% ALIGN_CLEAN, R.B. Russell, 1995 % Searching for domain descriptors... % 2 domain descriptions read in /disk3/pdb/pdb1pkm.ent 1pkm.1 { _ 12 _ to _ 115 _ _ 218 _ to _ 395 _ -0.60905 0.36431 0.70451 23.44435 0.40847 0.90548 -0.11519 34.26069 -0.67987 0.21758 -0.70032 73.34975 } /disk3/pdb/pdb4xia.ent 4xiaa { CHAIN A 0.74922 0.11826 -0.65163 21.14652 -0.02137 -0.97917 -0.20210 161.95177 -0.66194 0.16547 -0.73097 53.77890 } % Reading block file... Blocfile read: Length: 457 % Searching for STAMP data... % 268459416 STAMP fields found: T P A G % Block file contains 5 sequences; the alignment length is 457 % Cleaning up allowing continuous segments of 3 or greater... % Cleaning done. % The final alignment length is 432 % The alignment: >1pkm.1 (cluster A) sequence >4xiaa (cluster B) sequence >space >1pkm.1_dssp (cluster A) secondary structure from DSSP >4xiaa_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 * I - Q - T S Q T Q T L H H H A H A H M T A - D S T S F H L H E H H H M H C H R T L - D - I T D T S S P - P - IV -- 0 0.20000 2.49029 2.20000 TQ S- 0 0.35200 2.20677 3.72000 AP -- 0 0.10400 2.33175 1.24000 T - RP -G 0 0.02100 2.77290 0.41000 NA -G 0 0.11600 2.54570 1.36000 TD SG 0 0.17500 2.36722 1.95000 GH E- 0 0.42100 1.97356 4.41000 IF EE 1 0.60600 1.77070 6.26000 IT EE 1 0.58500 1.81848 6.05000 CF EE 1 0.74400 1.43651 7.64000 TG EE 1 0.73700 1.54222 7.57000 IL -H GW -H T H V H G H W - T - G - A - D B P T F T G B V - A - T S R S PA T- AN T- SL T- 1 0.44100 1.90856 4.61000 RD -- 1 0.53700 1.78395 5.57000 SP -H 1 0.50500 1.82668 5.25000 VV HH 1 0.65300 1.16394 6.73000 EE HH 1 0.52800 1.72034 5.48000 IA HH 1 0.44800 1.82729 4.68000 LV HH 1 0.73400 1.20891 7.54000 KH HH 1 0.89500 1.00799 9.15000 EK HH 1 0.84700 1.22661 8.67000 ML HH 1 0.87600 0.92308 8.96000 IA HH 1 0.75700 1.34309 7.77000 KE HH 1 0.68800 1.53755 7.08000 SL TH 1 0.74600 1.22716 7.66000 GG TT 1 0.56300 1.73535 5.83000 MA E- 1 0.61800 1.74021 6.38000 NY E- 1 0.58700 1.84829 6.07000 VG EE 1 0.50600 1.92314 5.26000 AI EE 1 0.64900 1.57955 6.69000 RT EE 1 0.65700 1.65672 6.77000 LF EE 1 0.60600 1.52088 6.26000 NH EE 1 0.44500 1.74105 4.65000 FD TH 0 0.22100 2.24342 2.41000 SN TH 0 0.01700 2.68883 0.37000 HD SH 0 0.05000 2.60313 0.70000 L H GI SS 0 0.03400 2.48711 0.54000 TP -- 0 0.18600 1.74060 2.06000 HF HT 0 0.17600 2.19350 1.96000 D T A - T - A H EA HH 0 0.05200 2.84115 0.72000 YE HH 0 0.10700 2.69668 1.27000 HR HH 0 0.12700 2.64212 1.47000 AE HH 0 0.17600 2.53810 1.96000 EK HH 0 0.26300 2.38586 2.83000 TI HH 0 0.29700 2.33200 3.17000 IL HH 0 0.37000 2.19392 3.90000 KG HH 1 0.44200 2.05571 4.62000 ND HH 1 0.53400 1.92488 5.54000 VF HH 1 0.54600 1.88240 5.66000 RN HH 1 0.70700 1.52374 7.27000 AQ HH 1 0.75000 1.34846 7.70000 AA HH 1 0.79500 1.27364 8.15000 TL HH 1 0.78700 1.36292 8.07000 EA HH 1 0.88400 0.78869 9.04000 SD TH 1 0.66500 0.83422 6.85000 F T A T S T D S P T I T R T YT -H 0 0.04100 2.56197 0.61000 RG -- 0 0.38300 1.96318 4.03000 PL -- 0 0.33300 2.03069 3.53000 VK -E 1 0.57900 1.10271 5.99000 AV EE 1 0.53900 1.21258 5.59000 VP EE 0 0.21800 2.18678 2.38000 AM EE 1 0.60300 1.68014 6.23000 LV EE 1 0.58300 1.64969 6.03000 DT EE 1 0.53000 1.50217 5.50000 TT -- 1 0.53900 1.69640 5.59000 N - L - F S S S H S P G V G F G K T D T KG -- 0 0.00000 2.75548 0.00000 GG -S 0 0.08900 2.18240 1.09000 PF -T 0 0.14000 1.81362 1.60000 T T S - N S D S R H AS SH VI SH 0 0.00000 3.10116 0.00000 SR -H 0 0.08500 1.66481 1.05000 ER HH 1 0.62000 1.53636 6.40000 KF HH 1 0.53800 1.77337 5.58000 DA HH 1 0.49600 1.66763 5.16000 IL HH 1 0.58700 1.43884 6.07000 QA HH 1 0.60500 1.62419 6.25000 DK HH 1 0.63600 1.61049 6.56000 LV HH 1 0.65600 1.50717 6.76000 KL HH 1 0.64100 1.57538 6.61000 FH HH 1 0.65300 1.54334 6.73000 GN HH 1 0.61000 1.35304 6.30000 VI HH 1 0.54300 1.67455 5.63000 ED HH 1 0.65100 1.64145 6.71000 QL TH 1 0.65200 1.41112 6.72000 A H A H E H M T DG TT VA -- 0 0.33600 2.12533 3.56000 DE SS 0 0.40900 1.97504 4.29000 MT EE 1 0.68600 1.48739 7.06000 VF EE 1 0.85400 1.12162 8.74000 FV EE 1 0.90200 1.00667 9.22000 AM EE 1 0.88600 0.76854 9.06000 SW S- 1 0.75700 1.30562 7.77000 FG -- G T R T E - G E S E E S Y S D G G G S G K - D - L H A H A H A H L H ID -H RR -H KM SH 0 0.00300 2.73643 0.23000 AR HH 0 0.12700 2.59501 1.47000 SE HH 0 0.14700 2.55758 1.67000 DG HH 0 0.18700 2.39345 2.07000 VV HH 0 0.42300 1.93744 4.43000 HD HH 1 0.56600 1.57112 5.86000 ET HH 1 0.46000 1.88653 4.80000 VA HH 1 0.56600 1.73760 5.86000 RA HH 1 0.71200 1.00573 7.32000 KG HH 1 0.62100 1.58452 6.41000 VY HH 0 0.40100 2.03328 4.21000 LI HH 1 0.47900 1.90288 4.99000 GK TH 0 0.28000 2.13062 3.00000 ED TH 1 0.54100 1.48187 5.61000 KK TH GG TT KY T- 0 0.26300 1.77100 2.83000 NN T- 1 0.72300 1.14137 7.43000 IL S- 1 0.80500 1.28921 8.25000 KR EE 1 0.70300 1.44253 7.23000 II EE 1 0.85800 0.86964 8.78000 IA EE 1 0.90900 0.93891 9.29000 SL EE 1 0.89900 0.94319 9.19000 KE E- 1 0.90300 0.79481 9.23000 IP E- 1 0.81900 1.23380 8.39000 EK -- 1 0.72600 1.33297 7.46000 P S N S E S P S R S G S ND SE 0 0.00600 2.56240 0.26000 HI SE 0 0.04800 2.63798 0.68000 EF HS 0 0.18000 2.36724 2.00000 L S P - GT HS 0 0.17500 2.24164 1.95000 VV HH 0 0.38900 2.01201 4.09000 RG HH 0 0.34600 2.05556 3.66000 RH TH 0 0.40300 1.79060 4.23000 FG HH 1 0.47700 1.94290 4.97000 DL HH 0 0.42300 1.81034 4.43000 EA HH 0 0.27200 1.84462 2.92000 IF HH 0 0.25600 2.13004 2.76000 LI HH 0 0.18000 2.43772 2.00000 EE HT AQ HT L - E T H T G G D G SI SG DV SE GG EE 0 0.38300 2.00779 4.03000 IL EE 1 0.65600 1.31973 6.76000 MN E- 1 0.78900 1.34996 8.09000 VP E- 1 0.56400 1.44749 5.84000 AE EB 0 0.31800 2.02819 3.38000 RT HH 0 0.20700 2.39570 2.27000 GG HH 0 0.16200 2.52467 1.82000 DH HH 0 0.20100 2.51276 2.21000 LE HH 0 0.22400 2.48529 2.44000 GQ HH 0 0.19300 2.54161 2.13000 IM HT EA HT I S P - A T E T K T V H FG HT LL H- AN H- 0 0.13000 2.29204 1.50000 QF HH 1 0.55200 1.57890 5.72000 KT HH 1 0.69500 1.62254 7.15000 MH HH 1 0.58600 1.68419 6.06000 MG HH 1 0.59500 1.50366 6.15000 II HH 1 0.80100 1.00102 8.21000 GA HH 1 0.88300 0.99082 9.03000 RQ HH 1 0.80100 1.26899 8.21000 CA HH 1 0.68700 1.61819 7.07000 NL HH 1 0.64100 1.76792 6.61000 RW HH 1 0.64400 1.70839 6.64000 AA HT 1 0.47000 2.03948 4.90000 GE TT 1 0.47500 2.08746 4.95000 K - L B KF -- PH -- 1 0.45600 1.97262 4.76000 VI E- 1 0.52500 1.81771 5.45000 ID EE 1 0.62000 1.75387 6.40000 CL EE AN E- TG SB QQ S- MR S- LG SS EI GS SK GS MY GS ID G- KQ T- KD -- PL SB RV S- PF -T TG -T RH HS AG HS ED H- GL HH ST HH 0 0.17000 2.55045 1.90000 DS HH 0 0.11400 2.64262 1.34000 VA HH 0 0.28800 2.28007 3.08000 AF HH 0 0.37500 2.19995 3.95000 NF HH 0 0.27600 2.33184 2.96000 AT HH 1 0.43500 2.00697 4.55000 VV HH 1 0.61900 1.58398 6.39000 LD HH DL HH L H E H N H G - F - P T N T G - G - P - K - Y - T - GG TS AP -- DR SE 0 0.02800 2.14408 0.48000 CH EE 1 0.51400 1.90009 5.34000 IF EE 1 0.48700 1.83294 5.07000 MD E- 1 0.47500 1.57355 4.95000 LY E- SK S- GP H- ES H- R T TT HT AD HS KG T- GY -H DD SH 0 0.01800 2.56484 0.38000 YG -H 0 0.19600 1.89095 2.16000 PV HH 1 0.57400 1.82022 5.94000 LW HH 1 0.74400 1.51035 7.64000 ED HH 1 0.81200 1.39362 8.32000 AS HH 1 0.82600 1.37469 8.46000 VA HH 1 0.85000 1.26970 8.70000 RK HH 1 0.90400 1.03675 9.24000 MA HH 1 0.91200 0.99553 9.32000 QN HH 1 0.92200 0.89553 9.42000 HM HH 1 0.92500 0.91759 9.45000 LS HH 1 0.94300 0.70830 9.63000 IM HH 1 0.92900 0.84469 9.49000 AY HH 1 0.92100 0.94127 9.41000 RL HH 1 0.90900 0.89643 9.29000 EL HH 1 0.87700 1.13727 8.97000 AL HH 1 0.90600 1.08139 9.26000 EK HH 1 0.84800 1.21639 8.68000 AE HH 1 0.78500 1.41678 8.05000 AR TH 1 0.78100 1.50406 8.01000 A H L H MA SH 0 0.03600 2.62468 0.56000 FF -H 0 0.16400 2.20413 1.84000 HR HH 0 0.13800 2.21084 1.58000 RA HH KD H- LP HH FE HH V H Q H E H A H M H K H T H S T G T V T F T E G L G G G E S T - T S L S N - A T G T E - S - A H A H D H L H M H N T D - S T A T S T F T A T G T F - D - A H E H A H A H A T E T R - N - F - A - F H I H R H L H N H Q H L H A H I H E H H H L H L T G T S - *