RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027775
(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 = 33.0 bits (76), Expect = 0.059
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 = 29.3 bits (67), Expect = 0.11
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 = 0.74
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 = 26.9 bits (61), Expect = 0.75
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 = 29.7 bits (68), Expect = 1.2
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 = 1.2
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|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 = 27.0 bits (61), Expect = 1.6
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|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 = 1.9
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|180330 PRK05965, PRK05965, hypothetical protein; Provisional.
Length = 459
Score = 29.3 bits (66), Expect = 1.9
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 = 28.5 bits (65), Expect = 2.3
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|237395 PRK13482, PRK13482, DNA integrity scanning protein DisA;
Provisional.
Length = 352
Score = 28.2 bits (64), Expect = 3.1
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|177810 PLN00417, PLN00417, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 348
Score = 28.4 bits (63), Expect = 3.2
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 151 DYSLRQYLLFADKLQAKAKELVSEENCF 178
+Y+++Q L+ +A A+ L EENCF
Sbjct: 166 EYTMKQRLVIEKFFKAMARSLELEENCF 193
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 28.1 bits (63), Expect = 4.2
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 108 VSELTVLKGVGPATASAVLA 127
EL L GVGP TA A+L+
Sbjct: 112 EEELAALPGVGPYTAGAILS 131
>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 = 27.7 bits (63), Expect = 4.8
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|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 = 5.4
Identities = 21/97 (21%), Positives = 33/97 (34%), Gaps = 14/97 (14%)
Query: 77 RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPF 136
LD + + KS +E K+ + A S GV A AS++L+ Y
Sbjct: 32 DSLDPGIKGVNETAKSINEAIQKTYQIIALAASNQ-NGGGVSFARASSILSPYG------ 84
Query: 137 MSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKELVS 173
+ A G + + AD KE+
Sbjct: 85 ----SRDYAKGSGTE---TDAVEAADAFNLALKEVGQ 114
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 27.5 bits (62), Expect = 5.7
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|224914 COG2003, RadC, DNA repair proteins [DNA replication, recombination,
and repair].
Length = 224
Score = 27.2 bits (61), Expect = 6.3
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|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 = 6.6
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 108 VSELTVLKGVGPATASAVLA 127
+L L GVG TA A+L+
Sbjct: 104 FEDLAALPGVGRYTAGAILS 123
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 27.7 bits (62), Expect = 6.6
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|237034 PRK12278, PRK12278, 50S ribosomal protein L21/unknown domain fusion
protein; Provisional.
Length = 221
Score = 27.1 bits (60), Expect = 6.8
Identities = 11/38 (28%), Positives = 14/38 (36%)
Query: 91 KSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128
A A +LT + GVGPA A + A
Sbjct: 140 APAPAAAAAPPAAAAAGADDLTKITGVGPALAKKLNEA 177
>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|235607 PRK05785, PRK05785, hypothetical protein; Provisional.
Length = 226
Score = 27.0 bits (60), Expect = 6.9
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|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 = 25.7 bits (57), Expect = 6.9
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|224859 COG1948, MUS81, ERCC4-type nuclease [DNA replication,
recombination, and repair].
Length = 254
Score = 26.9 bits (60), Expect = 7.5
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|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family
includes ribosomal protein S13 from prokaryotes and S18
from eukaryotes.
Length = 106
Score = 26.1 bits (58), Expect = 8.0
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|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 = 27.0 bits (60), Expect = 8.3
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|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 26.8 bits (60), Expect = 8.4
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|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 = 27.1 bits (60), Expect = 9.6
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
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
0.312 0.127 0.360
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: 10,601,205
Number of extensions: 961022
Number of successful extensions: 848
Number of sequences better than 10.0: 1
Number of HSP's gapped: 848
Number of HSP's successfully gapped: 45
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)