RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8351
(103 letters)
>gnl|CDD|224157 COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold
involved in RNA processing [Translation, ribosomal
structure and biogenesis].
Length = 427
Score = 90.9 bits (226), Expect = 4e-23
Identities = 29/80 (36%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 1 MTHATKAIYRWLLSDYIKVSNISTEQMLYTESDLEKSMDKIETINFHEEKDVNGIKFSAY 60
T T A+ + LL D +K++ + Y+E D+E+ D I + + E +V G+K + Y
Sbjct: 80 ATPPTAALLKVLLGDSLKLAEGPDKP-PYSEEDVERVPDLIRPLPYGEPVEVGGVKVTFY 138
Query: 61 NAGHVLGAAMFLIEIAGVKI 80
NAGH+LG+A L+E+ G +I
Sbjct: 139 NAGHILGSAAILLEVDGGRI 158
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 53.4 bits (129), Expect = 1e-09
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 1 MTHATKAIYRWLLSDYIKVSNISTEQMLYTESDLEKSMDKIETINFHEEKDVN-GIKFSA 59
T T+ + L DYI V+ ++ Y+ D+ +++ T+++ E D+ IK +
Sbjct: 259 CTPPTRDLMTLLQLDYIDVAQREGKKPPYSSKDVREALKHTITLDYGEVTDIAPDIKLTF 318
Query: 60 YNAGHVLGAAM 70
YNAGH+LG+A+
Sbjct: 319 YNAGHILGSAI 329
>gnl|CDD|224696 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
metallo-beta-lactamase domain and an RNA-binding KH
domain [General function prediction only].
Length = 637
Score = 50.4 bits (121), Expect = 1e-08
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 1 MTHATKAIYRWLLSDYIKVSNISTEQMLYTESDLEKSMDKIETINFHEEKDVN-GIKFSA 59
T T+ + L DYI+V+ + Y D+ K + T+++ E D+ I+ +
Sbjct: 265 CTPPTRDLMVLLQLDYIEVAEKEGGEPPYESKDVRKVLKHTITLDYGEVTDIAPDIRLTF 324
Query: 60 YNAGHVLGAAM 70
YNAGH+LG+AM
Sbjct: 325 YNAGHILGSAM 335
>gnl|CDD|200373 TIGR04122, Xnuc_lig_assoc, putative exonuclease, DNA
ligase-associated. Members of this protein family
frequently are found annotated as a putative exonuclease
involved in mRNA processing. This protein is found,
exclusively in bacteria, associated with three other
proteins: an ATP-dependent DNA ligase, a helicase, and
putative phosphoesterase.
Length = 326
Score = 43.0 bits (102), Expect = 4e-06
Identities = 16/37 (43%), Positives = 24/37 (64%)
Query: 41 IETINFHEEKDVNGIKFSAYNAGHVLGAAMFLIEIAG 77
I+T+ + E +NG+K S + AGHVLG+A +E G
Sbjct: 64 IQTVAYGETIRINGVKVSLHPAGHVLGSAQVRLEYGG 100
>gnl|CDD|181084 PRK07688, PRK07688, thiamine/molybdopterin biosynthesis
ThiF/MoeB-like protein; Validated.
Length = 339
Score = 31.1 bits (71), Expect = 0.059
Identities = 12/26 (46%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 15 DYIKVSNISTEQMLYTESDLEKSMDK 40
DY++ SN+ Q LYTESD++ ++ K
Sbjct: 57 DYVEWSNLQ-RQQLYTESDVKNNLPK 81
>gnl|CDD|237377 PRK13405, bchH, magnesium chelatase subunit H; Provisional.
Length = 1209
Score = 27.3 bits (61), Expect = 1.6
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 2 THATKAIYRWLLSDY 16
THA A YRWL D+
Sbjct: 581 THAFSAFYRWLREDF 595
>gnl|CDD|225296 COG2452, COG2452, Predicted site-specific integrase-resolvase
[DNA replication, recombination, and repair].
Length = 193
Score = 26.6 bits (59), Expect = 1.9
Identities = 8/39 (20%), Positives = 17/39 (43%)
Query: 4 ATKAIYRWLLSDYIKVSNISTEQMLYTESDLEKSMDKIE 42
+ + RW+ I+V + E +++K + K E
Sbjct: 14 SYSTLLRWIREGKIRVVTTEGGKYRIPEEEIKKYLGKRE 52
>gnl|CDD|183547 PRK12475, PRK12475, thiamine/molybdopterin biosynthesis MoeB-like
protein; Provisional.
Length = 338
Score = 26.6 bits (59), Expect = 2.4
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 15 DYIKVSNISTEQMLYTESDLEKSMDK 40
DY++ SN+ +Q LYTE D ++ K
Sbjct: 57 DYVEWSNLQRQQ-LYTEEDAKQKKPK 81
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in
yeast. Yra2p belongs to the evolutionarily conserved
REF (RNA and export factor binding proteins) family of
hnRNP-like proteins. It is a major component of
endogenous Yra1p complexes. It interacts with Yra1p and
functions as a negative regulator of Yra1p. Yra2p
consists of two highly conserved N- and C-terminal
boxes and a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 25.4 bits (56), Expect = 2.8
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 17 IKVSNISTEQMLYTESDLEKSMDKIETINFHEEKD 51
++++NI + YT DL K + F++ KD
Sbjct: 3 LRITNIPLDVSDYTIEDLIKEFGEPVYSKFYDHKD 37
>gnl|CDD|145103 pfam01770, Folate_carrier, Reduced folate carrier. The reduced
folate carrier (a transmembrane glycoprotein) transports
reduced folate into mammalian cells via the carrier
mediated mechanism (as opposed to the receptor mediated
mechanism) it also transports cytotoxic folate analogues
used in chemotherapy, such as methotrexate (MTX).
Mammalian cells have an absolute requirement for
exogenous folates which are needed for growth, and
biosynthesis of macromolecules.
Length = 410
Score = 26.1 bits (58), Expect = 4.4
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 62 AGHVL--GAAMFLIEIAGVKIARYL 84
G+VL + MFLI IA +IA L
Sbjct: 343 VGYVLFRASYMFLITIATFQIAANL 367
>gnl|CDD|226131 COG3603, COG3603, Uncharacterized conserved protein [Function
unknown].
Length = 128
Score = 25.5 bits (56), Expect = 4.5
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 19 VSNISTEQMLYTESDLEKSMDKIETINFH 47
VS T+ +L E DLEK++ +E
Sbjct: 97 VSTYDTDHILVREEDLEKAVKALEEAGHE 125
>gnl|CDD|149945 pfam09068, efhand_1, EF hand. Members of this family adopt a
helix-loop-helix motif, as per other EF hand domains.
However, since they do not contain the canonical
pattern of calcium binding residues found in many EF
hand domains, they do not bind calcium ions. The main
function of this domain is the provision of specificity
in beta-dystroglycan recognition, though in dystrophin
it serves an additional role: stabilisation of the WW
domain (pfam00397), enhancing dystroglycan binding.
Length = 125
Score = 24.9 bits (55), Expect = 6.7
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 45 NFHEEKDVNGIKFSAY 60
E D+N I+FSAY
Sbjct: 5 LMQELADLNNIRFSAY 20
>gnl|CDD|215491 PLN02906, PLN02906, xanthine dehydrogenase.
Length = 1319
Score = 25.4 bits (56), Expect = 7.8
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 7/33 (21%)
Query: 27 MLYTE-------SDLEKSMDKIETINFHEEKDV 52
ML TE +L KS ++I +NF E V
Sbjct: 916 MLITENWIQRIAVELNKSPEEIREMNFQGEGSV 948
>gnl|CDD|217489 pfam03315, SDH_beta, Serine dehydratase beta chain. L-serine
dehydratase (EC:4.2.1.13) is a found as a heterodimer of
alpha and beta chain or as a fusion of the two chains in
a single protein. This enzyme catalyzes the deamination
of serine to form pyruvate. This enzyme is part of the
gluconeogenesis pathway.
Length = 155
Score = 24.8 bits (55), Expect = 9.6
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 6/36 (16%)
Query: 31 ESDLEKSMDKIETINFHEEKDVNGIKFSAYNAGHVL 66
E D+ E + FH NG++F+A++ G L
Sbjct: 105 ERDIV--FHFKEILPFHP----NGMRFTAFDDGGEL 134
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
0.320 0.133 0.385
Gapped
Lambda K H
0.267 0.0846 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,104,327
Number of extensions: 419818
Number of successful extensions: 451
Number of sequences better than 10.0: 1
Number of HSP's gapped: 448
Number of HSP's successfully gapped: 26
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
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 (24.0 bits)