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= 006976
(623 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FLO|A Chain A, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|C Chain C, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|E Chain E, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|G Chain G, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
Length = 460
Score = 138 bits (348), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 113/410 (27%), Positives = 173/410 (42%), Gaps = 66/410 (16%)
Query: 239 TDPTVASQRTLFAVGMICCDG---DGHLNDKSVLLQSSVEHSGGQRVRLDLHKLGEFSLF 295
DPT+ SQ ++AVG I D D LN +S+ L++S G+RVRLDL ++ E S F
Sbjct: 39 ADPTIQSQSEIYAVGRIVPDSPTYDKFLNPESLSLETSRMGGVGRRVRLDLSQVNELSFF 98
Query: 296 PGQVVGIEGSNPSGHCLIASKLVDQIPLPVDAVVDVHPSMKQALDQEIHSTVVISRPEEI 355
GQ+V +G N +G + + +PLP +P+ + QE+ +
Sbjct: 99 LGQIVAFKGKNANGDYFTVNSI---LPLP-------YPNSPVSTSQELQEFQANLEGSSL 148
Query: 356 SMIIAAGPFTTTDNLYFEPLKELI-SYAKRKQPQLLILLGPFVDSEHPQIKKG------- 407
+I+ GP+ DN E L+E I S +P +LI+ GPF+D HP I G
Sbjct: 149 KVIVTCGPYFANDNFSLELLQEFIDSINNEVKPHVLIMFGPFIDITHPLIASGKLPNFPQ 208
Query: 408 --TTDSSFDEIFHLEILRRLQDYVEYMGSEVRAILVPSIRDA--NHDFVLXXXXXXXXXX 463
T + DE+F L+ ++ + ++ +L+PS +DA NH
Sbjct: 209 FKTQPKTLDELF----LKLFTPILKTISPHIQTVLIPSTKDAISNHAAYPQASLIRKALQ 264
Query: 464 XXXXXXTSLTNPGTFEANQIKVGCCTVDVLKQLS-----GEEMSRCSKDGTSND------ 512
+ NP +F+ N+I GC VD K L G SR D S
Sbjct: 265 LPKRNFKCMANPSSFQINEIYFGCSNVDTFKDLKEVIKGGTTSSRYRLDRVSEHILQQRR 324
Query: 513 ---------RMEIYSLDISLMGXXXXXXXXXXXX----EGIPLDFS-LAQEALTISTIPD 558
R I D+S G LD S L PD
Sbjct: 325 YYPIFPGSIRTRIKPKDVSTKKETNDMESKEEKVYEHISGADLDVSYLGLTEFVGGFSPD 384
Query: 559 IIILPSDMKYFIKVLSLGGRNEGEEQKKCVCVNPGRLAKGEGS-GTFAEI 607
I+I+PS++++F +V+ + V +NPGR + G+ G++A+I
Sbjct: 385 IMIIPSELQHFARVV-----------QNVVVINPGRFIRATGNRGSYAQI 423
>pdb|1BQK|A Chain A, Oxidized Pseudoazurin
pdb|1BQR|A Chain A, Reduced Pseudoazurin
pdb|1ZIA|A Chain A, Oxidized Pseudoazurin
pdb|1ZIB|A Chain A, Reduced Pseudoazurin
Length = 124
Score = 30.8 bits (68), Expect = 2.2, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 66 FMLHLQNEQKE-AIIKEEPSLHIYSSKDVDMILNDEDENIAEDILGTPPDNLKLYSDALD 124
F +H+ N+ K+ A++ E SL + V I D+ N+ E I G PD + + ++
Sbjct: 3 FEVHMLNKGKDGAMVFEPASLKVAPGDTVTFIPTDKGHNV-ETIKGMIPDGAEAFKSKIN 61
Query: 125 STYK 128
YK
Sbjct: 62 ENYK 65
>pdb|2UX6|A Chain A, Pseudoazurin With Engineered Amicyanin Ligand Loop,
Oxidized Form, Ph 7.5
pdb|2UX7|A Chain A, Pseudoazurin With Engineered Amicyanin Ligand Loop,
Reduced Form, Ph 7.5
pdb|2UXF|A Chain A, Pseudoazurin With Engineered Amicyanin Ligand Loop,
Oxidized Form, Ph 5.5
pdb|2UXG|A Chain A, Pseudoazurin With Engineered Amicyanin Ligand Loop,
Reduced Form, Ph 5.5
Length = 122
Score = 30.8 bits (68), Expect = 2.6, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 66 FMLHLQNEQKE-AIIKEEPSLHIYSSKDVDMILNDEDENIAEDILGTPPDNLKLYSDALD 124
F +H+ N+ K+ A++ E SL + V I D+ N+ E I G PD + + ++
Sbjct: 3 FEVHMLNKGKDGAMVFEPASLKVAPGDTVTFIPTDKGHNV-ETIKGMIPDGAEAFKSKIN 61
Query: 125 STYK 128
YK
Sbjct: 62 ENYK 65
>pdb|2JKW|A Chain A, Pseudoazurin M16f
pdb|2JKW|B Chain B, Pseudoazurin M16f
Length = 124
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 66 FMLHLQNEQKE-AIIKEEPSLHIYSSKDVDMILNDEDENIAEDILGTPPDNLKLYSDALD 124
F +H+ N+ K+ A + E SL + V I D+ N+ E I G PD + + ++
Sbjct: 3 FEVHMLNKGKDGAFVFEPASLKVAPGDTVTFIPTDKGHNV-ETIKGMIPDGAEAFKSKIN 61
Query: 125 STYK 128
YK
Sbjct: 62 ENYK 65
>pdb|3BIP|A Chain A, Crystal Structure Of Yeast Spt16 N-Terminal Domain
pdb|3BIP|B Chain B, Crystal Structure Of Yeast Spt16 N-Terminal Domain
pdb|3BIQ|A Chain A, Crystal Structure Of Yeast Spt16 N-Terminal Domain
Length = 467
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 32/93 (34%), Positives = 41/93 (44%), Gaps = 9/93 (9%)
Query: 40 LVSSWEVYYLNRQLDESTVKDDEMDGFMLHLQNEQKEAIIKEEPSLHIYSSKDVDMILND 99
L WEV +N Q S V D FM L NE A+ +E L I ++K D I N
Sbjct: 171 LSKVWEVKDVNEQAFLS-VSSKGSDKFMDLLSNEMVRAVDEE---LKITNAKLSDKIENK 226
Query: 100 EDE-----NIAEDILGTPPDNLKLYSDALDSTY 127
D+ ++ D+ P N K D LD TY
Sbjct: 227 IDDVKFLKQLSPDLSALCPPNYKFNFDLLDWTY 259
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
0.316 0.135 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,670,812
Number of Sequences: 62578
Number of extensions: 798328
Number of successful extensions: 1643
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1637
Number of HSP's gapped (non-prelim): 11
length of query: 623
length of database: 14,973,337
effective HSP length: 105
effective length of query: 518
effective length of database: 8,402,647
effective search space: 4352571146
effective search space used: 4352571146
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)