RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14628
(161 letters)
>gnl|CDD|197794 smart00569, L27, domain in receptor targeting proteins Lin-2 and
Lin-7.
Length = 53
Score = 29.0 bits (66), Expect = 0.16
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 62 ILESLDDIECLQEQLYEDKTMMNSLLEDKQLHILLELYDKISSKVISPNRTP 113
+LE L++++ L ED + LL+ L LL+++DK++ + P
Sbjct: 3 LLELLEELQSLLSP-SEDLQELRRLLQSPHLQALLKIHDKVAETELDPPLPE 53
>gnl|CDD|217245 pfam02828, L27, L27 domain. The L27 domain is found in receptor
targeting proteins Lin-2 and Lin-7.
Length = 51
Score = 29.1 bits (66), Expect = 0.18
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 58 AISMILESLDDIECLQEQLYEDKTMMNSLLEDKQLHILLELYDKISSKV 106
A+ LE L++++ L E + + +L+ L LLE++DK++ KV
Sbjct: 1 AVQRALELLEELQSLLEASEDLAELRK-VLQSPHLQSLLEVHDKVAEKV 48
>gnl|CDD|148959 pfam07637, PSD5, Protein of unknown function (DUF1595). A family
of proteins in Rhodopirellula baltica, associated with
pfam07635, pfam07626, pfam07631, pfam07627, and
pfam07624.
Length = 64
Score = 28.3 bits (64), Expect = 0.42
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 19/57 (33%)
Query: 123 DALDIIRDF-----ERSVSPTDV---------ELDLSGDFEE-----LKQILTSPHF 160
A +I+R F R ++ ++ + DFEE L IL SP F
Sbjct: 2 CAREILRRFARRAFRRPLTDAELDRLLALYDAAREAGKDFEEALKEALAAILCSPSF 58
>gnl|CDD|129290 TIGR00186, rRNA_methyl_3, rRNA methylase, putative, group 3. this
is part of the trmH (spoU) family of rRNA methylases
[Protein synthesis, tRNA and rRNA base modification].
Length = 237
Score = 29.2 bits (66), Expect = 0.78
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 73 QEQLYEDKTMMNSLLEDKQLHILLELYDKISSKVI 107
QE LY ++ +LL +++ IL L K K+I
Sbjct: 1 QEYLYGKNAVLEALLNQQRVFILKGLESKRLKKLI 35
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 28.2 bits (64), Expect = 1.9
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 111 RTPPSDVVTRCRDALDII 128
RT P +VV R +DA DI+
Sbjct: 32 RTSPEEVVERIKDA-DIV 48
>gnl|CDD|184858 PRK14856, nhaA, pH-dependent sodium/proton antiporter; Provisional.
Length = 438
Score = 27.8 bits (62), Expect = 2.5
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 68 DIECLQEQLYEDKTMMNSLLEDKQLHILLELYDKISSKVISP 109
++E L+ +T +LL +Q IL + +K +S + SP
Sbjct: 255 NVELLELGKRYAETSSGALLTKEQQEILHSIEEK-ASALQSP 295
>gnl|CDD|218754 pfam05795, Plasmodium_Vir, Plasmodium vivax Vir protein. This
family consists of several Vir proteins specific to
Plasmodium vivax. The vir genes are present at about
600-1,000 copies per haploid genome and encode proteins
that are immunovariant in natural infections, indicating
that they may have a functional role in establishing
chronic infection through antigenic variation.
Length = 348
Score = 27.9 bits (62), Expect = 2.6
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 77 YEDKTMMNSLLEDKQLHILLELYDKISSKVISPN 110
+ +++ + K L+ E YDKI K+ S N
Sbjct: 116 FNYIDILDEWKKRKDLYDYFENYDKIKKKIKSKN 149
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 28.0 bits (62), Expect = 2.7
Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 6/91 (6%)
Query: 21 RLKGAVLNAISSP-----KWNATDLDAQDHFSDCGEDELTSSAISMILESLDDIECLQEQ 75
L+ LN P + DLD F+ ++EL S + S+ +E E
Sbjct: 512 NLRKKFLNLNYFPAQRLLQVKIIDLDVDGLFNMPLDNELKRQVFSYQIGSISSLEKKLEP 571
Query: 76 LYEDKTMMNSLLEDKQLHILLELYDKISSKV 106
++ D ++ + + +QL +++ K +V
Sbjct: 572 IW-DVDVIQCIDDMEQLTAMVQFAQKTEGEV 601
>gnl|CDD|237505 PRK13783, PRK13783, adenylosuccinate synthetase; Provisional.
Length = 404
Score = 27.4 bits (61), Expect = 4.1
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 61 MILESLDDIECLQEQLYEDKTMMNSLLEDKQLHILLELYDKISSKVISP 109
+ E L+ I L ++LY + + ++ED LL Y+KI V+SP
Sbjct: 154 KLREFLEKILSLYKKLYGIEFDVEKMMED-----LLTFYEKIKDLVVSP 197
>gnl|CDD|168945 PRK07414, PRK07414, cob(I)yrinic acid a,c-diamide
adenosyltransferase; Validated.
Length = 178
Score = 26.2 bits (58), Expect = 6.9
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 134 SVSPTDVELDLSGDFEELKQILTSPH 159
VS + L L E L Q+ TS
Sbjct: 6 EVSSANSSLPLPYTIEGLVQVFTSSQ 31
>gnl|CDD|239533 cd03449, R_hydratase, (R)-hydratase [(R)-specific enoyl-CoA
hydratase] catalyzes the hydration of trans-2-enoyl CoA
to (R)-3-hydroxyacyl-CoA as part of the PHA
(polyhydroxyalkanoate) biosynthetic pathway.
(R)-hydratase contains a hot-dog fold similar to those
of thioesterase II, and beta-hydroxydecanoyl-ACP
dehydratase, MaoC dehydratase,
Hydratase-Dehydrogenase-Epimerase protein (HDE), and the
fatty acid synthase beta subunit. The active site lies
within a substrate-binding tunnel formed by the
(R)-hydratase homodimer. A subset of the bacterial
(R)-hydratases contain a C-terminal
phosphotransacetylase (PTA) domain.
Length = 128
Score = 25.6 bits (57), Expect = 8.3
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 131 FERSVSPTDVEL--DLSGDF 148
R+++ DVEL +LSGDF
Sbjct: 9 LTRTITEEDVELFAELSGDF 28
>gnl|CDD|218956 pfam06248, Zw10, Centromere/kinetochore Zw10. Zw10 and rough deal
proteins are both required for correct metaphase
check-pointing during mitosis. These proteins bind to
the centromere/kinetochore.
Length = 593
Score = 26.2 bits (58), Expect = 8.9
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 2/79 (2%)
Query: 78 EDKTMMNSLLEDKQLHILLELYDKISSKVI--SPNRTPPSDVVTRCRDALDIIRDFERSV 135
ED S L K E+ D I+ K PN + D++ + + I D +S
Sbjct: 10 EDLRGKISKLLSKVEEYKEEVRDMINKKYSDFLPNMSSAEDLLEQVSSLSEDISDLLKSE 69
Query: 136 SPTDVELDLSGDFEELKQI 154
++ DL+ EEL ++
Sbjct: 70 VSNEILQDLNDAVEELAEL 88
>gnl|CDD|211390 cd11378, DUF296, Domain of unknown function found in archaea,
bacteria, and plants. This domain is found in proteins
that contain AT-hook motifs, which suggests a role in
DNA-binding for the proteins as a whole. Three
conserved histidine residues appear to form a
zinc-binding site, and the domain has been observed to
form homotrimers. It co-occurs with a thioredoxin-like
domain in uncharacterized cyanobacterial proteins.
Length = 113
Score = 25.2 bits (56), Expect = 9.3
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 8 DCVEELKKFNVRRRLKGAVLNAISSPKWNAT 38
D VE L+ F +K AVL+ I + NAT
Sbjct: 12 DLVESLEAFAREEGIKAAVLSGIGAVS-NAT 41
>gnl|CDD|176759 cd08781, Death_UNC5-like, Death domain found in Uncoordinated-5
homolog family. Death Domain (DD) found in
Uncoordinated-5 (UNC-5) homolog family, which includes
Unc5A, B, C and D in vertebrates. UNC5 proteins are
receptors for secreted netrins (netrin-1, -3 and -4)
that are involved in diverse processes like axonal
guidance, neuronal migration, blood vessel patterning,
and apoptosis. They are transmembrane proteins with an
extracellular domain consisting of two immunoglobulin
repeats, two thrombospondin type-I modules and an
intracellular region containing a ZU-5 domain, UPA
domain and a DD. In general, DDs are protein-protein
interaction domains found in a variety of domain
architectures. Their common feature is that they form
homodimers by self-association or heterodimers by
associating with other members of the DD superfamily
including CARD (Caspase activation and recruitment
domain), DED (Death Effector Domain), and PYRIN. They
serve as adaptors in signaling pathways and can recruit
other proteins into signaling complexes.
Length = 83
Score = 25.0 bits (55), Expect = 10.0
Identities = 13/32 (40%), Positives = 14/32 (43%), Gaps = 7/32 (21%)
Query: 131 FERSVSPTDVELDL-------SGDFEELKQIL 155
F SPT V LDL G +L QIL
Sbjct: 39 FATKPSPTGVILDLWEARHRDDGALNDLAQIL 70
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 0.133 0.377
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,239,322
Number of extensions: 745731
Number of successful extensions: 772
Number of sequences better than 10.0: 1
Number of HSP's gapped: 771
Number of HSP's successfully gapped: 38
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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: 55 (24.8 bits)