RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1423
(125 letters)
>gnl|CDD|238107 cd00183, TFIIS_I, N-terminal domain (domain I) of transcription
elongation factor S-II (TFIIS); similar to a domain
found in elongin A and CRSP70; likely to be involved in
transcription; domain I from TFIIS interacts with RNA
polymerase II holoenzyme.
Length = 76
Score = 61.6 bits (150), Expect = 6e-14
Identities = 26/57 (45%), Positives = 39/57 (68%), Gaps = 1/57 (1%)
Query: 48 EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104
+ LDLL+ L+ L + + IL +T IG VN+LRK S ++++ LAK LIK+WKK +
Sbjct: 21 SRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHS-NEKIRKLAKALIKSWKKLVD 76
>gnl|CDD|197766 smart00509, TFS2N, Domain in the N-terminus of transcription
elongation factor S-II (and elsewhere).
Length = 75
Score = 60.0 bits (146), Expect = 3e-13
Identities = 27/58 (46%), Positives = 39/58 (67%), Gaps = 1/58 (1%)
Query: 48 EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRP 105
+ LD+LK L+ L I +++L +T IG VN LRK K++E+ LAK LIK+WKK +
Sbjct: 19 SRCLDILKKLKKLPITVDLLEETRIGKKVNGLRK-HKNEEIRKLAKKLIKSWKKLVYS 75
>gnl|CDD|204037 pfam08711, Med26, TFIIS helical bundle-like domain. Mediator is a
large complex of up to 33 proteins that is conserved
from plants to fungi to humans - the number and
representation of individual subunits varying with
species {1-2]. It is arranged into four different
sections, a core, a head, a tail and a kinase-activity
part, and the number of subunits within each of these is
what varies with species. Overall, Mediator regulates
the transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Mediator exists in
two major forms in human cells: a smaller form that
interacts strongly with pol II and activates
transcription, and a large form that does not interact
strongly with pol II and does not directly activate
transcription. Notably, the 'small' and 'large' Mediator
complexes differ in their subunit composition: the Med26
subunit preferentially associates with the small, active
complex, whereas cdk8, cyclin C, Med12 and Med13
associate with the large Mediator complex. This family
includesthe C terminal region of a number of eukaryotic
hypothetical proteins which are homologous to the
Saccharomyces cerevisiae protein IWS1. IWS1 is known to
be an Pol II transcription elongation factor and
interacts with Spt6 and Spt5.
Length = 51
Score = 56.8 bits (138), Expect = 3e-12
Identities = 25/52 (48%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 52 DLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
+LLK L+ L I +L +T IG VN LRK +++EV LAK LIK WK+ +
Sbjct: 1 ELLKELKKLPITEELLRETGIGKAVNKLRK-HENEEVKKLAKKLIKKWKRLV 51
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II. This model
represents eukaryotic transcription elongation factor
S-II. This protein allows stalled RNA transcription
complexes to perform a cleavage of the nascent RNA and
restart at the newly generated 3-prime end.
Length = 299
Score = 52.1 bits (125), Expect = 6e-09
Identities = 23/56 (41%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 48 EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
EQ LD+L L+ +L +T +G+ VN LRK +D + LAK +IK+WKK +
Sbjct: 21 EQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNED-ISKLAKKIIKSWKKVV 75
>gnl|CDD|132866 cd07228, Pat_NTE_like_bacteria, Bacterial patatin-like
phospholipase domain containing protein 6. Bacterial
patatin-like phospholipase domain containing protein 6.
PNPLA6 is commonly known as Neuropathy Target Esterase
(NTE). NTE has at least two functional domains: the
N-terminal domain putatively regulatory domain and the
C-terminal catalytic domain which shows esterase
activity. NTE shows phospholipase activity for
lysophosphatidylcholine (LPC) and phosphatidylcholine
(PC). Exposure of NTE to organophosphates leads to
organophosphate-induced delayed neurotoxicity (OPIDN).
OPIDN is a progressive neurological condition that is
characterized by weakness, paralysis, pain, and
paresthesia. This group includes YCHK and rssA from
Escherichia coli as well as Ylbk from Bacillus
amyloliquefaciens.
Length = 175
Score = 27.6 bits (62), Expect = 1.4
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 54 LKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104
L+AL+ I+++I+ + IG V L + D + ++L + + +R
Sbjct: 19 LRALEEEGIEIDIIAGSSIGALVGALYAAGHLDALEEWVRSL--SQRDVLR 67
>gnl|CDD|218331 pfam04926, PAP_RNA-bind, Poly(A) polymerase predicted RNA binding
domain. Based on its similarity structurally to the RNA
recognition motif this domain is thought to be RNA
binding.
Length = 141
Score = 26.8 bits (60), Expect = 2.6
Identities = 11/58 (18%), Positives = 27/58 (46%), Gaps = 15/58 (25%)
Query: 72 IGMTVNNLRKSSKDDEVINLA------KTLIKNWKKFIRP-------YVWRMNLPQDV 116
IG+ + +K + + +++ K ++++W ++ P +V R +LP V
Sbjct: 75 IGLELK--KKKEEGSKKLDITYAIQEFKDIVRSWPQYRPPGMDIEIKHVKRKDLPDFV 130
>gnl|CDD|222105 pfam13402, M60-like, Peptidase M60-like family. Members of this
family are related to the Enhancin peptidase family.
Therefore these proteins may act as peptidases.
Length = 303
Score = 26.5 bits (59), Expect = 4.3
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 71 HIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104
+ + NLRK +++D + L+K W + IR
Sbjct: 127 ILTVPSENLRKLTRND-----PEELLKLWDRIIR 155
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 26.6 bits (59), Expect = 4.4
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 26 SAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQT 59
+A+L R D L G VR +ALDLL A T
Sbjct: 209 TALLKTTLRMRPDRILVGEVRGPEALDLLMAWNT 242
>gnl|CDD|233413 TIGR01441, GPR, GPR endopeptidase. This model describes a
tetrameric protease that makes the rate-limiting first
cut in the small, acid-soluble spore proteins (SASP) of
Bacillus subtilis and related species. The enzyme lacks
clear homology to other known proteases. It processes
its own amino end before becoming active to cleave SASPs
[Protein fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 358
Score = 26.4 bits (58), Expect = 4.4
Identities = 11/45 (24%), Positives = 18/45 (40%)
Query: 15 KTRRPKRNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQT 59
+P R L + M ++R D L +++ L LL L
Sbjct: 256 SEDKPSRALAPAGMTFGERRELTDEDLPPEEKRKTFLGLLGTLDE 300
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 26.2 bits (58), Expect = 5.6
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 26 SAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQT 59
+ +L R D + G VR +ALDLLKA T
Sbjct: 194 TRLLKATLRLRPDRIIVGEVRGGEALDLLKAWNT 227
>gnl|CDD|187610 cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like,
classical (c) SDRs. NADP-mannitol dehydrogenase
catalyzes the conversion of fructose to mannitol, an
acyclic 6-carbon sugar. MDH is a tetrameric member of
the SDR family. This subgroup also includes various
other tetrameric SDRs, including Pichia stipitis
D-arabinitol dehydrogenase (aka polyol dehydrogenase),
Candida albicans Sou1p, a sorbose reductase, and Candida
parapsilosis (S)-specific carbonyl reductase (SCR, aka
S-specific alcohol dehydrogenase) which catalyzes the
enantioselective reduction of 2-hydroxyacetophenone into
(S)-1-phenyl-1,2-ethanediol. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser).
Length = 252
Score = 26.1 bits (58), Expect = 5.8
Identities = 11/18 (61%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 88 VINLAKTLIKNW-KKFIR 104
VI+LAK+L W K FIR
Sbjct: 167 VIHLAKSLAVEWAKYFIR 184
>gnl|CDD|112668 pfam03865, ShlB, Haemolysin secretion/activation protein
ShlB/FhaC/HecB. This family represents a group of
sequences that are related to ShlB from Serratia
marcescens. ShlB is an outer membrane protein pore
involved in the Type Vb or Two-partner secretion system
where it is functions to secrete and activate the
haemolysin ShlA. The activation of ShlA occurs during
secretion when ShlB imposes a conformational change in
the inactive haemolysin to form the active protein.
Length = 404
Score = 26.1 bits (57), Expect = 6.0
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 40 KLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLA 92
KL L +Q LD LQ+ L+IL +G +V LR IN A
Sbjct: 20 KLAEL---DQGLDQANRLQSNKTKLDILPGRELGGSVIKLRNQHAKPWHINAA 69
>gnl|CDD|238939 cd01981, Pchlide_reductase_B, Pchlide_reductase_B: B protein of the
NB protein complex of Protochlorophyllide
(Pchlide)_reductase. Pchlide reductase catalyzes the
reductive formation of chlorophyllide (chlide) from
protochlorophyllide (pchlide) during biosynthesis of
chlorophylls and bacteriochlorophylls. This group
contains both the light-independent Pchlide reductase
(DPOR) and light-dependent Pchlide reductase (LPOR).
Angiosperms contain only LPOR, cyanobacteria, algae and
gymnosperms contain both DPOR and LPOR, primitive
anoxygenic photosynthetic bacteria contain only DPOR. NB
is structurally similar to the FeMo protein of
nitrogenase, forming an N2B2 heterotetramer. N and B are
homologous to the FeMo alpha and beta subunits
respectively. Also in common with nitrogenase in vitro
DPOR activity requires ATP hydrolysis and dithoionite or
ferredoxin as electron donor. The NB protein complex may
serve as a catalytic site for Pchlide reduction similar
to MoFe for nitrogen reduction.
Length = 430
Score = 26.2 bits (58), Expect = 6.3
Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 14/65 (21%)
Query: 1 MAEPMSLRDSALWSKTRRPKRNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQTL 60
AE KT +P NLIG + L G + +L + L TL
Sbjct: 146 YAEKAR-PQGTPREKTEKPSVNLIGPSSL-------------GFHNRHDCRELKRLLHTL 191
Query: 61 NIDLN 65
I++N
Sbjct: 192 GIEVN 196
>gnl|CDD|234406 TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export
porin PgaA. Members of this protein family are the
poly-beta-1,6 N-acetyl-D-glucosamine (PGA) export porin
PgaA of Gram-negative bacteria. There is no counterpart
in the poly-beta-1,6 N-acetyl-D-glucosamine biosynthesis
systems of Gram-positive bacteria such as Staphylococcus
epidermidis. The PGA polysaccharide adhesin is a
critical determinant of biofilm formation. The conserved
C-terminal domain of this outer membrane protein is
preceded by a variable number of TPR repeats.
Length = 800
Score = 26.2 bits (58), Expect = 6.8
Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 6/71 (8%)
Query: 43 GLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKF 102
L + E+AL + + L N L T L + + E + A+ L+ K+
Sbjct: 322 ALRQPEKALPIYRELAAAEPADNNLELTI------KLFYAYLEAEQYDEAQALLDGLKES 375
Query: 103 IRPYVWRMNLP 113
P W
Sbjct: 376 TPPQRWDFTRS 386
>gnl|CDD|235382 PRK05270, PRK05270, galactose-1-phosphate uridylyltransferase;
Provisional.
Length = 493
Score = 25.6 bits (57), Expect = 8.9
Identities = 10/30 (33%), Positives = 21/30 (70%), Gaps = 3/30 (10%)
Query: 74 MTVNNLRKSSKD-DEVINLAKTLIKNWKKF 102
M+V +R +SK+ DE+I+ A +++ W+ +
Sbjct: 307 MSV--IRLTSKNKDELIDAADKILEAWRGY 334
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
0.317 0.131 0.373
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,171,810
Number of extensions: 515238
Number of successful extensions: 519
Number of sequences better than 10.0: 1
Number of HSP's gapped: 515
Number of HSP's successfully gapped: 33
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)