RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027752
(219 letters)
>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 158
Score = 34.1 bits (79), Expect = 0.019
Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 106 KAVSELTVLKGVGPATASAVLA-AYAPDLAP 135
A EL L GVG TA+ VL A PD P
Sbjct: 80 DAREELLALPGVGRKTANVVLLFALGPDAFP 110
>gnl|CDD|109681 pfam00633, HHH, Helix-hairpin-helix motif. The helix-hairpin-helix
DNA-binding motif is found to be duplicated in the
central domain of RuvA. The HhH domain of DisA, a
bacterial checkpoint control protein, is a DNA-binding
domain.
Length = 30
Score = 29.7 bits (68), Expect = 0.098
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 103 DLTKAVSELTVLKGVGPATASAVLAA 128
+ + EL L GVGP TA A+L+
Sbjct: 5 LIPASREELLALPGVGPKTAEAILSY 30
>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 29.5 bits (67), Expect = 0.66
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 106 KAVSELTVLKGVGPATASAVLA 127
EL L GVG TA+AVL+
Sbjct: 69 DDREELLKLPGVGRKTANAVLS 90
>gnl|CDD|197622 smart00278, HhH1, Helix-hairpin-helix DNA-binding motif class 1.
Length = 20
Score = 27.3 bits (62), Expect = 0.68
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 109 SELTVLKGVGPATASAVLAA 128
EL + G+GP TA +L A
Sbjct: 1 EELLKVPGIGPKTAEKILEA 20
>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 30.1 bits (69), Expect = 0.90
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAYAPD 132
K F SL + +A V EL + G+ A A+ A
Sbjct: 561 KHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHKK 598
>gnl|CDD|214836 smart00825, PKS_KS, Beta-ketoacyl synthase. The structure of
beta-ketoacyl synthase is similar to that of the
thiolase family and also chalcone synthase. The active
site of beta-ketoacyl synthase is located between the N
and C-terminal domains.
Length = 298
Score = 29.6 bits (68), Expect = 0.97
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 40 RKELPSLIHQRNPNPHINTTE-----LSKLVRWKLTRGKWRPRLLVFVSS 84
+P +H PNPHI+ E ++L W RPR VSS
Sbjct: 239 HGVIPPTLHFETPNPHIDLEESPLRVPTELTPW---PPPGRPR-RAGVSS 284
>gnl|CDD|177810 PLN00417, PLN00417, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 348
Score = 29.5 bits (66), Expect = 1.2
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 151 DYSLKQYLLFADKLQAKAKELVSEENCF 178
+Y++KQ L+ +A A+ L EENCF
Sbjct: 166 EYTMKQRLVIEKFFKAMARSLELEENCF 193
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 30.0 bits (68), Expect = 1.2
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 10/57 (17%)
Query: 80 VFVSSLDD----SSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPD 132
V V+ LD +++K A+EK L D V+ L A P
Sbjct: 832 VLVARLDVGVDAAALKEAAEKVIAKLGDPA------AVVLSSDEEKGKVSLVAAVPP 882
>gnl|CDD|205093 pfam12826, HHH_2, Helix-hairpin-helix motif. The HhH domain of
DisA, a bacterial checkpoint control protein, is a
DNA-binding domain.
Length = 64
Score = 27.4 bits (62), Expect = 1.3
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAV 125
K F SL L A V EL + +GP A ++
Sbjct: 21 KHFGSLDALANASVEELLEIDDIGPIVAQSI 51
>gnl|CDD|153083 cd00576, RNR_PFL, Ribonucleotide reductase and Pyruvate formate
lyase. Ribonucleotide reductase (RNR) and pyruvate
formate lyase (PFL) are believed to have diverged from a
common ancestor. They have a structurally similar
ten-stranded alpha-beta barrel domain that hosts the
active site, and are radical enzymes. RNRs are found in
all organisms and provide the only mechanism by which
nucleotides are converted to deoxynucleotides. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs use a diiron-tyrosyl
radical while Class II RNRs use coenzyme B12
(adenosylcobalamin, AdoCbl). Class III RNRs use an FeS
cluster and S-adenosylmethionine to generate a glycyl
radical. PFL, an essential enzyme in anaerobic bacteria,
catalyzes the conversion of pyruvate and CoA to
acteylCoA and formate in a mechanism that uses a glycyl
radical.
Length = 401
Score = 29.4 bits (66), Expect = 1.6
Identities = 20/84 (23%), Positives = 30/84 (35%), Gaps = 16/84 (19%)
Query: 91 KSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY-APDLAPFMSDEAMGAALGHS 149
KS +E K+ + A S GV A AS++L+ Y + D A G
Sbjct: 46 KSINEAIQKTYQIIALAASNQ-NGGGVSFARASSILSPYGSRD-----------YAKGSG 93
Query: 150 KDYSLKQYLLFADKLQAKAKELVS 173
+ + AD KE+
Sbjct: 94 TE---TDAVEAADAFNLALKEVGQ 114
>gnl|CDD|233862 TIGR02424, TF_pcaQ, pca operon transcription factor PcaQ. Members
of this family are LysR-family transcription factors
associated with operons for catabolism of
protocatechuate. Members occur only in Proteobacteria
[Energy metabolism, Other, Regulatory functions, DNA
interactions].
Length = 300
Score = 28.9 bits (65), Expect = 1.9
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 70 TRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGV 117
TR K+R L FV SVK A+E + P ++K + EL + G
Sbjct: 1 TRIKFR-HLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGT 47
>gnl|CDD|178801 PRK00024, PRK00024, hypothetical protein; Reviewed.
Length = 224
Score = 28.5 bits (65), Expect = 2.0
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 98 FKSLPDLTKA-VSELTVLKGVGPATASAVLAA 128
F SL L A + EL +KG+GPA A+ + AA
Sbjct: 54 FGSLRGLLDASLEELQSIKGIGPAKAAQLKAA 85
>gnl|CDD|198403 cd10456, GIY-YIG_UPF0213, The GIY-YIG domain of uncharacterized
protein family UPF0213 related to structure-specific
endonuclease SLX1. This family contains a group of
uncharacterized proteins found mainly in bacteria and
several in dsDNA viruses. Although their function roles
have not been recognized, these proteins show
significant sequence similarities with the N-terminal
GIY-YIG endonuclease domain of structure-specific
endonuclease subunit SLX1, which binds another
structure-specific endonuclease subunit SLX4 to form an
active heterodimeric SLX1-SLX4 complex. This complex
functions as a 5' flap endonuclease in yeast, and has
also been identified as a Holliday junction resolvase in
human.
Length = 68
Score = 27.0 bits (61), Expect = 2.0
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 68 KLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP 102
K TRG+ RP LV+ DD S E K L
Sbjct: 35 KYTRGR-RPVKLVYSEEFDDRSEALKREYRIKKLS 68
>gnl|CDD|180330 PRK05965, PRK05965, hypothetical protein; Provisional.
Length = 459
Score = 28.9 bits (65), Expect = 2.2
Identities = 12/42 (28%), Positives = 15/42 (35%), Gaps = 9/42 (21%)
Query: 121 TASAVLAAYAPDLAPFMSDE---------AMGAALGHSKDYS 153
A + + Y P A MSD A +GH YS
Sbjct: 282 VAKGLTSGYVPMGAVLMSDHVYQGIADGAGAAAPVGHGYTYS 323
>gnl|CDD|217002 pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family.
Transposases are needed for efficient transposition of
the insertion sequence or transposon DNA. This family
includes transposases for IS116, IS110 and IS902. This
region is often found with pfam01548. The exact function
of this region is uncertain. This family contains a HHH
motif suggesting a DNA-binding function.
Length = 87
Score = 27.1 bits (61), Expect = 2.5
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 111 LTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147
L + G+GP TA+A+LA D++ F S + A G
Sbjct: 4 LLSIPGIGPITAAALLAE-IGDISRFKSARQLAAYAG 39
>gnl|CDD|237395 PRK13482, PRK13482, DNA integrity scanning protein DisA;
Provisional.
Length = 352
Score = 28.6 bits (65), Expect = 2.6
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAV 125
+ F SL L A + +L ++G+G A A+
Sbjct: 305 EHFGSLQGLLAASIEDLDEVEGIGEVRARAI 335
>gnl|CDD|204791 pfam11945, WASH_WAHD, WAHD domain of WASH complex. This domain
forms part of the WASH-complex of domains and proteins
that activates the Arp2/3 complex, see pfam04062. The
Arp2/3 complex regulates endocytosis, sorting, and
trafficking within the cell. The WAHD domain attaches to
the FAM21 proteins via its N-terminal residues and to
the microtubules via its C-terminal residues.
Length = 297
Score = 28.6 bits (64), Expect = 2.7
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 100 SLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKD 151
LPDL +L +GP A + + P+L P +A+ A S++
Sbjct: 241 YLPDLPGIADDLMYSADLGPGIAPSAPSVIIPEL-PSFETDAIEVADHDSQE 291
>gnl|CDD|234014 TIGR02786, addB_alphas, double-strand break repair protein AddB,
alphaproteobacterial type. AddAB is a system well
described in the Firmicutes as a replacement for RecBCD
in many prokaryotes for the repair of double stranded
break DNA damage. More recently, a distantly related
gene pair conserved in many alphaproteobacteria was
shown also to function in double-stranded break repair
in Rhizobium etli. This family consists of AddB proteins
of the alphaproteobacteial type [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1021
Score = 28.5 bits (64), Expect = 2.9
Identities = 25/115 (21%), Positives = 41/115 (35%), Gaps = 8/115 (6%)
Query: 50 RNPNPHINTTELSK-LVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD-LTKA 107
R P L R L G P + + S+L + S+++A + L + L A
Sbjct: 461 RGGTPRAGILALPAFFERRLLALG-DDPEVPAWHSALPEQSIEAA-----RPLCELLEIA 514
Query: 108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFAD 162
+ L L G + + A + DE A + + K LFA+
Sbjct: 515 IEPLESLAGRREELDAELAEATVELMEALSRDEEGWLAALYEGEAGHKLASLFAE 569
>gnl|CDD|237034 PRK12278, PRK12278, 50S ribosomal protein L21/unknown domain fusion
protein; Provisional.
Length = 221
Score = 28.3 bits (63), Expect = 3.1
Identities = 18/76 (23%), Positives = 25/76 (32%), Gaps = 11/76 (14%)
Query: 91 KSASEKAFKSLPDLTKAVSELTVLKGVGPATAS----------AVLAAYAPDLAPFMSDE 140
A A +LT + GVGPA A A +AA + DE
Sbjct: 140 APAPAAAAAPPAAAAAGADDLTKITGVGPALAKKLNEAGVTTFAQIAALTDADIAKI-DE 198
Query: 141 AMGAALGHSKDYSLKQ 156
+ KD ++Q
Sbjct: 199 KLSFKGRIEKDGWIEQ 214
>gnl|CDD|235607 PRK05785, PRK05785, hypothetical protein; Provisional.
Length = 226
Score = 27.7 bits (62), Expect = 3.6
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 12 KWKEALASYEACVESLNKPN-LISL--DDYYRKELPSLIHQRNPNP 54
W+E +Y ++ ++ N IS D +R EL I + P
Sbjct: 7 TWEELQEAYNKIPKAYDRANRFISFNQDVRWRAELVKTILKYCGRP 52
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 28.1 bits (63), Expect = 4.1
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 108 VSELTVLKGVGPATASAVLA 127
EL L GVGP TA A+L+
Sbjct: 112 EEELAALPGVGPYTAGAILS 131
>gnl|CDD|234691 PRK00220, PRK00220, putative glycerol-3-phosphate acyltransferase
PlsY; Provisional.
Length = 198
Score = 27.4 bits (62), Expect = 4.9
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 115 KGVGPATASAVLAAYAPDLAPFM 137
KGV ATA+ VL P LA +
Sbjct: 106 KGV--ATAAGVLLGIGPLLALIL 126
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 27.9 bits (63), Expect = 4.9
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 82 VSSLDDSSVKSASE--KAFKSLPDLTKA-VSELTVLKGVGPATA 122
V SL D A + F S+ + A EL ++G+G TA
Sbjct: 717 VESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTA 760
>gnl|CDD|236091 PRK07768, PRK07768, long-chain-fatty-acid--CoA ligase; Validated.
Length = 545
Score = 27.7 bits (62), Expect = 5.1
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 116 GVGPATASAVLAAYAPDLAP 135
GVGP A AVLA ++AP
Sbjct: 50 GVGPGDAVAVLAGAPVEIAP 69
>gnl|CDD|233858 TIGR02414, pepN_proteo, aminopeptidase N, Escherichia coli type.
The M1 family of zinc metallopeptidases contains a
number of distinct, well-separated clades of proteins
with aminopeptidase activity. Several are designated
aminopeptidase N, EC 3.4.11.2, after the Escherichia
coli enzyme, suggesting a similar activity profile (see
SP|P04825 for a description of catalytic activity). This
family consists of all aminopeptidases closely related
to E. coli PepN and presumed to have similar (not
identical) function. Nearly all are found in
Proteobacteria, but members are found also in
Cyanobacteria, plants, and apicomplexan parasites. This
family differs greatly in sequence from the family of
aminopeptidases typified by Streptomyces lividans PepN
(TIGR02412), from the membrane bound aminopeptidase N
family in animals, etc [Protein fate, Degradation of
proteins, peptides, and glycopeptides].
Length = 863
Score = 28.1 bits (63), Expect = 5.2
Identities = 14/56 (25%), Positives = 29/56 (51%)
Query: 75 RPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYA 130
R L ++S+ DD+ +++ + + FKS ++T ++ L+ L LAA+
Sbjct: 675 RNACLSYLSAADDAEIRNLALEQFKSADNMTDRLAALSALVHFESDFRERALAAFY 730
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include the fungal mating type gene products
MC, MATA1 and Ste11.
Length = 77
Score = 26.1 bits (58), Expect = 5.5
Identities = 7/33 (21%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 39 YRKELPSLIHQRNPNPHINTTELSKLV--RWKL 69
YR++ + + NP + E+S+++ W+
Sbjct: 12 YRQDKHAQLKT--ENPGLTNNEISRIIGRMWRS 42
>gnl|CDD|224914 COG2003, RadC, DNA repair proteins [DNA replication, recombination,
and repair].
Length = 224
Score = 27.2 bits (61), Expect = 5.6
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 4/44 (9%)
Query: 89 SVKSASE---KAFKSLPDLTKA-VSELTVLKGVGPATASAVLAA 128
SV ++ + F SL +L KA V EL+ +KG+G A A + AA
Sbjct: 42 SVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAA 85
>gnl|CDD|223474 COG0397, COG0397, Uncharacterized conserved protein [Function
unknown].
Length = 488
Score = 27.7 bits (62), Expect = 6.2
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 126 LAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYL-LFADKL 164
L A L+P + A+ AAL D Y L D+L
Sbjct: 302 LQRLAGALSPLIDQAALEAALNSFSDLYRAAYRGLMRDRL 341
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family
includes ribosomal protein S13 from prokaryotes and S18
from eukaryotes.
Length = 106
Score = 26.5 bits (59), Expect = 6.4
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
L K LT +KG+G A+ +L
Sbjct: 7 LDGNKKIEIALTYIKGIGRRKANQILKK 34
>gnl|CDD|130156 TIGR01084, mutY, A/G-specific adenine glycosylase. This equivalog
model identifies mutY members of the pfam00730
superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro
rich loop followed by a conserved aspartate). The major
members of the superfamily are nth and mutY [DNA
metabolism, DNA replication, recombination, and repair].
Length = 275
Score = 27.4 bits (61), Expect = 6.7
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 108 VSELTVLKGVGPATASAVLA 127
+L L GVG TA A+L+
Sbjct: 104 FEDLAALPGVGRYTAGAILS 123
>gnl|CDD|190277 pfam02320, UCR_hinge, Ubiquinol-cytochrome C reductase hinge
protein. The ubiquinol-cytochrome C reductase complex
(cytochrome bc1 complex) is a respiratory multienzyme
complex. This Pfam family represents the 'hinge'
protein of the complex which is thought to mediate
formation of the cytochrome c1 and cytochrome c
complex.
Length = 65
Score = 25.3 bits (56), Expect = 6.8
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 2 QLEFECSNVNKWKEALASYEACVESLNK 29
L EC N K +A Y+ CVE +N
Sbjct: 6 TLREECKNKEKCVKAKHEYQECVERVNS 33
>gnl|CDD|143386 cd00141, NT_POLXc, Nucleotidyltransferase (NT) domain of family X
DNA Polymerases. X family polymerases fill in short
gaps during DNA repair. They are relatively inaccurate
enzymes and play roles in base excision repair, in
non-homologous end joining (NHEJ) which acts mainly to
repair damage due to ionizing radiation, and in V(D)J
recombination. This family includes eukaryotic Pol beta,
Pol lambda, Pol mu, and terminal deoxyribonucleotidyl
transferase (TdT). Pol beta and Pol lambda are primarily
DNA template-dependent polymerases. TdT is a DNA
template-independent polymerase. Pol mu has both
template dependent and template independent activities.
This subgroup belongs to the Pol beta-like NT
superfamily. In the majority of enzymes in this
superfamily, two carboxylates, Dx[D/E], together with a
third more distal carboxylate, coordinate two divalent
metal cations involved in a two-metal ion mechanism of
nucleotide addition. These three carboxylate residues
are fairly well conserved in this family.
Length = 307
Score = 26.8 bits (60), Expect = 9.9
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 94 SEKAFKSLPDLTKAVSELTVLKGVGPATA 122
K + D+ + L + GVGP TA
Sbjct: 70 LRKLEELREDVPPGLLLLLRVPGVGPKTA 98
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
0.313 0.127 0.361
Gapped
Lambda K H
0.267 0.0940 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,508,707
Number of extensions: 945531
Number of successful extensions: 806
Number of sequences better than 10.0: 1
Number of HSP's gapped: 804
Number of HSP's successfully gapped: 51
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.4 bits)