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= 008728
(556 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 270
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 40/183 (21%), Positives = 78/183 (42%), Gaps = 2/183 (1%)
Query: 276 LMGCGIGERWKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVRD 335
L+ + K ++ +L +G+ + + L +F DLE + +V +
Sbjct: 32 LLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-LKTRVAYLHSKNFSK 90
Query: 336 EGIANMLVKFPSLLTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLE 395
+A M+ K P LL +S+ +++ + F + +S + + P LL S+ E
Sbjct: 91 ADVAQMVRKAPFLLNFSV-ERLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKE 149
Query: 396 VNVKYFLSLGIKLHQLGAMIADFPMLLRYNIDIFRPKYRYLRRTMVRPLQDLIEFPRFFS 455
Y L LG K +++ MI P +L N + ++ M P +++FP+ F+
Sbjct: 150 NMKVYRLELGFKHNEIQHMITRIPKMLTANKMKLTETFDFVHNVMSIPHHIIVKFPQVFN 209
Query: 456 YSL 458
L
Sbjct: 210 TRL 212
Score = 35.4 bits (80), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 34/145 (23%), Positives = 66/145 (45%), Gaps = 8/145 (5%)
Query: 140 ESIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRDWMGYVM 199
+ I+ + +LK V ++ LG L K I +E L V YL + + + ++
Sbjct: 39 KDIKQMLLFLKDVGIEDNQLGAFLTKNHA-IFSEDLENLKTRVAYLHSKNFSKADVAQMV 97
Query: 200 SRCPQLLSQSIEEVKTRVHFY---LDMGMNKNDFGTMVFDYPKIL-GFLTLEEMHQKVTY 255
+ P LL+ S+E + R+ F+ L++ + K +V P++L G L + + KV Y
Sbjct: 98 RKAPFLLNFSVERLDNRLGFFQKELELSVKKT--RDLVVRLPRLLTGSLEPVKENMKV-Y 154
Query: 256 LKEFGLSTEDVGRLLAFRPHLMGCG 280
E G ++ ++ P ++
Sbjct: 155 RLELGFKHNEIQHMITRIPKMLTAN 179
>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 298
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 40/183 (21%), Positives = 78/183 (42%), Gaps = 2/183 (1%)
Query: 276 LMGCGIGERWKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVRD 335
L+ + K ++ +L +G+ + + L +F DLE + +V +
Sbjct: 60 LLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-LKTRVAYLHSKNFSK 118
Query: 336 EGIANMLVKFPSLLTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLE 395
+A M+ K P LL +S+ +++ + F + +S + + P LL S+ E
Sbjct: 119 ADVAQMVRKAPFLLNFSV-ERLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKE 177
Query: 396 VNVKYFLSLGIKLHQLGAMIADFPMLLRYNIDIFRPKYRYLRRTMVRPLQDLIEFPRFFS 455
Y L LG K +++ MI P +L N + ++ M P +++FP+ F+
Sbjct: 178 NMKVYRLELGFKHNEIQHMITRIPKMLTANKMKLTETFDFVHNVMSIPHHIIVKFPQVFN 237
Query: 456 YSL 458
L
Sbjct: 238 TRL 240
Score = 36.2 bits (82), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 34/145 (23%), Positives = 66/145 (45%), Gaps = 8/145 (5%)
Query: 140 ESIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRDWMGYVM 199
+ I+ + +LK V ++ LG L K I +E L V YL + + + ++
Sbjct: 67 KDIKQMLLFLKDVGIEDNQLGAFLTKNHA-IFSEDLENLKTRVAYLHSKNFSKADVAQMV 125
Query: 200 SRCPQLLSQSIEEVKTRVHFY---LDMGMNKNDFGTMVFDYPKIL-GFLTLEEMHQKVTY 255
+ P LL+ S+E + R+ F+ L++ + K +V P++L G L + + KV Y
Sbjct: 126 RKAPFLLNFSVERLDNRLGFFQKELELSVKKT--RDLVVRLPRLLTGSLEPVKENMKV-Y 182
Query: 256 LKEFGLSTEDVGRLLAFRPHLMGCG 280
E G ++ ++ P ++
Sbjct: 183 RLELGFKHNEIQHMITRIPKMLTAN 207
>pdb|3MVB|O Chain O, Crystal Structure Of A Triple Rfy Mutant Of Human Mterf1
Bound To The Termination Sequence
Length = 343
Score = 35.4 bits (80), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 60/291 (20%), Positives = 119/291 (40%), Gaps = 20/291 (6%)
Query: 180 EIVEYLETNGVRRDWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPK 239
++++ L T GV D R P + + I + F L G +K +++ YP+
Sbjct: 21 DLLKNLLTMGVDID---MARKRQPGVFHRMITNEQDLKMFLLSKGASKEVIASIISRYPR 77
Query: 240 ILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPH-LMGCGIGERWKPLVKYLYYLGVS 298
+ T E + ++ ++ S ++ +L P + +K+LY +G++
Sbjct: 78 AIT-RTPENLSKRWDLWRKIVTSDLEIVNILEASPESFFRSNNNLNLENNIKFLYSVGLT 136
Query: 299 RDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVR------DEGIANMLVKFPSLLTYS 352
R + R+L P F L+ V F Q G+ + + ++ K P++L S
Sbjct: 137 RKCLCRLLTNAPRTFSNSLDLN-KQMVEFLQAAGLSLGHNDPADFVRKIIFKNPAILIQS 195
Query: 353 LYKKIRPVVIFLMTKAGVSERDIGKCLALGP--ELLGCS--IGNKLEVNVK-YFLSLGIK 407
K+++ + FL + ++ ++ L GP E+L S + N+K SLG
Sbjct: 196 -TKRVKANIEFLRSTFNLNSEEL-LVLICGPGAEILDLSNDAARRSYANIKEKLFSLGCT 253
Query: 408 LHQLGAMIADFPMLLRYNIDIFRPKYRYLRRTMVRPLQDLIEFPRFFSYSL 458
++ + +P ++ F K L + + +IE PR S+
Sbjct: 254 EEEVQKFVLSYPDVIFLAEKKFNDKIDCLMEENI-SISQIIENPRVLDSSI 303
>pdb|2BI4|A Chain A, Lactaldehyde:1,2-Propanediol Oxidoreductase Of Escherichia
Coli
pdb|2BI4|B Chain B, Lactaldehyde:1,2-Propanediol Oxidoreductase Of Escherichia
Coli
pdb|2BL4|A Chain A, Lactaldehyde:1,2-Propanediol Oxidoreductase Of Escherichia
Coli
pdb|2BL4|B Chain B, Lactaldehyde:1,2-Propanediol Oxidoreductase Of Escherichia
Coli
Length = 392
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 56/134 (41%), Gaps = 15/134 (11%)
Query: 316 DLETTIVPKVRFFQDIGVRDEGIANMLVKFPSLLTYSLYKKIRPVVIFLMTKAGVSERDI 375
D+ + P ++ + I + + LT +L+ K ++ + + ++D
Sbjct: 189 DMMDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDA 248
Query: 376 GKCLALGPELLGCSIGNKLEVNVKYFLSLGIKLHQLGAM------IAD---FPMLLRYNI 426
G+ +ALG + G N V L G+ H LGA +A+ P ++RYN
Sbjct: 249 GEEMALGQYVAGMGFSN-----VGLGLVHGMA-HPLGAFYNTPHGVANAILLPHVMRYNA 302
Query: 427 DIFRPKYRYLRRTM 440
D KYR + R M
Sbjct: 303 DFTGEKYRDIARVM 316
>pdb|3MVA|O Chain O, Crystal Structure Of Human Mterf1 Bound To The Termination
Sequence
Length = 343
Score = 32.3 bits (72), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 60/291 (20%), Positives = 118/291 (40%), Gaps = 20/291 (6%)
Query: 180 EIVEYLETNGVRRDWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPK 239
++++ L T GV D R P + + I + F L G +K +++ YP+
Sbjct: 21 DLLKNLLTMGVDID---MARKRQPGVFHRMITNEQDLKMFLLSKGASKEVIASIISRYPR 77
Query: 240 ILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPH-LMGCGIGERWKPLVKYLYYLGVS 298
+ T E + ++ ++ S ++ +L P + +K+LY +G++
Sbjct: 78 AIT-RTPENLSKRWDLWRKIVTSDLEIVNILERSPESFFRSNNNLNLENNIKFLYSVGLT 136
Query: 299 RDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVR------DEGIANMLVKFPSLLTYS 352
R + R+L P F L+ V F Q G+ + + ++ K P +L S
Sbjct: 137 RKCLCRLLTNAPRTFSNSLDLN-KQMVEFLQAAGLSLGHNDPADFVRKIIFKNPFILIQS 195
Query: 353 LYKKIRPVVIFLMTKAGVSERDIGKCLALGP--ELLGCS--IGNKLEVNVK-YFLSLGIK 407
K+++ + FL + ++ ++ L GP E+L S + N+K SLG
Sbjct: 196 -TKRVKANIEFLRSTFNLNSEEL-LVLICGPGAEILDLSNDYARRSYANIKEKLFSLGCT 253
Query: 408 LHQLGAMIADFPMLLRYNIDIFRPKYRYLRRTMVRPLQDLIEFPRFFSYSL 458
++ + +P ++ F K L + + +IE PR S+
Sbjct: 254 EEEVQKFVLSYPDVIFLAEKKFNDKIDCLMEENI-SISQIIENPRVLDSSI 303
>pdb|3N6S|A Chain A, Crystal Structure Of Human Mitochondrial Mterf In Complex
With A 15- Mer Dna Encompassing The Trnaleu(Uur) Binding
Sequence
Length = 353
Score = 32.3 bits (72), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 60/291 (20%), Positives = 118/291 (40%), Gaps = 20/291 (6%)
Query: 180 EIVEYLETNGVRRDWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPK 239
++++ L T GV D R P + + I + F L G +K +++ YP+
Sbjct: 22 DLLKNLLTMGVDID---MARKRQPGVFHRMITNEQDLKMFLLSKGASKEVIASIISRYPR 78
Query: 240 ILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPH-LMGCGIGERWKPLVKYLYYLGVS 298
+ T E + ++ ++ S ++ +L P + +K+LY +G++
Sbjct: 79 AIT-RTPENLSKRWDLWRKIVTSDLEIVNILERSPESFFRSNNNLNLENNIKFLYSVGLT 137
Query: 299 RDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVR------DEGIANMLVKFPSLLTYS 352
R + R+L P F L+ V F Q G+ + + ++ K P +L S
Sbjct: 138 RKCLCRLLTNAPRTFSNSLDLN-KQMVEFLQAAGLSLGHNDPADFVRKIIFKNPFILIQS 196
Query: 353 LYKKIRPVVIFLMTKAGVSERDIGKCLALGP--ELLGCS--IGNKLEVNVK-YFLSLGIK 407
K+++ + FL + ++ ++ L GP E+L S + N+K SLG
Sbjct: 197 -TKRVKANIEFLRSTFNLNSEEL-LVLICGPGAEILDLSNDYARRSYANIKEKLFSLGCT 254
Query: 408 LHQLGAMIADFPMLLRYNIDIFRPKYRYLRRTMVRPLQDLIEFPRFFSYSL 458
++ + +P ++ F K L + + +IE PR S+
Sbjct: 255 EEEVQKFVLSYPDVIFLAEKKFNDKIDCLMEENI-SISQIIENPRVLDSSI 304
>pdb|4FP9|B Chain B, Human Mterf4-Nsun4 Protein Complex
pdb|4FP9|E Chain E, Human Mterf4-Nsun4 Protein Complex
pdb|4FP9|G Chain G, Human Mterf4-Nsun4 Protein Complex
pdb|4FP9|H Chain H, Human Mterf4-Nsun4 Protein Complex
Length = 335
Score = 32.3 bits (72), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 24/111 (21%), Positives = 57/111 (51%), Gaps = 2/111 (1%)
Query: 174 SIEELNEIVEYLETNGVRRDWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTM 233
S+++L +I+ G+ + + V+ + PQLL I +++ R + +G+ + +
Sbjct: 74 SLQQLLDIISEFILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRV 133
Query: 234 VFDYPKILGFLTLEEMHQKVTYLKEFGLST-EDVGRLLAFRPHLMGCGIGE 283
++ P+I + ++++ V LKE L T + V ++L P ++ +G+
Sbjct: 134 LYCCPEIFT-MRQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQ 183
>pdb|3N7Q|A Chain A, Crystal Structure Of Human Mitochondrial Mterf Fragment
(Aa 99-399) In Complex With A 12-Mer Dna Encompassing
The Trnaleu(Uur) Binding Sequence
Length = 310
Score = 32.0 bits (71), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 52/252 (20%), Positives = 103/252 (40%), Gaps = 17/252 (6%)
Query: 219 FYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPH-LM 277
F L G +K +++ YP+ + T E + ++ ++ S ++ +L P
Sbjct: 15 FLLSKGASKEVIASIISRYPRAIT-RTPENLSKRWDLWRKIVTSDLEIVNILERSPESFF 73
Query: 278 GCGIGERWKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVR--- 334
+ +K+LY +G++R + R+L P F L+ V F Q G+
Sbjct: 74 RSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSLDLN-KQMVEFLQAAGLSLGH 132
Query: 335 ---DEGIANMLVKFPSLLTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGP--ELLGCS 389
+ + ++ K P +L S K+++ + FL + ++ ++ L GP E+L S
Sbjct: 133 NDPADFVRKIIFKNPFILIQS-TKRVKANIEFLRSTFNLNSEEL-LVLICGPGAEILDLS 190
Query: 390 --IGNKLEVNVK-YFLSLGIKLHQLGAMIADFPMLLRYNIDIFRPKYRYLRRTMVRPLQD 446
+ N+K SLG ++ + +P ++ F K L + +
Sbjct: 191 NDYARRSYANIKEKLFSLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDCLMEENI-SISQ 249
Query: 447 LIEFPRFFSYSL 458
+IE PR S+
Sbjct: 250 IIENPRVLDSSI 261
>pdb|3P3D|A Chain A, Crystal Structure Of The Nup53 Rrm Domain From Pichia
Guilliermondii
Length = 132
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 9/62 (14%)
Query: 223 MGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPHLMGCGIG 282
M ++ + +VF YP+ + +Q + Y +EFG ED L +P M G+
Sbjct: 1 MSLSNGELAILVFGYPETMA-------NQVIAYFQEFGTILEDFEVLR--KPQAMTVGLQ 51
Query: 283 ER 284
+R
Sbjct: 52 DR 53
>pdb|4FZV|B Chain B, Crystal Structure Of The Human Mterf4:nsun4:sam Ternary
Complex
Length = 239
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/109 (21%), Positives = 55/109 (50%), Gaps = 2/109 (1%)
Query: 176 EELNEIVEYLETNGVRRDWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVF 235
++L +I+ G+ + + V+ + PQLL I +++ R + +G+ + +++
Sbjct: 31 QQLLDIISEFILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLY 90
Query: 236 DYPKILGFLTLEEMHQKVTYLKEFGLST-EDVGRLLAFRPHLMGCGIGE 283
P+I + ++++ V LKE L T + V ++L P ++ +G+
Sbjct: 91 CCPEIFT-MRQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQ 138
>pdb|3ZZM|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Purh With
A Novel Bound Nucleotide Cfair, At 2.2 A Resolution.
pdb|3ZZM|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Purh With
A Novel Bound Nucleotide Cfair, At 2.2 A Resolution.
pdb|4A1O|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Purh
Complexed With Aicar And A Novel Nucleotide Cfair, At
2.48 A Resolution.
pdb|4A1O|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Purh
Complexed With Aicar And A Novel Nucleotide Cfair, At
2.48 A Resolution
Length = 523
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 28/96 (29%), Positives = 40/96 (41%), Gaps = 13/96 (13%)
Query: 441 VRPLQDLIEFPRFFSYSLEERIIPRHKIMVENRVNFKLRYMLACSNEEFNQKVADKVEGR 500
V P++ L FP L+ R+ H RV+ L L + A + G
Sbjct: 54 VTPVEQLTGFPEV----LDGRVKTLHP-----RVHAGLLADL----RKSEHAAALEQLGI 100
Query: 501 RLYELGLINEAPHSQTVDDSLRQQDAVDYTDIGSKA 536
+EL ++N P SQTV+ D V+ DIG A
Sbjct: 101 EAFELVVVNLYPFSQTVESGASVDDCVEQIDIGGPA 136
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
0.323 0.140 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,435,856
Number of Sequences: 62578
Number of extensions: 700435
Number of successful extensions: 1518
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1496
Number of HSP's gapped (non-prelim): 25
length of query: 556
length of database: 14,973,337
effective HSP length: 104
effective length of query: 452
effective length of database: 8,465,225
effective search space: 3826281700
effective search space used: 3826281700
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)