RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15261
(292 letters)
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 150 bits (380), Expect = 7e-41
Identities = 88/243 (36%), Positives = 129/243 (53%), Gaps = 38/243 (15%)
Query: 4 YLQSVCNHPKLVLGPSHAQYEALVSRPGLNLSDI--------RHAAKLPALKQLLMDCGI 55
L+ +CNHP LV A ++ +V + KL AL +LL+
Sbjct: 647 RLRQICNHPALVDEGLEATFDRIVLLLREDKDFDYLKKPLIQLSKGKLQALDELLL---- 702
Query: 56 GASPGMSGSGPHYDPGAPPPSILTQ---HRALIFCQLRAMLDIVENDLFKCEMPGVTYLR 112
+L + H+ LIF Q +LD++E + G+ Y+R
Sbjct: 703 -------------------DKLLEEGHYHKVLIFSQFTPVLDLLE---DYLKALGIKYVR 740
Query: 113 LDGSVVSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFVDHDWSPMKDLQA 172
LDGS + R ++ +FN+D V LL+ + GGLGLNLTGADTVI D W+P +LQA
Sbjct: 741 LDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQA 800
Query: 173 MDRAHRIGQKKVVNVYRLITKNTLEEKIMNLQKFKLLTANTVINSENRNLDTMATGK-IL 231
+DRAHRIGQK+ V VYRLIT+ T+EEKI+ LQ+ K +++I++E + + + +L
Sbjct: 801 IDRAHRIGQKRPVKVYRLITRGTIEEKILELQEKKQELLDSLIDAEGEKELSKLSIEDLL 860
Query: 232 DLF 234
DLF
Sbjct: 861 DLF 863
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 131 bits (330), Expect = 4e-34
Identities = 81/229 (35%), Positives = 106/229 (46%), Gaps = 47/229 (20%)
Query: 5 LQSVCNHPKLVLG----PSHAQYEALVSRPG-LNLSDIRHAAKLPALKQLLMDCGIGASP 59
L+ CNHP L G P + E LV G + L D LP LK+
Sbjct: 441 LRKCCNHPYLFQGAEPGPPYTTGEHLVENSGKMVLLD----KLLPKLKE----------- 485
Query: 60 GMSGSGPHYDPGAPPPSILTQHRALIFCQLRAMLDIVENDLFKCEMPGVTYLRLDGSVVS 119
R LIF Q+ +LDI+E+ G Y R+DG+
Sbjct: 486 -------------------RDSRVLIFSQMTRLLDILED---YLMYRGYQYCRIDGNTGG 523
Query: 120 TARHAIVTKFNSDPTID-VLLLTTQVGGLGLNLTGADTVIFVDHDWSPMKDLQAMDRAHR 178
R A + FN + V LL+T+ GGLG+NL AD VI D DW+P DLQA DRAHR
Sbjct: 524 EDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHR 583
Query: 179 IGQKKVVNVYRLITKNTLEEKIMNLQKFKLLTANTVIN----SENRNLD 223
IGQKK V V+R T+ T+EEK++ KL VI +E + ++
Sbjct: 584 IGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQGRLAEQKTVN 632
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 98.8 bits (247), Expect = 9e-26
Identities = 36/112 (32%), Positives = 49/112 (43%), Gaps = 5/112 (4%)
Query: 77 ILTQHRALIFCQLRAMLDIVENDLFKCEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTID 136
+ + LIFC + MLD + L K + V L DGS R ++ F
Sbjct: 25 LKKGGKVLIFCPSKKMLDELAELLRKPGIK-VAALHGDGSQ--EEREEVLKDFREGEI-- 79
Query: 137 VLLLTTQVGGLGLNLTGADTVIFVDHDWSPMKDLQAMDRAHRIGQKKVVNVY 188
V+L+ T V G++L VI D WSP LQ + RA R GQK +
Sbjct: 80 VVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 80.3 bits (199), Expect = 2e-19
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 102 KCEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFVD 161
PG+ RL G + R I+ F + + +L+ T V G G++L + VI D
Sbjct: 2 LLRKPGIKVARLHGGLSQEEREEILEDFRNGKS--KVLVATDVAGRGIDLPDVNLVINYD 59
Query: 162 HDWSPMKDLQAMDRAHRIG 180
W+P +Q + RA R G
Sbjct: 60 LPWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 77.3 bits (191), Expect = 3e-18
Identities = 29/87 (33%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 94 DIVENDLFKCEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTG 153
+ + L + G+ RL G + R I+ KFN+ +L+ T V GL+L G
Sbjct: 1 EELAELL---KELGIKVARLHGGLSQEEREEILDKFNNGKI--KVLVATDVAERGLDLPG 55
Query: 154 ADTVIFVDHDWSPMKDLQAMDRAHRIG 180
D VI D WSP +Q + RA R G
Sbjct: 56 VDLVIIYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 40.4 bits (95), Expect = 8e-04
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 139 LLTTQVGGLGLNLTGADTVIFVDHDWSPMKDLQAMDRAHRIGQKKVVNVYRLITKNTLEE 198
L+ T VG GL++ D VIF + S ++ +Q R G+K+ V L+T+ T +E
Sbjct: 429 LVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRT---GRKRKGRVVVLVTEGTRDE 485
>gnl|CDD|237222 PRK12837, PRK12837, 3-ketosteroid-delta-1-dehydrogenase;
Provisional.
Length = 513
Score = 31.0 bits (70), Expect = 0.74
Identities = 20/48 (41%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 71 GAPPPSILTQHRALIFCQLRAMLDIVENDLFKCEMPGVTYLRLDGSVV 118
GAPPP L RALI L A L N + P V + DG VV
Sbjct: 162 GAPPPDYLVGGRALIGRFLAA-LARFPNARLRLNTPLVELVVEDGRVV 208
>gnl|CDD|221342 pfam11960, DUF3474, Domain of unknown function (DUF3474). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and eukaryotes. This domain
is typically between 126 to 140 amino acids in length.
This domain is found associated with pfam00487.
Length = 135
Score = 30.0 bits (68), Expect = 0.77
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 63 GSGPHYDPGAPPPSILTQHRALI 85
+DPGAPPP L RA I
Sbjct: 85 EEEEEFDPGAPPPFKLADIRAAI 107
>gnl|CDD|215275 PLN02498, PLN02498, omega-3 fatty acid desaturase.
Length = 450
Score = 30.6 bits (69), Expect = 1.1
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 56 GASPGMSGSGPHYDPGAPPPSILTQHRALI 85
G + +DPGAPPP L RA I
Sbjct: 82 GVNGVGEDEEGEFDPGAPPPFNLADIRAAI 111
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 30.3 bits (69), Expect = 1.2
Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 15/76 (19%)
Query: 118 VSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLN------LTGADTVIFVDHDWSPMKDLQ 171
V T HA+V P VL++ +GGLGLN GA VI VD +
Sbjct: 150 VLTPYHAVVRAGEVKPGETVLVIG--LGGLGLNAVQIAKAMGA-AVIAVD------IKEE 200
Query: 172 AMDRAHRIGQKKVVNV 187
++ A +G +V+N
Sbjct: 201 KLELAKELGADEVLNS 216
>gnl|CDD|237325 PRK13267, PRK13267, archaemetzincin-like protein; Reviewed.
Length = 179
Score = 29.6 bits (67), Expect = 1.3
Identities = 21/84 (25%), Positives = 31/84 (36%), Gaps = 18/84 (21%)
Query: 51 MDCGIGASPGMSGSGPHYDPGAPPPSILTQHRALIFCQL---------RAMLDIVENDLF 101
+DC + S YD Q+RA F L + I + DL+
Sbjct: 29 LDCDVTVDSRQSLPISAYDWER------GQYRAEKFLPLLSRIGRFNGDKNIGITDCDLY 82
Query: 102 KCEMP---GVTYLRLDGSVVSTAR 122
+ G+ Y L G+V+ST R
Sbjct: 83 YRGLNFVFGLAYPNLRGAVISTYR 106
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 28.9 bits (65), Expect = 3.1
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 138 LLLTTQVGGLGLNLTGADTVIFVDHDWSPMKDL-QAMDRAHRIGQKKVVNVYRLI 191
+++ TQV L+++ D +I + +P+ L Q + R HR G+K VY +
Sbjct: 277 VIVATQVIEASLDIS-VDVMI---TELAPIDSLIQRLGRLHRYGEKNGEEVYIIT 327
>gnl|CDD|211387 cd11301, Fut1_Fut2_like, Alpha-1,2-fucosyltransferase.
Alpha-1,2-fucosyltransferases (Fut1, Fut2) catalyze the
transfer of alpha-L-fucose to the terminal
beta-D-galactose residue of glycoconjugates via an
alpha-1,2-linkage, generating carbohydrate structures
that exhibit H-antigenicity for blood-group
carbohydrates. These structures also act as ligands for
morphogenesis, the adhesion of microbes, and
metastasizing cancer cells. Fut1 is responsible for
producing the H antigen on red blood cells. Fut2 is
expressed in epithelia of secretory tissues, and
individuals termed "secretors" have at least one
functional copy of the gene; they secrete H antigen
which is further processed into A and/or B antigens
depending on the ABO genotype. O-fucosyltransferase-like
proteins are GDP-fucose dependent enzymes with
similarities to the family 1 glycosyltransferases (GT1).
They are soluble ER proteins that may be proteolytically
cleaved from a membrane-associated preprotein, and are
involved in the O-fucosylation of protein substrates,
the core fucosylation of growth factor receptors, and
other processes.
Length = 265
Score = 28.6 bits (64), Expect = 3.9
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 149 LNLTGADTVIFVDHDWSPMKDLQAM 173
L LT + V FVD + S +DL M
Sbjct: 196 LALTSKENVYFVDGNNSSYEDLYLM 220
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 28.6 bits (64), Expect = 4.0
Identities = 28/107 (26%), Positives = 50/107 (46%), Gaps = 5/107 (4%)
Query: 78 LTQHRALIFCQLRAMLDIVENDLFKCEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTIDV 137
LT +A+I+C R +D + + + + T + G + R I+ +F S T
Sbjct: 265 LTITQAIIYCNTRRKVDYLTKKMHERDF---TVSCMHGDMDQKDRDLIMREFRSGST--R 319
Query: 138 LLLTTQVGGLGLNLTGADTVIFVDHDWSPMKDLQAMDRAHRIGQKKV 184
+L+TT + G+++ VI D SP + + R+ R G+K V
Sbjct: 320 VLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGV 366
>gnl|CDD|188633 cd00502, DHQase_I, Type I 3-dehydroquinase, (3-dehydroquinate
dehydratase or DHQase). Type I 3-dehydroquinase,
(3-dehydroquinate dehydratase or DHQase). Catalyzes the
cis-dehydration of 3-dehydroquinate via a covalent imine
intermediate to produce dehydroshikimate. Dehydroquinase
is the third enzyme in the shikimate pathway, which is
involved in the biosynthesis of aromatic amino acids.
Type I DHQase exists as a homodimer. Type II
3-dehydroquinase also catalyzes the same overall
reaction, but is unrelated in terms of sequence and
structure, and utilizes a completely different reaction
mechanism.
Length = 225
Score = 28.1 bits (63), Expect = 4.4
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 11/81 (13%)
Query: 162 HDWSPMKDLQAMDRAHRIGQKKVVNVYRLITKNTLEEKIMNLQKFKLLTANTVINSENRN 221
HD+S + + ++ ++ E + L KF V N +
Sbjct: 121 HDFSGTPSDEELVSRLEKMAALGADIVKIAVMANSIEDNLRLLKFT----RQVKNLYDIP 176
Query: 222 LDTMATGKILDLFCLDGQDSR 242
L + G++ G+ SR
Sbjct: 177 LIAINMGEL-------GKLSR 190
>gnl|CDD|129799 TIGR00716, rnhC, ribonuclease HIII. This enzyme cleaves RNA from
DNA-RNA hybrids. Two types of ribonuclease H in Bacillus
subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are
both known experimentally and are quite similar to each
other. The only RNase H homolog in the Mycoplasmas
resembles rnhC. Archaeal forms resemble HII more closely
than HIII. This model describes bacterial RNase III [DNA
metabolism, DNA replication, recombination, and repair].
Length = 284
Score = 28.0 bits (62), Expect = 5.4
Identities = 23/154 (14%), Positives = 48/154 (31%), Gaps = 31/154 (20%)
Query: 100 LFKCEMPGVT-YLRLDGSVVSTARHA-IVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTV 157
+F+ E PGV G ++ +++ V K + LL ++ ++ G D
Sbjct: 30 VFQLEGPGVKVTYYQSGKLLIQGKNSEKVLKRWGTAEVLNLLEKKKLPADPRSVIGCDES 89
Query: 158 -------------IFVDHDWSP-MKDLQAMDRAHRIGQKKVVNVYRLITK---------- 193
+++ + + L D + R+ K++ + +
Sbjct: 90 GKGDIFGPLVLCCVYIPEENYLKVSSLNPRD-SKRLSDKRIERLALNLKPLVKAYCYELK 148
Query: 194 ----NTLEEKIMNLQKFKLLTANTVINSENRNLD 223
N L K NL K +I +
Sbjct: 149 PEKYNKLYRKFRNLNKMMAHFHKLLIERLLKEEC 182
>gnl|CDD|219337 pfam07217, Het-C, Heterokaryon incompatibility protein Het-C. In
filamentous fungi, het loci (for heterokaryon
incompatibility) are believed to regulate
self/nonself-recognition during vegetative growth. As
filamentous fungi grow, hyphal fusion occurs within an
individual colony to form a network. Hyphal fusion can
occur also between different individuals to form a
heterokaryon, in which genetically distinct nuclei
occupy a common cytoplasm. However, heterokaryotic cells
are viable only if the individuals involved have
identical alleles at all het loci.
Length = 602
Score = 28.5 bits (64), Expect = 5.6
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 235 CLDGQDSRQEAGSSGTNPGGLKGLLDTLPE 264
L+G E SSG++ L LL +P
Sbjct: 296 ELEGALGDAENSSSGSSGSDLIDLLSKIPG 325
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 27.8 bits (62), Expect = 8.3
Identities = 28/135 (20%), Positives = 53/135 (39%), Gaps = 7/135 (5%)
Query: 82 RALIFCQLRAMLDIVENDLFKCEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTIDVLLLT 141
R ++F + + +++ + L K V L G + R + KF + VL+
Sbjct: 275 RVIVFVRTKRLVEELAESLRKRGFK-VAALH--GDLPQEERDRALEKFKDG-ELRVLV-A 329
Query: 142 TQVGGLGLNLTGADTVIFVDHDWSPMKDLQAMDRAHRIGQKKVVNVYRLITKNTLEEKIM 201
T V GL++ VI D P + + R R G+K V +T+ +K+
Sbjct: 330 TDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAIS--FVTEEEEVKKLK 387
Query: 202 NLQKFKLLTANTVIN 216
++K + +
Sbjct: 388 RIEKRLERKLPSAVL 402
>gnl|CDD|237036 PRK12284, PRK12284, tryptophanyl-tRNA synthetase; Reviewed.
Length = 431
Score = 27.7 bits (62), Expect = 8.9
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 16 LGPSHAQYEALVSRPGLNLSDIRH--AAKLPALKQLLM 51
L P +YEAL++RP + DI AAK + +
Sbjct: 286 LAPMRERYEALIARPAD-IEDILLAGAAKARRIATPFL 322
>gnl|CDD|178129 PLN02513, PLN02513, adenylosuccinate synthase.
Length = 427
Score = 27.3 bits (61), Expect = 9.8
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 16 LGPSHAQYEALVSRPGLNLSDIRHAAKLPA-LKQLLMD 52
+GP+ Y + +R GL + D+RH L++LL D
Sbjct: 135 IGPA---YSSKATRNGLRVGDLRHMDTFAEKLRELLAD 169
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 0.135 0.399
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,809,522
Number of extensions: 1412815
Number of successful extensions: 1187
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1179
Number of HSP's successfully gapped: 30
Length of query: 292
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 196
Effective length of database: 6,679,618
Effective search space: 1309205128
Effective search space used: 1309205128
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: 59 (26.4 bits)