RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9488
(114 letters)
>gnl|CDD|176383 cd01788, ElonginB, Ubiquitin-like domain of Elongin B. Elongin B
is part of an E3 ubiquitin ligase complex called VEC
that activates ubiquitylation by the E2
ubiquitin-conjugating enzyme Ubc5. VEC is composed of
von Hippel-Lindau tumor suppressor protein (pVHL),
elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds
elonginC to form the elonginBC complex which is a
positive regulator of RNA polymerase II elongation
factor Elongin A. The BC complex then binds VHL (von
Hippel-Lindau) tumour suppressor protein to form a VCB
ternary complex. Elongin B has a ubiquitin-llike
domain.
Length = 119
Score = 80.5 bits (198), Expect = 6e-21
Identities = 44/90 (48%), Positives = 61/90 (67%), Gaps = 8/90 (8%)
Query: 24 RYHKGITKVPPKDQKLFNKDNREMEEGNLLQEYGLTSAVAKAQSPALVGLAFRQENGEFE 83
R +GI K PP+DQ+L+ KD++ +++G L + G TS A+ Q+PA VGLAFR + FE
Sbjct: 29 RIVEGILKRPPEDQRLY-KDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFRSSDDTFE 87
Query: 84 PLELTPYSSPPDLPYVMK-------ASEQA 106
PL + P+SSPP+LP VMK A+EQA
Sbjct: 88 PLRIEPFSSPPELPDVMKPQDSGSSANEQA 117
>gnl|CDD|227851 COG5564, COG5564, Predicted TIM-barrel enzyme, possibly a
dioxygenase [General function prediction only].
Length = 276
Score = 27.9 bits (62), Expect = 1.1
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 57 GLTSAVAKAQSPALVGLAFRQENGEFEP----LELTPYSSPPDLPYVMKASEQANG 108
G SA++ A L+ LA G + P S P D Y++ +G
Sbjct: 193 GARSALSLADCVELIELAAEAARGVRKDVIPLCHGGPISMPEDARYILDRCPGCDG 248
>gnl|CDD|132417 TIGR03374, ABALDH, 1-pyrroline dehydrogenase. Members of this
protein family are 1-pyrroline dehydrogenase (1.5.1.35),
also called gamma-aminobutyraldehyde dehydrogenase. This
enzyme can follow putrescine transaminase (EC 2.6.1.82)
for a two-step conversion of putrescine to
gamma-aminobutyric acid (GABA). The member from
Escherichia coli is characterized as a homotetramer that
binds one NADH per momomer. This enzyme belongs to the
medium-chain aldehyde dehydrogenases, and is quite
similar in sequence to the betaine aldehyde
dehydrogenase (EC 1.2.1.8) family.
Length = 472
Score = 26.5 bits (58), Expect = 3.5
Identities = 14/31 (45%), Positives = 16/31 (51%)
Query: 83 EPLELTPYSSPPDLPYVMKASEQANGQENIT 113
E EL P SS L VMKA E+A +I
Sbjct: 314 ESTELGPLSSLAHLERVMKAVEEAKALGHIK 344
>gnl|CDD|225625 COG3083, COG3083, Predicted hydrolase of alkaline phosphatase
superfamily [General function prediction only].
Length = 600
Score = 26.6 bits (59), Expect = 3.5
Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 10/60 (16%)
Query: 45 REMEEGNLLQE------YGL----TSAVAKAQSPALVGLAFRQENGEFEPLELTPYSSPP 94
GN Q YGL +V A++P + A RQ+N +F + SP
Sbjct: 295 NHYSSGNSTQAGLFGLFYGLSATYWDSVLSARTPPALIEALRQQNYQFGLFSSDGFKSPL 354
>gnl|CDD|163566 TIGR03854, F420_MSMEG_3544, probable F420-dependent oxidoreductase,
MSMEG_3544 family. Coenzyme F420 has a limited
phylogenetic distribution, including methanogenic
archaea, Mycobacterium tuberculosis and related species,
Colwellia psychrerythraea 34H, Rhodopseudomonas
palustris HaA2, and others. Partial phylogenetic
profiling identifies protein subfamilies, within the
larger family called luciferase-like monooxygenanases
(pfam00296), that appear only in F420-positive genomes
and are likely to be F420-dependent. This model
describes a small family, closely related to other such
families in the putative F420-binding region,
exemplified by MSMEG_3544 in Mycobacterium smegmatis
[Unknown function, Enzymes of unknown specificity].
Length = 290
Score = 26.3 bits (58), Expect = 3.8
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 45 REMEEGNLLQEYGLTSAVAKAQSPALVGLAFRQENGEFEPLELTP 89
RE+E +G++ AVA PA V A R+ + +P EL
Sbjct: 203 REIEP----DHFGISLAVADGDLPAPVIAALRRRRPDVDPAELIA 243
>gnl|CDD|240079 cd04728, ThiG, Thiazole synthase (ThiG) is the tetrameric enzyme
that is involved in the formation of the thiazole moiety
of thiamin pyrophosphate, an essential ubiquitous
cofactor that plays an important role in carbohydrate
and amino acid metabolism. ThiG catalyzes the formation
of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP)
and dehydroglycine, with the help of the sulfur carrier
protein ThiS that carries the sulfur needed for thiazole
assembly on its carboxy terminus (ThiS-COSH).
Length = 248
Score = 26.3 bits (59), Expect = 4.1
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 58 LTSAVAKAQSPALVGLAFRQ 77
L +A+AKA+ P + AF+
Sbjct: 203 LNTAIAKAKDPVAMARAFKL 222
>gnl|CDD|234687 PRK00208, thiG, thiazole synthase; Reviewed.
Length = 250
Score = 25.0 bits (56), Expect = 9.5
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 58 LTSAVAKAQSPALVGLAFRQ 77
L +A+A A P + AF+
Sbjct: 203 LNTAIAVAGDPVAMARAFKL 222
>gnl|CDD|218097 pfam04463, DUF523, Protein of unknown function (DUF523). Family of
uncharacterized bacterial proteins.
Length = 143
Score = 24.8 bits (55), Expect = 9.5
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 13/57 (22%)
Query: 23 PRYHKGITKVPPKDQ-KLFNKDN-----REMEEG-----NLLQEYGLTSAVAKAQSP 68
PR I V + ++ + D +M G L+EYG+ A+ KA+SP
Sbjct: 48 PR--PPIRIVGLDGRARVVDTDTGRDVTEKMLAGAARALEELKEYGIDGAILKAKSP 102
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.313 0.133 0.377
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,701,386
Number of extensions: 475030
Number of successful extensions: 228
Number of sequences better than 10.0: 1
Number of HSP's gapped: 227
Number of HSP's successfully gapped: 12
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.2 bits)