RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2587
(210 letters)
>gnl|CDD|144618 pfam01091, PTN_MK_C, PTN/MK heparin-binding protein family,
C-terminal domain.
Length = 63
Score = 60.2 bits (146), Expect = 1e-12
Identities = 24/59 (40%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 60 CKYDKSSWSECDPNTHMKNRTLTLKKGSPTT-CEATKSISRKCKKACRY----EKGSWS 113
CKY +W ECD T K RT TLKK C+ T +IS+ C K +Y +KG
Sbjct: 4 CKYKFEAWGECDAKTGTKTRTGTLKKALYNAECQQTVTISKPCTKKTKYKPKAKKGKGK 62
Score = 45.6 bits (108), Expect = 3e-07
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 105 CRYEKGSWSQCSVAGDM-TRTDMLKEANSDANCEKSRTLTKKCKAK 149
C+Y+ +W +C TRT LK+A +A C+++ T++K C K
Sbjct: 4 CKYKFEAWGECDAKTGTKTRTGTLKKALYNAECQQTVTISKPCTKK 49
>gnl|CDD|128490 smart00193, PTN, Pleiotrophin / midkine family. Heparin-binding
domain family.
Length = 80
Score = 31.8 bits (72), Expect = 0.045
Identities = 16/26 (61%), Positives = 18/26 (69%)
Query: 60 CKYDKSSWSECDPNTHMKNRTLTLKK 85
CKY SW ECD NT +K R+ TLKK
Sbjct: 48 CKYKFESWGECDANTGLKTRSGTLKK 73
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 32.3 bits (74), Expect = 0.19
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 87 SPTTCEATKSISRKC 101
SP TCEA +S+ RKC
Sbjct: 283 SPLTCEAARSVCRKC 297
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 29.8 bits (67), Expect = 1.0
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 87 SPTTCEATKSISRKC 101
SP TCEA +S+ RKC
Sbjct: 281 SPLTCEAARSVCRKC 295
>gnl|CDD|216330 pfam01149, Fapy_DNA_glyco, Formamidopyrimidine-DNA glycosylase
N-terminal domain. Formamidopyrimidine-DNA glycosylase
(Fpg) is a DNA repair enzyme that excises oxidized
purines from damaged DNA. This family is the N-terminal
domain contains eight beta-strands, forming a
beta-sandwich with two alpha-helices parallel to its
edges.
Length = 117
Score = 26.8 bits (60), Expect = 4.5
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 12/39 (30%)
Query: 165 LGLGLSDGRTCVVYKARHLGLSGSL--------IDRHTR 195
L L L G V+ HLG++G L +HT
Sbjct: 60 LLLELDGGLVLVI----HLGMTGRLRVVEPEDPPPKHTH 94
>gnl|CDD|215648 pfam00003, 7tm_3, 7 transmembrane sweet-taste receptor of 3 GCPR.
This is a domain of seven transmembrane regions that
forms the C-terminus of some subclass 3
G-coupled-protein receptors. It is often associated with
a downstream cysteine-rich linker domain, NCD3G
pfam07562, which is the human sweet-taste receptor, and
the N-terminal domain, ANF_receptor pfam01094. The seven
TM regions assemble in such a way as to produce a
docking pocket into which such molecules as cyclamate
and lactisole have been found to bind and consequently
confer the taste of sweetness.
Length = 238
Score = 27.2 bits (61), Expect = 5.5
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 10 PYQDIRMWGVFGTVLVLCLVSIINANHAENWEENAHE 46
++ V G V +L L+ A A EN +E
Sbjct: 145 KGSNVDFVLVLGYVGLLLLLCFFLAFKARKLPENFNE 181
>gnl|CDD|212471 cd01724, Sm_D1, Sm protein D1. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit D1
heterodimerizes with subunit D2 and three such
heterodimers form a hexameric ring structure with
alternating D1 and D2 subunits. The D1 - D2 heterodimer
also assembles into a heptameric ring containing DB,
D3, E, F, and G subunits.
Length = 92
Score = 26.0 bits (58), Expect = 6.0
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 70 CDP--NTHMKNRTLTLKKGSPTTCE 92
D NTH+KN LTLK +P + +
Sbjct: 31 VDVSMNTHLKNVKLTLKGKNPVSLD 55
>gnl|CDD|238175 cd00283, GIY-YIG_Cterm, GIYX(10-11)YIG family of class I homing
endonucleases C-terminus (GIY-YIG_Cterm). Homing
endonucleases promote the mobility of intron or intein
by recognizing and cleaving a homologous allele that
lacks the sequence. They catalyze a double-strand break
in the DNA near the insertion site of that element to
facilitate homing at that site. Class I homing
endonucleases are sorted into four families based on the
presence of these motifs in their respective N-termini:
LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD
contains several but not all members of the GIY-YIG
family. The C-terminus of GIY-YIG is a DNA-binding
domain which is separated from the N-terminus by a long,
flexible linker. The DNA-binding domain consists of a
minor-groove binding alpha-helix, and a
helix-turn-helix. Some also contain a zinc finger (i.e.
I-TevI) which is not required for DNA binding or
catalysis, but is a component of the linker and directs
the catalytic domain to cleave the homing site at a
fixed distance from the intron insertion site.
Length = 113
Score = 25.9 bits (57), Expect = 8.2
Identities = 14/53 (26%), Positives = 18/53 (33%), Gaps = 1/53 (1%)
Query: 144 KKCKAKNSGRKNKANNDCLTDLGLGLSDGRTCVVYKARHLGLSGSLIDRHTRS 196
K AK GRKN N G AR L + I ++ +S
Sbjct: 52 AKISAKKKGRKNL-NAKKKQSDTDGYIGIFDSTTEAARFLKVHSGTISKNIKS 103
>gnl|CDD|183516 PRK12416, PRK12416, protoporphyrinogen oxidase; Provisional.
Length = 463
Score = 27.1 bits (60), Expect = 8.2
Identities = 8/40 (20%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 49 IRNTRGAEKQPCKYDKSSWSECDPNTHMKN----RTLTLK 84
I + G + +P + ++W + P H+++ ++L K
Sbjct: 384 IEKSLGIKGEPEVVEVTNWKDLMPKYHLEHNQAVQSLQEK 423
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
0.314 0.128 0.401
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,708,786
Number of extensions: 791311
Number of successful extensions: 567
Number of sequences better than 10.0: 1
Number of HSP's gapped: 564
Number of HSP's successfully gapped: 14
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
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: 57 (26.0 bits)