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= 023027
(288 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 = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 39/126 (30%), Positives = 64/126 (50%), Gaps = 8/126 (6%)
Query: 88 LDMHPK----LLTADIPRDLEPIIDFLLEEVLIPFNDLPKSLTRCPRILVSDLKT-QLRP 142
++ HP+ LL D +D++ ++ FL ++V I N L LT+ I DL+ + R
Sbjct: 22 IEKHPEAANLLLRLDFEKDIKQMLLFL-KDVGIEDNQLGAFLTKNHAIFSEDLENLKTRV 80
Query: 143 SFKFLVEFGFKGSHKINCQTTVLLVSSVERTLKPKIDFL-KNLGLSDEEVERMVIRSPGL 201
++ F ++ + LL SVER L ++ F K L LS ++ +V+R P L
Sbjct: 81 AYLHSKNFSKADVAQMVRKAPFLLNFSVER-LDNRLGFFQKELELSVKKTRDLVVRLPRL 139
Query: 202 LTFSVE 207
LT S+E
Sbjct: 140 LTGSLE 145
Score = 27.7 bits (60), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 45/83 (54%), Gaps = 4/83 (4%)
Query: 162 TTVLLVSSVERTLKPKIDFLKNLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQE- 220
+LL E+ +K + FLK++G+ D ++ + ++ + + +E NL +V + +
Sbjct: 29 ANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLE-NLKTRVAYLHSKN 87
Query: 221 -MKGDLDEL-KKFPQYFSFSLER 241
K D+ ++ +K P +FS+ER
Sbjct: 88 FSKADVAQMVRKAPFLLNFSVER 110
>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 298
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 39/126 (30%), Positives = 64/126 (50%), Gaps = 8/126 (6%)
Query: 88 LDMHPK----LLTADIPRDLEPIIDFLLEEVLIPFNDLPKSLTRCPRILVSDLKT-QLRP 142
++ HP+ LL D +D++ ++ FL ++V I N L LT+ I DL+ + R
Sbjct: 50 IEKHPEAANLLLRLDFEKDIKQMLLFL-KDVGIEDNQLGAFLTKNHAIFSEDLENLKTRV 108
Query: 143 SFKFLVEFGFKGSHKINCQTTVLLVSSVERTLKPKIDFL-KNLGLSDEEVERMVIRSPGL 201
++ F ++ + LL SVER L ++ F K L LS ++ +V+R P L
Sbjct: 109 AYLHSKNFSKADVAQMVRKAPFLLNFSVER-LDNRLGFFQKELELSVKKTRDLVVRLPRL 167
Query: 202 LTFSVE 207
LT S+E
Sbjct: 168 LTGSLE 173
Score = 27.7 bits (60), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 45/83 (54%), Gaps = 4/83 (4%)
Query: 162 TTVLLVSSVERTLKPKIDFLKNLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQE- 220
+LL E+ +K + FLK++G+ D ++ + ++ + + +E NL +V + +
Sbjct: 57 ANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLE-NLKTRVAYLHSKN 115
Query: 221 -MKGDLDEL-KKFPQYFSFSLER 241
K D+ ++ +K P +FS+ER
Sbjct: 116 FSKADVAQMVRKAPFLLNFSVER 138
>pdb|3O21|A Chain A, High Resolution Structure Of Glua3 N-Terminal Domain (Ntd)
pdb|3O21|B Chain B, High Resolution Structure Of Glua3 N-Terminal Domain (Ntd)
pdb|3O21|C Chain C, High Resolution Structure Of Glua3 N-Terminal Domain (Ntd)
pdb|3O21|D Chain D, High Resolution Structure Of Glua3 N-Terminal Domain (Ntd)
pdb|3P3W|A Chain A, Structure Of A Dimeric Glua3 N-Terminal Domain (Ntd) At
4.2 A Resolution
pdb|3P3W|B Chain B, Structure Of A Dimeric Glua3 N-Terminal Domain (Ntd) At
4.2 A Resolution
pdb|3P3W|C Chain C, Structure Of A Dimeric Glua3 N-Terminal Domain (Ntd) At
4.2 A Resolution
pdb|3P3W|D Chain D, Structure Of A Dimeric Glua3 N-Terminal Domain (Ntd) At
4.2 A Resolution
Length = 389
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 10/85 (11%)
Query: 181 LKNLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFSFSLE 240
L NLG +D +ER++ + F + NN P V FIQ LDE ++FP E
Sbjct: 219 LANLGFTDILLERVMHGGANITGFQIVNNENPMVQQFIQRWV-RLDE-REFP-------E 269
Query: 241 RKIKP-RYRILVDHGFKLPLAQMLR 264
K P +Y + H L +A+ R
Sbjct: 270 AKNAPLKYTSALTHDAILVIAEAFR 294
>pdb|2LEM|A Chain A, Monomeric Mouse Apoai(1-216)
Length = 216
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 200 GLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFSFSLERKIK 244
G LT +NL + D+ QEM DL+E+K+ Q + ++K K
Sbjct: 64 GPLTRDFWDNLEKETDWVRQEMNKDLEEVKQKVQPYLDEFQKKWK 108
>pdb|3MVB|O Chain O, Crystal Structure Of A Triple Rfy Mutant Of Human Mterf1
Bound To The Termination Sequence
Length = 343
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 5/94 (5%)
Query: 183 NLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFSFSLERK 242
+LG ++EEV++ V+ P ++ F E K+D ++E + ++ + P+ S+
Sbjct: 249 SLGCTEEEVQKFVLSYPDVI-FLAEKKFNDKIDCLMEE-NISISQIIENPRVLDSSIS-T 305
Query: 243 IKPRYRILVDHGFKLPLAQ--MLRVSDGEFNARL 274
+K R + LV+ G L +L S + A+L
Sbjct: 306 LKSRIKELVNAGCNLSTLNITLLSWSKKRYEAKL 339
>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 = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 5/94 (5%)
Query: 183 NLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFSFSLERK 242
+LG ++EEV++ V+ P ++ F E K+D ++E + ++ + P+ S+
Sbjct: 250 SLGCTEEEVQKFVLSYPDVI-FLAEKKFNDKIDCLMEE-NISISQIIENPRVLDSSIS-T 306
Query: 243 IKPRYRILVDHGFKLPLAQ--MLRVSDGEFNARL 274
+K R + LV+ G L +L S + A+L
Sbjct: 307 LKSRIKELVNAGCNLSTLNITLLSWSKKRYEAKL 340
>pdb|3MVA|O Chain O, Crystal Structure Of Human Mterf1 Bound To The Termination
Sequence
Length = 343
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 5/94 (5%)
Query: 183 NLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFSFSLERK 242
+LG ++EEV++ V+ P ++ F E K+D ++E + ++ + P+ S+
Sbjct: 249 SLGCTEEEVQKFVLSYPDVI-FLAEKKFNDKIDCLMEE-NISISQIIENPRVLDSSIS-T 305
Query: 243 IKPRYRILVDHGFKLPLAQ--MLRVSDGEFNARL 274
+K R + LV+ G L +L S + A+L
Sbjct: 306 LKSRIKELVNAGCNLSTLNITLLSWSKKRYEAKL 339
>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 = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 5/94 (5%)
Query: 183 NLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFSFSLERK 242
+LG ++EEV++ V+ P ++ F E K+D ++E + ++ + P+ S+
Sbjct: 207 SLGCTEEEVQKFVLSYPDVI-FLAEKKFNDKIDCLMEE-NISISQIIENPRVLDSSIS-T 263
Query: 243 IKPRYRILVDHGFKLPLAQ--MLRVSDGEFNARL 274
+K R + LV+ G L +L S + A+L
Sbjct: 264 LKSRIKELVNAGCNLSTLNITLLSWSKKRYEAKL 297
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 27.7 bits (60), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 244 KPRYRILVDHGFKLPLA 260
+ R ++LVDHGF+LP A
Sbjct: 355 RARKQVLVDHGFRLPSA 371
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
Length = 658
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 244 KPRYRILVDHGFKLPLA 260
+ R ++LVDHGF+LP A
Sbjct: 355 RARKQVLVDHGFRLPSA 371
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 27.7 bits (60), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 244 KPRYRILVDHGFKLPLA 260
+ R ++LVDHGF+LP A
Sbjct: 355 RARKQVLVDHGFRLPSA 371
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 27.7 bits (60), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 244 KPRYRILVDHGFKLPLA 260
+ R ++LVDHGF+LP A
Sbjct: 354 RARKQVLVDHGFRLPSA 370
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 244 KPRYRILVDHGFKLPLA 260
+ R ++LVDHGF+LP A
Sbjct: 380 RARKQVLVDHGFRLPSA 396
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 0.141 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,650,849
Number of Sequences: 62578
Number of extensions: 288805
Number of successful extensions: 736
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 730
Number of HSP's gapped (non-prelim): 27
length of query: 288
length of database: 14,973,337
effective HSP length: 98
effective length of query: 190
effective length of database: 8,840,693
effective search space: 1679731670
effective search space used: 1679731670
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)