RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16849
(371 letters)
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 42.0 bits (98), Expect = 4e-04
Identities = 42/250 (16%), Positives = 85/250 (34%), Gaps = 5/250 (2%)
Query: 71 INYAAEQHSFSNMKKLEDDNFYVCSNVMFDSQNQLYPSENNNNLNVDESCVQISPLAYNA 130
N HS + + + + ++ S + N + + + +
Sbjct: 119 DNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTPQSNSLHPPLPANSLSK 178
Query: 131 LMTFVPNNENIINDMSPPASPTNRINGSFTKMIIADEVVCKEATENYQNKVITPPMSPML 190
+ + N + S + S + I + + + T
Sbjct: 179 DPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPK 238
Query: 191 TDPLLLNRTEVPPVNNNNNNNNTRVNINTPSKTKTRERRSGSRK-KLTSHACFHPGCGKT 249
+ + ++++ + + R ++ T S + S S K S C +
Sbjct: 239 SLLSQSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNIS 298
Query: 250 YTKSSHLKAHLRT--HTGE--KPYQCKWKGCGWKFARSDELTRHFRKHTGDRPFQCKPNL 305
+++SS L HLR+ H+GE KP+ C + CG F+R+D L RH HT P + K
Sbjct: 299 FSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLN 358
Query: 306 VNPSIKEGKD 315
+ +
Sbjct: 359 SSSKFSPLLN 368
Score = 35.1 bits (80), Expect = 0.052
Identities = 29/96 (30%), Positives = 48/96 (50%), Gaps = 8/96 (8%)
Query: 201 VPPVNNNNNNNNTRVNINTPSKTKTRERRSGSRKKLTSHACFHPGCGKTYTKSSHLKAHL 260
+ ++++NN+ ++ S K +C P C ++++ HL H+
Sbjct: 2 TLTSSQSSSSNNSVLSSTPKSTLK------SLSNAPRPDSC--PNCTDSFSRLEHLTRHI 53
Query: 261 RTHTGEKPYQCKWKGCGWKFARSDELTRHFRKHTGD 296
R+HTGEKP QC + GC F+R EL+RH R H +
Sbjct: 54 RSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89
Score = 30.0 bits (67), Expect = 2.1
Identities = 24/119 (20%), Positives = 42/119 (35%)
Query: 183 TPPMSPMLTDPLLLNRTEVPPVNNNNNNNNTRVNINTPSKTKTRERRSGSRKKLTSHACF 242
+L T + P N++++ + ++ ++ K
Sbjct: 331 KLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETL 390
Query: 243 HPGCGKTYTKSSHLKAHLRTHTGEKPYQCKWKGCGWKFARSDELTRHFRKHTGDRPFQC 301
C + + + S+L H+ TH +PY CK C F R L H + HT P C
Sbjct: 391 SNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLC 449
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 35.8 bits (83), Expect = 0.001
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 255 HLKAHLRTHTGEKPYQCK 272
+L+ H+RTHTGEKPY+C
Sbjct: 1 NLRRHMRTHTGEKPYKCP 18
Score = 33.1 bits (76), Expect = 0.008
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 285 ELTRHFRKHTGDRPFQCK 302
L RH R HTG++P++C
Sbjct: 1 NLRRHMRTHTGEKPYKCP 18
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 33.9 bits (78), Expect = 0.005
Identities = 12/20 (60%), Positives = 17/20 (85%)
Query: 244 PGCGKTYTKSSHLKAHLRTH 263
P CGK++++ S+LK HLRTH
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
Score = 29.6 bits (67), Expect = 0.18
Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 2/24 (8%)
Query: 270 QCKWKGCGWKFARSDELTRHFRKH 293
+C CG F+R L RH R H
Sbjct: 1 KCP--DCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 32.1 bits (73), Expect = 0.019
Identities = 9/25 (36%), Positives = 10/25 (40%), Gaps = 2/25 (8%)
Query: 269 YQCKWKGCGWKFARSDELTRHFRKH 293
Y+C CG F L H R H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
Score = 27.4 bits (61), Expect = 0.84
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 239 HACFHPGCGKTYTKSSHLKAHLRTH 263
+ C CGK + S L+ H+RTH
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 29.9 bits (67), Expect = 0.12
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 269 YQCKWKGCGWKFARSDELTRHFRKH 293
++C CG F+ D L RH RKH
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
Score = 26.8 bits (59), Expect = 1.5
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 239 HACFHPGCGKTYTKSSHLKAHLRTH 263
C P CGK+++ LK HLR H
Sbjct: 1 FKC--PLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|218591 pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein.
This family consists of several ROS/MUCR transcriptional
regulator proteins. The ros chromosomal gene is present
in octopine and nopaline strains of Agrobacterium
tumefaciens as well as in Rhizobium meliloti. This gene
encodes a 15.5-kDa protein that specifically represses
the virC and virD operons in the virulence region of the
Ti plasmid and is necessary for succinoglycan
production. Sinorhizobium meliloti can produce two types
of acidic exopolysaccharides, succinoglycan and
galactoglucan, that are interchangeable for infection of
alfalfa nodules. MucR from Sinorhizobium meliloti acts
as a transcriptional repressor that blocks the
expression of the exp genes responsible for
galactoglucan production therefore allowing the
exclusive production of succinoglycan.
Length = 130
Score = 32.1 bits (74), Expect = 0.17
Identities = 15/30 (50%), Positives = 18/30 (60%), Gaps = 5/30 (16%)
Query: 246 CGKTYTKSSHLKAHLRTHTGEKP--YQCKW 273
GK + K+ LK HLRTH G P Y+ KW
Sbjct: 76 DGKKF-KT--LKRHLRTHHGLTPEEYRAKW 102
>gnl|CDD|212104 cd10792, GH57N_AmyC_like, N-terminal catalytic domain of
alpha-amylase ( AmyC ) and similar proteins.
Alpha-amylases (alpha-1,4-glucan-4-glucanohydrolases, EC
3.2.1.1) play essential roles in alpha-glucan metabolism
by catalyzing the hydrolysis of polysaccharides such as
amylose starch, and beta-limit dextrin. This subfamily
is represented by a novel alpha-amylase (AmyC) encoded
by hyperthermophilic organism Thermotoga maritime ORF
tm1438, and its prokaryotic homologs. AmyC functions as
a homotetramer and shows thermostable amylolytic
activity. It is strongly inhibited by acarbose. AmyC is
composed of a N-terminal catalytic domain, containing a
distorted TIM-barrel structure with a characteristic
(beta/alpha)7 fold motif, and two additional less
conserved domains. There are other two canonical
alpha-amylases encoded from T. maritime that lack the
sequence similarity to AmyC, and belong to a different
superfamily.
Length = 412
Score = 32.1 bits (74), Expect = 0.51
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 181 VITPPMSPMLTDPLLLNR 198
++P + ML DPLL R
Sbjct: 58 SLSPTLCSMLADPLLQER 75
>gnl|CDD|223628 COG0554, GlpK, Glycerol kinase [Energy production and conversion].
Length = 499
Score = 31.0 bits (71), Expect = 0.99
Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 7/32 (21%)
Query: 239 HACFHPGCGK-TY-TKSSHLKAHLRTHTGEKP 268
CF PG K TY T L +TGEKP
Sbjct: 253 QGCFEPGMAKNTYGTGCFLL-----MNTGEKP 279
>gnl|CDD|227293 COG4957, COG4957, Predicted transcriptional regulator
[Transcription].
Length = 148
Score = 29.6 bits (67), Expect = 1.4
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 246 CGKTYTKSSHLKAHLRTHTGEKP--YQCKWK 274
GK + KS LK HL TH G P Y+ KW
Sbjct: 82 DGKKF-KS--LKRHLTTHYGLTPDEYRAKWG 109
>gnl|CDD|223410 COG0333, RpmF, Ribosomal protein L32 [Translation, ribosomal
structure and biogenesis].
Length = 57
Score = 27.2 bits (61), Expect = 2.0
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 2/50 (4%)
Query: 218 NTPSKTKTRERRSGSRKKLTSHACFHPGCGKTYTKSSHLKAHLRTHTGEK 267
SK++ R RRS K P CG+ Y + + G +
Sbjct: 6 RKTSKSRRRMRRSHDALKA-PTLSVCPNCGE-YKLPHRVCLKCGYYKGRQ 53
>gnl|CDD|235853 PRK06701, PRK06701, short chain dehydrogenase; Provisional.
Length = 290
Score = 29.6 bits (67), Expect = 2.1
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 62 EEFVDLDMLINYAAEQHSFSNMKKLEDDNF 91
E LD+L+N AA Q+ +++ + +
Sbjct: 120 RELGRLDILVNNAAFQYPQQSLEDITAEQL 149
>gnl|CDD|221143 pfam11593, Med3, Mediator complex subunit 3 fungal. 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. 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 subunit
Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast
transcriptional co-repressor.
Length = 381
Score = 29.2 bits (65), Expect = 3.2
Identities = 17/61 (27%), Positives = 25/61 (40%)
Query: 96 NVMFDSQNQLYPSENNNNLNVDESCVQISPLAYNALMTFVPNNENIINDMSPPASPTNRI 155
N M N + P N N + + Q++P A N M ++ M+P AS N
Sbjct: 259 NAMASPLNNMSPMRNLNQMGNQNNGGQMTPSANNGNMNNQSRENSMNQGMTPSASMINLN 318
Query: 156 N 156
N
Sbjct: 319 N 319
>gnl|CDD|198363 cd07791, FGGY_GK2_bacteria, bacterial glycerol kinase 2-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
putative bacterial glycerol kinases (GK), which may be
coded by the GK-like gene, GK2. Sequence comparison
shows members in this CD are homologs of Escherichia
coli GK. They retain all functionally important
residues, and may catalyze the Mg-ATP dependent
phosphorylation of glycerol to yield glycerol
3-phosphate (G3P). GKs belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 484
Score = 29.3 bits (66), Expect = 3.4
Identities = 12/25 (48%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 232 SRKKLTSHACFHPGCGK-TY-TKSS 254
S L H F PG K TY T SS
Sbjct: 240 SHAALFGHGAFAPGEVKATYGTGSS 264
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 26.5 bits (58), Expect = 3.8
Identities = 13/30 (43%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 244 PGCGKTYTKSSHLKAHLRTH-TGEKPYQCK 272
P CG+ Y K + HLR H T K CK
Sbjct: 9 PICGEIYIKRKSMITHLRKHNTNLKLSNCK 38
>gnl|CDD|187613 cd05355, SDR_c1, classical (c) SDR, subgroup 1. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. 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 catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). 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) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 270
Score = 28.8 bits (65), Expect = 4.6
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 61 NEEFVDLDMLINYAAEQHSFSNMKKLEDDNFY 92
+EF LD+L+N AA QH +++ + +
Sbjct: 100 VKEFGKLDILVNNAAYQHPQESIEDITTEQLE 131
>gnl|CDD|222972 PHA03080, PHA03080, putative virion core protein; Provisional.
Length = 366
Score = 28.1 bits (63), Expect = 8.0
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 205 NNNNNNNNTRVNINTPSKTKT 225
N+ N +NIN+P KT T
Sbjct: 338 NSGKKNGGITLNINSPFKTIT 358
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1034
Score = 28.3 bits (63), Expect = 8.5
Identities = 20/106 (18%), Positives = 31/106 (29%), Gaps = 1/106 (0%)
Query: 130 ALMTFVPNNENIINDMSPPASPTNRINGSFTKMIIADEVVCKEATENYQNKVITPPMSPM 189
A+ T N I+D N ++ TK + TE N + S
Sbjct: 538 AIPTEGTQNLQGISDHPEQFEFQNELSPLETKNN-ESNLSSDAETEGSPNPEMPSWSSVT 596
Query: 190 LTDPLLLNRTEVPPVNNNNNNNNTRVNINTPSKTKTRERRSGSRKK 235
+ L N P N N I T + ++ + S
Sbjct: 597 VPSEALDNYETTNPSNAKEVRNFAETGIQTTNVGESADLLLISNPM 642
>gnl|CDD|129369 TIGR00268, TIGR00268, TIGR00268 family protein. The N-terminal
region of the model shows similarity to
Argininosuccinate synthase proteins using PSI-blast and
using the recognize protein identification server
[Hypothetical proteins, Conserved].
Length = 252
Score = 27.8 bits (62), Expect = 8.7
Identities = 11/47 (23%), Positives = 23/47 (48%)
Query: 270 QCKWKGCGWKFARSDELTRHFRKHTGDRPFQCKPNLVNPSIKEGKDL 316
K G +F + D++ FR + +R + CK +++ +KE +
Sbjct: 60 IAKEIGVNHEFVKIDKMINPFRANVEERCYFCKKMVLSILVKEAEKR 106
>gnl|CDD|226444 COG3934, COG3934, Endo-beta-mannanase [Carbohydrate transport and
metabolism].
Length = 587
Score = 27.9 bits (62), Expect = 9.0
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 7/60 (11%)
Query: 36 SSSQIVKEEYGFPTAKYVEEPQLNQNEEFVDLDMLINYAAEQH---SFSNMKKLEDDNFY 92
+ EE+GF TA E F+ + + ++ + S+ DD+ Y
Sbjct: 235 GWQPVNLEEFGFSTAFGQENSPA----YFIWIRLALDTGGDGALIWCLSDFHLGSDDSEY 290
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
0.314 0.129 0.392
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,984,415
Number of extensions: 1627770
Number of successful extensions: 1305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1298
Number of HSP's successfully gapped: 30
Length of query: 371
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 273
Effective length of database: 6,590,910
Effective search space: 1799318430
Effective search space used: 1799318430
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 (21.5 bits)
S2: 60 (27.0 bits)