RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16020
(151 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 30.4 bits (69), Expect = 0.26
Identities = 19/117 (16%), Positives = 44/117 (37%), Gaps = 16/117 (13%)
Query: 28 VVCALADGSVAIFRRGPDGQWDLSKYHTVTLGLPH-HSVRSLAAVYNK---VWCGYKNKI 83
+ + D ++ + WD+ +T H V S+A + I
Sbjct: 108 LSSSSRDKTIKV--------WDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTI 159
Query: 84 HVVDPKSLVVLKSFDAHPRRESQVRQMTWAGDGVW-VSIRLDSTLRMYNAHTYQHLQ 139
+ D ++ + + H +V + ++ DG +S D T+++++ T + L
Sbjct: 160 KLWDLRTGKCVATLTGH---TGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLG 213
>gnl|CDD|225189 COG2307, COG2307, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 313
Score = 29.3 bits (66), Expect = 0.70
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 112 WAGDGVWVSIRLDSTLRMYNAH-TYQHLQDVDIEP 145
AGDG W S+ LR +AH TY+ I+P
Sbjct: 187 AAGDGAWESL-----LRSGSAHETYRRRYRAVIDP 216
>gnl|CDD|223378 COG0301, ThiI, Thiamine biosynthesis ATP pyrophosphatase [Coenzyme
metabolism].
Length = 383
Score = 28.8 bits (65), Expect = 1.00
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 19/79 (24%)
Query: 21 PVHVQGRVVCALADG---SVAIF---RRGPDGQWDLSKYHTVTLGLP---HHSVRSLAAV 71
PV QG+V+ L+ G VA + +RG + V G P R
Sbjct: 171 PVGTQGKVLLLLSGGIDSPVAAWLMMKRG-------VEVIPVHFGNPPYTSEKAREKVVA 223
Query: 72 YNKVWC---GYKNKIHVVD 87
+ G K +++VV
Sbjct: 224 LALLRLTSYGGKVRLYVVP 242
>gnl|CDD|130398 TIGR01331, bisphos_cysQ, 3'(2'),5'-bisphosphate nucleotidase,
bacterial. Sulfate is incorporated into
3-phosphoadenylylsulfate, PAPS, for utilization in
pathways such as methionine biosynthesis. Transfer of
sulfate from PAPS to an acceptor leaves adenosine
3'-5'-bisphosphate, APS. This model describes a form
found in bacteria of the enzyme 3'(2'),5'-bisphosphate
nucleotidase, which removes the 3'-phosphate from APS to
regenerate AMP and help drive the cycle [Central
intermediary metabolism, Sulfur metabolism].
Length = 249
Score = 28.2 bits (63), Expect = 1.5
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 30 CALADGSVAIF-RRGPDGQWDLSKYHTV 56
C +A+GS I+ R GP G+WD + H V
Sbjct: 189 CLVAEGSADIYPRLGPTGEWDTAAGHAV 216
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 28.3 bits (62), Expect = 2.1
Identities = 16/39 (41%), Positives = 20/39 (51%)
Query: 6 PTPYPLNKILDTALPPVHVQGRVVCALADGSVAIFRRGP 44
P P P++ L PPV GR V A+G+VA R P
Sbjct: 103 PQPVPMDASLSLFTPPVPDCGRDVGEEAEGAVAPSWRAP 141
>gnl|CDD|187887 cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
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;
Zn-finger domain containing protein, distant homologs of
Cas8 proteins; signature gene for I-C subtype; also
known as Csd1 family.
Length = 569
Score = 27.6 bits (62), Expect = 2.7
Identities = 7/41 (17%), Positives = 14/41 (34%)
Query: 44 PDGQWDLSKYHTVTLGLPHHSVRSLAAVYNKVWCGYKNKIH 84
D L T + +++A + K GY+ +
Sbjct: 275 EDPFAALFDPPDDTKPDDAATTQAVALLLKKPITGYRADLD 315
>gnl|CDD|192248 pfam09322, DUF1979, Domain of unknown function (DUF1979).
Members of this family of functionally uncharacterized
domains are found in various Oryza sativa mutator-like
transposases.
Length = 58
Score = 26.0 bits (57), Expect = 2.8
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 41 RRGPDGQWDLSKYHTVTLGLPHHSVRSLAAVYNKVWCGYKNKIHVVDP 88
R GP G DLS + G+ + RS ++ N + G++ +DP
Sbjct: 17 RYGPTGV-DLSDFIVSERGIDRPAERSFPSIKNWLMRGFR-----IDP 58
>gnl|CDD|240114 cd04801, CBS_pair_M50_like, This cd contains two tandem repeats of
the cystathionine beta-synthase (CBS pair) domains in
association with the metalloprotease peptidase M50. CBS
is a small domain originally identified in cystathionine
beta-synthase and subsequently found in a wide range of
different proteins. CBS domains usually come in tandem
repeats, which associate to form a so-called Bateman
domain or a CBS pair which is reflected in this model.
The interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is unknown.
Length = 114
Score = 26.8 bits (60), Expect = 3.0
Identities = 19/81 (23%), Positives = 29/81 (35%), Gaps = 9/81 (11%)
Query: 18 ALPPVHVQGRVVCALADGSVAIFRRGPDGQWDLSKYHTVTLGLPHHSVR-----SLAAVY 72
V +GR V + S+A R P QW + V V SLA V
Sbjct: 27 RFVVVDNEGRYVGII---SLADLRAIPTSQWAQTTVIQVM-TPAAKLVTVLSEESLAEVL 82
Query: 73 NKVWCGYKNKIHVVDPKSLVV 93
+ +++ VV+ V+
Sbjct: 83 KLLEEQGLDELAVVEDSGQVI 103
>gnl|CDD|226769 COG4319, COG4319, Ketosteroid isomerase homolog [Function unknown].
Length = 137
Score = 26.2 bits (58), Expect = 5.2
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 8/38 (21%)
Query: 20 PPVHVQGRVVCALADGSVAIFRRGPDGQWDLSKYHTVT 57
PP + GR +FR+ DG W L+ H
Sbjct: 102 PPADLAGRAT--------YVFRKEADGGWKLAHDHIPN 131
>gnl|CDD|178120 PLN02504, PLN02504, nitrilase.
Length = 346
Score = 26.3 bits (58), Expect = 7.4
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 37 VAIFRRGPDGQWDLSKYHTVTLGLPHHSVRSLAAVYNKVWCGYKNKIHVV 86
+AI R P G+ D KYH + +P V LAA+ K K+++V
Sbjct: 79 LAIGDRSPKGREDFRKYHASAIDVPGPEVDRLAAMAG------KYKVYLV 122
>gnl|CDD|106970 PHA00661, PHA00661, hypothetical protein.
Length = 734
Score = 26.4 bits (58), Expect = 8.0
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 23 HVQGRVVCALADGSVAIFRRGPDGQWDL-SKYHTVTLGLP 61
H++G+ V LADG+V R DG L + TV +GLP
Sbjct: 587 HLEGKTVSILADGAVHPQRVVTDGAITLDVEAGTVHIGLP 626
>gnl|CDD|211988 TIGR04265, bac_cardiolipin, cardiolipin synthase. This model is
based on experimentally characterized bacterial
cardiolipin synthases (cls) from E. coli, Staphylococcus
aureus (two), and Bacillus pseudofirmus OF4. This model
describes just one of several homologous but
non-orthologous forms of cls. The cutoff score is set
arbitrarily high to avoid false-positives. Note that
there are two enzymatic activites called cardiolipin
synthase. This model represents type 1, which does not
rely on a CDP-linked donor, but instead does a
reversible transfer of a phosphatidyl group from one
phosphatidylglycerol molecule to another.
Length = 483
Score = 26.3 bits (58), Expect = 8.6
Identities = 7/38 (18%), Positives = 9/38 (23%)
Query: 16 DTALPPVHVQGRVVCALADGSVAIFRRGPDGQWDLSKY 53
+ I GPD W+ KY
Sbjct: 284 RIIPYDPDYFPMPNEQAGGHGIQIIASGPDFPWEQIKY 321
>gnl|CDD|239118 cd02652, nuc_hydro_2, NH_2: A subgroup of nucleoside hydrolases.
This group contains eukaryotic and bacterial proteins
similar to nucleoside hydrolases. Nucleoside hydrolases
cleave the N-glycosidic bond in nucleosides generating
ribose and the respective base. These enzymes vary in
their substrate specificity. .
Length = 293
Score = 25.9 bits (57), Expect = 9.5
Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 3/41 (7%)
Query: 75 VWCGYKNKIHVVDPKSLVVLKSFDAHPRR---ESQVRQMTW 112
VW GY+ V P LV+ F+ R+ W
Sbjct: 191 VWSGYELGEAVSYPHVLVIAHPFNTPVFAAYWPRSHRRPLW 231
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
0.322 0.136 0.440
Gapped
Lambda K H
0.267 0.0618 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,835,679
Number of extensions: 681668
Number of successful extensions: 518
Number of sequences better than 10.0: 1
Number of HSP's gapped: 518
Number of HSP's successfully gapped: 15
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
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 (21.9 bits)
S2: 54 (24.8 bits)