BLASTP 2.2.26 [Sep-21-2011]
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.
Query= 002016
(981 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3Q7M|A Chain A, The Crystal Structure Of Bamb From The Bam Complex In
Spacegroup I222
pdb|3Q7N|A Chain A, The Crystal Structure Of Bamb From The Bam Complex In
Spacegroup P212121
Length = 376
Score = 36.6 bits (83), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 99 ITLSSDGSTLRAWNLPDGQMVWESFLRGSKHSKPLLLVPTNLKVDKDSLILV-SSKGCLH 157
+ + S+ + + A N DG + W++ + G S+P++ D L+L+ +S G L
Sbjct: 106 VYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVV---------SDGLVLIHTSNGQLQ 156
Query: 158 AVSSIDGEILWTRDFAAESVEVQ 180
A++ DG + WT + S+ ++
Sbjct: 157 ALNEADGAVKWTVNLDXPSLSLR 179
Score = 32.0 bits (71), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 2/98 (2%)
Query: 82 GINDVVDGIDIALGKYVITLSSDGSTLRAWNLPDGQMVWESFL--RGSKHSKPLLLVPTN 139
GI + + AL V+ + ++A N DG+ +W L + SK L+
Sbjct: 39 GIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGG 98
Query: 140 LKVDKDSLILVSSKGCLHAVSSIDGEILWTRDFAAESV 177
+ V + + S K ++A+++ DG + W A E++
Sbjct: 99 VTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEAL 136
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 51/109 (46%), Gaps = 24/109 (22%)
Query: 65 IASLDLRHGEIFWRHVLG-IND-VVDGIDIAL---GKYVITLSSDGSTLRAWNLPDGQMV 119
+ +LDLR G+I W+ LG +ND +VDG I L V L+ DG G +
Sbjct: 251 LTALDLRSGQIXWKRELGSVNDFIVDGNRIYLVDQNDRVXALTIDG----------GVTL 300
Query: 120 W-ESFLRGSKHSKPLLLVPTNLKVDKDSLILVSSKGCLHAVSSIDGEIL 167
W +S L + P+L +L++ S+G LH ++ DG +
Sbjct: 301 WTQSDLLHRLLTSPVLY--------NGNLVVGDSEGYLHWINVEDGRFV 341
>pdb|3Q54|A Chain A, Crystal Structure Of Escherichia Coli Bamb
Length = 368
Score = 36.6 bits (83), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 99 ITLSSDGSTLRAWNLPDGQMVWESFLRGSKHSKPLLLVPTNLKVDKDSLILV-SSKGCLH 157
+ + S+ + + A N DG + W++ + G S+P++ D L+L+ +S G L
Sbjct: 98 VYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVV---------SDGLVLIHTSNGQLQ 148
Query: 158 AVSSIDGEILWTRDFAAESVEVQ 180
A++ DG + WT + S+ ++
Sbjct: 149 ALNEADGAVKWTVNLDMPSLSLR 171
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 24/109 (22%)
Query: 65 IASLDLRHGEIFWRHVLG-IND-VVDGIDIAL---GKYVITLSSDGSTLRAWNLPDGQMV 119
+ +LDLR G+I W+ LG +ND +VDG I L V+ L+ DG G +
Sbjct: 243 LTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDG----------GVTL 292
Query: 120 W-ESFLRGSKHSKPLLLVPTNLKVDKDSLILVSSKGCLHAVSSIDGEIL 167
W +S L + P+L +L++ S+G LH ++ DG +
Sbjct: 293 WTQSDLLHRLLTSPVLY--------NGNLVVGDSEGYLHWINVEDGRFV 333
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 2/98 (2%)
Query: 82 GINDVVDGIDIALGKYVITLSSDGSTLRAWNLPDGQMVWESFL--RGSKHSKPLLLVPTN 139
GI + + AL V+ + ++A N DG+ +W L + SK L+
Sbjct: 31 GIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGG 90
Query: 140 LKVDKDSLILVSSKGCLHAVSSIDGEILWTRDFAAESV 177
+ V + + S K ++A+++ DG + W A E++
Sbjct: 91 VTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEAL 128
>pdb|3Q7O|A Chain A, The Crystal Structure Of Bamb From The Bam Complex In
Spacegroup P213
Length = 376
Score = 36.6 bits (83), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 99 ITLSSDGSTLRAWNLPDGQMVWESFLRGSKHSKPLLLVPTNLKVDKDSLILV-SSKGCLH 157
+ + S+ + + A N DG + W++ + G S+P++ D L+L+ +S G L
Sbjct: 106 VYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVV---------SDGLVLIHTSNGQLQ 156
Query: 158 AVSSIDGEILWTRDFAAESVEVQ 180
A++ DG + WT + S+ ++
Sbjct: 157 ALNEADGAVKWTVNLDMPSLSLR 179
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 24/109 (22%)
Query: 65 IASLDLRHGEIFWRHVLG-IND-VVDGIDIAL---GKYVITLSSDGSTLRAWNLPDGQMV 119
+ +LDLR G+I W+ LG +ND +VDG I L V+ L+ DG G +
Sbjct: 251 LTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDG----------GVTL 300
Query: 120 W-ESFLRGSKHSKPLLLVPTNLKVDKDSLILVSSKGCLHAVSSIDGEIL 167
W +S L + P+L +L++ S+G LH ++ DG +
Sbjct: 301 WTQSDLLHRLLTSPVLY--------NGNLVVGDSEGYLHWINVEDGRFV 341
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 2/98 (2%)
Query: 82 GINDVVDGIDIALGKYVITLSSDGSTLRAWNLPDGQMVWESFL--RGSKHSKPLLLVPTN 139
GI + + AL V+ + ++A N DG+ +W L + SK L+
Sbjct: 39 GIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGG 98
Query: 140 LKVDKDSLILVSSKGCLHAVSSIDGEILWTRDFAAESV 177
+ V + + S K ++A+++ DG + W A E++
Sbjct: 99 VTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEAL 136
>pdb|2YH3|A Chain A, The Structure Of Bamb From E. Coli
Length = 379
Score = 36.6 bits (83), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 99 ITLSSDGSTLRAWNLPDGQMVWESFLRGSKHSKPLLLVPTNLKVDKDSLILV-SSKGCLH 157
+ + S+ + + A N DG + W++ + G S+P++ D L+L+ +S G L
Sbjct: 101 VYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVV---------SDGLVLIHTSNGQLQ 151
Query: 158 AVSSIDGEILWTRDFAAESVEVQ 180
A++ DG + WT + S+ ++
Sbjct: 152 ALNEADGAVKWTVNLDMPSLSLR 174
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 24/109 (22%)
Query: 65 IASLDLRHGEIFWRHVLG-IND-VVDGIDIAL---GKYVITLSSDGSTLRAWNLPDGQMV 119
+ +LDLR G+I W+ LG +ND +VDG I L V+ L+ DG G +
Sbjct: 246 LTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDG----------GVTL 295
Query: 120 W-ESFLRGSKHSKPLLLVPTNLKVDKDSLILVSSKGCLHAVSSIDGEIL 167
W +S L + P+L +L++ S+G LH ++ DG +
Sbjct: 296 WTQSDLLHRLLTSPVLY--------NGNLVVGDSEGYLHWINVEDGRFV 336
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 2/98 (2%)
Query: 82 GINDVVDGIDIALGKYVITLSSDGSTLRAWNLPDGQMVWESFL--RGSKHSKPLLLVPTN 139
GI + + AL V+ + ++A N DG+ +W L + SK L+
Sbjct: 34 GIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGG 93
Query: 140 LKVDKDSLILVSSKGCLHAVSSIDGEILWTRDFAAESV 177
+ V + + S K ++A+++ DG + W A E++
Sbjct: 94 VTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEAL 131
>pdb|3P1L|A Chain A, Crystal Structure Of Escherichia Coli Bamb, A Lipoprotein
Component Of The Beta-Barrel Assembly Machinery Complex,
Native Crystals
Length = 393
Score = 36.6 bits (83), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 99 ITLSSDGSTLRAWNLPDGQMVWESFLRGSKHSKPLLLVPTNLKVDKDSLILV-SSKGCLH 157
+ + S+ + + A N DG + W++ + G S+P++ D L+L+ +S G L
Sbjct: 123 VYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVV---------SDGLVLIHTSNGQLQ 173
Query: 158 AVSSIDGEILWTRDFAAESVEVQ 180
A++ DG + WT + S+ ++
Sbjct: 174 ALNEADGAVKWTVNLDMPSLSLR 196
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 2/98 (2%)
Query: 82 GINDVVDGIDIALGKYVITLSSDGSTLRAWNLPDGQMVWESFL--RGSKHSKPLLLVPTN 139
GI + + AL V+ + ++A N DG+ +W L + SK L+
Sbjct: 56 GIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGG 115
Query: 140 LKVDKDSLILVSSKGCLHAVSSIDGEILWTRDFAAESV 177
+ V + + S K ++A+++ DG + W A E++
Sbjct: 116 VTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEAL 153
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 24/109 (22%)
Query: 65 IASLDLRHGEIFWRHVLG-IND-VVDGIDIAL---GKYVITLSSDGSTLRAWNLPDGQMV 119
+ +LDLR G+I W+ LG +ND +VDG I L V+ L+ DG G +
Sbjct: 268 LTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDG----------GVTL 317
Query: 120 W-ESFLRGSKHSKPLLLVPTNLKVDKDSLILVSSKGCLHAVSSIDGEIL 167
W +S L + P+L +L++ S+G LH ++ DG +
Sbjct: 318 WTQSDLLHRLLTSPVLY--------NGNLVVGDSEGYLHWINVEDGRFV 358
>pdb|3PRW|A Chain A, Crystal Structure Of The Lipoprotein Bamb
Length = 377
Score = 36.6 bits (83), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 99 ITLSSDGSTLRAWNLPDGQMVWESFLRGSKHSKPLLLVPTNLKVDKDSLILV-SSKGCLH 157
+ + S+ + + A N DG + W++ + G S+P++ D L+L+ +S G L
Sbjct: 107 VYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVV---------SDGLVLIHTSNGQLQ 157
Query: 158 AVSSIDGEILWTRDFAAESVEVQ 180
A++ DG + WT + S+ ++
Sbjct: 158 ALNEADGAVKWTVNLDMPSLSLR 180
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 24/109 (22%)
Query: 65 IASLDLRHGEIFWRHVLG-IND-VVDGIDIAL---GKYVITLSSDGSTLRAWNLPDGQMV 119
+ +LDLR G+I W+ LG +ND +VDG I L V+ L+ DG G +
Sbjct: 252 LTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDG----------GVTL 301
Query: 120 W-ESFLRGSKHSKPLLLVPTNLKVDKDSLILVSSKGCLHAVSSIDGEIL 167
W +S L + P+L +L++ S+G LH ++ DG +
Sbjct: 302 WTQSDLLHRLLTSPVLY--------NGNLVVGDSEGYLHWINVEDGRFV 342
Score = 32.0 bits (71), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 2/98 (2%)
Query: 82 GINDVVDGIDIALGKYVITLSSDGSTLRAWNLPDGQMVWESFL--RGSKHSKPLLLVPTN 139
GI + + AL V+ + ++A N DG+ +W L + SK L+
Sbjct: 40 GIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGG 99
Query: 140 LKVDKDSLILVSSKGCLHAVSSIDGEILWTRDFAAESV 177
+ V + + S K ++A+++ DG + W A E++
Sbjct: 100 VTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEAL 137
>pdb|1TSF|A Chain A, Crystal Structure Of The Archaeal Homolog Of Human Rnase P
Protein Rpp29 From Archaeoglobus Fulgidus
Length = 102
Score = 29.6 bits (65), Expect = 8.7, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 414 ASIIDVTTSELPV--EKEGVSVAKVEHSLFEWLKGHMLKLKGTLMLASPED 462
++D T + L + EK VAK + W KG ++++KG L+ PED
Sbjct: 35 GEVVDETQNTLKIMTEKGLKVVAKRGRTFRVWYKGKIMRIKGDLINFRPED 85
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.134 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,891,428
Number of Sequences: 62578
Number of extensions: 1127147
Number of successful extensions: 2975
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2929
Number of HSP's gapped (non-prelim): 46
length of query: 981
length of database: 14,973,337
effective HSP length: 108
effective length of query: 873
effective length of database: 8,214,913
effective search space: 7171619049
effective search space used: 7171619049
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)