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= 040121
(368 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 15 KRHNCYNYGMVFCHSSSSKKTLKASMAPNPNKPYRICDNCFSKLR 59
+RH+C G +FC S+K L P+ KP R+CD CF+ L+
Sbjct: 84 RRHHCRQCGNIFCAECSAKNAL----TPSSKKPVRVCDACFNDLQ 124
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 15 KRHNCYNYGMVFCHSSSSKKTLKASMAPNPNKPYRICDNCFSKLR 59
+RH+C G +FC S+K L P+ KP R+CD CF+ L+
Sbjct: 24 RRHHCRQCGNIFCAECSAKNAL----TPSSKKPVRVCDACFNDLQ 64
>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 = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 11/61 (18%)
Query: 5 CRLPFNNFKRKRHNCYNYGMVFCHSSSSKKTLKASMAPNP----NKPYRICDNCFSKLRK 60
CR+ F F ++H+C N G VFC ++K+ P P K R+CD CF+ L++
Sbjct: 167 CRVEFT-FTNRKHHCRNCGQVFCGQCTAKQ------CPLPKYGIEKEVRVCDGCFAALQR 219
Query: 61 A 61
Sbjct: 220 G 220
>pdb|2YQM|A Chain A, Solution Structure Of The Fyve Domain In Zinc Finger
Fyve Domain-Containing Protein 12
Length = 89
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 11 NFKRKRHNCYNYGMVFCHSSSSKKTLKASMAPNPNKPYRICDNCFSKL 58
+ R++H+C N G +FC++ SS + P+ KP R+CD+C + L
Sbjct: 37 SISRRKHHCRNCGHIFCNTCSSNEL----ALPSYPKPVRVCDSCHTLL 80
>pdb|2YW8|A Chain A, Crystal Structure Of Human Run And Fyve
Domain-Containing Protein
Length = 82
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 11 NFKRKRHNCYNYGMVFCHSSSSKKTLKASMAPNPNKPYRICDNCFSKL 58
+ R++H+C N G +FC++ SS + P+ KP R+CD+C + L
Sbjct: 30 SISRRKHHCRNCGHIFCNTCSSNEL----ALPSYPKPVRVCDSCHTLL 73
>pdb|1VFY|A Chain A, Phosphatidylinositol-3-Phosphate Binding Fyve Domain Of
Vps27p Protein From Saccharomyces Cerevisiae
Length = 73
Score = 35.4 bits (80), Expect = 0.053, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 11/55 (20%)
Query: 5 CRLPFNNFKRKRHNCYNYGMVFCHSSSSKKTLKASMAPNPN----KPYRICDNCF 55
C F+ RK H+C + G VFC SS P P+ +P R+CD+CF
Sbjct: 17 CSKKFSLLNRK-HHCRSCGGVFCQEHSSNSI------PLPDLGIYEPVRVCDSCF 64
>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 = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 5 CRLPFNNFKRKRHNCYNYGMVFCHSSSSKKTLKASMAPNPNKPYRICDNCFSKL-RKA 61
CR+ F RK H+C G +FC SSK + K R+C+ C+ +L RKA
Sbjct: 170 CRVQFGVMTRK-HHCRACGQIFCGKCSSKYSTIPKFG--IEKEVRVCEPCYEQLNRKA 224
>pdb|1Z2Q|A Chain A, High-Resolution Solution Structure Of The Lm5-1 Fyve
Domain From Leishmania Major
Length = 84
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 3 SGCRLPFNNFKRKRHNCYNYGMVFCHSSSSKKTLKASMAPNPNKPYRICDNCFSKLRKA 61
+GC F R RH+C N G V C S + A +P R+CD C+ LR +
Sbjct: 25 NGCGCVFTTTVR-RHHCRNCGYVLCGDCSRHRA--AIPMRGITEPERVCDACYLALRSS 80
>pdb|3MPX|A Chain A, Crystal Structure Of The Dh And Ph-1 Domains Of Human Fgd5
Length = 434
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 15 KRHNCYNYGMVFCHSSSSKKTLKASMAPNPNKPYRICDNCFSKLRK 60
+RH+C+ G + C + S K + ++ ++CD CF +L+K
Sbjct: 390 RRHHCHACGKIVCRNCSRNKY---PLKYLKDRXAKVCDGCFGELKK 432
>pdb|3T7L|A Chain A, Crystal Structure Of The Fyve Domain Of Endofin
(Zfyve16) At 1.1a Resolution
Length = 90
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 5 CRLPFNNFKRKRHNCYNYGMVFCHSSSSKKTLKASMAPNPNKPYRICDNCFSKLRKA 61
C++ F F ++RH+C G VFC ++K + K R+C C+ + KA
Sbjct: 26 CQVKFT-FTKRRHHCRACGKVFCGVCCNRKCKLQYL----EKEARVCVVCYETISKA 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
0.316 0.130 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,252,724
Number of Sequences: 62578
Number of extensions: 264366
Number of successful extensions: 639
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 626
Number of HSP's gapped (non-prelim): 18
length of query: 368
length of database: 14,973,337
effective HSP length: 100
effective length of query: 268
effective length of database: 8,715,537
effective search space: 2335763916
effective search space used: 2335763916
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)