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= psy336
(121 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3E4W|A Chain A, Crystal Structure Of A 33kda Catalase-Related Protein
From Mycobacterium Avium Subsp. Paratuberculosis.
P2(1)2(1)2(1) Crystal Form.
pdb|3E4W|B Chain B, Crystal Structure Of A 33kda Catalase-Related Protein
From Mycobacterium Avium Subsp. Paratuberculosis.
P2(1)2(1)2(1) Crystal Form.
pdb|3E4Y|A Chain A, Crystal Structure Of A 33kda Catalase-Related Protein
From Mycobacterium Avium Subsp. Paratuberculosis.
I2(1)2(1)2(1) Crystal Form
Length = 320
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 19 DRIIDLQFGTGEAE-----YHIIVELYDRGNIVLTDKDYIILNVLRPHSDGEEVRFYVRE 73
D+ ID GTG A+ H LY RG T +D ++L+ PH DG V +R
Sbjct: 15 DQAIDAIRGTGGAQPGCRALHAKGTLY-RGTFTAT-RDAVMLSAA-PHLDGSTVPALIRF 71
Query: 74 KYPVDLAKVRSGAPTQEMLYELFT 97
K R GAP + FT
Sbjct: 72 SNGSGNPKQRDGAPGVRGMAVKFT 95
>pdb|3FFZ|A Chain A, Domain Organization In Clostridium Butulinum Neurotoxin Type
E Is Unique: Its Implication In Faster Translocation
pdb|3FFZ|B Chain B, Domain Organization In Clostridium Butulinum Neurotoxin Type
E Is Unique: Its Implication In Faster Translocation
Length = 1252
Score = 29.3 bits (64), Expect = 0.65, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 43 GNIVLTDKDYIILNVLRPHS 62
GN +L DK+Y +LNVL+P++
Sbjct: 1077 GNYLLYDKEYYLLNVLKPNN 1096
>pdb|2ZWM|A Chain A, Crystal Structure Of Yycf Receiver Domain From Bacillus
Subtilis
pdb|2ZWM|B Chain B, Crystal Structure Of Yycf Receiver Domain From Bacillus
Subtilis
Length = 130
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 51 DYIILNVLRPHSDGEEVRFYVREKY 75
D I+L+++ P+ DG EV VR+KY
Sbjct: 48 DLILLDIMLPNKDGVEVCREVRKKY 72
>pdb|3F6P|A Chain A, Crystal Structure Of Unphosphorelated Receiver Domain Of
Yycf
Length = 120
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 51 DYIILNVLRPHSDGEEVRFYVREKY 75
D I+L+++ P+ DG EV VR+KY
Sbjct: 48 DLILLDIMLPNKDGVEVCREVRKKY 72
>pdb|3DOA|A Chain A, The Crystal Structure Of The Fibrinogen Binding Protein
From Staphylococcus Aureus
Length = 288
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 36/61 (59%), Gaps = 6/61 (9%)
Query: 1 MRKHLKNKRLESLKLLGLDRIIDLQFGT----GEAEYH-IIVELYDR-GNIVLTDKDYII 54
RKHL+ +ES+K +G DR I++ + G+ Y +I+E+ + N++L D++ I
Sbjct: 78 FRKHLEGGIIESIKQIGNDRRIEIDIKSKDEIGDTIYRTVILEIMGKHSNLILVDENRKI 137
Query: 55 L 55
+
Sbjct: 138 I 138
>pdb|1Z82|A Chain A, Crystal Structure Of Glycerol-3-Phosphate Dehydrogenase
(Tm0378) From Thermotoga Maritima At 2.00 A Resolution
pdb|1Z82|B Chain B, Crystal Structure Of Glycerol-3-Phosphate Dehydrogenase
(Tm0378) From Thermotoga Maritima At 2.00 A Resolution
Length = 335
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 61 HSDGEEVRFYVREKYPVDLAKVRSGAP 87
H +GEEV + R K VDL V +P
Sbjct: 34 HENGEEVILWARRKEIVDLINVSHTSP 60
>pdb|3EQZ|A Chain A, Crystal Structure Of A Response Regulator From Colwellia
Psychrerythraea
pdb|3EQZ|B Chain B, Crystal Structure Of A Response Regulator From Colwellia
Psychrerythraea
Length = 135
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 18 LDRIIDLQFGTGEAEYHIIVELYDRGNIVLTDKDYIILNVLRPHSDGEEV-RFYVREKYP 76
L I++ FG EA H L + L +D IIL+++ P DG EV R K P
Sbjct: 19 LKTIVEPIFGNVEAFQHPRAFL----TLSLNKQDIIILDLMMPDMDGIEVIRHLAEHKSP 74
Query: 77 VDL 79
L
Sbjct: 75 ASL 77
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
0.320 0.142 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,705,245
Number of Sequences: 62578
Number of extensions: 148719
Number of successful extensions: 292
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 285
Number of HSP's gapped (non-prelim): 14
length of query: 121
length of database: 14,973,337
effective HSP length: 83
effective length of query: 38
effective length of database: 9,779,363
effective search space: 371615794
effective search space used: 371615794
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)