RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10510
(91 letters)
>gnl|CDD|218289 pfam04845, PurA, PurA ssDNA and RNA-binding protein. This family
represents most of the length of the protein.
Length = 218
Score = 74.1 bits (182), Expect = 6e-18
Identities = 30/50 (60%), Positives = 37/50 (74%), Gaps = 3/50 (6%)
Query: 45 VSQTIPRG--GPRSQIAIPAQGMIEFRDALTDLLEEFGTEDGG-YKGELP 91
++QT+ RG G R QIA+PAQGMIEFRDALTDL+E++G D ELP
Sbjct: 110 IAQTVMRGGSGQRQQIALPAQGMIEFRDALTDLIEDYGEGDEEDEPAELP 159
Score = 28.6 bits (64), Expect = 0.38
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 41 VYCTVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLLEE 78
V+ +S+ + R+ I +P + FRD EE
Sbjct: 182 VFMRISEV--KPNYRNSITVPEKAWTRFRDIFCKYSEE 217
>gnl|CDD|197840 smart00712, PUR, DNA/RNA-binding repeats in PUR-alpha/beta/gamma
and in hypothetical proteins from spirochetes and the
Bacteroides-Cytophaga-Flexibacter bacteria.
Length = 63
Score = 49.5 bits (119), Expect = 7e-10
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 41 VYCTVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLLEEFG 80
+ +S+ GG RS I +P QG EFRDALT L+E++G
Sbjct: 25 RFLRISEVKNNGG-RSSITVPEQGAAEFRDALTKLIEKYG 63
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 29.8 bits (68), Expect = 0.14
Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 23/55 (41%)
Query: 37 KPILVYCTVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLLEEFGTE----DGGYK 87
L+YC RGG RS + L+E G + +GGYK
Sbjct: 89 PRGLLYCW------RGGLRSGS-------------VQQWLKEAGIDVPRLEGGYK 124
>gnl|CDD|183947 PRK13283, PRK13283, flagellar assembly protein FliW; Provisional.
Length = 134
Score = 26.3 bits (58), Expect = 2.1
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 20/66 (30%)
Query: 29 VYCTVVLTKPI----------LVYCTVSQTIPRGGPRSQIAIPAQGMIEFRD-ALTDLLE 77
VYC VVL K + LV+ + + +Q+A+ M+++ D + D L+
Sbjct: 74 VYCVVVLQKNLEDSMVNFLAPLVFNSKNGF------AAQVALS---MMDYPDFSFRDPLK 124
Query: 78 EFGTED 83
F ++
Sbjct: 125 SFVVKE 130
>gnl|CDD|187745 cd09223, Photo_RC, D1, D2 subunits of photosystem II (PSII); M,
L subunits of bacterial photosynthetic reaction center.
This protein superfamily contains the D1, D2 subunits
of the photosystem II (PS II) and the M, L subunits of
the bacterial photosynthetic reaction center (RC).
These four proteins are highly homologous and share a
common fold. PS II is a multi-subunit protein found in
the photosynthetic membranes of plants, algae, and
cyanobacteria. It utilizes light-induced electron
transfer and water-splitting reactions to produce
protons, electrons, and molecular oxygen. The protons
generated are instrumental in ATP formation. Bacterial
photosynthetic reaction center (RC) complex is found in
photosynthetic bacteria, such as purple bacteria and
other proteobacteria species. It couples light-induced
electron transfer to proton pumping across the membrane
by reactions of a quinone molecule (QB) that binds two
electrons and two protons at the active site. Protons
are translocated from the bacterial cytoplasm to the
periplasmic space, generating an electrochemical
gradient of protons (the protonmotive force) that can
be used to power reactions such as the synthesis of
ATP.
Length = 199
Score = 26.3 bits (58), Expect = 2.5
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 19 VAVVLTKPILVYCTVVLTKPIL 40
+AV + PI + + L +PI
Sbjct: 58 IAVAFSAPIASFFVLFLIRPIG 79
>gnl|CDD|193531 cd05654, M20_ArgE_RocB, M20 Peptidase Arginine utilization protein,
RocB. Peptidase M20 family, ArgE RocB (Arginine
utilization protein, RocB; arginine degradation protein,
RocB) subfamily. This group of proteins is possibly
related to acetylornithine deacetylase (ArgE) and may be
involved in the arginine and/or ornithine degradation
pathway. In Bacillus subtilis, RocB is one of the three
genes found in the rocABC operon, which is sigma L
dependent and induced by arginine. The function of
members of this family is as yet unknown, although they
are predicted as deacetylases.
Length = 535
Score = 26.0 bits (58), Expect = 3.0
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 63 QGMIEFRDALTDLLEEFG 80
GM L +L E++G
Sbjct: 169 AGMRAAVPELLELKEKYG 186
>gnl|CDD|166363 PLN02722, PLN02722, indole-3-acetamide amidohydrolase.
Length = 422
Score = 26.0 bits (57), Expect = 3.5
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 67 EFRDALTDLLEEFG 80
E R ALT LL EFG
Sbjct: 329 ELRAALTTLLGEFG 342
>gnl|CDD|238089 cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta
fold domain found duplicated in the rhodanese protein.
The cysteine containing enzymatically active version of
the domain is also found in the Cdc25 class of protein
phosphatases and a variety of proteins such as sulfide
dehydrogenases and certain stress proteins such as
senesence specific protein 1 in plants, PspE and GlpE
in bacteria and cyanide and arsenate resistance
proteins. Inactive versions (no active site cysteine)
are also seen in dual specificity phosphatases,
ubiquitin hydrolases from yeast and in
sulfuryltransferases, where they are believed to play a
regulatory role in multidomain proteins.
Length = 89
Score = 25.0 bits (55), Expect = 3.9
Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 7/23 (30%)
Query: 37 KPILVYCTVSQTIPRGGPRSQIA 59
KPI+VYC R G RS A
Sbjct: 51 KPIVVYC-------RSGNRSARA 66
>gnl|CDD|148415 pfam06794, UPF0270, Uncharacterized protein family (UPF0270).
Length = 70
Score = 24.4 bits (54), Expect = 4.6
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 60 IPAQGMIEFRDALTDLLEEFGTEDGGYKGE 89
IP Q + + L +L+EEF +G GE
Sbjct: 3 IPWQQLPP--ETLNNLIEEFVLREGTDYGE 30
>gnl|CDD|147720 pfam05718, Pox_int_trans, Poxvirus intermediate transcription
factor. This family consists of several highly related
Poxvirus sequences which are thought to be intermediate
transcription factors.
Length = 383
Score = 25.3 bits (56), Expect = 5.6
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 28 LVYCTVVLTKPIL---VYCTVSQTIPRGGPRSQ 57
LVYC + LTK I+ Y T ++ SQ
Sbjct: 63 LVYCDIHLTKHIINQAAYPTYNRDNVNSNKCSQ 95
>gnl|CDD|215734 pfam00124, Photo_RC, Photosynthetic reaction centre protein.
Length = 257
Score = 24.9 bits (55), Expect = 6.7
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 19 VAVVLTKPILVYCTVVLTKPIL 40
VA + I Y + L +PIL
Sbjct: 96 VAWAFSAAIFAYLVLGLIRPIL 117
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
0.322 0.140 0.419
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,524,928
Number of extensions: 361621
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 16
Length of query: 91
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 33
Effective length of database: 8,365,070
Effective search space: 276047310
Effective search space used: 276047310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)