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= psy8680
(180 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SQW|A Chain A, Crystal Structure Of Kd93, A Novel Protein Expressed In
The Human Pro
Length = 188
Score = 189 bits (480), Expect = 8e-49, Method: Compositional matrix adjust.
Identities = 93/171 (54%), Positives = 115/171 (67%), Gaps = 38/171 (22%)
Query: 3 DRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQFKVWVKP 62
DRV+YVSEKI+ LA N D L++LGTCFGKFTK+ KFRLH+TAL YLAPYA++KV
Sbjct: 42 DRVYYVSEKIMKLAANISGDKLVSLGTCFGKFTKTHKFRLHVTALDYLAPYAKYKV---- 97
Query: 63 QADQQFLYGHNILKSGLARITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITE 122
W+KP AEQ FLYG+++LKSGL RITE
Sbjct: 98 ----------------------------------WIKPGAEQSFLYGNHVLKSGLGRITE 123
Query: 123 NTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYIR 173
NT +YQGV+V +M D+PLGFGVAAKST +C+ DP+AIV F+Q+DIGEY+R
Sbjct: 124 NTSQYQGVVVYSMADIPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEYVR 174
>pdb|1T5Y|A Chain A, Crystal Structure Of Northeast Structural Genomics
Consortium Target Hr2118: A Human Homolog Of
Saccharomyces Cerevisiae Nip7p
Length = 190
Score = 183 bits (464), Expect = 5e-47, Method: Compositional matrix adjust.
Identities = 91/176 (51%), Positives = 114/176 (64%), Gaps = 38/176 (21%)
Query: 3 DRVFYVSEKILTLAENFGPDHLLALGTCFGKFTKSGKFRLHITALSYLAPYAQFKVWVKP 62
DRV+YVSEKI LA N D L++LGTCFGKFTK+ KFRLH+TAL YLAPYA++KVW+KP
Sbjct: 52 DRVYYVSEKIXKLAANISGDKLVSLGTCFGKFTKTHKFRLHVTALDYLAPYAKYKVWIKP 111
Query: 63 QADQQFLYGHNILKSGLARITENTPKYQGVIFKVWVKPQAEQQFLYGHNILKSGLARITE 122
A+Q FLYG+++LKSGL RITENT +YQ
Sbjct: 112 GAEQSFLYGNHVLKSGLGRITENTSQYQ-------------------------------- 139
Query: 123 NTPKYQGVIVLNMNDVPLGFGVAAKSTAECKLADPLAIVGFNQSDIGEYIRYMTNM 178
GV+V + D+PLGFGVAAKST +C+ DP AIV F+Q+DIGEY+R+ +
Sbjct: 140 ------GVVVYSXADIPLGFGVAAKSTQDCRKVDPXAIVVFHQADIGEYVRHEETL 189
>pdb|1ACO|A Chain A, Crystal Structure Of Aconitase With Transaconitate Bound
pdb|1FGH|A Chain A, Complex With 4-Hydroxy-Trans-Aconitate
pdb|8ACN|A Chain A, Crystal Structures Of Aconitase With Isocitrate And
Nitroisocitrate Bound
Length = 754
Score = 26.9 bits (58), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 103 EQQFLYGHNILKSGLARITENTPKYQGVIVLNMND 137
E +FL G I+ ARI E K QG++ L D
Sbjct: 650 EPRFLGGRAIITKSFARIHETNLKKQGLLPLTFAD 684
>pdb|1NIS|A Chain A, Crystal Structure Of Aconitase With Trans-Aconitate And
Nitrocitrate Bound
pdb|1NIT|A Chain A, Crystal Structure Of Aconitase With Trans-Aconitate And
Nitrocitrate Bound
Length = 754
Score = 26.9 bits (58), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 103 EQQFLYGHNILKSGLARITENTPKYQGVIVLNMND 137
E +FL G I+ ARI E K QG++ L D
Sbjct: 650 EPRFLGGRAIITKSFARIHETNLKKQGLLPLTFAD 684
>pdb|1AMI|A Chain A, Steric And Conformational Features Of The Aconitase
Mechanism
pdb|1AMJ|A Chain A, Steric And Conformational Features Of The Aconitase
Mechanism
Length = 754
Score = 26.9 bits (58), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 103 EQQFLYGHNILKSGLARITENTPKYQGVIVLNMND 137
E +FL G I+ ARI E K QG++ L D
Sbjct: 650 EPRFLGGRAIITKSFARIHETNLKKQGLLPLTFAD 684
>pdb|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
pdb|2EY4|B Chain B, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
Length = 333
Score = 26.9 bits (58), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAEC 152
KVW+K A +G ++ G+A++ + V ++ + D + G A ++ E
Sbjct: 252 KVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEM 309
>pdb|3LWO|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
Length = 340
Score = 26.9 bits (58), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAEC 152
KVW+K A +G ++ G+A++ + V ++ + D + G A ++ E
Sbjct: 252 KVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEM 309
>pdb|2HVY|A Chain A, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|A Chain A, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|A Chain A, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 346
Score = 26.9 bits (58), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAEC 152
KVW+K A +G ++ G+A++ + V ++ + D + G A ++ E
Sbjct: 252 KVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEM 309
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing
Aca Trinucleotide
Length = 328
Score = 26.9 bits (58), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAEC 152
KVW+K A +G ++ G+A++ + V ++ + D + G A ++ E
Sbjct: 245 KVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEM 302
>pdb|3HJW|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
pdb|3HJY|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 327
Score = 26.9 bits (58), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAEC 152
KVW+K A +G ++ G+A++ + V ++ + D + G A ++ E
Sbjct: 245 KVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEM 302
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
Length = 334
Score = 26.9 bits (58), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 95 KVWVKPQAEQQFLYGHNILKSGLARITENTPKYQGVIVLNMNDVPLGFGVAAKSTAEC 152
KVW+K A +G ++ G+A++ + V ++ + D + G A ++ E
Sbjct: 248 KVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEM 305
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 0.139 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,493,244
Number of Sequences: 62578
Number of extensions: 222937
Number of successful extensions: 407
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 385
Number of HSP's gapped (non-prelim): 22
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)