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= 040101
(101 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NUP|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
pdb|2NUT|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
Length = 196
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 35/72 (48%), Positives = 48/72 (66%)
Query: 1 TFIQKTKKLYQDTRTQRNIAKLNDELYEVHQIMTRNVQEVLGVGEKLDQVSEMSSRLTSE 60
TFIQKTKKLY D+R +RN+ +N EL +V +IM N++EVL GE L + ++ L+S
Sbjct: 118 TFIQKTKKLYIDSRARRNLGSINTELQDVQRIMVANIEEVLQRGEALSALDSKANNLSSL 177
Query: 61 SRIYADKAKDLN 72
S+ Y AK LN
Sbjct: 178 SKKYRQDAKYLN 189
>pdb|3EGD|C Chain C, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22 AND
BOUND To The Transport Signal Sequence Of Vesicular
Stomatitis Virus Glycoprotein
pdb|3EGX|C Chain C, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22B AND
Bound To The Transport Signal Sequence Of The Snare
Protein Bet1
Length = 157
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/41 (58%), Positives = 32/41 (78%)
Query: 1 TFIQKTKKLYQDTRTQRNIAKLNDELYEVHQIMTRNVQEVL 41
TFIQKTKKLY D+R +RN+ +N EL +V +IM N++EVL
Sbjct: 117 TFIQKTKKLYIDSRARRNLGSINTELQDVQRIMVANIEEVL 157
>pdb|2NPS|A Chain A, Crystal Structure Of The Early Endosomal Snare Complex
Length = 74
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 35/56 (62%)
Query: 19 IAKLNDELYEVHQIMTRNVQEVLGVGEKLDQVSEMSSRLTSESRIYADKAKDLNRQ 74
I + +++ EV +M N+ +V+ GE+LD++ + S L+ + +++++K L RQ
Sbjct: 10 IKHVQNQVDEVIDVMQENITKVIERGERLDELQDKSESLSDNATAFSNRSKQLRRQ 65
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion
Activity Of Longin Domain Snare Ykt6
Length = 199
Score = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%)
Query: 10 YQDTRTQRNIAKLNDELYEVHQIMTRNVQEVLGVGEKLDQVSEMSSRLTSESRIYADKAK 69
YQ+ R ++K+ EL E I+ ++ +L GEKLD + S L ++S+ + A+
Sbjct: 131 YQNPREADPMSKVQAELDETKIILHNTMESLLERGEKLDDLVSKSEVLGTQSKAFYKTAR 190
Query: 70 DLNRQALI 77
N I
Sbjct: 191 KQNSCCAI 198
>pdb|1GL2|A Chain A, Crystal Structure Of An Endosomal Snare Core Complex
Length = 65
Score = 28.5 bits (62), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 19 IAKLNDELYEVHQIMTRNVQEVLGVGEKLDQV 50
+ L E+ V IMT+NV+ +L GE LD +
Sbjct: 11 VRNLQSEVEGVKNIMTQNVERILARGENLDHL 42
>pdb|3C3W|A Chain A, Crystal Structure Of The Mycobacterium Tuberculosis
Hypoxic Response Regulator Dosr
pdb|3C3W|B Chain B, Crystal Structure Of The Mycobacterium Tuberculosis
Hypoxic Response Regulator Dosr
Length = 225
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 26 LYEVHQIMTRNVQEVLGVGEKLDQVSEMSSRLTSESRIYA 65
L + H+++ R + ++LG +LD V E S + +R+ A
Sbjct: 6 LVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPA 45
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 26.2 bits (56), Expect = 4.4, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 19/22 (86%), Gaps = 1/22 (4%)
Query: 36 NVQEVLGVGEKLD-QVSEMSSR 56
NV++VLGVG+K+ +++E+ SR
Sbjct: 711 NVEDVLGVGQKVQVEIAEIDSR 732
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 26.2 bits (56), Expect = 4.8, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 19/22 (86%), Gaps = 1/22 (4%)
Query: 36 NVQEVLGVGEKLD-QVSEMSSR 56
NV++VLGVG+K+ +++E+ SR
Sbjct: 711 NVEDVLGVGQKVQVEIAEIDSR 732
>pdb|3ZYM|A Chain A, Structure Of Calm (Picalm) In Complex With Vamp8
pdb|3ZYM|B Chain B, Structure Of Calm (Picalm) In Complex With Vamp8
pdb|3ZYM|C Chain C, Structure Of Calm (Picalm) In Complex With Vamp8
Length = 310
Score = 25.4 bits (54), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 19 IAKLNDELYEVHQIMTRNVQEVLGVGEKL 47
+ L E+ V IMT+NV+ +L GE L
Sbjct: 282 VRNLQSEVEGVKNIMTQNVERILARGENL 310
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
0.317 0.129 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,139,938
Number of Sequences: 62578
Number of extensions: 59665
Number of successful extensions: 201
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 186
Number of HSP's gapped (non-prelim): 19
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)