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= 048759
(442 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 = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/126 (24%), Positives = 57/126 (45%), Gaps = 7/126 (5%)
Query: 243 SVIAQYPQIIGLPLK---AKMSSQLYFFNLKLKIDPDEFAQVVEKMPQVVSLNQHVIMKS 299
S I ++P+ L L+ K Q+ F + I+ ++ + K + S + +
Sbjct: 20 SKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTR 79
Query: 300 VEFLLGRGIPSGDLAKMVVQCPQLIACRVELMKNSFYFFKSEMGRPIKE----LIEFPEY 355
V +L + D+A+MV + P L+ VE + N FF+ E+ +K+ ++ P
Sbjct: 80 VAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLGFFQKELELSVKKTRDLVVRLPRL 139
Query: 356 FTYSLE 361
T SLE
Sbjct: 140 LTGSLE 145
Score = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 35/162 (21%), Positives = 67/162 (41%), Gaps = 39/162 (24%)
Query: 58 LGLTIDDINEYP----LMLGCSMRKNMIPVFSYLEKIGIAKSKLGEFVKKYPQV------ 107
LG+ + I ++P L+L K++ + +L+ +GI ++LG F+ K +
Sbjct: 15 LGVDLSKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLE 74
Query: 108 --------LHA-----SVVVELMPVVKFLRGLDVEKED--IGY--------------VLM 138
LH+ + V +++ FL VE+ D +G+ +++
Sbjct: 75 NLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLGFFQKELELSVKKTRDLVV 134
Query: 139 KYPELLGFKLEGTMSTSVAYLVSIGVSPRDIGPMVTQYPYFL 180
+ P LL LE Y + +G +I M+T+ P L
Sbjct: 135 RLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRIPKML 176
>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 298
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 31/126 (24%), Positives = 57/126 (45%), Gaps = 7/126 (5%)
Query: 243 SVIAQYPQIIGLPLK---AKMSSQLYFFNLKLKIDPDEFAQVVEKMPQVVSLNQHVIMKS 299
S I ++P+ L L+ K Q+ F + I+ ++ + K + S + +
Sbjct: 48 SKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTR 107
Query: 300 VEFLLGRGIPSGDLAKMVVQCPQLIACRVELMKNSFYFFKSEMGRPIKE----LIEFPEY 355
V +L + D+A+MV + P L+ VE + N FF+ E+ +K+ ++ P
Sbjct: 108 VAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLGFFQKELELSVKKTRDLVVRLPRL 167
Query: 356 FTYSLE 361
T SLE
Sbjct: 168 LTGSLE 173
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 35/162 (21%), Positives = 67/162 (41%), Gaps = 39/162 (24%)
Query: 58 LGLTIDDINEYP----LMLGCSMRKNMIPVFSYLEKIGIAKSKLGEFVKKYPQV------ 107
LG+ + I ++P L+L K++ + +L+ +GI ++LG F+ K +
Sbjct: 43 LGVDLSKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLE 102
Query: 108 --------LHA-----SVVVELMPVVKFLRGLDVEKED--IGY--------------VLM 138
LH+ + V +++ FL VE+ D +G+ +++
Sbjct: 103 NLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLGFFQKELELSVKKTRDLVV 162
Query: 139 KYPELLGFKLEGTMSTSVAYLVSIGVSPRDIGPMVTQYPYFL 180
+ P LL LE Y + +G +I M+T+ P L
Sbjct: 163 RLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRIPKML 204
>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 = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 33/145 (22%), Positives = 69/145 (47%), Gaps = 5/145 (3%)
Query: 232 ISFGIRREKLASVIAQYPQIIGLPLKAKMSSQLYFFNLKLKIDPDEFAQVVEKMPQVVSL 291
I G+ E + V+ + PQ++ LP+ Y KL + + +V+ P++ ++
Sbjct: 86 ILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYL--QKLGLGEGKLKRVLYCCPEIFTM 143
Query: 292 NQHVIMKSVEFLLGRGIPS-GDLAKMVVQCPQLIACRVELMKNSFYFFKSEMGRPIKELI 350
Q I +V L + + + + K++ CP ++ + ++ F + MG +++
Sbjct: 144 RQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQLEYKFQYAYFRMGIKHPDIV 203
Query: 351 EFPEYFTYSLESRIKPRYQRLQSKG 375
+ EY YSL ++IK R+ L+ G
Sbjct: 204 K-SEYLQYSL-TKIKQRHIYLERLG 226
>pdb|4FZV|B Chain B, Crystal Structure Of The Human Mterf4:nsun4:sam Ternary
Complex
Length = 239
Score = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 33/146 (22%), Positives = 69/146 (47%), Gaps = 5/146 (3%)
Query: 231 LISFGIRREKLASVIAQYPQIIGLPLKAKMSSQLYFFNLKLKIDPDEFAQVVEKMPQVVS 290
I G+ E + V+ + PQ++ LP+ Y KL + + +V+ P++ +
Sbjct: 40 FILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYL--QKLGLGEGKLKRVLYCCPEIFT 97
Query: 291 LNQHVIMKSVEFLLGRGIPS-GDLAKMVVQCPQLIACRVELMKNSFYFFKSEMGRPIKEL 349
+ Q I +V L + + + + K++ CP ++ + ++ F + MG ++
Sbjct: 98 MRQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQLEYKFQYAYFRMGIKHPDI 157
Query: 350 IEFPEYFTYSLESRIKPRYQRLQSKG 375
++ EY YSL ++IK R+ L+ G
Sbjct: 158 VK-SEYLQYSL-TKIKQRHIYLERLG 181
>pdb|2A1T|S Chain S, Structure Of The Human Mcad:etf E165betaa Complex
pdb|2A1U|B Chain B, Crystal Structure Of The Human Etf E165betaa Mutant
Length = 255
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 349 LIEFPEYFTYSLESRIKPRYQRLQSKGIRCSMNWFLNCSDQ---RFEERLLGNYIESESS 405
L+ Y+++ R+KP + + G++ SMN F + + R +E+ L + + S
Sbjct: 7 LVAVKRVIDYAVKIRVKPDRTGVVTDGVKHSMNPFCEIAVEEAVRLKEKKLVKEVIAVSC 66
Query: 406 GPSFC 410
GP+ C
Sbjct: 67 GPAQC 71
>pdb|1EFV|B Chain B, Three-Dimensional Structure Of Human Electron Transfer
Flavoprotein To 2.1 A Resolution
pdb|1T9G|S Chain S, Structure Of The Human Mcad:etf Complex
Length = 255
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 349 LIEFPEYFTYSLESRIKPRYQRLQSKGIRCSMNWFLNCSDQ---RFEERLLGNYIESESS 405
L+ Y+++ R+KP + + G++ SMN F + + R +E+ L + + S
Sbjct: 7 LVAVKRVIDYAVKIRVKPDRTGVVTDGVKHSMNPFCEIAVEEAVRLKEKKLVKEVIAVSC 66
Query: 406 GPSFC 410
GP+ C
Sbjct: 67 GPAQC 71
>pdb|3MVA|O Chain O, Crystal Structure Of Human Mterf1 Bound To The Termination
Sequence
Length = 343
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 54/112 (48%), Gaps = 4/112 (3%)
Query: 231 LISFGIRREKLASVIAQYPQIIGLPLKAKMSSQLYFFNLKLKIDPDEFAQVVEKMPQVV- 289
L+S G +E +AS+I++YP+ I + S+ + K+ E ++E+ P+
Sbjct: 58 LLSKGASKEVIASIISRYPRAITRT--PENLSKRWDLWRKIVTSDLEIVNILERSPESFF 115
Query: 290 -SLNQHVIMKSVEFLLGRGIPSGDLAKMVVQCPQLIACRVELMKNSFYFFKS 340
S N + +++FL G+ L +++ P+ + ++L K F ++
Sbjct: 116 RSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQA 167
>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 = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 54/112 (48%), Gaps = 4/112 (3%)
Query: 231 LISFGIRREKLASVIAQYPQIIGLPLKAKMSSQLYFFNLKLKIDPDEFAQVVEKMPQVV- 289
L+S G +E +AS+I++YP+ I + S+ + K+ E ++E+ P+
Sbjct: 59 LLSKGASKEVIASIISRYPRAITRT--PENLSKRWDLWRKIVTSDLEIVNILERSPESFF 116
Query: 290 -SLNQHVIMKSVEFLLGRGIPSGDLAKMVVQCPQLIACRVELMKNSFYFFKS 340
S N + +++FL G+ L +++ P+ + ++L K F ++
Sbjct: 117 RSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQA 168
>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 = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 54/112 (48%), Gaps = 4/112 (3%)
Query: 231 LISFGIRREKLASVIAQYPQIIGLPLKAKMSSQLYFFNLKLKIDPDEFAQVVEKMPQVV- 289
L+S G +E +AS+I++YP+ I + S+ + K+ E ++E+ P+
Sbjct: 16 LLSKGASKEVIASIISRYPRAITRT--PENLSKRWDLWRKIVTSDLEIVNILERSPESFF 73
Query: 290 -SLNQHVIMKSVEFLLGRGIPSGDLAKMVVQCPQLIACRVELMKNSFYFFKS 340
S N + +++FL G+ L +++ P+ + ++L K F ++
Sbjct: 74 RSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQA 125
>pdb|3MVB|O Chain O, Crystal Structure Of A Triple Rfy Mutant Of Human Mterf1
Bound To The Termination Sequence
Length = 343
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 53/112 (47%), Gaps = 4/112 (3%)
Query: 231 LISFGIRREKLASVIAQYPQIIGLPLKAKMSSQLYFFNLKLKIDPDEFAQVVEKMPQVV- 289
L+S G +E +AS+I++YP+ I + S+ + K+ E ++E P+
Sbjct: 58 LLSKGASKEVIASIISRYPRAITRT--PENLSKRWDLWRKIVTSDLEIVNILEASPESFF 115
Query: 290 -SLNQHVIMKSVEFLLGRGIPSGDLAKMVVQCPQLIACRVELMKNSFYFFKS 340
S N + +++FL G+ L +++ P+ + ++L K F ++
Sbjct: 116 RSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQA 167
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 0.142 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,000,800
Number of Sequences: 62578
Number of extensions: 486639
Number of successful extensions: 1190
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1170
Number of HSP's gapped (non-prelim): 18
length of query: 442
length of database: 14,973,337
effective HSP length: 102
effective length of query: 340
effective length of database: 8,590,381
effective search space: 2920729540
effective search space used: 2920729540
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: 53 (25.0 bits)