RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028836
(203 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 = 32.6 bits (75), Expect = 0.060
Identities = 14/31 (45%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 106 KAVSELTVLKGVGPATASAVLA-AYAPGVAP 135
A EL L GVG TA+ VL A P 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 = 30.1 bits (69), Expect = 0.066
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 103 DLTKAVSELTVLKGVGPATASAVLAA 128
+ + EL L GVGP TA A+L+
Sbjct: 5 LIPASREELLALPGVGPKTAEAILSY 30
>gnl|CDD|197622 smart00278, HhH1, Helix-hairpin-helix DNA-binding motif class 1.
Length = 20
Score = 27.3 bits (62), Expect = 0.48
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 109 SELTVLKGVGPATASAVLAA 128
EL + G+GP TA +L A
Sbjct: 1 EELLKVPGIGPKTAEKILEA 20
>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 = 29.9 bits (68), Expect = 0.52
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 106 KAVSELTVLKGVGPATASAVLA 127
EL L GVG TA+AVL+
Sbjct: 69 DDREELLKLPGVGRKTANAVLS 90
>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 29.7 bits (68), Expect = 0.96
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAYAPG 132
K F SL + +A V EL + G+ A A+ A
Sbjct: 561 KHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHKK 598
>gnl|CDD|176206 cd08244, MDR_enoyl_red, Possible enoyl reductase. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 29.6 bits (67), Expect = 1.1
Identities = 16/40 (40%), Positives = 17/40 (42%), Gaps = 7/40 (17%)
Query: 100 SLPDLTKAVSELT-------VLKGVGPATASAVLAAYAPG 132
+ PD V E VL GVG A A LA APG
Sbjct: 195 TRPDWPDQVREALGGGGVTVVLDGVGGAIGRAALALLAPG 234
>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 = 27.6 bits (62), Expect = 1.1
Identities = 7/43 (16%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 39 YRKELPSLIHQRNPNPHINTTELSKLV--RWKL----TRGKWR 75
YR++ + + NP + E+S+++ W+ + ++
Sbjct: 12 YRQDKHAQLKT--ENPGLTNNEISRIIGRMWRSESPEVKAYYK 52
>gnl|CDD|237034 PRK12278, PRK12278, 50S ribosomal protein L21/unknown domain fusion
protein; Provisional.
Length = 221
Score = 28.7 bits (64), Expect = 1.6
Identities = 16/55 (29%), Positives = 20/55 (36%), Gaps = 3/55 (5%)
Query: 91 KSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAA 145
A A +LT + GVGPA A + A GV F A+ A
Sbjct: 140 APAPAAAAAPPAAAAAGADDLTKITGVGPALAKKLNEA---GVTTFAQIAALTDA 191
>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 = 29.2 bits (66), Expect = 1.6
Identities = 14/56 (25%), Positives = 29/56 (51%)
Query: 75 RPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYA 130
R L ++S+ DD+ +++ + + FKS ++T ++ L+ L LAA+
Sbjct: 675 RNACLSYLSAADDAEIRNLALEQFKSADNMTDRLAALSALVHFESDFRERALAAFY 730
>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 = 26.7 bits (60), Expect = 2.0
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|180330 PRK05965, PRK05965, hypothetical protein; Provisional.
Length = 459
Score = 28.9 bits (65), Expect = 2.0
Identities = 12/42 (28%), Positives = 15/42 (35%), Gaps = 9/42 (21%)
Query: 121 TASAVLAAYAPGVAPFMSDE---------AMGAALGHSKDYS 153
A + + Y P A MSD A +GH YS
Sbjct: 282 VAKGLTSGYVPMGAVLMSDHVYQGIADGAGAAAPVGHGYTYS 323
>gnl|CDD|178801 PRK00024, PRK00024, hypothetical protein; Reviewed.
Length = 224
Score = 28.1 bits (64), Expect = 2.4
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|224859 COG1948, MUS81, ERCC4-type nuclease [DNA replication,
recombination, and repair].
Length = 254
Score = 28.1 bits (63), Expect = 2.7
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 75 RPRLLDFVSSLDDSSVKSASE--KAFKSLPDLTKA-VSELTVLKGVGPATASAV 125
+ L + S+ K A K F S+ D+ A EL +KG+G A +
Sbjct: 177 KELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREI 230
>gnl|CDD|237395 PRK13482, PRK13482, DNA integrity scanning protein DisA;
Provisional.
Length = 352
Score = 28.2 bits (64), Expect = 2.8
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|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 28.3 bits (64), Expect = 2.8
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|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 28.1 bits (63), Expect = 3.7
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 108 VSELTVLKGVGPATASAVLA 127
EL L GVGP TA A+L+
Sbjct: 112 EEELAALPGVGPYTAGAILS 131
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 28.1 bits (63), Expect = 4.4
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 11/59 (18%)
Query: 81 FVSSLDD----SSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL-AAYAPGVA 134
V+ LD +++K A+EK L D V+ L AA PGV
Sbjct: 833 LVARLDVGVDAAALKEAAEKVIAKLGDPA------AVVLSSDEEKGKVSLVAAVPPGVV 885
>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 = 4.6
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|178588 PLN03014, PLN03014, carbonic anhydrase.
Length = 347
Score = 27.8 bits (61), Expect = 4.7
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 18/88 (20%)
Query: 88 SSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147
SS S+S + +S+P L + V AA AP +AP+ S+E MG
Sbjct: 40 SSSSSSSSSSSRSVPTLIRN---------------EPVFAAPAPIIAPYWSEE-MGTEAY 83
Query: 148 HSKDYSLRQYLLFADKLQ--AKAKVSDI 173
+L++ L+ ++L+ A AKV I
Sbjct: 84 DEAIEALKKLLIEKEELKTVAAAKVEQI 111
>gnl|CDD|220426 pfam09823, DUF2357, Domain of unknown function (DUF2357). This
entry was previously the N terminal portion of DUF524
(pfam04411) before it was split into two. This domain
has no known function. It is predicted to adopt an all
beta secondary structure pattern followed by mainly
alpha-helical structures.
Length = 246
Score = 27.3 bits (61), Expect = 5.1
Identities = 22/116 (18%), Positives = 38/116 (32%), Gaps = 19/116 (16%)
Query: 7 CSNVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVR 66
S V + + VE RK LP + Q ++T E ++ V+
Sbjct: 123 DSAVLRELAKNPARLQWVEDGG-----------RKYLPRRVRQDKKELTVDTPE-NRFVK 170
Query: 67 WKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSEL---TVLKGVGP 119
+ L R R +L D L + L ++ + + L + VG
Sbjct: 171 YVLER--LRKKLSDLKERL--PEKSRTELAFLEELKEMQRQLERLLRHPFFREVGE 222
>gnl|CDD|233135 TIGR00804, nupC, nucleoside transporter. The Concentrative
Nucleoside Transporter (CNT) Family (TC 2.A.41) Members
of the CNT family mediate nucleoside uptake. In bacteria
they are energized by H+ symport, but in mammals they
are energized by Na+ symport. The different transporters
exhibit differing specificities for nucleosides. The E.
coli NupC permease transports all nucleosides (both
ribo- and deoxyribonucleosides) except hypoxanthine and
guanine nucleosides. The B. subtilis NupC is specific
for pyrimidine nucleosides (cytidine and uridine and the
corresponding deoxyribonucleosides). The mammalian
permease members of the CNT family also exhibit
differing specificities. Thus, rats possess at least two
NupC homologues, one specific for both purine and
pyrimidine nucleosides and one specific for purine
nucleosides. At least three paralogues have been
characterized from humans. One human homologue(CNT1)
transports pyrimidine nucleosides and adenosine, but
deoxyadenosine and guanosine are poor substrates of this
permease. Another (CNT2) is selective for purine
nucleosides. Alteration of just a few amino acyl
residues in TMSs 7 and 8 interconverts their
specificities [Transport and binding proteins,
Nucleosides, purines and pyrimidines].
Length = 401
Score = 27.7 bits (62), Expect = 5.3
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 166 AKAKVSDIFFFKCLCTFQFVVCLI-VLHHL-LLQLDLDI 202
+ +F F+ L F LI +L++L ++Q +
Sbjct: 78 PLVQDLFVFAFQVLPIIIFFSALISILYYLGIMQWVIRK 116
>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 = 5.4
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 108 VSELTVLKGVGPATASAVLA 127
+L L GVG TA A+L+
Sbjct: 104 FEDLAALPGVGRYTAGAILS 123
>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 = 27.3 bits (62), Expect = 5.4
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 40 RKELPSLIHQRNPNPHINTTE-----LSKLVRWKLTRGKWRPRLLDFVSS 84
+P +H PNPHI+ E ++L W RPR VSS
Sbjct: 239 HGVIPPTLHFETPNPHIDLEESPLRVPTELTPW---PPPGRPR-RAGVSS 284
>gnl|CDD|173858 cd08493, PBP2_DppA_like, The substrate-binding component of an
ABC-type dipeptide import system contains the type 2
periplasmic binding fold. This family represents the
substrate-binding domain of an ATP-binding cassette
(ABC)-type dipeptide import system. The DppA binds
dipeptides and some tripeptides and is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 amino acid
residues) and plays a role in recycling of cell wall
peptides, which precludes any involvement in chemotaxis.
Most of other periplasmic binding proteins are
comprised of only two globular subdomains corresponding
to domains I and III of the dipeptide/oligopeptide
binding proteins. The structural topology of these
domains is most similar to that of the type 2
periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 27.5 bits (62), Expect = 5.8
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 134 APFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKVSDI 173
APF+++ AM A S +Y AD+L A K +
Sbjct: 136 APFLANLAMPFASILSPEY--------ADQLLAAGKPEQL 167
>gnl|CDD|224914 COG2003, RadC, DNA repair proteins [DNA replication, recombination,
and repair].
Length = 224
Score = 27.2 bits (61), Expect = 5.8
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|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 = 27.5 bits (61), Expect = 5.9
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 77 RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY 129
LD + + KS +E K+ + A S GV A AS++L+ Y
Sbjct: 32 DSLDPGIKGVNETAKSINEAIQKTYQIIALAASNQ-NGGGVSFARASSILSPY 83
>gnl|CDD|235607 PRK05785, PRK05785, hypothetical protein; Provisional.
Length = 226
Score = 27.0 bits (60), Expect = 6.4
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 12 KWKEALASYEARVESLNKPN-LISL--DDYYRKELPSLIHQRNPNP 54
W+E +Y ++ ++ N IS D +R EL I + P
Sbjct: 7 TWEELQEAYNKIPKAYDRANRFISFNQDVRWRAELVKTILKYCGRP 52
>gnl|CDD|180528 PRK06321, PRK06321, replicative DNA helicase; Provisional.
Length = 472
Score = 27.1 bits (60), Expect = 6.5
Identities = 15/41 (36%), Positives = 19/41 (46%)
Query: 139 DEAMGAALGHSKDYSLRQYLLFADKLQAKAKVSDIFFFKCL 179
DEA S+ +L QY+L ADKL+ D F L
Sbjct: 147 DEAQNLLFKISQTTNLAQYVLVADKLKGLTSSKDKPFLLQL 187
>gnl|CDD|132358 TIGR03315, Se_ygfK, putative selenate reductase, YgfK subunit.
Members of this protein family are YgfK, predicted to be
one subunit of a three-subunit, molybdopterin-containing
selenate reductase. This enzyme is found, typically, in
genomic regions associated with xanthine dehydrogenase
homologs predicted to belong to the selenium-dependent
molybdenum hydroxylases (SDMH). Therefore, the selenate
reductase is suggested to play a role in furnishing
selenide for SelD, the selenophosphate synthase.
Length = 1012
Score = 27.4 bits (61), Expect = 6.6
Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 14/92 (15%)
Query: 39 YRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKS-ASEKA 97
Y + L +I+ +NP P I T ++K TR LD+ S++ +K A+EK
Sbjct: 469 YLEAL-EVIYDKNPLPAITGTICDHQCQYKCTR-------LDYDESVNIREMKKVAAEKG 520
Query: 98 F-KSLPDLTKAVSELTVLK----GVGPATASA 124
+ + K + + K G GPA SA
Sbjct: 521 YDEYKTRWHKPQGKSSAHKVAVIGAGPAGLSA 552
>gnl|CDD|223145 COG0067, GltB, Glutamate synthase domain 1 [Amino acid transport
and metabolism].
Length = 371
Score = 27.3 bits (61), Expect = 6.8
Identities = 30/115 (26%), Positives = 35/115 (30%), Gaps = 28/115 (24%)
Query: 45 SLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104
L+H N INT W RG F S D E K LP L
Sbjct: 227 LLVH----NGEINT--YGGNRNWLEARGYK------FESPTD-------GEVLAKLLPIL 267
Query: 105 TKAVS---------ELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSK 150
+ S EL +L G A+ +L A V M E HS
Sbjct: 268 MRGGSDSASLDNALELLLLGGRDLYHAAMLLGPEAWVVGTDMDPEGRAFYEDHSA 322
>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 = 25.6 bits (57), Expect = 7.2
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 16/41 (39%)
Query: 111 LTVLKGVGPATASAVLA---------------AYAPGVAPF 136
L + G+GP TA+A+LA AYA G+AP
Sbjct: 4 LLSIPGIGPITAAALLAEIGDISRFKSARQLAAYA-GLAPR 43
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 26.8 bits (60), Expect = 8.0
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 106 KAVSELTVLKGVGPATASAVLA-AY-APGVA 134
EL L GVG TA+ VL+ A+ P +A
Sbjct: 106 DTREELLSLPGVGRKTANVVLSFAFGIPAIA 136
>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 = 8.3
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 94 SEKAFKSLPDLTKAVSELTVLKGVGPATA 122
K + D+ + L + GVGP TA
Sbjct: 70 LRKLEELREDVPPGLLLLLRVPGVGPKTA 98
>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 = 26.6 bits (59), Expect = 8.7
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 70 TRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGV 117
TR K+R L FV SVK A+E + P ++K + EL + G
Sbjct: 1 TRIKFR-HLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGT 47
>gnl|CDD|192651 pfam10666, Phage_Gp14, Phage protein Gp14. This phage protein
family is of unknown function but is expressed from
within a cluster of tail- and base plate-producing
genes.
Length = 140
Score = 26.2 bits (57), Expect = 9.6
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 12 KWKEALASYEARVESLNKPNLISLDDYYRKELPSL 46
KW EA Y+ ++E LNK N+ + D+ ++ +L
Sbjct: 36 KWIEADEKYKKKLEKLNKYNIDNTDEMSSEDYFAL 70
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 0.134 0.393
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: 10,039,928
Number of extensions: 909825
Number of successful extensions: 1033
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1033
Number of HSP's successfully gapped: 47
Length of query: 203
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 111
Effective length of database: 6,857,034
Effective search space: 761130774
Effective search space used: 761130774
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: 57 (25.4 bits)