BLASTP 2.2.22 [Sep-27-2009] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Reference for composition-based statistics starting in round 2: Schaffer, Alejandro A., L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005. Query= batch____ (88 letters) Database: uniref50.fasta 3,077,464 sequences; 1,040,396,356 total letters Searching..................................................done Results from round 1 Score E Sequences producing significant alignments: (bits) Value UniRef50_P37590 Signal transduction protein pmrD n=99 Tax=Entero... 184 1e-45 UniRef50_C1M702 PmrD n=2 Tax=Citrobacter RepID=C1M702_9ENTR 95 9e-19 UniRef50_A6TB93 Polymyxin resistance protein B n=5 Tax=Klebsiell... 54 2e-06 UniRef50_B5RK41 Putative polymyxin B resistance protein pmrD n=1... 52 7e-06 >UniRef50_P37590 Signal transduction protein pmrD n=99 Tax=Enterobacteriaceae RepID=PMRD_ECOLI Length = 88 Score = 184 bits (466), Expect = 1e-45, Method: Compositional matrix adjust. Identities = 88/88 (100%), Positives = 88/88 (100%) Query: 1 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK 60 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK Sbjct: 1 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK 60 Query: 61 LHTVKVLSASSYSPDEWERQCKVAGKTQ 88 LHTVKVLSASSYSPDEWERQCKVAGKTQ Sbjct: 61 LHTVKVLSASSYSPDEWERQCKVAGKTQ 88 >UniRef50_C1M702 PmrD n=2 Tax=Citrobacter RepID=C1M702_9ENTR Length = 87 Score = 94.7 bits (234), Expect = 9e-19, Method: Compositional matrix adjust. Identities = 41/84 (48%), Positives = 62/84 (73%) Query: 1 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK 60 MEW VKK+CC+K+ R ++LCD+GG++KM+A+ +S +K GDLLSPL++A YCINR+ Sbjct: 1 MEWHVKKTCCHKKAGRLYIVLCDSGGSLKMLAQAQSSERIKPGDLLSPLKDAQYCINRDT 60 Query: 61 LHTVKVLSASSYSPDEWERQCKVA 84 +K++ A Y DEWER +++ Sbjct: 61 SRVIKIIDARQYICDEWERLLRLS 84 >UniRef50_A6TB93 Polymyxin resistance protein B n=5 Tax=Klebsiella RepID=A6TB93_KLEP7 Length = 81 Score = 53.9 bits (128), Expect = 2e-06, Method: Compositional matrix adjust. Identities = 32/81 (39%), Positives = 47/81 (58%), Gaps = 9/81 (11%) Query: 1 MEWLVKKSCCNKQDNRHVLMLCDA---GGAIKMIAEVKS-DFAVKVGDLLSPLQNALYCI 56 MEW VKK QDN LC GA++MIAE+++ ++ GD L+PL +A YC+ Sbjct: 1 MEWWVKKV----QDNASA-SLCRVVLQSGALEMIAEIEACRLRLREGDKLTPLADARYCL 55 Query: 57 NREKLHTVKVLSASSYSPDEW 77 N T+K+ +A+ YS + W Sbjct: 56 NNNPTQTLKIRNATHYSSERW 76 >UniRef50_B5RK41 Putative polymyxin B resistance protein pmrD n=1 Tax=Klebsiella pneumoniae 342 RepID=B5RK41_KLEP3 Length = 95 Score = 51.6 bits (122), Expect = 7e-06, Method: Compositional matrix adjust. Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 2/83 (2%) Query: 1 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK 60 MEW+V +++ + L L G +KMIAEV S + D+L P+++A Y +N+ + Sbjct: 1 MEWIVCDVIYFAKNDIYFLKLY--GRPLKMIAEVVSTEPIFRSDILYPIKDAKYLVNKNE 58 Query: 61 LHTVKVLSASSYSPDEWERQCKV 83 VKV+ AS YS W Q K+ Sbjct: 59 NRPVKVIRASEYSASYWLSQKKI 81 Searching..................................................done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: UniRef50_P37590 Signal transduction protein pmrD n=99 Tax=Entero... 139 2e-32 UniRef50_C1M702 PmrD n=2 Tax=Citrobacter RepID=C1M702_9ENTR 127 8e-29 UniRef50_B5RK41 Putative polymyxin B resistance protein pmrD n=1... 116 3e-25 UniRef50_A6TB93 Polymyxin resistance protein B n=5 Tax=Klebsiell... 91 1e-17 Sequences not found previously or not previously below threshold: CONVERGED! >UniRef50_P37590 Signal transduction protein pmrD n=99 Tax=Enterobacteriaceae RepID=PMRD_ECOLI Length = 88 Score = 139 bits (350), Expect = 2e-32, Method: Composition-based stats. Identities = 88/88 (100%), Positives = 88/88 (100%) Query: 1 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK 60 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK Sbjct: 1 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK 60 Query: 61 LHTVKVLSASSYSPDEWERQCKVAGKTQ 88 LHTVKVLSASSYSPDEWERQCKVAGKTQ Sbjct: 61 LHTVKVLSASSYSPDEWERQCKVAGKTQ 88 >UniRef50_C1M702 PmrD n=2 Tax=Citrobacter RepID=C1M702_9ENTR Length = 87 Score = 127 bits (320), Expect = 8e-29, Method: Composition-based stats. Identities = 41/84 (48%), Positives = 62/84 (73%) Query: 1 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK 60 MEW VKK+CC+K+ R ++LCD+GG++KM+A+ +S +K GDLLSPL++A YCINR+ Sbjct: 1 MEWHVKKTCCHKKAGRLYIVLCDSGGSLKMLAQAQSSERIKPGDLLSPLKDAQYCINRDT 60 Query: 61 LHTVKVLSASSYSPDEWERQCKVA 84 +K++ A Y DEWER +++ Sbjct: 61 SRVIKIIDARQYICDEWERLLRLS 84 >UniRef50_B5RK41 Putative polymyxin B resistance protein pmrD n=1 Tax=Klebsiella pneumoniae 342 RepID=B5RK41_KLEP3 Length = 95 Score = 116 bits (289), Expect = 3e-25, Method: Composition-based stats. Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 2/83 (2%) Query: 1 MEWLVKKSCCNKQDNRHVLMLCDAGGAIKMIAEVKSDFAVKVGDLLSPLQNALYCINREK 60 MEW+V +++ + L L G +KMIAEV S + D+L P+++A Y +N+ + Sbjct: 1 MEWIVCDVIYFAKNDIYFLKLY--GRPLKMIAEVVSTEPIFRSDILYPIKDAKYLVNKNE 58 Query: 61 LHTVKVLSASSYSPDEWERQCKV 83 VKV+ AS YS W Q K+ Sbjct: 59 NRPVKVIRASEYSASYWLSQKKI 81 >UniRef50_A6TB93 Polymyxin resistance protein B n=5 Tax=Klebsiella RepID=A6TB93_KLEP7 Length = 81 Score = 91.0 bits (224), Expect = 1e-17, Method: Composition-based stats. Identities = 32/81 (39%), Positives = 47/81 (58%), Gaps = 9/81 (11%) Query: 1 MEWLVKKSCCNKQDNRHVLMLCDA---GGAIKMIAEVKS-DFAVKVGDLLSPLQNALYCI 56 MEW VKK QDN LC GA++MIAE+++ ++ GD L+PL +A YC+ Sbjct: 1 MEWWVKKV----QDNASA-SLCRVVLQSGALEMIAEIEACRLRLREGDKLTPLADARYCL 55 Query: 57 NREKLHTVKVLSASSYSPDEW 77 N T+K+ +A+ YS + W Sbjct: 56 NNNPTQTLKIRNATHYSSERW 76 Database: uniref50.fasta Posted date: Mar 8, 2010 10:38 AM Number of letters in database: 1,040,396,356 Number of sequences in database: 3,077,464 Lambda K H 0.310 0.125 0.353 Lambda K H 0.267 0.0386 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 308,983,797 Number of Sequences: 3077464 Number of extensions: 8095674 Number of successful extensions: 20262 Number of sequences better than 1.0e-01: 4 Number of HSP's better than 0.1 without gapping: 8 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 20251 Number of HSP's gapped (non-prelim): 8 length of query: 88 length of database: 1,040,396,356 effective HSP length: 58 effective length of query: 30 effective length of database: 861,903,444 effective search space: 25857103320 effective search space used: 25857103320 T: 11 A: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.3 bits) S2: 87 (38.2 bits)