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= psy12925
(83 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IQ2|A Chain A, Human Sorting Nexin 7, Phox Homology (Px) Domain
pdb|3IQ2|B Chain B, Human Sorting Nexin 7, Phox Homology (Px) Domain
Length = 138
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 6/58 (10%)
Query: 21 VWRRYSEFEQMKNYLQATYPYVILPPLPEKKPTFVWKHDAASTDITDPDFVDRRRASL 78
V RRY +F +K L+ +P +I+PPLPEK F+ K + + DF++ RR +L
Sbjct: 47 VRRRYQDFLWLKGKLEEAHPTLIIPPLPEK---FIVK---GMVERFNDDFIETRRKAL 98
>pdb|2CSK|A Chain A, Solution Structure Of Px Domain From Human Snx12
Length = 146
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 17 KLSIVWRRYSEFEQMKNYLQATYPYVILPPLPEK--KPTFVWKHDAASTDITDPDFVDRR 74
K S V RRYS+FE +KN L+ +++PPLP K K ++ D I + F++ R
Sbjct: 45 KESCVRRRYSDFEWLKNELERD-SKIVVPPLPGKALKRQLPFRGDEG---IFEESFIEER 100
Query: 75 RASLE 79
R LE
Sbjct: 101 RQGLE 105
>pdb|1XTN|A Chain A, Crystal Structure Of Cisk-Px Domain With Sulfates
pdb|1XTN|B Chain B, Crystal Structure Of Cisk-Px Domain With Sulfates
Length = 120
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 10/59 (16%)
Query: 20 IVWRRYSEFEQMKNYLQATYPYVILPPLPEKKPTFVWKHDAASTDITDPDFVDRRRASL 78
V+RRY+EF+++ N L+ +P + L +P K+ D DPDF+ +RRA L
Sbjct: 40 FVFRRYAEFDKLYNSLKKQFPAMAL-KIPAKR---------IFGDNFDPDFIKQRRAGL 88
>pdb|1XTE|A Chain A, Crystal Structure Of Cisk-Px Domain
Length = 154
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 10/59 (16%)
Query: 20 IVWRRYSEFEQMKNYLQATYPYVILPPLPEKKPTFVWKHDAASTDITDPDFVDRRRASL 78
V+RRY+EF+++ N L+ +P + L +P K+ D DPDF+ +RRA L
Sbjct: 40 FVFRRYAEFDKLYNSLKKQFPAMAL-KIPAKR---------IFGDNFDPDFIKQRRAGL 88
>pdb|2I4K|A Chain A, Solution Structure Of The Px Domain Of Sorting Nexin 1
Length = 128
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 15 QNKLSIVWRRYSEFEQMKNYLQATYPY--VILPPLPEKKPTFVWKHDAASTDITDPDFVD 72
++K V RR+S+F + L + I+PP PEK + K D + +F++
Sbjct: 36 RSKQFAVKRRFSDFLGLYEKLSEKHSQNGFIVPPPPEKSLIGMTKVKVGKEDSSSAEFLE 95
Query: 73 RRRASLE 79
+RRA+LE
Sbjct: 96 KRRAALE 102
>pdb|4AKV|A Chain A, Crystal Structure Of Human Sorting Nexin 33 (Snx33)
pdb|4AKV|B Chain B, Crystal Structure Of Human Sorting Nexin 33 (Snx33)
Length = 386
Score = 32.3 bits (72), Expect = 0.077, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 10/60 (16%)
Query: 19 SIVWRRYSEFEQMKNYLQATYPYVILPPLPEKKPTFVWKHDAASTDITDPDFVDRRRASL 78
S V+RRY F+ + N L + + +P LPEK+ T ++ DF+++R+ L
Sbjct: 73 SPVYRRYKHFDWLYNRLLHKFTVISVPHLPEKQATGRFEE----------DFIEKRKRRL 122
>pdb|1KMD|A Chain A, Solution Structure Of The Vam7p Px Domain
Length = 117
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 21 VWRRYSEFEQMKNYLQATYPYVILPPLPEKKPTFVWKHDAASTDITDPDFVDRRRASLE 79
+++RYSEF ++K L+ I PE KP + + D DP+ +D RR LE
Sbjct: 31 LYKRYSEFWKLKTRLERDVGSTIPYDFPE-KPGVLDRRWQRRYD--DPEMIDERRIGLE 86
>pdb|1OCS|A Chain A, Crystal Structure Of The Yeast Px-Doamin Protein Grd19p
(Sorting Nexin3) Complexed To
Phosphatidylinosytol-3-Phosphate.
pdb|1OCU|A Chain A, Crystal Structure Of The Yeast Px-Domain Protein Grd19p
(Sorting Nexin 3) Complexed To
Phosphatidylinosytol-3-Phospahte.
pdb|1OCU|B Chain B, Crystal Structure Of The Yeast Px-Domain Protein Grd19p
(Sorting Nexin 3) Complexed To
Phosphatidylinosytol-3-Phospahte
Length = 162
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 11/54 (20%)
Query: 8 DWSLIPKQN------KLSIVWRRYSEFEQMKNYL-----QATYPYVILPPLPEK 50
D+ +I + N ++S V RRYS+FE + L +P V++P LP K
Sbjct: 59 DYEIICRTNLPSFHKRVSKVRRRYSDFEFFRKXLIKEISMLNHPKVMVPHLPGK 112
>pdb|3EUW|A Chain A, Crystal Structure Of A Myo-Inositol Dehydrogenase From
Corynebacterium Glutamicum Atcc 13032
pdb|3EUW|B Chain B, Crystal Structure Of A Myo-Inositol Dehydrogenase From
Corynebacterium Glutamicum Atcc 13032
pdb|3EUW|C Chain C, Crystal Structure Of A Myo-Inositol Dehydrogenase From
Corynebacterium Glutamicum Atcc 13032
pdb|3EUW|D Chain D, Crystal Structure Of A Myo-Inositol Dehydrogenase From
Corynebacterium Glutamicum Atcc 13032
Length = 344
Score = 26.6 bits (57), Expect = 3.5, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 51 KPTFVWKHDAASTDITDPDF 70
+PT V KH+A ST+ DP F
Sbjct: 256 RPTTVRKHNAESTEQADPIF 275
>pdb|3J21|T Chain T, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 86
Score = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 3 LVTDEDWSLIPKQNKLSIVWRRYSEFEQMKNYLQATYPY------VILPPLPEKKPTFVW 56
+VT++ SLI K+NKL+ + R + + +K ++ + ++ P EKK
Sbjct: 11 VVTEKAISLIEKENKLTFIVDRRATKQDIKRAVEEIFNVKVEKVNTLITPRGEKKAYVKL 70
Query: 57 KHDAASTDIT 66
K + +++++
Sbjct: 71 KPEYSASEVA 80
>pdb|3A5Y|A Chain A, Crystal Structure Of Genx From Escherichia Coli In Complex
With Lysyladenylate Analog
pdb|3A5Y|B Chain B, Crystal Structure Of Genx From Escherichia Coli In Complex
With Lysyladenylate Analog
pdb|3A5Y|C Chain C, Crystal Structure Of Genx From Escherichia Coli In Complex
With Lysyladenylate Analog
pdb|3A5Y|D Chain D, Crystal Structure Of Genx From Escherichia Coli In Complex
With Lysyladenylate Analog
Length = 345
Score = 25.4 bits (54), Expect = 9.2, Method: Composition-based stats.
Identities = 13/48 (27%), Positives = 22/48 (45%)
Query: 29 EQMKNYLQATYPYVILPPLPEKKPTFVWKHDAASTDITDPDFVDRRRA 76
E LQ + + + P + ++KPTFV+ A+ + D R A
Sbjct: 206 EDRDTLLQLLFTFGVEPNIGKEKPTFVYHFPASQASLAQISTEDHRVA 253
>pdb|3A5Z|A Chain A, Crystal Structure Of Escherichia Coli Genx In Complex With
Elongation Factor P
pdb|3A5Z|C Chain C, Crystal Structure Of Escherichia Coli Genx In Complex With
Elongation Factor P
pdb|3A5Z|E Chain E, Crystal Structure Of Escherichia Coli Genx In Complex With
Elongation Factor P
pdb|3A5Z|G Chain G, Crystal Structure Of Escherichia Coli Genx In Complex With
Elongation Factor P
Length = 328
Score = 25.0 bits (53), Expect = 9.8, Method: Composition-based stats.
Identities = 13/48 (27%), Positives = 22/48 (45%)
Query: 29 EQMKNYLQATYPYVILPPLPEKKPTFVWKHDAASTDITDPDFVDRRRA 76
E LQ + + + P + ++KPTFV+ A+ + D R A
Sbjct: 189 EDRDTLLQLLFTFGVEPNIGKEKPTFVYHFPASQASLAQISTEDHRVA 236
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 0.136 0.436
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,648,757
Number of Sequences: 62578
Number of extensions: 88984
Number of successful extensions: 203
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 191
Number of HSP's gapped (non-prelim): 12
length of query: 83
length of database: 14,973,337
effective HSP length: 51
effective length of query: 32
effective length of database: 11,781,859
effective search space: 377019488
effective search space used: 377019488
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)