RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2702
(87 letters)
>gnl|CDD|197321 cd09087, Ape1-like_AP-endo, Human Ape1-like subfamily of the
ExoIII family purinic/apyrimidinic (AP) endonucleases.
This subfamily includes human Ape1 (also known as Apex,
Hap1, or Ref-1) and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiences. Many organisms
have two AP endonucleases, usually one is the dominant
AP endonuclease, the other has weak AP endonuclease
activity; for example, Ape1 and Ape2 in humans. Ape1 is
found in this subfamily, it exhibits strong
AP-endonuclease activity but shows weak 3'-5'
exonuclease and 3'-phosphodiesterase activities. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes exonuclease
III (ExoIII) and endonuclease IV (EndoIV). This
subfamily belongs to the ExoIII family; the EndoIV
family belongs to a different superfamily.
Length = 253
Score = 27.1 bits (61), Expect = 0.88
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 44 LMKNELLDLMQKEKPDL--VQE 63
L+K LLD ++KE PD+ +QE
Sbjct: 14 LLKKGLLDYVKKEDPDILCLQE 35
>gnl|CDD|237216 PRK12821, PRK12821, aspartyl/glutamyl-tRNA amidotransferase subunit
C-like protein; Provisional.
Length = 477
Score = 27.2 bits (60), Expect = 0.97
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 1/83 (1%)
Query: 3 DLMREEKPDLMQEGKPDLMKDELPALMKEEKPDLMKDAKYDLMKNELLDLMQKEKPDLVQ 62
+ E + +++ DL P +K L KD L + + DL E + +Q
Sbjct: 356 TELSETQTKGIKKSFSDLQSPLFPKHWTSKKQQLNKDELKKLARLVMFDLDDAEL-EKLQ 414
Query: 63 EEMSDLMKHKMSVLMKDEKSVRP 85
E D+ V D +V+P
Sbjct: 415 VEFKDITSSFKQVEKIDTTNVKP 437
>gnl|CDD|99993 cd03823, GT1_ExpE7_like, This family is most closely related to the
GT1 family of glycosyltransferases. ExpE7 in
Sinorhizobium meliloti has been shown to be involved in
the biosynthesis of galactoglucans (exopolysaccharide
II).
Length = 359
Score = 27.2 bits (61), Expect = 1.1
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 7 EEKPDLMQEGKPDLMKDELPALMKEEKPDLMKDAKYDL--MKNELLDLMQKEKPDLV 61
+ D G + L DL + YD + E L++ +PD+V
Sbjct: 44 PPRQDKEVIGVVVYGRPIDEVLRSALPRDLFHLSDYDNPAVVAEFARLLEDFRPDVV 100
>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 27.0 bits (61), Expect = 1.2
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 36 LMKDAKYDLMKNELLDLMQKEKPDLVQE 63
+ DA+YD + EL+ L + E P+L+
Sbjct: 30 SISDAEYDRLYRELVAL-EAEHPELITP 56
>gnl|CDD|179345 PRK01885, greB, transcription elongation factor GreB; Reviewed.
Length = 157
Score = 26.4 bits (59), Expect = 1.4
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 36 LMKDAKYDLMKNELLDLMQKEKPDLVQ 62
+ Y +K EL L ++E+P++ Q
Sbjct: 6 YITREGYARLKQELDYLWREERPEVTQ 32
>gnl|CDD|131388 TIGR02335, hydr_PhnA, phosphonoacetate hydrolase. This family
consists of examples of phosphonoacetate hydrolase, an
enzyme specific for the cleavage of the C-P bond in
phosphonoacetate. Phosphonates are organic compounds
with a direct C-P bond that is far less labile that the
C-O-P bonds of phosphate attachment sites. Phosphonates
may be degraded for phosphorus and energy by broad
spectrum C-P lyase encoded by large operon or by
specific enzymes for some of the more common
phosphonates in nature. This family represents an enzyme
from the latter category. It may be found encoded near
genes for phosphonate transport and for pther specific
phosphonatases.
Length = 408
Score = 26.0 bits (57), Expect = 2.8
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 50 LDLMQKEKPDLVQEEMSDLMKHK 72
L L+ E+PDL+ SD ++HK
Sbjct: 181 LSLLTNERPDLMYLSTSDYVQHK 203
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 25.7 bits (57), Expect = 3.0
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 8/77 (10%)
Query: 4 LMREEKPDLMQEGKPDLMKDELPALMKEEKPDLMKDA-----KYDLMKNELLDLMQK--- 55
+ E L + K +E + E D++ +A + + L+ + +
Sbjct: 515 YEQVEGVFLGRYQKAKNYSEETAQEIDREVKDIIDEAYERAKELLNENKDALETLAEMLL 574
Query: 56 EKPDLVQEEMSDLMKHK 72
EK + EE+ D++ +
Sbjct: 575 EKETIDAEEIKDILAGR 591
>gnl|CDD|236454 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
Validated.
Length = 395
Score = 25.5 bits (57), Expect = 3.8
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 6/25 (24%)
Query: 37 MKDAKYDLMKNELLDLMQKEKPDLV 61
M D + L ++++EKPD +
Sbjct: 61 MLDG------DALRAVIEREKPDYI 79
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 25.2 bits (56), Expect = 4.5
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 27 ALMKEEKPDLMKDAKYDLMKNELLDLMQKEKPDLVQE---EMSDLMKH--KMSVLMKDEK 81
L + +K+A +LMK+E L KE L Q+ E+ L K K+ + DE+
Sbjct: 793 VLEIAAENGDVKEAIKELMKDEELRKHGKEVAKLAQKIVKEVLKLDKEVRKLILKNIDEE 852
Query: 82 SV 83
V
Sbjct: 853 EV 854
>gnl|CDD|184905 PRK14941, PRK14941, DNA polymerase III subunit beta; Provisional.
Length = 374
Score = 24.7 bits (54), Expect = 6.7
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 30 KEEKPDLMKDAKYDLMKNELLDLMQK 55
K EK + D DL +ELLDL+QK
Sbjct: 119 KPEKQEKNFDISLDLETSELLDLIQK 144
>gnl|CDD|184179 PRK13608, PRK13608, diacylglycerol glucosyltransferase;
Provisional.
Length = 391
Score = 24.8 bits (54), Expect = 6.7
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 47 NELLDLMQKEKPDLV 61
N+L++L+ KEKPDL+
Sbjct: 94 NKLINLLIKEKPDLI 108
>gnl|CDD|233396 TIGR01399, hrcV, type III secretion protein, HrcV family. Members
of this family are closely homologous to the flagellar
biosynthesis protein FlhA (TIGR01398) and should all
participate in type III secretion systems. Examples
include InvA (Salmonella enterica), LcrD (Yersinia
enterocolitica), HrcV (Xanthomonas), etc. Type III
secretion systems resemble flagellar biogenesis systems,
and may share the property of translocating special
classes of peptides through the membrane [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 677
Score = 24.6 bits (54), Expect = 7.9
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 49 LLDLMQKEKPDLVQE 63
LLD M++E P+LV+E
Sbjct: 496 LLDQMEREYPELVKE 510
>gnl|CDD|99850 cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain of yeast
Rrp6p, human polymyositis/scleroderma autoantigen
100kDa, and similar proteins. Yeast Rrp6p and its human
homolog, the polymyositis/scleroderma autoantigen 100kDa
(PM/Scl-100), are exosome-associated proteins involved
in the degradation and processing of precursors to
stable RNAs. Both proteins contain a DEDDy-type
DnaQ-like 3'-5' exonuclease domain possessing three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific YX(3)D pattern at ExoIII. The motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. PM/Scl-100, an
autoantigen present in the nucleolar compartment of the
cell, reacts with autoantibodies produced by about 50%
of patients with polymyositis-scleroderma overlap
syndrome.
Length = 192
Score = 24.5 bits (54), Expect = 8.7
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 42 YDLMKNELLDLMQKEKPDLVQ 62
YD ++NELL+ P+L++
Sbjct: 165 YDRLRNELLERANALAPNLLE 185
>gnl|CDD|179310 PRK01622, PRK01622, OxaA-like protein precursor; Validated.
Length = 256
Score = 24.3 bits (53), Expect = 9.1
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 29 MKEEKPDLMK-DAKYDLMKNELLDLMQKEKPDLVQEEMSDLMK 70
M KP+L K AK + K+ EK Q+EM +L K
Sbjct: 93 MAVMKPELDKIQAKLKVTKD-------LEKQKEYQKEMMELYK 128
>gnl|CDD|119430 cd05170, PIKKc_SMG1, Suppressor of morphogenetic effect on
genitalia-1 (SMG-1), catalytic domain; The SMG-1
catalytic domain subfamily is part of a larger
superfamily that includes the catalytic domains of other
kinases such as the typical serine/threonine/tyrosine
protein kinases (PKs), aminoglycoside
phosphotransferase, choline kinase, and RIO kinases.
SMG-1 is a member of the phosphoinositide
3-kinase-related protein kinase (PIKK) subfamily. PIKKs
have intrinsic serine/threonine kinase activity and are
distinguished from other PKs by their unique catalytic
domain, similar to that of lipid PI3K, and their large
molecular weight (240-470 kDa). In addition to its
catalytic domain, SMG-1 contains a FATC (FRAP, ATM and
TRRAP, C-terminal) domain at the C-terminus. SMG-1 plays
a critical role in the mRNA surveillance mechanism known
as non-sense mediated mRNA decay (NMD). NMD protects the
cells from the accumulation of aberrant mRNAs with
premature termination codons (PTCs) generated by genome
mutations and by errors during transcription and
splicing. SMG-1 phosphorylates Upf1, another central
component of NMD, at the C-terminus upon recognition of
PTCs. The phosphorylation/dephosphorylation cycle of
Upf1 is essential for promoting NMD.
Length = 307
Score = 24.3 bits (53), Expect = 9.5
Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 19 DLMKDELPALMKEEKPDLM---KDAKYDLMKNELLDLMQKEKPDLVQEEM 65
DL +++ +K L +D +++ L +LMQ+ DL+ E+
Sbjct: 131 DLFYNKITPALKAHGLSLDVSRRDWPLSVLRQVLDELMQETPKDLLAREL 180
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
0.310 0.130 0.347
Gapped
Lambda K H
0.267 0.0816 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,443,932
Number of extensions: 369524
Number of successful extensions: 463
Number of sequences better than 10.0: 1
Number of HSP's gapped: 461
Number of HSP's successfully gapped: 48
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.0 bits)