% ALIGN_CLEAN, R.B. Russell, 1995 % Searching for domain descriptors... % 2 domain descriptions read in /disk3/pdb/pdb1cpt.ent 1cpt { ALL 1.00000 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 } /disk3/pdb/pdb1oxa.ent 1oxa { ALL 0.87235 -0.16763 0.45926 40.63050 -0.48857 -0.33288 0.80653 4.28102 0.01768 -0.92794 -0.37228 101.38055 } % Reading block file... Blocfile read: Length: 441 % Searching for STAMP data... % 268459416 STAMP fields found: T P A G % Block file contains 5 sequences; the alignment length is 441 % Cleaning up allowing continuous segments of 3 or greater... % Cleaning done. % The final alignment length is 434 % The alignment: >1cpt (cluster A) sequence >1oxa (cluster B) sequence >space >1cpt_dssp (cluster A) secondary structure from DSSP >1oxa_dssp (cluster B) secondary structure from DSSP #T -- '1' = equivalenced residues #P -- averaged Pij #A -- distance between averaged CA atoms in angtroms #G -- Pij' value * M - D - A T R T A - T - I S P - E H H H IA H- AT H- RV H- TP H- VD HB IL HT LE ST PS SS 0 0.00100 2.64782 0.21000 QD GG 0 0.24100 2.26072 2.61000 GS GG 0 0.30100 2.23920 3.21000 YF GG 0 0.32100 2.23334 3.41000 AH GT 0 0.40100 2.10107 4.21000 DV -S 1 0.57800 1.79054 5.98000 D H E H VD HS 1 0.47900 1.82316 4.99000 IW HH 1 0.77100 1.18148 7.91000 YY HH 1 0.88900 1.12483 9.09000 PS HH 1 0.86300 1.22082 8.83000 AT HH 1 0.87700 1.13740 8.97000 FY HH 1 0.92500 0.74217 9.45000 KA HH 1 0.93500 0.60296 9.55000 WE HH 1 0.90900 0.86357 9.29000 LL HH 1 0.87000 1.10500 8.90000 RR HH 1 0.87900 1.07555 8.99000 DE HH 1 0.91200 0.93027 9.32000 ET HH 1 0.91100 0.95288 9.31000 QA -- 1 0.91500 0.91215 9.35000 PP SS 1 0.89700 0.94644 9.17000 LV EE 1 0.83600 0.94310 8.56000 AT EE 1 0.76200 1.42097 7.82000 MP EE 1 0.81700 1.32044 8.37000 AV EE 1 0.67900 1.49972 6.99000 HR -E 0 0.36800 1.99178 3.88000 I - EF TE 0 0.01500 2.73374 0.35000 GL TT 0 0.16900 2.26612 1.89000 YG ST 1 0.49700 1.60322 5.17000 DQ -E 1 0.74200 1.55569 7.62000 PD -E 1 0.81200 1.41546 8.32000 MA EE 1 0.86200 1.28977 8.82000 WW EE 1 0.87000 1.23411 8.90000 IL EE 1 0.90200 0.96738 9.22000 AV EE 1 0.91400 0.91931 9.34000 TT -- 1 0.91700 0.77719 9.37000 KG SS 1 0.87900 1.09756 8.99000 HY HH 1 0.86700 1.25856 8.87000 AD HH 1 0.86900 1.26041 8.89000 DE HH 1 0.85900 1.29239 8.79000 VA HH 1 0.86300 1.29437 8.83000 MK HH 1 0.87400 1.26114 8.94000 QA HH 1 0.87500 1.23170 8.95000 IA HH 1 0.88400 1.17974 9.04000 GL HH 1 0.88700 1.15299 9.07000 KS HH 1 0.82200 1.33234 8.42000 QD -- 1 0.66200 1.60580 6.82000 P T GL TT 0 0.34000 1.71413 3.60000 LR TT 1 0.73300 0.87635 7.53000 FL EE 1 0.93600 0.76410 9.56000 SS EE 1 0.94200 0.54479 9.62000 NS S- 1 0.92300 0.89560 9.43000 D - P T K T K - K - Y - P T G T AV S- EE S- 0 0.00000 3.01687 0.00000 GV S- 0 0.14600 1.92801 1.66000 SE -- 0 0.42900 2.08261 4.49000 EF S- 0 0.41000 2.13653 4.30000 IP SG 0 0.36700 2.06344 3.87000 LA -G 0 0.29200 2.06387 3.12000 YY -G D - Q H N H N H E H A H FL HT MG HT RF H- 0 0.06400 2.51252 0.84000 SP H- 0 0.32200 1.98064 3.42000 IE HH 1 0.45100 1.93975 4.71000 SD TH 0 0.19300 1.68489 2.13000 G T G T CV SH PR SH 0 0.04200 2.45824 0.62000 HN -H 0 0.16800 2.17765 1.88000 VY SH 0 0.19000 2.29697 2.10000 F H IA SS 0 0.38700 2.03237 4.07000 DT -S 1 0.62500 1.50032 6.45000 SN -S 1 0.68500 1.67676 7.05000 LM GG 1 0.76000 1.53336 7.80000 TG GG 1 0.76600 1.52166 7.86000 ST GG 1 0.80200 1.39653 8.22000 MS -- 1 0.88200 1.12941 9.02000 DD -- 1 0.89500 1.12965 9.15000 PP TT 1 0.89300 1.12490 9.13000 PP TT 1 0.92400 0.96169 9.44000 TT HH 1 0.91800 0.98417 9.38000 HH HH 1 0.88100 1.14932 9.01000 TT HH 1 0.88200 1.15622 9.02000 AR HH 1 0.90600 1.05637 9.26000 YL HH 1 0.88900 1.10243 9.09000 RR HH 1 0.85700 1.26252 8.77000 GK HH 1 0.85700 1.23920 8.77000 LL HH 1 0.84400 1.28424 8.64000 TV HH 1 0.82200 1.32280 8.42000 LS HH 1 0.57100 1.39653 5.91000 NQ TT 0 0.31700 2.11224 3.37000 WE TT 1 0.52800 1.96328 5.48000 FF SS 1 0.50400 1.95799 5.24000 QT S- 0 0.42600 2.08014 4.46000 PV HH 1 0.55200 1.83366 5.72000 AR HH 1 0.46700 2.00565 4.87000 SR HH 1 0.44500 1.98455 4.65000 IV HH 1 0.70300 1.38676 7.23000 RE GH 1 0.86600 1.13871 8.86000 KA GT 1 0.84400 1.29351 8.64000 LM GT 1 0.87800 1.21344 8.98000 ER HH 1 0.89100 1.15644 9.11000 EP HH 1 0.89400 1.15961 9.14000 NR HH 1 0.89700 1.16497 9.17000 IV HH 1 0.89400 1.17456 9.14000 RE HH 1 0.90100 1.11406 9.21000 RQ HH 1 0.89800 1.03151 9.18000 II HH 1 0.87600 1.16281 8.96000 AT HH 1 0.87300 1.24403 8.93000 QA HH 1 0.89200 1.11976 9.12000 AE HH 1 0.86000 1.13428 8.80000 SL HH 1 0.78600 1.43830 8.06000 VL HH 1 0.76500 1.51302 7.85000 QD HH 1 0.81400 1.35321 8.34000 RE HH 1 0.74700 1.55014 7.67000 LV HH 1 0.65000 1.72984 6.70000 LG H- 0 0.41300 1.93995 4.33000 D T FD SS 0 0.13500 2.13760 1.55000 DS SS 1 0.55300 1.22396 5.73000 GG SS 1 0.52800 1.79596 5.48000 EV EE 1 0.76300 1.26703 7.83000 CV EE 1 0.89400 0.91756 9.14000 DD EE 1 0.88900 1.14647 9.09000 FI HH 1 0.90700 1.01671 9.27000 MV HH 1 0.92400 0.70776 9.44000 TD HH 1 0.88500 1.07303 9.05000 DR HH 1 0.85900 1.22341 8.79000 CF TT 1 0.88100 1.07162 9.01000 AA TT 1 0.89900 0.89086 9.19000 LH TT 1 0.90100 0.92629 9.21000 YP TH 1 0.93700 0.52110 9.57000 YL HH 1 0.95300 0.55715 9.73000 PP HH 1 0.94700 0.71050 9.67000 LI HH 1 0.94100 0.71872 9.61000 HK HH 1 0.92300 0.94421 9.43000 VV HH 1 0.92200 0.99958 9.42000 VI HH 1 0.92500 0.90595 9.45000 MC HH 1 0.90000 1.00263 9.20000 TE HH 1 0.85600 1.25964 8.76000 AL HH 1 0.87500 1.19289 8.95000 LL HH 1 0.86500 1.05580 8.85000 GG TT 1 0.74000 1.47327 7.60000 VV -- 1 0.78100 1.42008 8.01000 PD -- 1 0.65900 1.56173 6.79000 EE GT 0 0.39500 2.02744 4.15000 DA GT 0 0.31800 2.18836 3.38000 DA GT 1 0.49000 1.87650 5.10000 E H P H L H MR HT 1 0.60200 1.72702 6.22000 LG HT 1 0.74100 1.56488 7.61000 KA HH 1 0.77300 1.32657 7.93000 L H TF HH 1 0.43400 1.91874 4.54000 QG HH 1 0.65500 1.63889 6.75000 DR TH 1 0.71500 1.58247 7.35000 FW TH 1 0.72900 1.58296 7.49000 FS TH 1 0.64100 1.76283 6.61000 GS -H VE -H EI -H AL HH AV H- M - D - P G E G R G A H E H Q H R H G H RQ HH RA HH FA HH HR HH EE HH TV HH 0 0.05700 2.54702 0.77000 IV HH 0 0.35600 1.67975 3.76000 AN HH 1 0.47100 1.75831 4.91000 TF HH 0 0.30700 2.17422 3.27000 FI HH 0 0.35700 1.94661 3.77000 YL HH 1 0.62000 0.95539 6.40000 DD HH 1 0.69500 1.45613 7.15000 YL HH 0 0.42000 1.79961 4.40000 FV HH 1 0.47500 1.66586 4.95000 NE HH 1 0.80400 1.15604 8.24000 GR HH 1 0.89500 0.71046 9.15000 FR HH 1 0.78000 1.06739 8.00000 TR HH 1 0.52100 1.66061 5.41000 VT HH 1 0.56500 1.66848 5.85000 D H R H R T S T CE SS PP -- 0 0.32400 2.22118 3.44000 KG -- 1 0.45300 1.98936 4.73000 DD SS 1 0.50800 1.91914 5.28000 DD SS 1 0.62200 1.60635 6.42000 VL HH 1 0.77000 1.13055 7.90000 ML HH 1 0.85400 0.78744 8.74000 SS HH 1 0.71800 1.28082 7.38000 LA HH 1 0.74400 1.29196 7.64000 LL HH 1 0.86900 0.98836 8.89000 AI HH 1 0.90200 0.99172 9.22000 NS HH 1 0.83300 0.85492 8.53000 SV -- 1 0.67800 1.40005 6.98000 KQ BE 0 0.41700 1.84942 4.37000 LD SE D T DD ST GD ST NG SE 0 0.09900 2.50222 1.19000 YR BE 0 0.26300 2.26019 2.83000 IL -- 1 0.57100 1.65324 5.91000 DS -- 1 0.68500 1.62820 7.05000 DA HH 1 0.74000 1.49302 7.60000 KD HH 1 0.81200 1.44522 8.32000 YE HH 1 0.83500 1.34731 8.55000 IL HH 1 0.87200 1.12526 8.92000 NT HH 1 0.83200 1.32206 8.52000 AS HH 1 0.86800 1.24109 8.88000 YI HH 1 0.88300 1.13553 9.03000 YA HH 1 0.87000 1.20524 8.90000 VL HH 1 0.86900 1.11653 8.89000 AV HH 1 0.89800 0.56445 9.18000 IL HH 1 0.90300 0.94998 9.23000 AL HH 1 0.89000 1.12493 9.10000 TL HH 1 0.92600 0.87999 9.46000 AA HH 1 0.87900 0.83894 8.99000 GG HH 1 0.74600 1.35605 7.66000 HF HH 1 0.78600 1.27102 8.06000 DE HH 1 0.80600 1.30765 8.26000 TA HH 1 0.90500 0.94271 9.25000 TS HH 1 0.93800 0.77998 9.58000 SV HH 1 0.92800 0.91654 9.48000 SS HH 1 0.91600 1.04566 9.36000 SL HH 1 0.90800 1.06630 9.28000 SI HH 1 0.93100 0.84535 9.51000 GG HH 1 0.92200 0.93394 9.42000 GI HH 1 0.92000 0.93457 9.40000 AG HH 1 0.91100 0.98767 9.31000 IT HH 1 0.90200 1.02871 9.22000 IY HH 1 0.91200 0.96359 9.32000 GL HH 1 0.89600 0.94245 9.16000 LL HH 1 0.88200 1.02896 9.02000 SL HH 1 0.90900 1.01124 9.29000 RT HH 1 0.90600 0.94940 9.26000 NH -- 1 0.85800 1.11090 8.78000 PP HH 1 0.85300 1.20613 8.73000 ED HH 1 0.81800 1.42029 8.38000 QQ HH 1 0.83700 1.39268 8.57000 LL HH 1 0.82800 1.40796 8.48000 AA HH 1 0.85800 1.29974 8.78000 LL HH 1 0.88200 1.19099 9.02000 AV HH 1 0.91100 0.97374 9.31000 KR HH 1 0.89200 1.13610 9.12000 SA HH 1 0.89100 1.17512 9.11000 DD -- 1 0.91500 1.03210 9.35000 PP GG 1 0.91900 0.94595 9.39000 AS GG 1 0.92400 0.58069 9.44000 LA GG 1 0.90300 1.00080 9.23000 IL HH 1 0.88500 1.09138 9.05000 PP HH 1 0.89100 0.66995 9.11000 RN HH 1 0.84400 1.12316 8.64000 LA HH 1 0.84600 1.23748 8.66000 VV HH 1 0.90900 1.03595 9.29000 DE HH 1 0.91400 0.97796 9.34000 EE HH 1 0.86200 1.24948 8.82000 AI HH 1 0.84800 1.34238 8.68000 VL HH 1 0.86700 1.28489 8.87000 RR HH 1 0.86000 1.30614 8.80000 WY HH 1 0.81400 1.38399 8.34000 TI HS 1 0.65600 1.56318 6.76000 AA -- 1 0.80500 1.03346 8.25000 PP -S 1 0.90800 1.10199 9.28000 VP BS 1 0.86600 1.13673 8.86000 KE -- 1 0.76800 1.40221 7.88000 ST -- 1 0.85600 1.10890 8.76000 FT -E 1 0.78300 1.33704 8.03000 MT EE 1 0.85200 1.03436 8.72000 RR EE 1 0.93200 0.85109 9.52000 TF EE 1 0.89600 0.97339 9.16000 AA EE 1 0.86200 1.12149 8.82000 LA SS 1 0.82500 1.37563 8.45000 AE SS 1 0.84100 1.35279 8.61000 DE -- 1 0.82600 1.39745 8.46000 TV EE 1 0.74900 1.53945 7.69000 EE EE 1 0.83400 1.29380 8.54000 VI EE 1 0.84000 1.30924 8.60000 RG TT 1 0.89200 1.02800 9.12000 GG TT 1 0.91600 0.99979 9.36000 QV EE 1 0.90500 1.06152 9.25000 NA EE 1 0.86900 1.16680 8.89000 II EE 1 0.80500 1.41218 8.25000 KP -- 1 0.75500 1.54839 7.75000 RQ TT 1 0.79700 1.34530 8.17000 GY TT 1 0.86900 1.03030 8.89000 DS -- 1 0.85000 1.27170 8.70000 RT EE 1 0.86100 1.20852 8.81000 IV EE 1 0.92200 0.85467 9.42000 ML EE 1 0.94000 0.73269 9.60000 LV EE 1 0.91300 0.99295 9.33000 SA -- 1 0.92400 0.76621 9.44000 YN HH 1 0.87300 1.11286 8.93000 PG HH 1 0.85800 1.09138 8.78000 SA HH 1 0.89900 0.44765 9.19000 AA HH 1 0.90100 0.95959 9.21000 NN TT 1 0.89600 1.09352 9.16000 RR TT 1 0.93100 0.87862 9.51000 DD -- 1 0.93200 0.92321 9.52000 EP TT 1 0.93000 0.85063 9.50000 ES TT 1 0.88700 1.08996 9.07000 VQ TT 1 0.87200 1.16420 8.92000 FF -S 1 0.87200 1.09699 8.92000 SP SS 1 0.78600 1.44035 8.06000 ND SS 1 0.79800 1.45705 8.18000 PP TT 1 0.85100 1.29599 8.71000 DH TT 1 0.81600 1.41778 8.36000 ER SS 1 0.77600 1.53928 7.96000 FF -- 1 0.80300 1.46967 8.23000 DD -- 1 0.83000 1.37459 8.50000 IV TT 1 0.88100 1.19062 9.01000 TT TT 1 0.86700 1.23366 8.87000 RR -S FD -- PT S- NR -T 0 0.24300 1.97994 2.63000 RG -T 1 0.62000 1.64419 6.40000 HH -- 1 0.81700 1.22043 8.37000 LL -S 1 0.91500 0.93800 9.35000 GS TT 1 0.89800 0.99359 9.18000 FF TT 1 0.85600 1.20927 8.76000 GG -- 1 0.87100 1.19211 8.91000 WQ -- 1 0.90100 1.03436 9.21000 GG SS 1 0.87400 1.21878 8.94000 AI TT 1 0.86700 1.27066 8.87000 HH TT 1 0.87900 1.22601 8.99000 MF -- 1 0.86300 1.29488 8.83000 CC -- 1 0.85300 1.33344 8.73000 LM TT 1 0.86100 1.28049 8.81000 GG TT 1 0.90500 1.05714 9.25000 QR HH 1 0.87600 1.13255 8.96000 HP HH 1 0.87000 1.10382 8.90000 LL HH 1 0.91100 0.87734 9.31000 AA HH 1 0.93700 0.70385 9.57000 KK HH 1 0.93300 0.75925 9.53000 LL HH 1 0.90200 1.00963 9.22000 EE HH 1 0.86800 1.20743 8.88000 MG HH 1 0.87900 1.10889 8.99000 KE HH 1 0.89200 1.02824 9.12000 IV HH 1 0.85800 1.22717 8.78000 FA HH 1 0.84700 1.25661 8.67000 FL HH 1 0.77000 1.48396 7.90000 ER HH 1 0.71000 1.65149 7.30000 EA HH 1 0.75000 1.55650 7.70000 LL HH 1 0.72800 1.58687 7.48000 LF GH 1 0.70900 1.56023 7.29000 PG GH 1 0.78100 1.32956 8.01000 KR GH 1 0.86600 1.09207 8.86000 LF E- 1 0.72600 1.40019 7.46000 KP ET 1 0.70000 1.20312 7.20000 SA ET 1 0.67500 1.54538 6.95000 VL E- 1 0.79500 1.46497 8.15000 ES EE 1 0.83000 1.35551 8.50000 LL EE 1 0.86500 1.16125 8.85000 SG SS 1 0.81900 1.18441 8.39000 I S D - A G GD SG 0 0.00000 2.78200 0.20000 PD -G 0 0.20700 1.61741 2.27000 PV -- 1 0.77200 1.48246 7.92000 RV E- 1 0.82200 1.34387 8.42000 LW EB 1 0.85100 1.19086 8.71000 VR -- 1 0.88600 1.09220 9.06000 AR -- 1 0.89500 1.12701 9.15000 TS -- 1 0.86000 1.25683 8.80000 NL SS 1 0.77400 1.44029 7.94000 FL SS 1 0.87800 0.99770 8.98000 VL BS 1 0.86000 1.12739 8.80000 GR -- 1 0.66900 1.52667 6.89000 GG S- 1 0.77800 1.17292 7.98000 PI EB 1 0.90600 0.96230 9.26000 KD ES 1 0.92900 0.96294 9.49000 NH E- 1 0.92600 0.98862 9.46000 VL -- 1 0.91000 1.00181 9.30000 PP EE 1 0.90900 0.99679 9.29000 IV EE 1 0.91700 0.99171 9.37000 RR EE 1 0.84300 1.12633 8.63000 FL ES TD E- K E *