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= psy4518
(376 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z2Q|A Chain A, High-Resolution Solution Structure Of The Lm5-1 Fyve
Domain From Leishmania Major
Length = 84
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 42 PIKKKNHEQAIVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKAR 101
P+ +Q+ W + +D P C C F R+HHCR CG ++C DCS R
Sbjct: 2 PLGSMGEKQSKGYWQEDEDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHRAAIPMR 61
Query: 102 QILVEPE 108
I EPE
Sbjct: 62 GI-TEPE 67
>pdb|3T7L|A Chain A, Crystal Structure Of The Fyve Domain Of Endofin
(Zfyve16) At 1.1a Resolution
Length = 90
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 21/37 (56%)
Query: 55 WLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDC 91
W+ + P C NC F F KR+HHCR CG + C C
Sbjct: 14 WVPDSEAPNCMNCQVKFTFTKRRHHCRACGKVFCGVC 50
>pdb|1JOC|A Chain A, Eea1 Homodimer Of C-Terminal Fyve Domain Bound To Inositol
1,3-Diphosphate
pdb|1JOC|B Chain B, Eea1 Homodimer Of C-Terminal Fyve Domain Bound To Inositol
1,3-Diphosphate
Length = 125
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 12/90 (13%)
Query: 15 DRYERFSHEINKL---IIRLDKLLTNM--PIDPIKKKN------HEQAI-VPWLDGKDVP 62
+R + EI KL ++ L + L N + + ++N H QA+ W + +V
Sbjct: 11 ERCLKGEGEIEKLQTKVLELQRKLDNTTAAVQELGRENQSLQIKHTQALNRKWAEDNEVQ 70
Query: 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
C C + F+ R+HHCR CG I C +CS
Sbjct: 71 NCMACGKGFSVTVRRHHCRQCGNIFCAECS 100
>pdb|1HYI|A Chain A, Solution Structure Of The Eea1 Fyve Domain Complexed
With Inositol 1,3-Bisphosphate
pdb|1HYJ|A Chain A, Solution Structure Of The Eea1 Fyve Domain
Length = 65
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 22/38 (57%)
Query: 55 WLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
W + +V C C + F+ R+HHCR CG I C +CS
Sbjct: 3 WAEDNEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECS 40
>pdb|1Z0K|B Chain B, Structure Of Gtp-Bound Rab4q67l Gtpase In Complex With The
Central Rab Binding Domain Of Rabenosyn-5
pdb|1Z0K|D Chain D, Structure Of Gtp-Bound Rab4q67l Gtpase In Complex With The
Central Rab Binding Domain Of Rabenosyn-5
Length = 69
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 306 EAWSP--AGTKSVSSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLK 353
E W P G DPL+QQI NI FI++A+ A R +EV +L+ +L+
Sbjct: 7 EGWLPLSGGQGQSEDSDPLLQQIHNITSFIRQAKAAGRMDEVRTLQENLR 56
>pdb|2YQM|A Chain A, Solution Structure Of The Fyve Domain In Zinc Finger
Fyve Domain-Containing Protein 12
Length = 89
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 43 IKKKNHEQAIVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
IK+ N WL + C C + F+ ++R+HHCR CG I C+ CS
Sbjct: 8 IKEVNQALKGHAWLKDDEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCS 57
>pdb|2YW8|A Chain A, Crystal Structure Of Human Run And Fyve
Domain-Containing Protein
Length = 82
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 43 IKKKNHEQAIVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
IK+ N WL + C C + F+ ++R+HHCR CG I C+ CS
Sbjct: 1 IKEVNQALKGHAWLKDDEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCS 50
>pdb|3ZYQ|A Chain A, Crystal Structure Of The Tandem Vhs And Fyve Domains Of
Hepatocyte Growth Factor-Regulated Tyrosine Kinase
Substrate (Hgs-Hrs) At 1.48 A Resolution
pdb|4AVX|A Chain A, Hepatocyte Growth Factor-Regulated Tyrosine Kinase
Substrate (Hgs-Hrs) Bound To An Ip2 Compound At 1.68 A
Resolution
Length = 226
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 55 WLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
W+D ++ C C F R+HHCR CG I C CS
Sbjct: 161 WVDAEE---CHRCRVQFGVMTRKHHCRACGQIFCGKCS 195
>pdb|3MPX|A Chain A, Crystal Structure Of The Dh And Ph-1 Domains Of Human Fgd5
Length = 434
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 19/32 (59%)
Query: 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
V C NC F+ R+HHC CG I+C +CS
Sbjct: 375 VXXCXNCGCDFSLTLRRHHCHACGKIVCRNCS 406
>pdb|1DVP|A Chain A, Crystal Structure Of The Vhs And Fyve Tandem Domains Of
Hrs, A Protein Involved In Membrane Trafficking And
Signal Transduction
Length = 220
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 55 WLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
W DG+ C C F F R+HHCR CG + C C+
Sbjct: 158 WADGR---VCHRCRVEFTFTNRKHHCRNCGQVFCGQCT 192
>pdb|1VFY|A Chain A, Phosphatidylinositol-3-Phosphate Binding Fyve Domain Of
Vps27p Protein From Saccharomyces Cerevisiae
Length = 73
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 55 WLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
W+D C CS+ F+ R+HHCR CG + C + S
Sbjct: 8 WIDSD---ACMICSKKFSLLNRKHHCRSCGGVFCQEHS 42
>pdb|1YZM|A Chain A, Structure Of Rabenosyn (458-503), Rab4 Binding Domain
Length = 51
Score = 37.0 bits (84), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 25/33 (75%)
Query: 321 PLVQQITNIKQFIKEARMAHRYNEVASLENHLK 353
PL+QQI NI FI++A+ A R +EV +L+ +L+
Sbjct: 6 PLLQQIHNITSFIRQAKAAGRMDEVRTLQENLR 38
>pdb|3V1E|A Chain A, Crystal Structure Of De Novo Designed Mid1-Zinc H12e
Mutant
pdb|3V1E|B Chain B, Crystal Structure Of De Novo Designed Mid1-Zinc H12e
Mutant
Length = 48
Score = 35.8 bits (81), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 317 SSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHL 352
S PL QQI NI+ FI +A+ A R +EV +L+ +L
Sbjct: 1 GSGSPLAQQIKNIESFIHQAKAAGRMDEVRTLQENL 36
>pdb|3V1F|A Chain A, Crystal Structure Of De Novo Designed Mid1-Zinc H35e
Mutant
pdb|3V1F|B Chain B, Crystal Structure Of De Novo Designed Mid1-Zinc H35e
Mutant
Length = 48
Score = 35.4 bits (80), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 24/37 (64%)
Query: 317 SSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLK 353
S PL QQI NI FI +A+ A R +EV +L+ +L+
Sbjct: 1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLE 37
>pdb|3V1A|A Chain A, Crystal Structure Of De Novo Designed Mid1-Apo1
pdb|3V1B|A Chain A, Crystal Structure Of De Novo Designed Mid1-Apo2
pdb|3V1B|B Chain B, Crystal Structure Of De Novo Designed Mid1-Apo2
pdb|3V1C|A Chain A, Crystal Structure Of De Novo Designed Mid1-Zinc
pdb|3V1C|B Chain B, Crystal Structure Of De Novo Designed Mid1-Zinc
pdb|3V1D|A Chain A, Crystal Structure Of De Novo Designed Mid1-Cobalt
pdb|3V1D|B Chain B, Crystal Structure Of De Novo Designed Mid1-Cobalt
pdb|3V1D|C Chain C, Crystal Structure Of De Novo Designed Mid1-Cobalt
pdb|3V1D|D Chain D, Crystal Structure Of De Novo Designed Mid1-Cobalt
pdb|3V1D|E Chain E, Crystal Structure Of De Novo Designed Mid1-Cobalt
pdb|3V1D|F Chain F, Crystal Structure Of De Novo Designed Mid1-Cobalt
pdb|3V1D|G Chain G, Crystal Structure Of De Novo Designed Mid1-Cobalt
pdb|3V1D|H Chain H, Crystal Structure Of De Novo Designed Mid1-Cobalt
Length = 48
Score = 35.0 bits (79), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 317 SSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHL 352
S PL QQI NI FI +A+ A R +EV +L+ +L
Sbjct: 1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENL 36
>pdb|1WFK|A Chain A, Fyve Domain Of Fyve Domain Containing 19 Protein From
Mus Musculus
Length = 88
Score = 31.6 bits (70), Expect = 0.84, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPL 97
RC C+ F K+++ C+ CG C+ C F L
Sbjct: 11 RCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSAL 45
>pdb|1X4U|A Chain A, Solution Structure Of The Fyve Domain From Human Fyve
Domain Containing 27 Isoform B Protein
Length = 84
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 64 CPNCSRSFNFAKRQHHCRLCGCIMCHD-CSFFLPLNKARQILVEPELGESQLSASANSDL 122
C CS +F+ K++ C CG C CSF +P + E + + AS N L
Sbjct: 17 CTGCSATFSVLKKRRSCSNCGNSFCSRCCSFKVPKSSMGATAPEAQRETVFVCASCNQTL 76
Query: 123 N 123
+
Sbjct: 77 S 77
>pdb|1UKR|A Chain A, Structure Of Endo-1,4-Beta-Xylanase C
pdb|1UKR|B Chain B, Structure Of Endo-1,4-Beta-Xylanase C
pdb|1UKR|C Chain C, Structure Of Endo-1,4-Beta-Xylanase C
pdb|1UKR|D Chain D, Structure Of Endo-1,4-Beta-Xylanase C
Length = 184
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 285 FNVETHHGRHSVSKENNVSLLEAWSPAGTKSVS 317
FN HHG + V +EAWS AG+ SV+
Sbjct: 149 FNFWAHHGFGNSDFNYQVVAVEAWSGAGSASVT 181
>pdb|2VCP|D Chain D, Crystal Structure Of N-wasp Vc Domain In Complex With
Skeletal Actin
pdb|2VCP|E Chain E, Crystal Structure Of N-wasp Vc Domain In Complex With
Skeletal Actin
Length = 93
Score = 28.9 bits (63), Expect = 5.0, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 107 PELGESQLSASANSDLNL--RLLESREVLKESRNSRPLICDLYDALMGKKQEASKLRAM 163
P G+ Q+ +A + L ++ E ++ K +NSRP+ C DAL+ + ++ +L+++
Sbjct: 1 PSDGDHQVPTTAGNKAALLDQIREGAQLKKVEQNSRPVSCSGRDALLDQIRQGIQLKSV 59
>pdb|3GLJ|A Chain A, A Polymorph Of Carboxypeptidase B Zymogen Structure
Length = 401
Score = 28.1 bits (61), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 282 EENFNVETHHGRHSVSKENNVSLLEAWSPAGTKSVSSQDP 321
E F+ HS K NN +EAW TK V+S++P
Sbjct: 87 EAQFDSRVRTTGHSYEKYNNWETIEAW----TKQVTSENP 122
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
0.319 0.131 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,295,208
Number of Sequences: 62578
Number of extensions: 265349
Number of successful extensions: 885
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 865
Number of HSP's gapped (non-prelim): 22
length of query: 376
length of database: 14,973,337
effective HSP length: 100
effective length of query: 276
effective length of database: 8,715,537
effective search space: 2405488212
effective search space used: 2405488212
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: 52 (24.6 bits)