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= 047127
(322 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F0R|A Chain A, Crystallographic Structure Of Human Tsg101 Uev Domain
pdb|2F0R|B Chain B, Crystallographic Structure Of Human Tsg101 Uev Domain
Length = 159
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/124 (26%), Positives = 59/124 (47%), Gaps = 4/124 (3%)
Query: 32 LIRKQLLSLLQNYPSFNLSNDTFTHNDGTAVNLFKVSGCFHVS--QSTPPIHFTLWLHEN 89
L ++ ++++ Y D++ NDG++ L ++G V +T I LWL +
Sbjct: 34 LTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDT 93
Query: 90 YPSMAPMAFIVSSNSMYPIRQNHPFVSPCGTITTPYLQTWSYPGYNLNDLVHNLVQIFSH 149
YP P+ F+ ++SM H V G I PYL W +P +L L+ ++ +F
Sbjct: 94 YPYNPPICFVKPTSSMTIKTGKH--VDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGD 151
Query: 150 DHPL 153
+ P+
Sbjct: 152 EPPV 155
>pdb|1KPP|A Chain A, Structure Of The Tsg101 Uev Domain
pdb|1KPQ|A Chain A, Structure Of The Tsg101 Uev Domain
pdb|1M4P|A Chain A, Structure Of The Tsg101 Uev Domain In Complex With A Hiv-1
Ptap "late Domain" Peptide, Dyana Ensemble
pdb|1M4Q|A Chain A, Structure Of The Tsg101 Uev Domain In Complex With A Hiv-1
Ptap "late Domain" Peptide, Cns Ensemble
Length = 145
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 33/124 (26%), Positives = 59/124 (47%), Gaps = 4/124 (3%)
Query: 32 LIRKQLLSLLQNYPSFNLSNDTFTHNDGTAVNLFKVSGCFHVS--QSTPPIHFTLWLHEN 89
L ++ ++++ Y D++ NDG++ L ++G V +T I LWL +
Sbjct: 20 LTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDT 79
Query: 90 YPSMAPMAFIVSSNSMYPIRQNHPFVSPCGTITTPYLQTWSYPGYNLNDLVHNLVQIFSH 149
YP P+ F+ ++SM H V G I PYL W +P +L L+ ++ +F
Sbjct: 80 YPYNPPICFVKPTSSMTIKTGKH--VDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGD 137
Query: 150 DHPL 153
+ P+
Sbjct: 138 EPPV 141
>pdb|1S1Q|A Chain A, Tsg101(Uev) Domain In Complex With Ubiquitin
pdb|1S1Q|C Chain C, Tsg101(Uev) Domain In Complex With Ubiquitin
Length = 145
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 57/124 (45%), Gaps = 4/124 (3%)
Query: 32 LIRKQLLSLLQNYPSFNLSNDTFTHNDGTAVNLFKVSGCFHVS--QSTPPIHFTLWLHEN 89
L ++ ++++ Y D++ NDG++ L ++G V +T I LWL +
Sbjct: 20 LTVRETVNVITLYKDLKPVLDSYVFNDGSSRELXNLTGTIPVPYRGNTYNIPICLWLLDT 79
Query: 90 YPSMAPMAFIVSSNSMYPIRQNHPFVSPCGTITTPYLQTWSYPGYNLNDLVHNLVQIFSH 149
YP P+ F+ ++S H V G I PYL W +P +L L+ + +F
Sbjct: 80 YPYNPPICFVKPTSSXTIKTGKH--VDANGKIYLPYLHEWKHPQSDLLGLIQVXIVVFGD 137
Query: 150 DHPL 153
+ P+
Sbjct: 138 EPPV 141
>pdb|3P9G|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
Fa459 Peptide
pdb|3P9H|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
Fa258 Peptide
Length = 145
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 4/97 (4%)
Query: 59 GTAVNLFKVSGCFHVS--QSTPPIHFTLWLHENYPSMAPMAFIVSSNSMYPIRQNHPFVS 116
G + L ++G V +T I LWL + YP P+ F+ ++SM H V
Sbjct: 47 GGSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKH--VD 104
Query: 117 PCGTITTPYLQTWSYPGYNLNDLVHNLVQIFSHDHPL 153
G I PYL W +P +L L+ ++ +F + P+
Sbjct: 105 ANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPV 141
>pdb|3OBQ|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
A Human Hrs Psap Peptide
pdb|3OBS|A Chain A, Crystal Structure Of Tsg101 Uev Domain
pdb|3OBU|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
A Hiv-1 Ptap Peptide
pdb|3OBX|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
A Hiv-1 Gag P7a Mutant Peptide
Length = 146
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 80 IHFTLWLHENYPSMAPMAFIVSSNSMYPIRQNHPFVSPCGTITTPYLQTWSYPGYNLNDL 139
I LWL + YP P+ F+ ++SM H V G I PYL W +P +L L
Sbjct: 71 IPICLWLLDTYPYNPPICFVKPTSSMTIKTGKH--VDANGKIYLPYLHEWKHPQSDLLGL 128
Query: 140 VHNLVQIFSHDHPL 153
+ ++ +F + P+
Sbjct: 129 IQVMIVVFGDEPPV 142
>pdb|2F66|A Chain A, Structure Of The Escrt-I Endosomal Trafficking Complex
pdb|2F66|D Chain D, Structure Of The Escrt-I Endosomal Trafficking Complex
pdb|2F6M|A Chain A, Structure Of A Vps23-C:vps28-N Subcomplex
pdb|2F6M|C Chain C, Structure Of A Vps23-C:vps28-N Subcomplex
Length = 65
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 27/42 (64%)
Query: 267 AADEAIEDVIYALDKALERGVVSFDSYIRQVRILAREQFFHR 308
A D A+ D I AL + L RG + D++++Q R LAR+QF R
Sbjct: 13 AQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVR 54
>pdb|2CAZ|A Chain A, Escrt-I Core
pdb|2CAZ|D Chain D, Escrt-I Core
Length = 82
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 26/42 (61%)
Query: 267 AADEAIEDVIYALDKALERGVVSFDSYIRQVRILAREQFFHR 308
A D A+ D I L + L RG + D++++Q R LAR+QF R
Sbjct: 30 AQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVR 71
>pdb|2P22|A Chain A, Structure Of The Yeast Escrt-i Heterotetramer Core
Length = 174
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 32/114 (28%), Positives = 52/114 (45%), Gaps = 22/114 (19%)
Query: 206 LKNRARKLKETVVELAGKADVLT-NWLKV----------NGDPKAIGVILGDRVEDAFEA 254
L+ + +++T+ L + DVLT N KV + D +I V D + +
Sbjct: 61 LRAVEQAIEQTMHSLNAQIDVLTANRAKVQQFSSTSHVDDEDVNSIAVAKTDGLNQLYNL 120
Query: 255 IDAESKAELEGSAADEAIEDVIYALDKALERGVVSFDSYIRQVRILAREQFFHR 308
+ A D A+ D I L + L RG + D++++Q R LAR+QF R
Sbjct: 121 V-----------AQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVR 163
>pdb|3R3Q|A Chain A, Crystal Structure Of The Yeast Vps23 Uev Domain
pdb|3R42|A Chain A, Crystal Structure Of The Yeast Vps23 Uev Domain In Complex
With A Vps27 Psdp Peptide
Length = 162
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/125 (28%), Positives = 52/125 (41%), Gaps = 14/125 (11%)
Query: 38 LSLLQNYPSFNLSNDTFTHNDGTAVNLFKVSGCFHVSQ--STP-PIHFTLWLHENYPSMA 94
L+LL N+ S FTH+DGT L + G + S+P I +W+ YP
Sbjct: 38 LALLDNFHSLRPRTRVFTHSDGTPQLLLSIYGTISTGEDGSSPHSIPVIMWVPSMYPVKP 97
Query: 95 PMAFIVSSN-------SMYPIRQNHPFVSPCGTITTPYLQTWSYPGYNLNDLVHNLVQIF 147
P I N S PI++ ++ G I P L W NL +V L+ +
Sbjct: 98 PFISINLENFDMNTISSSLPIQE---YIDSNGWIALPILHAWDPAAMNLIMVVQELMSLL 154
Query: 148 SHDHP 152
H+ P
Sbjct: 155 -HEPP 158
>pdb|1UZX|A Chain A, A Complex Of The Vps23 Uev With Ubiquitin
Length = 169
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 36/125 (28%), Positives = 50/125 (40%), Gaps = 14/125 (11%)
Query: 38 LSLLQNYPSFNLSNDTFTHNDGTAVNLFKVSGCFHVSQ--STP-PIHFTLWLHENYPSMA 94
L+LL N+ S FTH+DGT L + G + S+P I W+ YP
Sbjct: 44 LALLDNFHSLRPRTRVFTHSDGTPQLLLSIYGTISTGEDGSSPHSIPVIXWVPSXYPVKP 103
Query: 95 PMAFIVSSN-------SMYPIRQNHPFVSPCGTITTPYLQTWSYPGYNLNDLVHNLVQIF 147
P I N S PI++ ++ G I P L W NL +V L +
Sbjct: 104 PFISINLENFDXNTISSSLPIQE---YIDSNGWIALPILHCWDPAAXNLIXVVQELXSLL 160
Query: 148 SHDHP 152
H+ P
Sbjct: 161 -HEPP 164
>pdb|2GTT|A Chain A, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|B Chain B, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|C Chain C, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|D Chain D, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|E Chain E, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|F Chain F, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|G Chain G, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|H Chain H, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|I Chain I, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|J Chain J, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|K Chain K, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|L Chain L, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|M Chain M, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|N Chain N, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|O Chain O, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|P Chain P, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|Q Chain Q, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|R Chain R, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|S Chain S, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|T Chain T, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|U Chain U, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
pdb|2GTT|V Chain V, Crystal Structure Of The Rabies Virus Nucleoprotein-rna
Complex
Length = 450
Score = 30.8 bits (68), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 25/38 (65%), Gaps = 5/38 (13%)
Query: 286 GVVSFDSYIRQVRILAREQ---FFHRDLLVKLEVKRGF 320
G+VSF +I+Q+ + ARE FFH++ + E++R F
Sbjct: 238 GLVSFTGFIKQINLTAREAILYFFHKNF--EEEIRRMF 273
>pdb|1XAF|A Chain A, Crystal Structure Of Protein Of Unknown Function Yfih From
Shigella Flexneri 2a Str. 2457t
pdb|1XAF|B Chain B, Crystal Structure Of Protein Of Unknown Function Yfih From
Shigella Flexneri 2a Str. 2457t
Length = 246
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 213 LKETVVELAGKADVLTNWLKVNGDPKAIGVILGDRVEDAFEAIDAESKA 261
L+ETV A K + + WL P+A V G V +AF A+DA++ A
Sbjct: 138 LEETVSCFADKPENILAWLGPAIGPRAFEV--GAEVREAFXAVDAKASA 184
>pdb|1U05|A Chain A, Crystal Structure Of Protein Yfih From Shigella Flexneri,
Pfam Duf152
pdb|1U05|B Chain B, Crystal Structure Of Protein Yfih From Shigella Flexneri,
Pfam Duf152
Length = 243
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 213 LKETVVELAGKADVLTNWLKVNGDPKAIGVILGDRVEDAFEAIDAESKA 261
L+ETV A K + + WL P+A V G V +AF A+DA++ A
Sbjct: 135 LEETVSCFADKPENILAWLGPAIGPRAFEV--GAEVREAFMAVDAKASA 181
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.5 bits (62), Expect = 4.7, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 214 KETVVELAGKADVLTNWLKVNGDPKAIGVILGDRVEDAFEAIDAESKAELEGSA 267
+ET+ E+ KA + NG K I EDA EA+++ +K E+EG A
Sbjct: 29 EETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRA 82
>pdb|1Z9T|A Chain A, Crystal Structure Of A Putative Laccase (yfih) From
Escherichia Coli At 1.54 A Resolution
Length = 255
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 213 LKETVVELAGKADVLTNWLKVNGDPKAIGVILGDRVEDAFEAIDAESKA 261
L+ETV A + + WL P+A V G V +AF A+DA++ A
Sbjct: 147 LEETVSCFADNPENILAWLGPAIGPRAFEV--GGEVREAFXAVDAKASA 193
>pdb|1TW2|A Chain A, Crystal Structure Of Carminomycin-4-O-Methyltransferase
(Dnrk) In Complex With S-Adenosyl-L-Homocystein (Sah)
And 4-Methoxy-E-Rhodomycin T (M-Et)
pdb|1TW2|B Chain B, Crystal Structure Of Carminomycin-4-O-Methyltransferase
(Dnrk) In Complex With S-Adenosyl-L-Homocystein (Sah)
And 4-Methoxy-E-Rhodomycin T (M-Et)
pdb|1TW3|A Chain A, Crystal Structure Of Carminomycin-4-o-methyltransferase
(dnrk) In Complex With S-adenosyl-l-homocystein (sah)
And 4-methoxy-e-rhodomycin T (m-et)
pdb|1TW3|B Chain B, Crystal Structure Of Carminomycin-4-o-methyltransferase
(dnrk) In Complex With S-adenosyl-l-homocystein (sah)
And 4-methoxy-e-rhodomycin T (m-et)
Length = 360
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 208 NRARKLKETVVELAGKADVLTNWLKVNGDPKAIGVILGD 246
RA + TV+E+AG D ++LK G + V+ GD
Sbjct: 203 RRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGD 241
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
0.321 0.135 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,030,049
Number of Sequences: 62578
Number of extensions: 345169
Number of successful extensions: 990
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 973
Number of HSP's gapped (non-prelim): 16
length of query: 322
length of database: 14,973,337
effective HSP length: 99
effective length of query: 223
effective length of database: 8,778,115
effective search space: 1957519645
effective search space used: 1957519645
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)