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= 047553
(377 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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 36/108 (33%), Positives = 53/108 (49%), Gaps = 5/108 (4%)
Query: 213 ELKIRHLVSRLLDMGFSTNS-RMFVYGLVVLSCLNEETFGRKLELFRSYGFSKEEVLQMF 271
E I+ ++ L D+G N F+ + + E ++ S FSK +V QM
Sbjct: 66 EKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSKNFSKADVAQMV 125
Query: 272 RKAPLILKASEERLQLGLEFFLKEIECE----KSVLVRIPICLACSIE 315
RKAP +L S ERL L FF KE+E + ++VR+P L S+E
Sbjct: 126 RKAPFLLNFSVERLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLE 173
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 43/209 (20%), Positives = 83/209 (39%), Gaps = 40/209 (19%)
Query: 100 DVDKTLKPKIEFFQHLGLVGSDLGKFISKNPSLFAASLERKLIPCVEILKKILVDDSNNE 159
D +K +K + F + +G+ + LG F++KN ++F+ LE + K + +
Sbjct: 64 DFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSK----NFSKA 119
Query: 160 DLTRVFRRCCWNLIMDTEKSGLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIRHL 219
D+ ++ R+ + L E+ L N G +L + + K R L
Sbjct: 120 DVAQMVRKAPFLLNFSVER---LDN-----RLGFFQKELELSVK-----------KTRDL 160
Query: 220 VSRLLDMGFSTNSRMFVYGLVVLSCLNEETFGRKLELFR-SYGFSKEEVLQMFRKAPLIL 278
V RL R+ L E ++++R GF E+ M + P +L
Sbjct: 161 VVRL--------PRLLTGSL--------EPVKENMKVYRLELGFKHNEIQHMITRIPKML 204
Query: 279 KASEERLQLGLEFFLKEIECEKSVLVRIP 307
A++ +L +F + ++V+ P
Sbjct: 205 TANKMKLTETFDFVHNVMSIPHHIIVKFP 233
>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 270
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 248 ETFGRKLELFRSYGFSKEEVLQMFRKAPLILKASEERLQLGLEFFLKEIECE----KSVL 303
E ++ S FSK +V QM RKAP +L S ERL L FF KE+E + ++
Sbjct: 74 ENLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLGFFQKELELSVKKTRDLV 133
Query: 304 VRIPICLACSIE 315
VR+P L S+E
Sbjct: 134 VRLPRLLTGSLE 145
Score = 31.2 bits (69), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 25/39 (64%)
Query: 100 DVDKTLKPKIEFFQHLGLVGSDLGKFISKNPSLFAASLE 138
D +K +K + F + +G+ + LG F++KN ++F+ LE
Sbjct: 36 DFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLE 74
>pdb|2WKN|A Chain A, Gamma Lactamase From Delftia Acidovorans
pdb|2WKN|B Chain B, Gamma Lactamase From Delftia Acidovorans
pdb|2WKN|C Chain C, Gamma Lactamase From Delftia Acidovorans
pdb|2WKN|D Chain D, Gamma Lactamase From Delftia Acidovorans
pdb|2WKN|E Chain E, Gamma Lactamase From Delftia Acidovorans
pdb|2WKN|F Chain F, Gamma Lactamase From Delftia Acidovorans
pdb|2WKN|G Chain G, Gamma Lactamase From Delftia Acidovorans
pdb|2WKN|H Chain H, Gamma Lactamase From Delftia Acidovorans
Length = 409
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 38/93 (40%), Gaps = 16/93 (17%)
Query: 117 LVGSDLGKFISKNPSLFAASLERKLIPCVEILKKILVDDSNNE---DLTRVFRRCCWNLI 173
L+ + K+ KNP +F S I + I VD+ + D+T +R+ C
Sbjct: 278 LIKGGMAKYGIKNP-IFKPSPMTPNYKDYLIFEGISVDEKGKQHYLDVTVAYRQAC---- 332
Query: 174 MDTEKSGLLRNIEYLKSCGIVGSQLSMLLVWQP 206
L IEYLK G G+Q LL P
Sbjct: 333 --------LNAIEYLKKFGYSGAQAYSLLGTAP 357
>pdb|3L2O|B Chain B, Structure-Based Mechanism Of Dimerization-Dependent
Ubiquitination By The Scffbx4 Ubiquitin Ligase
Length = 312
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 135 ASLERKLIPCVEILKKIL--VDDSNNEDLTRVFRRCCWNLIMDTE 177
+S++ K +P +EILKK + V D D V+R CC LI+ E
Sbjct: 57 SSVDWKSLPDLEILKKPISEVTDGAFFDYMAVYRMCCPYLIIQNE 101
>pdb|2R5K|A Chain A, Pentamer Structure Of Major Capsid Protein L1 Of Human
Papilloma Virus Type 11
pdb|2R5K|B Chain B, Pentamer Structure Of Major Capsid Protein L1 Of Human
Papilloma Virus Type 11
pdb|2R5K|C Chain C, Pentamer Structure Of Major Capsid Protein L1 Of Human
Papilloma Virus Type 11
pdb|2R5K|D Chain D, Pentamer Structure Of Major Capsid Protein L1 Of Human
Papilloma Virus Type 11
pdb|2R5K|E Chain E, Pentamer Structure Of Major Capsid Protein L1 Of Human
Papilloma Virus Type 11
Length = 424
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 78 NVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQH--LGLVGSDLGKFISKNPSLFAA 135
N+ + + +L P V+KT+ PK+ +Q+ +V D KF + SLF
Sbjct: 13 NIFYHASSSRLLAVGHPYYSIKKVNKTVVPKVSGYQYRVFKVVLPDPNKFALPDSSLFDP 72
Query: 136 SLERKLIPCVEI 147
+ +R + C +
Sbjct: 73 TTQRLVWACTGL 84
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
0.325 0.141 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,786,200
Number of Sequences: 62578
Number of extensions: 369540
Number of successful extensions: 961
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 956
Number of HSP's gapped (non-prelim): 16
length of query: 377
length of database: 14,973,337
effective HSP length: 100
effective length of query: 277
effective length of database: 8,715,537
effective search space: 2414203749
effective search space used: 2414203749
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)