RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13665
(105 letters)
>gnl|CDD|177922 PLN02284, PLN02284, glutamine synthetase.
Length = 354
Score = 32.0 bits (73), Expect = 0.035
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 40 DPVLV------PGGVAIETNKRRKDAKVIPEPD 66
+ +LV P G I TNKR K AK+ PD
Sbjct: 86 NNILVMCDAYTPAGEPIPTNKRAKAAKIFSHPD 118
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 27.9 bits (63), Expect = 0.76
Identities = 17/58 (29%), Positives = 22/58 (37%), Gaps = 16/58 (27%)
Query: 16 KVTATTVHTY--DKPLQR-KHVK-----SGALDPVLVPGGVAIETNKRRKD-AKVIPE 64
K TTVH Y D+ L H + AL+ + G A K V+PE
Sbjct: 172 KGLMTTVHAYTNDQKLVDGPHKDLRRARAAALNIIPTSTGAA-------KAVGLVLPE 222
>gnl|CDD|225800 COG3261, HycE, Ni,Fe-hydrogenase III large subunit [Energy
production and conversion].
Length = 382
Score = 27.7 bits (62), Expect = 0.97
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 48 VAIETNKRRKDAKVIPEPDWP-LVVLTSMA-GYAMAPAPFEWSSFLICFS 95
V + N + K K I P + L L M G +A AP +S C+S
Sbjct: 315 VKLGDNGKIKRWK-IRTPSYANLPALKYMLRGNTVADAPLIIASLDPCYS 363
>gnl|CDD|233472 TIGR01570, A_thal_3588, uncharacterized plant-specific domain
TIGR01570. This model represents a region of about 170
amino acids found at the C-terminus of a family of
plant proteins. These proteins typically have
additional highly divergent N-terminal regions rich in
low complexity sequence. PSI-BLAST reveals no clear
similarity to any characterized protein. At least 12
distinct members are found in Arabidopsis thaliana.
Length = 161
Score = 26.3 bits (58), Expect = 3.1
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 48 VAIETNKR--RKDAKVIPEPDWPLVVLTSMAGYAMAPAPFE 86
+A+E R KD+K++ EP W + GYA+ + E
Sbjct: 49 IALECETRKQDKDSKLLSEPVWTMYCNGRKVGYAVKRSASE 89
>gnl|CDD|215631 PLN03202, PLN03202, protein argonaute; Provisional.
Length = 900
Score = 26.6 bits (59), Expect = 3.2
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 7/46 (15%)
Query: 27 KPLQRKHVKSGAL-------DPVLVPGGVAIETNKRRKDAKVIPEP 65
KP +R V + AL DP+L G++I + + + +V+P P
Sbjct: 407 KPQERMKVLTDALKSSNYDADPMLRSCGISISSQFTQVEGRVLPAP 452
>gnl|CDD|176473 cd06444, DNA_pol_A, Family A polymerase primarily fills DNA gaps
that arise during DNA repair, recombination and
replication. DNA polymerase family A, 5'-3' polymerase
domain. Family A polymerase functions primarily to fill
DNA gaps that arise during DNA repair, recombination and
replication. DNA-dependent DNA polymerases can be
classified into six main groups based upon phylogenetic
relationships with E. coli polymerase I (classA), E.
coli polymerase II (class B), E.coli polymerase III
(class C), euryarchaeota polymerase II (class D), human
polymerase beta (class X), E. coli UmuC/DinB and
eukaryotic RAP 30/Xeroderma pigmentosum variant (class
Y). Family A polymerases are found primarily in
organisms related to prokaryotes and include prokaryotic
DNA polymerase I, mitochondrial polymerase gamma, and
several bacteriophage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic
polymerase I (pol I) has two functional domains located
on the same polypeptide; a 5'-3' polymerase and a 5'-3'
exonuclease. Pol I uses its 5' nuclease activity to
remove the ribonucleotide portion of newly synthesized
Okazaki fragments and the DNA polymerase activity to
fill in the resulting gap. The structure of these
polymerases resembles in overall morphology a cupped
human right hand, with fingers (which bind an incoming
nucleotide and interact with the single-stranded
template), palm (which harbors the catalytic amino acid
residues and also binds an incoming dNTP) and thumb
(which binds double-stranded DNA) subdomains.
Length = 347
Score = 26.2 bits (58), Expect = 3.9
Identities = 14/64 (21%), Positives = 19/64 (29%), Gaps = 16/64 (25%)
Query: 24 TYDKPLQRKHVKSGALDPVLVPGGVA----------------IETNKRRKDAKVIPEPDW 67
P + V+ G P VPGG + R + +P W
Sbjct: 44 ANGWPWLDQWVRDGRFHPEYVPGGTVTGRWASRGGNAQQIPRRDPLGRDIRQAFVADPGW 103
Query: 68 PLVV 71
LVV
Sbjct: 104 TLVV 107
>gnl|CDD|223472 COG0395, UgpE, ABC-type sugar transport system, permease component
[Carbohydrate transport and metabolism].
Length = 281
Score = 26.0 bits (58), Expect = 3.9
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 70 VVLTSMAGYAMAPAPFEWSSFL 91
++L+S+A YA+A F+ L
Sbjct: 90 LLLSSLAAYALARFRFKGRKLL 111
>gnl|CDD|233428 TIGR01473, cyoE_ctaB, protoheme IX farnesyltransferase. This
model describes protoheme IX farnesyltransferase, also
called heme O synthase, an enzyme that creates an
intermediate in the biosynthesis of heme A. Prior to
the description of its enzymatic function, this protein
was often called a cytochrome o ubiquinol oxidase
assembly factor [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 280
Score = 26.1 bits (58), Expect = 4.2
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 67 WPLVVLTSMAGYAMAPAPFEWSSFLICF 94
L+++T+ AG +AP + L+
Sbjct: 12 ISLLLITAFAGMWLAPGGALVNPPLLLL 39
>gnl|CDD|223581 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha
subunit - helicase superfamily I member [DNA
replication, recombination, and repair].
Length = 696
Score = 25.9 bits (57), Expect = 4.7
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 6/40 (15%)
Query: 47 GVAIETNKRRKDAKVIPEPDWPLVVLTS------MAGYAM 80
GV + KRR+ ++ + D VV+ YAM
Sbjct: 586 GVILSIVKRRQGDVLVVDFDGREVVVARSELPELELAYAM 625
>gnl|CDD|165288 PHA02985, PHA02985, hypothetical protein; Provisional.
Length = 271
Score = 25.8 bits (57), Expect = 5.2
Identities = 10/64 (15%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 21 TVHTYDKPLQRKHVKSGALDPVLV------PGGVAIETNKRRKDAKVIPEPDWPLVVLTS 74
++ ++K + L +++ GG I N + K+I +++L+
Sbjct: 60 SIEVFNKKKKYYQNIPSRLSKIIICIQSAKKGGCIIIINNITNNKKIITLNINHIIILSP 119
Query: 75 MAGY 78
++ Y
Sbjct: 120 LSKY 123
>gnl|CDD|183446 PRK12331, PRK12331, oxaloacetate decarboxylase; Provisional.
Length = 448
Score = 25.8 bits (57), Expect = 5.3
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 11/39 (28%)
Query: 20 TTVHTYDKPLQRKHVKSGALDPVL-----------VPGG 47
+ + Y P++ + + G L+P + VPGG
Sbjct: 264 SEIAEYFNPIRDHYREEGILNPKVKDVEPKTLIYQVPGG 302
>gnl|CDD|233637 TIGR01920, Shik_kin_archae, shikimate kinase. This model
represents the shikimate kinase (SK) gene found in
archaea which is only distantly related to homoserine
kinase (thrB) and not atr all to the bacterial SK
enzyme. The SK from M. janaschii has been overexpressed
in E. coli and characterized. SK catalyzes the fifth
step of the biosynthesis of chorismate from
D-erythrose-4-phosphate and phosphoenolpyruvate [Amino
acid biosynthesis, Aromatic amino acid family].
Length = 261
Score = 25.5 bits (56), Expect = 7.0
Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 36 SGALDPVLVP--GGVAIETNKRRKDAKVIPEPDWPLVVLT 73
+GA D GG+ I N+R K K VL
Sbjct: 122 TGAFDDAAASYLGGIVITDNRRMKILKRDKLEGCTAAVLV 161
>gnl|CDD|237829 PRK14834, PRK14834, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 249
Score = 25.1 bits (55), Expect = 8.5
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 32 KHVKSGALDPVLVPGGVAIETNKRRKDAKVIPEPDWPLVVLTS 74
+ V G LDP + ET D IP+PD L++ TS
Sbjct: 157 REVAEGRLDP----ASIDAETISANLDTADIPDPD--LIIRTS 193
>gnl|CDD|173627 cd05037, PTK_Jak_rpt1, Pseudokinase (repeat 1) domain of the
Protein Tyrosine Kinases, Janus kinases. Protein
Tyrosine Kinase (PTK) family; Janus kinase (Jak)
subfamily; pseudokinase domain (repeat1). The Jak
subfamily is composed of Jak1, Jak2, Jak3, TYK2, and
similar proteins. The PTKc (catalytic domain) family to
which this subfamily belongs, is part of a larger
superfamily that includes the catalytic domains of other
kinases such as protein serine/threonine kinases, RIO
kinases, and phosphoinositide 3-kinase (PI3K). PTKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to tyrosine (tyr) residues in protein substrates.
Jak subfamily proteins are cytoplasmic (or nonreceptor)
tyr kinases containing an N-terminal FERM domain,
followed by a Src homology 2 (SH2) domain, a
pseudokinase domain, and a C-terminal catalytic tyr
kinase domain. The pseudokinase domain shows similarity
to tyr kinases but lacks crucial residues for catalytic
activity and ATP binding. It modulates the kinase
activity of the C-terminal catalytic domain. Most Jaks
are expressed in a wide variety of tissues, except for
Jak3, which is expressed only in hematopoietic cells.
Jaks are crucial for cytokine receptor signaling. They
are activated by autophosphorylation upon
cytokine-induced receptor aggregation, and subsequently
trigger downstream signaling events such as the
phosphorylation of signal transducers and activators of
transcription (STATs). Jaks are also involved in
regulating the surface expression of some cytokine
receptors. The Jak-STAT pathway is involved in many
biological processes including hematopoiesis,
immunoregulation, host defense, fertility, lactation,
growth, and embryogenesis.
Length = 259
Score = 25.1 bits (55), Expect = 9.4
Identities = 9/47 (19%), Positives = 14/47 (29%), Gaps = 2/47 (4%)
Query: 51 ETNKRRKDAKVIPEPDWPLVVLTSMAGYAMAPAPFEWSSFLICFSQL 97
E + +D +P PD + P + SF L
Sbjct: 214 EKERFYQDQHRLPMPDCAELANLINQC--WTYDPTKRPSFRAILRDL 258
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
0.318 0.132 0.399
Gapped
Lambda K H
0.267 0.0573 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,185,298
Number of extensions: 427071
Number of successful extensions: 336
Number of sequences better than 10.0: 1
Number of HSP's gapped: 335
Number of HSP's successfully gapped: 27
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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 (21.7 bits)
S2: 53 (24.5 bits)