RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2073
(126 letters)
>gnl|CDD|219532 pfam07717, OB_NTP_bind, Oligonucleotide/oligosaccharide-binding
(OB)-fold. This family is found towards the C-terminus
of the DEAD-box helicases (pfam00270). In these
helicases it is apparently always found in association
with pfam04408. There do seem to be a couple of
instances where it occurs by itself - . The structure
PDB:3i4u adopts an OB-fold. helicases (pfam00270). In
these helicases it is apparently always found in
association with pfam04408. This C-terminal domain of
the yeast helicase contains an
oligonucleotide/oligosaccharide-binding (OB)-fold which
seems to be placed at the entrance of the putative
nucleic acid cavity. It also constitutes the binding
site for the G-patch-containing domain of Pfa1p. When
found on DEAH/RHA helicases, this domain is central to
the regulation of the helicase activity through its
binding of both RNA and G-patch domain proteins.
Length = 109
Score = 90.1 bits (224), Expect = 9e-25
Identities = 35/69 (50%), Positives = 45/69 (65%), Gaps = 3/69 (4%)
Query: 30 QVAHLEKDGRY-LTIKDNQVVQLHPSTCLDHK--PEWVVYNEFVLTTKNYIRTVTDVKPE 86
VA L + T+K+ Q V +HPS+ L K PEWVVY+E V TTK Y+R VT + PE
Sbjct: 41 NVARLVDEKGEYKTLKEGQPVFIHPSSVLFGKKPPEWVVYHELVETTKEYMRDVTAIDPE 100
Query: 87 WLIKLAPQY 95
WL++LAP Y
Sbjct: 101 WLLELAPHY 109
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 53.9 bits (130), Expect = 2e-09
Identities = 27/84 (32%), Positives = 39/84 (46%), Gaps = 14/84 (16%)
Query: 24 LSESLLQVAHLEKDGR-YLTIKDNQVVQLHP-STCL-DHKPEWVVYNEFVLTTKNYIR-- 78
+ L +A L+ DGR Y+T+ DN V HP S L EW+ Y EF+ T K Y+R
Sbjct: 624 AAGRKLNIAQLQLDGRPYVTLSDNTPVFAHPSSVRLGLVLLEWIKYAEFLRTRKGYLREG 683
Query: 79 ---------TVTDVKPEWLIKLAP 93
T+ ++ WL +
Sbjct: 684 RGERWPDVQTLIELLKLWLKEQVK 707
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 47.1 bits (112), Expect = 4e-07
Identities = 28/96 (29%), Positives = 46/96 (47%), Gaps = 3/96 (3%)
Query: 15 NYSILFYSTLSESLLQVAHLEKDGRYLTIKDNQVVQLHPSTCLDHK-PEWVVYNEFVLTT 73
+Y + + LS L Q+ ++ Y + + + P + L K P+WV+ E V T+
Sbjct: 605 DYDAIHKALLSGLLSQIGMKDEKHEYDGAR-GRKFHIFPGSPLFKKPPKWVMAAELVETS 663
Query: 74 KNYIRTVTDVKPEWLIKLAPQYYELQNF-PQCEAKR 108
K Y R V ++PEW+ +A + F P E KR
Sbjct: 664 KLYARLVAKIEPEWVEPVAGHLIKKNYFEPHWEKKR 699
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 33.1 bits (76), Expect = 0.027
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 61 PEWVVYNEFVLTTKNYIRTVTDVKPEWLIKLA 92
P+WV+ E V T++ + R ++PEW+ LA
Sbjct: 661 PKWVMVAELVETSRLWGRIAARIEPEWIEPLA 692
>gnl|CDD|233634 TIGR01914, cas_Csa4, CRISPR-associated protein Cas8a2/Csa4, subtype
I-A/APERN. CRISPR loci appear to be mobile elements
with a wide host range. This model represents a protein
that tends to be found near CRISPR repeats. The species
range for this species, so far, is exclusively archaeal.
It is found so far in only four different species, and
includes two tandem genes in Pyrococcus furiosus DSM
3638. This subfamily is found in a CRISPR/Cas locus we
designate APERN, so the family is designated Csa4, for
CRISPR/Cas Subtype Protein 4 [Mobile and
extrachromosomal element functions, Other].
Length = 354
Score = 27.9 bits (62), Expect = 1.7
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 1 MPYQEIPFGFIYNKNYSILFYSTLSESL 28
MPY F F + ++L++ +ESL
Sbjct: 215 MPYILRDFHFKISNELALLYHLLYTESL 242
>gnl|CDD|180124 PRK05537, PRK05537, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Validated.
Length = 568
Score = 26.6 bits (59), Expect = 4.6
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 22 STLSESLLQVAHLEKDGRYLTIKDNQVVQLHPSTCL 57
ST++++L V +E GR +T+ D VV+ H S+ L
Sbjct: 406 STIAKAL-MVKLMEMRGRPVTLLDGDVVRKHLSSEL 440
>gnl|CDD|225065 COG2154, COG2154, Pterin-4a-carbinolamine dehydratase [Coenzyme
metabolism].
Length = 101
Score = 25.8 bits (57), Expect = 4.6
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 46 NQVVQLHPSTCLDHKPEW-VVYNEFVLT-TKNYIRTVTDVKPEWLIKLA 92
N+V ++ + L+H P+ VVYN +T T + +TD+ KLA
Sbjct: 47 NRVAEI--AEKLNHHPDIEVVYNRVTVTLTTHDAGGLTDLD----FKLA 89
>gnl|CDD|167649 PRK03963, PRK03963, V-type ATP synthase subunit E; Provisional.
Length = 198
Score = 25.9 bits (57), Expect = 6.6
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 8/38 (21%)
Query: 84 KPEWLIKLAPQYYELQNFPQCEAKRQLEILQAKMETRQ 121
K EW+++ A Q E ++Q I AK+E R+
Sbjct: 44 KAEWILRKAKT--------QAELEKQRIIANAKLEVRR 73
>gnl|CDD|198325 cd10292, GST_C_YghU_like, C-terminal, alpha helical domain of
Escherichia coli Yghu Glutathione S-transferases and
related uncharacterized proteins. Glutathione
S-transferase (GST) C-terminal domain family, YghU-like
subfamily; composed of the Escherichia coli YghU and
related proteins. GSTs are cytosolic dimeric proteins
involved in cellular detoxification by catalyzing the
conjugation of glutathione (GSH) with a wide range of
endogenous and xenobiotic alkylating agents, including
carcinogens, therapeutic drugs, environmental toxins and
products of oxidative stress. GSTs also show GSH
peroxidase activity and are involved in the synthesis of
prostaglandins and leukotrienes. The GST active site is
located in a cleft between the N- and C-terminal
domains. GSH binds to the N-terminal domain while the
hydrophobic substrate occupies a pocket in the
C-terminal domain. YghU is one of nine GST homologs in
the genome of Escherichia coli. It is similar to
Escherichia coli YfcG in that it has poor GSH
transferase activity towards typical substrates. It
shows modest reductase activity towards some organic
hydroperoxides. Like YfcG, YghU also shows good
disulfide bond oxidoreductase activity comparable to the
activities of glutaredoxins and thioredoxins. YghU does
not contain a redox active cysteine residue, and may use
a bound thiol disulfide couple such as 2GSH/GSSG for
activity. The crystal structure of YghU reveals two GSH
molecules bound in its active site.
Length = 118
Score = 25.1 bits (55), Expect = 7.7
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 105 EAKRQLEILQAKMETRQYQDG 125
EAKRQL++L ++ T +Y G
Sbjct: 44 EAKRQLDVLDRQLATHKYLAG 64
>gnl|CDD|226195 COG3669, COG3669, Alpha-L-fucosidase [Carbohydrate transport and
metabolism].
Length = 430
Score = 25.6 bits (56), Expect = 9.0
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 2/32 (6%)
Query: 38 GRYLTIKDNQVVQLHPSTCLDHKPEWVVYNEF 69
YL + + HP+T D EW EF
Sbjct: 16 LAYLYQEGSPFYHFHPNTYGD--QEWFGGQEF 45
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
0.321 0.137 0.416
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,303,581
Number of extensions: 523792
Number of successful extensions: 478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 476
Number of HSP's successfully gapped: 24
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
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 (21.8 bits)
S2: 53 (24.2 bits)