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= 010002
(520 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
Structure
Length = 63
Score = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 252 YRGVTLHKCGRWEARM-GQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNF 307
YRGV G++ A + V+LG F+T +AA AYDRAA + G A+ NF
Sbjct: 3 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59
Score = 29.3 bits (64), Expect = 5.3, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 159 QYRGVTFYRRTGRWESHIWD---SGKQVYLGGFDTXXXXXXXXXXXXIKFRGAEADINFS 215
YRGV R G++ + I D +G +V+LG F+T + RG+ A +NF
Sbjct: 2 HYRGVR-QRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60
Query: 216 I 216
+
Sbjct: 61 L 61
>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
Minimized Mean Structure
pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr, 46
Structures
Length = 70
Score = 36.6 bits (83), Expect = 0.031, Method: Composition-based stats.
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 252 YRGVTLHKCGRWEARMGQ-FLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNF 307
YRGV G++ A + V+LG F+T +AA AYDRAA + G A+ NF
Sbjct: 6 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62
Score = 28.9 bits (63), Expect = 6.6, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 159 QYRGVTFYRRTGRWESHIWD---SGKQVYLGGFDTXXXXXXXXXXXXIKFRGAEADINFS 215
YRGV R G++ + I D +G +V+LG F+T + RG+ A +NF
Sbjct: 5 HYRGVR-QRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63
Query: 216 I 216
+
Sbjct: 64 L 64
>pdb|3EJ6|A Chain A, Neurospora Crassa Catalase-3 Crystal Structure
pdb|3EJ6|B Chain B, Neurospora Crassa Catalase-3 Crystal Structure
pdb|3EJ6|C Chain C, Neurospora Crassa Catalase-3 Crystal Structure
pdb|3EJ6|D Chain D, Neurospora Crassa Catalase-3 Crystal Structure
Length = 688
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 434 SHLLHMVPPQCNQSNYQTHQLTPGSSKRGRIGNELSLSTNDHHQQWQSGPHMF 486
S+L P Q NQ+ + TPG + G + ELS + +DH+ Q P +F
Sbjct: 406 SYLNKGYPAQANQTVGRGFFTTPGRTASGVLNRELSATFDDHYTQ----PRLF 454
>pdb|3LAW|A Chain A, Structure Of Gtp-Bound L129f Mutant Rab7
pdb|3LAW|B Chain B, Structure Of Gtp-Bound L129f Mutant Rab7
pdb|3LAW|C Chain C, Structure Of Gtp-Bound L129f Mutant Rab7
pdb|3LAW|D Chain D, Structure Of Gtp-Bound L129f Mutant Rab7
pdb|3LAW|E Chain E, Structure Of Gtp-Bound L129f Mutant Rab7
Length = 207
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 361 LPNEVDWHNRGYRPKQQQEAYSRQHDLPYKRDGYSEAETMQLLSQTHLQSPASSSLNKSS 420
L N++D+ NR K+ Q ++++PY EA + + Q+ A ++L + +
Sbjct: 123 LGNKIDFENRQVATKRAQAWCYSKNNIPYFETSAKEAINV----EQAFQTIARNALKQET 178
Query: 421 EMQRYEQF 428
E++ Y +F
Sbjct: 179 EVELYNEF 186
>pdb|1T91|A Chain A, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
pdb|1T91|B Chain B, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
pdb|1T91|C Chain C, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
pdb|1T91|D Chain D, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
pdb|1YHN|A Chain A, Structure Basis Of Rilp Recruitment By Rab7
Length = 207
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 361 LPNEVDWHNRGYRPKQQQEAYSRQHDLPYKRDGYSEAETMQLLSQTHLQSPASSSLNKSS 420
L N++D NR K+ Q ++++PY EA + + Q+ A ++L + +
Sbjct: 123 LGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINV----EQAFQTIARNALKQET 178
Query: 421 EMQRYEQF 428
E++ Y +F
Sbjct: 179 EVELYNEF 186
>pdb|1VG0|B Chain B, The Crystal Structures Of The Rep-1 Protein In Complex
With Monoprenylated Rab7 Protein
pdb|1VG8|A Chain A, Gppnhp-Bound Rab7
pdb|1VG8|B Chain B, Gppnhp-Bound Rab7
pdb|1VG8|C Chain C, Gppnhp-Bound Rab7
pdb|1VG8|D Chain D, Gppnhp-Bound Rab7
Length = 207
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 361 LPNEVDWHNRGYRPKQQQEAYSRQHDLPYKRDGYSEAETMQLLSQTHLQSPASSSLNKSS 420
L N++D NR K+ Q ++++PY EA + + Q+ A ++L + +
Sbjct: 123 LGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINV----EQAFQTIARNALKQET 178
Query: 421 EMQRYEQF 428
E++ Y +F
Sbjct: 179 EVELYNEF 186
>pdb|3SYJ|A Chain A, Crystal Structure Of The Haemophilus Influenzae Hap
Adhesin
Length = 1011
Score = 28.5 bits (62), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 452 HQLTPGSSKRGR-IGNELSLSTNDHHQQWQSGPHMFATAAASSGFPQQIRSSHSQNWLQN 510
H LT G++ R GN S D + + GP A + SG P I + Q WL N
Sbjct: 176 HYLTAGNTHNQRGAGNGYSYLGGDVRKAGEYGPLPIAGSKGDSGSPMFIYDAEKQKWLIN 235
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
0.314 0.130 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,573,655
Number of Sequences: 62578
Number of extensions: 529974
Number of successful extensions: 685
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 680
Number of HSP's gapped (non-prelim): 13
length of query: 520
length of database: 14,973,337
effective HSP length: 103
effective length of query: 417
effective length of database: 8,527,803
effective search space: 3556093851
effective search space used: 3556093851
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)