RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14233
(122 letters)
>gnl|CDD|214634 smart00358, DSRM, Double-stranded RNA binding motif.
Length = 67
Score = 76.9 bits (190), Expect = 5e-20
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 8 KAFLNEWCQKNSKQPEFD-VRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDAQTNAAK 66
K+ L E QK PE++ V+ GP H RF +++ G G G ++KK+A+ AA+
Sbjct: 2 KSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGK-RTGEGEGSSKKEAKQRAAE 60
Query: 67 DFVQYL 72
++ L
Sbjct: 61 AALRSL 66
>gnl|CDD|238007 cd00048, DSRM, Double-stranded RNA binding motif. Binding is not
sequence specific but is highly specific for double
stranded RNA. Found in a variety of proteins including
dsRNA dependent protein kinase PKR, RNA helicases,
Drosophila staufen protein, E. coli RNase III, RNases
H1, and dsRNA dependent adenosine deaminases.
Length = 68
Score = 69.6 bits (171), Expect = 3e-17
Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 8 KAFLNEWCQKNSK-QPEFD-VRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDAQTNAA 65
K+ L E QK K PE++ V GP H RF E+ + G G G ++KK+A+ NAA
Sbjct: 3 KSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGK-ITGEGEGSSKKEAKQNAA 61
Query: 66 KDFVQYL 72
+ ++ L
Sbjct: 62 EAALRKL 68
>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif. Sequences
gathered for seed by HMM_iterative_training Putative
motif shared by proteins that bind to dsRNA. At least
some DSRM proteins seem to bind to specific RNA
targets. Exemplified by Staufen, which is involved in
localisation of at least five different mRNAs in the
early Drosophila embryo. Also by interferon-induced
protein kinase in humans, which is part of the cellular
response to dsRNA.
Length = 66
Score = 62.7 bits (153), Expect = 1e-14
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 8 KAFLNEWCQKNSKQPEF-DVRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDAQTNAAK 66
K+ L E CQK +P + V GP H F + + G Y G G ++KK+A+ AA+
Sbjct: 2 KSLLQELCQKKGPKPPYEYVEEEGPPHSPTFTVTVTVNGKKY-GTGTGSSKKEAKQLAAE 60
Query: 67 DFVQYL 72
+Q L
Sbjct: 61 KALQKL 66
>gnl|CDD|222987 PHA03103, PHA03103, double-strand RNA-binding protein; Provisional.
Length = 183
Score = 45.9 bits (109), Expect = 5e-07
Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 11 LNEWCQKNSKQPEFDVRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDAQTNAAK 66
+NE+CQ S+ ++ ++GP H F + I+GI + A ST KK+A+ NAAK
Sbjct: 115 INEYCQITSRDWSINITSSGPSHSPTFTASVIISGIKFKPAIGST-KKEAKNNAAK 169
>gnl|CDD|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial. This family
consists of bacterial examples of ribonuclease III. This
enzyme cleaves double-stranded rRNA. It is involved in
processing ribosomal RNA precursors. It is found even in
minimal genones such as Mycoplasma genitalium and
Buchnera aphidicola, and in some cases has been shown to
be an essential gene. These bacterial proteins contain a
double-stranded RNA binding motif (pfam00035) and a
ribonuclease III domain (pfam00636). Eukaryotic homologs
tend to be much longer proteins with additional domains,
localized to the nucleus, and not included in this
family [Transcription, RNA processing].
Length = 220
Score = 41.8 bits (99), Expect = 2e-05
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 11 LNEWCQKNSKQ-PEFD-VRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDAQTNAAKD 67
L EW Q K PE+ ++ GP H + F E+ + G G G +KK+A+ NAAK
Sbjct: 158 LQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNG-EPYGEGKGKSKKEAEQNAAKA 215
>gnl|CDD|234633 PRK00102, rnc, ribonuclease III; Reviewed.
Length = 229
Score = 40.9 bits (97), Expect = 3e-05
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 11 LNEWCQKNSK-QPEFD-VRAAGPKHRQRFLCELRIAGIGY-VGAGNSTNKKDAQTNAAK 66
L E Q PE++ V+ GP H + F E+ + G G G+S KK+A+ AAK
Sbjct: 164 LQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKELGEGTGSS--KKEAEQAAAK 220
>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription].
Length = 235
Score = 40.7 bits (96), Expect = 4e-05
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 7 VKAFLNEWCQKNSKQ-PEFD-VRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDAQTNA 64
K L E Q PE+ V+ GP H + F E+ + G +G G +KK+A+ A
Sbjct: 163 PKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGK-ELGTGKGRSKKEAEQAA 221
Query: 65 AKD 67
A+
Sbjct: 222 AEQ 224
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed.
Length = 235
Score = 35.1 bits (81), Expect = 0.004
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 8 KAFLNEWC-QKNSKQPEFDV-RAAGPKHRQRFLCELRIAGIG-YVGAGNSTNKKDAQTNA 64
K L EW + P + V +GP H RF E+ + G G G S K+ A+ A
Sbjct: 164 KTELQEWAHAQFGVTPVYRVDSRSGPDHDPRFTVEVEVKGFAPETGEGRS--KRAAEQVA 221
Query: 65 A 65
A
Sbjct: 222 A 222
>gnl|CDD|133475 cd06583, PGRP, Peptidoglycan recognition proteins (PGRPs) are
pattern recognition receptors that bind, and in certain
cases, hydrolyze peptidoglycans (PGNs) of bacterial cell
walls. PGRPs have been divided into three classes: short
PGRPs (PGRP-S), that are small (20 kDa) extracellular
proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa
and are predicted to be transmembrane proteins; and long
PGRPs (PGRP-L), up to 90 kDa, which may be either
intracellular or transmembrane. Several structures of
PGRPs are known in insects and mammals, some bound with
substrates like Muramyl Tripeptide (MTP) or Tracheal
Cytotoxin (TCT). The substrate binding site is conserved
in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This
family includes Zn-dependent N-Acetylmuramoyl-L-alanine
Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond
between N-acetylmuramoyl and L-amino acids,
preferentially D-lactyl-L-Ala, in bacterial cell walls.
The structure for the bacteriophage T7 lysozyme shows
that two of the conserved histidines and a cysteine are
zinc binding residues. Site-directed mutagenesis of T7
lysozyme indicates that two conserved residues, a Tyr
and a Lys, are important for amidase activity.
Length = 126
Score = 31.1 bits (71), Expect = 0.061
Identities = 9/38 (23%), Positives = 15/38 (39%)
Query: 45 GIGYVGAGNSTNKKDAQTNAAKDFVQYLVRSGQVNERD 82
GI +G + AQ A + + YLV+ +
Sbjct: 71 GIELIGNFDGGPPTAAQLEALAELLAYLVKRYGIPPDY 108
>gnl|CDD|241290 cd01259, PH_APBB1IP, Amyloid beta (A4) Precursor protein-Binding,
family B, member 1 Interacting Protein pleckstrin
homology (PH) domain. APBB1IP consists of a
Ras-associated (RA) domain, a PH domain, a
family-specific BPS region, and a C-terminal SH2
domain. Grb7, Grb10 and Grb14 are paralogs that are
also present in this hierarchy. These adapter proteins
bind a variety of receptor tyrosine kinases, including
the insulin and insulin-like growth factor-1 (IGF1)
receptors. Grb10 and Grb14 are important
tissue-specific negative regulators of insulin and IGF1
signaling based and may contribute to type 2
(non-insulin-dependent) diabetes in humans. RA-PH
function as a single structural unit and is dimerized
via a helical extension of the PH domain. The PH domain
here are proposed to bind phosphoinositides
non-cannonically ahd are unlikely to bind an activated
GTPase. The tandem RA-PH domains are present in a
second adapter-protein family, MRL proteins,
Caenorhabditis elegans protein MIG-1012, the mammalian
proteins RIAM and lamellipodin and the Drosophila
melanogaster protein Pico12, all of which are
Ena/VASP-binding proteins involved in
actin-cytoskeleton rearrangement. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They
share little sequence conservation, but all have a
common fold, which is electrostatically polarized. Less
than 10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 124
Score = 27.2 bits (61), Expect = 1.7
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 22 PEFD----VRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDAQTNAAKDFVQYLV 73
PE + ++ G K ++ LR +G+ Y G S +D Q A F Y V
Sbjct: 6 PEIEGFLYLKEDGKKSWKKRYFVLRASGLYYSPKGKSKESRDLQCLA--QFDDYNV 59
>gnl|CDD|185607 PTZ00422, PTZ00422, glideosome-associated protein 50;
Provisional.
Length = 394
Score = 27.1 bits (60), Expect = 2.5
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 39 CELRIAGIGYVGAGNSTNKKDAQT---NAAKDFVQYLVRSG 76
+LR A +G G G+ K A A + V +LV G
Sbjct: 25 AQLRFASLGNWGTGSKQQKLVASYLKQYAKNERVTFLVSPG 65
>gnl|CDD|220830 pfam10637, Ofd1_CTDD, Oxoglutarate and iron-dependent oxygenase
degradation C-term. Ofd1 is a prolyl
4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase
that accelerates the degradation of Sre1N in the
presence of oxygen. The domain is conserved from yeasts
to humans. Yeast Sre1 is the orthologue of mammalian
sterol regulatory element binding protein (SREBP), and
it responds to changes in oxygen-dependent sterol
synthesis as an indirect measure of oxygen
availability. However, unlike the prolyl 4-hydroxylases
that regulate mammalian hypoxia-inducible factor, Ofd1
uses multiple domains to regulate Sre1N degradation by
oxygen; the Ofd1 N-terminal dioxygenase domain is
required for oxygen sensing and this Ofd1 C-terminal
domain accelerates Sre1N degradation in yeasts.
Length = 246
Score = 26.5 bits (59), Expect = 3.5
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 15 CQKNSKQPEFDVRAAGPKHRQRFLC 39
++SK+ E + AGP H+ R+L
Sbjct: 60 LPQSSKEIELPWKVAGPPHKHRYLY 84
>gnl|CDD|224567 COG1653, UgpB, ABC-type sugar transport system, periplasmic
component [Carbohydrate transport and metabolism].
Length = 433
Score = 26.5 bits (58), Expect = 3.8
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 43 IAGIGYVGAGNSTNKKDAQTNAAKDFVQYL 72
+ G G + S K+A A F+++L
Sbjct: 309 VGGGGLGVSKKSKKHKEA----AWKFLEFL 334
>gnl|CDD|200087 TIGR01237, D1pyr5carbox2, delta-1-pyrroline-5-carboxylate
dehydrogenase, group 2, putative. This enzyme is the
second of two in the degradation of proline to
glutamate. This model represents one of several related
branches of delta-1-pyrroline-5-carboxylate
dehydrogenase. Members of this branch may be associated
with proline dehydrogenase (the other enzyme of the
pathway from proline to glutamate) but have not been
demonstrated experimentally. The branches are not as
closely related to each other as some distinct aldehyde
dehydrogenases are to some; separate models were built
to let each model describe a set of equivalogs [Energy
metabolism, Amino acids and amines].
Length = 511
Score = 26.4 bits (58), Expect = 4.3
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 51 AGNSTNKKDAQTNAAKDFVQYLVRS-------GQVNERDVPVENIPMTPTGPSVTV 99
G N+ DA+ A DF++Y R VN R+ TPTG +V +
Sbjct: 119 VGKPWNEADAEVAEAIDFMEYYARQMIELAKGKPVNSREGETNQYVYTPTGVTVVI 174
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 26.4 bits (58), Expect = 4.7
Identities = 25/92 (27%), Positives = 38/92 (41%), Gaps = 8/92 (8%)
Query: 1 MSGDGLVKAFLNEWCQKNSKQPEFDVRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDA 60
++GD LVKA Q K P R A ++ L L G T++ A
Sbjct: 324 IAGDELVKAL-----QIRGKIPR---RKALSSLEEKVLSILTEEGYVSKDESFGTSETRA 375
Query: 61 QTNAAKDFVQYLVRSGQVNERDVPVENIPMTP 92
+D + +V G+V+E DV ++ IP
Sbjct: 376 DLLEDEDEDEEVVVDGEVDEGDVHIKPIPRKS 407
>gnl|CDD|168170 PRK05677, PRK05677, long-chain-fatty-acid--CoA ligase; Validated.
Length = 562
Score = 26.3 bits (58), Expect = 5.9
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 86 ENIPMTPTGPSVTVNTSKRFSFIRRSSIGLP 116
E MT T P V+VN I+ +IG+P
Sbjct: 356 EGYGMTETSPVVSVNP---SQAIQVGTIGIP 383
>gnl|CDD|233218 TIGR00975, 3a0107s03, phosphate ABC transporter, phosphate-binding
protein. This family represents one type of
(periplasmic, in Gram-negative bacteria)
phosphate-binding protein found in phosphate ABC
(ATP-binding cassette) transporters. This protein is
accompanied, generally in the same operon, by an ATP
binding protein and (usually) two permease proteins
[Transport and binding proteins, Anions].
Length = 314
Score = 25.9 bits (57), Expect = 6.5
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 53 NSTNKKDAQTNAAKDFVQYLVRSGQ 77
K A+ A K F+ + + +GQ
Sbjct: 263 YKKQKDPAKAKALKAFLTWALTNGQ 287
>gnl|CDD|180761 PRK06935, PRK06935, 2-deoxy-D-gluconate 3-dehydrogenase;
Provisional.
Length = 258
Score = 25.9 bits (57), Expect = 7.2
Identities = 8/14 (57%), Positives = 8/14 (57%)
Query: 5 GLVKAFLNEWCQKN 18
GL KAF NE N
Sbjct: 172 GLTKAFANELAAYN 185
>gnl|CDD|111223 pfam02308, MgtC, MgtC family. The MgtC protein is found in an
operon with the Mg2+ transporter protein MgtB. The
function of MgtC and its homologues is not known.
Length = 130
Score = 25.4 bits (56), Expect = 7.4
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 43 IAGIGYVGAGNSTNKKDA 60
++GIG++GAG + D
Sbjct: 58 VSGIGFLGAGVILREGDN 75
>gnl|CDD|236194 PRK08236, PRK08236, hypothetical protein; Provisional.
Length = 212
Score = 25.4 bits (56), Expect = 8.1
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 21 QPEFDVRAAGPKHRQRFLCELRIAGIGYVGAGNSTNKKDAQTNAAKDFV 69
E D G + RF ++ AG+G A ST + A A D V
Sbjct: 11 PAERDAVLRGLGNDSRF--DVLAAGVGPAAAAASTARALAAAAAPYDLV 57
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
0.316 0.132 0.389
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,048,879
Number of extensions: 501454
Number of successful extensions: 436
Number of sequences better than 10.0: 1
Number of HSP's gapped: 427
Number of HSP's successfully gapped: 28
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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 (21.6 bits)
S2: 53 (24.1 bits)