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= 007270
(610 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 298
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 48/205 (23%), Positives = 90/205 (43%), Gaps = 36/205 (17%)
Query: 393 LKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRILGRC 452
+K ML L ++G+E+ +LG + K+ + + + V++L F + +V +++ +
Sbjct: 69 IKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSKNFSKADVAQMVRKA 128
Query: 453 PELFASNIERTLMKKIDFLIGIGISKDHLPRTIKKYPELLVSDVDRTLLPRI-------- 504
P L ++ER + +G + L ++KK +L+V LPR+
Sbjct: 129 PFLLNFSVERLDNR-------LGFFQKELELSVKKTRDLVVR------LPRLLTGSLEPV 175
Query: 505 -----KYLMEMGLSKRDIAFMVRRFSPLLGYS---IDEVFRPKLAFLLNTMEKSLQDVVA 556
Y +E+G +I M+ R +L + + E F F+ N M +V
Sbjct: 176 KENMKVYRLELGFKHNEIQHMITRIPKMLTANKMKLTETF----DFVHNVMSIPHHIIVK 231
Query: 557 YPRYFSYSLEKKIKPR--FWVLKGR 579
+P+ F+ L K+K R F GR
Sbjct: 232 FPQVFNTRL-FKVKERHLFLTYLGR 255
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 48/164 (29%), Positives = 84/164 (51%), Gaps = 18/164 (10%)
Query: 397 LDQLGELGVENKKLGQVIAKSPQ---LLLRK--PQEFRQVVSFLEDVGFDRENVGRILGR 451
L +L LGV+ K I K P+ LLLR ++ +Q++ FL+DVG + +G L +
Sbjct: 37 LQKLVLLGVDLSK----IEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTK 92
Query: 452 CPELFASNIERTLMKKIDFLIGIGISKDHLPRTIKKYPELLVSDVDRTLLPRIKYLM-EM 510
+F+ ++E L ++ +L SK + + ++K P LL V+R L R+ + E+
Sbjct: 93 NHAIFSEDLE-NLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVER-LDNRLGFFQKEL 150
Query: 511 GLSKRDIAFMVRRFSPLLGYSID------EVFRPKLAFLLNTME 548
LS + +V R LL S++ +V+R +L F N ++
Sbjct: 151 ELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQ 194
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 78/165 (47%), Gaps = 7/165 (4%)
Query: 278 LLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEIGAVDN 337
LL L E +K ++ FL+ VG+ + +G L + +++ ++T+
Sbjct: 60 LLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSKNFSKA 119
Query: 338 DVGKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRA---IRSWPHLLGCSTSKLK 394
DV +M+ K P++L+ S+ E + L F +E +LSV + + P LL S +K
Sbjct: 120 DVAQMVRKAPFLLNFSV-ERLDNRLGFFQKE--LELSVKKTRDLVVRLPRLLTGSLEPVK 176
Query: 395 LMLDQLG-ELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDV 438
+ ELG ++ ++ +I + P++L + + F+ +V
Sbjct: 177 ENMKVYRLELGFKHNEIQHMITRIPKMLTANKMKLTETFDFVHNV 221
>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 270
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 48/205 (23%), Positives = 90/205 (43%), Gaps = 36/205 (17%)
Query: 393 LKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRILGRC 452
+K ML L ++G+E+ +LG + K+ + + + V++L F + +V +++ +
Sbjct: 41 IKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSKNFSKADVAQMVRKA 100
Query: 453 PELFASNIERTLMKKIDFLIGIGISKDHLPRTIKKYPELLVSDVDRTLLPRI-------- 504
P L ++ER + +G + L ++KK +L+V LPR+
Sbjct: 101 PFLLNFSVERLDNR-------LGFFQKELELSVKKTRDLVVR------LPRLLTGSLEPV 147
Query: 505 -----KYLMEMGLSKRDIAFMVRRFSPLLGYS---IDEVFRPKLAFLLNTMEKSLQDVVA 556
Y +E+G +I M+ R +L + + E F F+ N M +V
Sbjct: 148 KENMKVYRLELGFKHNEIQHMITRIPKMLTANKMKLTETF----DFVHNVMSIPHHIIVK 203
Query: 557 YPRYFSYSLEKKIKPR--FWVLKGR 579
+P+ F+ L K+K R F GR
Sbjct: 204 FPQVFNTRL-FKVKERHLFLTYLGR 227
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 48/164 (29%), Positives = 84/164 (51%), Gaps = 18/164 (10%)
Query: 397 LDQLGELGVENKKLGQVIAKSPQ---LLLRK--PQEFRQVVSFLEDVGFDRENVGRILGR 451
L +L LGV+ K I K P+ LLLR ++ +Q++ FL+DVG + +G L +
Sbjct: 9 LQKLVLLGVDLSK----IEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTK 64
Query: 452 CPELFASNIERTLMKKIDFLIGIGISKDHLPRTIKKYPELLVSDVDRTLLPRIKYLM-EM 510
+F+ ++E L ++ +L SK + + ++K P LL V+R L R+ + E+
Sbjct: 65 NHAIFSEDLE-NLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVER-LDNRLGFFQKEL 122
Query: 511 GLSKRDIAFMVRRFSPLLGYSID------EVFRPKLAFLLNTME 548
LS + +V R LL S++ +V+R +L F N ++
Sbjct: 123 ELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQ 166
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 78/165 (47%), Gaps = 7/165 (4%)
Query: 278 LLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEIGAVDN 337
LL L E +K ++ FL+ VG+ + +G L + +++ ++T+
Sbjct: 32 LLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSKNFSKA 91
Query: 338 DVGKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRA---IRSWPHLLGCSTSKLK 394
DV +M+ K P++L+ S+ E + L F +E +LSV + + P LL S +K
Sbjct: 92 DVAQMVRKAPFLLNFSV-ERLDNRLGFFQKE--LELSVKKTRDLVVRLPRLLTGSLEPVK 148
Query: 395 LMLDQLG-ELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDV 438
+ ELG ++ ++ +I + P++L + + F+ +V
Sbjct: 149 ENMKVYRLELGFKHNEIQHMITRIPKMLTANKMKLTETFDFVHNV 193
>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 = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 75/155 (48%), Gaps = 22/155 (14%)
Query: 391 SKLKLMLDQLGE---LGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGR 447
+ L+ +LD + E LG+ + + V+ KSPQLL + R+ S+L+ +G + R
Sbjct: 73 ASLQQLLDIISEFILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKR 132
Query: 448 ILGRCPELFASNIERTLMKKIDFLIGIGISKDHLPRTIKKYPELLVS--DVDRTLLPRIK 505
+L CPE+F M++ D + + K+ T+++ ++L S V R L +++
Sbjct: 133 VLYCCPEIFT-------MRQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQLE 185
Query: 506 YLME-----MGLSKRDIAFMVRRFSPLLGYSIDEV 535
Y + MG+ DI S L YS+ ++
Sbjct: 186 YKFQYAYFRMGIKHPDIV-----KSEYLQYSLTKI 215
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 1/84 (1%)
Query: 378 AIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFL-E 436
++ P LL +++ L +LG+ KL +V+ P++ + Q+ V L E
Sbjct: 98 VLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMRQQDINDTVRLLKE 157
Query: 437 DVGFDRENVGRILGRCPELFASNI 460
F + V +IL CP + ++
Sbjct: 158 KCLFTVQQVTKILHSCPSVLREDL 181
>pdb|4FZV|B Chain B, Crystal Structure Of The Human Mterf4:nsun4:sam Ternary
Complex
Length = 239
Score = 36.6 bits (83), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 40/150 (26%), Positives = 72/150 (48%), Gaps = 22/150 (14%)
Query: 396 MLDQLGE---LGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRILGRC 452
+LD + E LG+ + + V+ KSPQLL + R+ S+L+ +G + R+L C
Sbjct: 33 LLDIISEFILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLYCC 92
Query: 453 PELFASNIERTLMKKIDFLIGIGISKDHLPRTIKKYPELLVS--DVDRTLLPRIKYLME- 509
PE+F M++ D + + K+ T+++ ++L S V R L +++Y +
Sbjct: 93 PEIFT-------MRQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQLEYKFQY 145
Query: 510 ----MGLSKRDIAFMVRRFSPLLGYSIDEV 535
MG+ DI S L YS+ ++
Sbjct: 146 AYFRMGIKHPDIV-----KSEYLQYSLTKI 170
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 1/84 (1%)
Query: 378 AIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFL-E 436
++ P LL +++ L +LG+ KL +V+ P++ + Q+ V L E
Sbjct: 53 VLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMRQQDINDTVRLLKE 112
Query: 437 DVGFDRENVGRILGRCPELFASNI 460
F + V +IL CP + ++
Sbjct: 113 KCLFTVQQVTKILHSCPSVLREDL 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
0.321 0.139 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,878,795
Number of Sequences: 62578
Number of extensions: 601726
Number of successful extensions: 1369
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1353
Number of HSP's gapped (non-prelim): 20
length of query: 610
length of database: 14,973,337
effective HSP length: 105
effective length of query: 505
effective length of database: 8,402,647
effective search space: 4243336735
effective search space used: 4243336735
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: 54 (25.4 bits)