RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014334
(426 letters)
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and
repair].
Length = 285
Score = 64.4 bits (157), Expect = 2e-11
Identities = 41/145 (28%), Positives = 69/145 (47%), Gaps = 16/145 (11%)
Query: 252 FPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKL 311
FP+P +LA DE L + G +A I+ LAR +G++ L EL+ + +E
Sbjct: 144 FPTPEQLAAADEEALRRCGLSGRKAEYIISLARAAAEGELDLSELKPLSDEE-------A 196
Query: 312 AEQLSQINGFGPFTRNNVLV-CIGFYHVIPTDSETIRH-LKQVHA--RNCTSKTVQMIAE 367
E+L+ + G GP+T L+ +G V P D +R +K+++ T K V+ +AE
Sbjct: 197 IEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPTEKEVRELAE 256
Query: 368 SIYGKYAPFQFLAYWSELWHFYEKR 392
+ P++ A LW +
Sbjct: 257 R----WGPYRSYAALY-LWRYARAT 276
>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 = 41.5 bits (98), Expect = 2e-04
Identities = 34/145 (23%), Positives = 59/145 (40%), Gaps = 29/145 (20%)
Query: 252 FPSPRELANLDESFLAK--RCNLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTA 307
FP+P +LA DE L + R Y +A +++LAR +V+ ++ ++
Sbjct: 21 FPTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILVE-----EYGGEVPDDR---- 71
Query: 308 YVKLAEQLSQINGFGPFTRNNVLVCIGF-YHVIPTDSETIRHLKQVHARNCTSKT--VQM 364
E+L ++ G G T N VL IP D+ +R K++ + S V+
Sbjct: 72 -----EELLKLPGVGRKTANAVL-SFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEK 125
Query: 365 IAESIYGKYAPFQFLAYWSELWHFY 389
+ E + + W EL
Sbjct: 126 LLEKLLPE-------EDWRELNLLL 143
>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 = 41.5 bits (98), Expect = 2e-04
Identities = 31/144 (21%), Positives = 48/144 (33%), Gaps = 23/144 (15%)
Query: 253 PSPRELANLDESFLAK---RCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYV 309
P+P LA DE L + +A + +LAR IV+G L +
Sbjct: 31 PTPEALAAADEEELRELIRSLGYRRKAKYLKELARAIVEGFGGLVLDDP----------- 79
Query: 310 KLAEQLSQINGFGPFTRNNVLVCIGFYH-VIPTDSETIRHLKQV--HARNCTSKTVQMIA 366
E+L + G G T N VL P D H+++V K
Sbjct: 80 DAREELLALPGVGRKTANVVL-LFALGPDAFPVD----THVRRVLKRLGLIPKKKTPEEL 134
Query: 367 ESIYGKYAPFQFLAYWSE-LWHFY 389
E + + P + ++ L
Sbjct: 135 EELLEELLPKPYWGEANQALMDLG 158
Score = 27.6 bits (62), Expect = 8.9
Identities = 6/28 (21%), Positives = 8/28 (28%)
Query: 124 FEDMVKCMLLCNCQWPRTLSMARALCEL 151
FE +V +L L E
Sbjct: 1 FEVLVSEILSQQTTDKAVNKAYERLFER 28
>gnl|CDD|236671 PRK10308, PRK10308, 3-methyl-adenine DNA glycosylase II;
Provisional.
Length = 283
Score = 34.4 bits (79), Expect = 0.078
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 15/79 (18%)
Query: 252 FPSPRELANLDESFLAKRCNLGY---RAGRILKLARGIVDGQIQLRELEDMCNEASLTAY 308
FP+P LA D L LG RA ++ LA ++G + L D+ E ++
Sbjct: 155 FPTPERLAAADPQALKA---LGMPLKRAEALIHLANAALEGTLPLTIPGDV--EQAM--- 206
Query: 309 VKLAEQLSQINGFGPFTRN 327
+ L G G +T N
Sbjct: 207 ----KTLQTFPGIGRWTAN 221
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair
protein. This family contains a diverse range of
structurally related DNA repair proteins. The
superfamily is called the HhH-GPD family after its
hallmark Helix-hairpin-helix and Gly/Pro rich loop
followed by a conserved aspartate. This includes
endonuclease III, EC:4.2.99.18 and MutY an A/G-specific
adenine glycosylase, both have a C terminal 4Fe-4S
cluster. The family also includes 8-oxoguanine DNA
glycosylases. The methyl-CPG binding protein MBD4 also
contains a related domain that is a thymine DNA
glycosylase. The family also includes
DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other
members of the AlkA family.
Length = 144
Score = 32.7 bits (75), Expect = 0.13
Identities = 29/129 (22%), Positives = 45/129 (34%), Gaps = 22/129 (17%)
Query: 251 NFPSPRELANLDESFLA---KRCNL-GYRAGRILKLARGIVDGQIQLRELEDMCNEASLT 306
FP+P +LA DE L K +A I +LAR +V+G + L L+
Sbjct: 26 GFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKELARILVEGYLGLVPLDLE------- 78
Query: 307 AYVKLAEQLSQINGFGPFTRNNVLVCIGFYH---VIPTDSETIR---HLKQVHARNCTSK 360
E L + G G +T VL D+ R L + + +
Sbjct: 79 ----ELEALLALPGVGRWTAEAVL-LFALGRPDVFPAVDTHVRRVAKRLGLIDTKPPKKE 133
Query: 361 TVQMIAESI 369
+ + E
Sbjct: 134 VERELEELW 142
>gnl|CDD|240354 PTZ00310, PTZ00310, AMP deaminase; Provisional.
Length = 1453
Score = 34.4 bits (79), Expect = 0.14
Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 13/88 (14%)
Query: 259 ANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQI 318
A L +SFL+ G G++L R ++ + + ++ + E SL Y E+L+ +
Sbjct: 297 AELRQSFLSLH---GNLCGKLL---RRELE-RREYQKQQPQATEYSLPLYGHHPEELTDL 349
Query: 319 ------NGFGPFTRNNVLVCIGFYHVIP 340
GFGPF+RN ++ I F + P
Sbjct: 350 AEWVRRQGFGPFSRNRWILAISFKELGP 377
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 33.5 bits (77), Expect = 0.17
Identities = 29/116 (25%), Positives = 45/116 (38%), Gaps = 25/116 (21%)
Query: 252 FPSPRELANLDESFLAKR-CNLGY--RAGRILKLARGIVD---GQIQLRELEDMCNEASL 305
FP+ + LA E + K LGY RA + K A+ +V+ G+ E
Sbjct: 63 FPTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDE---------- 112
Query: 306 TAYVKLAEQLSQINGFGPFTRNNVLVCIGFYHVIPT-DSETIRHLKQVHARNCTSK 360
E+L+ + G GP+T +L F P D R L ++ A +
Sbjct: 113 -------EELAALPGVGPYTAGAIL-SFAFNQPEPVLDGNVKRVLSRLFAISGDIG 160
>gnl|CDD|233910 TIGR02522, pilus_cpaD, pilus (Caulobacter type) biogenesis
lipoprotein CpaD. This family consists of a pilus
biogenesis protein, CpaD, from Caulobacter, and
homologs in other bacteria, including three in the root
nodule bacterium Bradyrhizobium japonicum. The
molecular function is not known [Cell envelope, Surface
structures].
Length = 198
Score = 31.7 bits (72), Expect = 0.54
Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 7/64 (10%)
Query: 22 NSLDNTDIPSVSVDVTICQP---QQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRM 78
S D D+ ++ D P Q+ S+ + V G LS QQD LL +K
Sbjct: 15 ASTDIIDVGALPDDYRQRHPIAVQESSVSIDLLVAPGDRG----LSASQQDQLLGFLKDW 70
Query: 79 LRLS 82
R S
Sbjct: 71 GRAS 74
>gnl|CDD|235849 PRK06666, fliM, flagellar motor switch protein FliM; Validated.
Length = 337
Score = 31.0 bits (71), Expect = 1.2
Identities = 19/45 (42%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 63 LSQEQQDALLAQV-----KRMLRLSEADERNVR--DFK---RIVR 97
LSQE+ DALL+ V E DE+ VR DFK R R
Sbjct: 6 LSQEEIDALLSGVSDGEVDDEELKEEGDEKKVRPYDFKRQERFSR 50
>gnl|CDD|234944 PRK01345, PRK01345, heat shock protein HtpX; Provisional.
Length = 317
Score = 30.4 bits (69), Expect = 1.5
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 75 VKRMLRLSEADERNVRDFKRIVRQVAQEEG 104
V RM E DER+ + R+VR +A+ G
Sbjct: 52 VLRMYGAQEVDERSAPELYRMVRDLARRAG 81
>gnl|CDD|202394 pfam02783, MCR_beta_N, Methyl-coenzyme M reductase beta subunit,
N-terminal domain. Methyl-coenzyme M reductase (MCR) is
the enzyme responsible for microbial formation of
methane. It is a hexamer composed of 2 alpha
(pfam02249), 2 beta (this family), and 2 gamma
(pfam02240) subunits with two identical nickel
porphinoid active sites. The N-terminal domain has an
alpha/beta ferredoxin-like fold.
Length = 182
Score = 29.7 bits (67), Expect = 1.7
Identities = 12/37 (32%), Positives = 24/37 (64%), Gaps = 3/37 (8%)
Query: 66 EQQDALLAQVKRMLRLSEADERNVR---DFKRIVRQV 99
+A+ +VK+M+++SE D+ NV+ K+++ QV
Sbjct: 75 GNAEAIAEKVKKMVQVSEDDDTNVKLINGGKQLLVQV 111
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 30.0 bits (67), Expect = 2.6
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 72 LAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTDFSGRVFR-SPTLFEDMVKC 130
L Q R LSE NVR+ +R++ ++ Q GE + GR+ TL +++
Sbjct: 595 LEQEFRRNGLSEDSCANVRELRRVIMELGQRGGENG--LPTAGGRLSEWRITLTFAIIRF 652
Query: 131 MLLCNCQWPRT 141
+ C PR
Sbjct: 653 I----CGTPRR 659
>gnl|CDD|225025 COG2114, CyaA, Adenylate cyclase, family 3 (some proteins contain
HAMP domain) [Signal transduction mechanisms].
Length = 227
Score = 29.4 bits (66), Expect = 3.2
Identities = 25/128 (19%), Positives = 38/128 (29%), Gaps = 33/128 (25%)
Query: 80 RLSEADERNV------RDFKRIVRQVAQEEGEESQYMTDFSGRVFRSPTLFEDMVKCMLL 133
LSE+ F + VA+ G +++ D VF P+ ED V C
Sbjct: 59 ELSESLGDEALVELLNLYFDAVAEVVARHGGRVVKFIGDGFLAVFGRPSPLEDAVACA-- 116
Query: 134 CNCQWPRTLSMARALCELQWELQ----------HCSPSISEDFIPQTPAGKESKRRQKVS 183
L + AL L+ H + + T G
Sbjct: 117 --------LDLQLALRNPLARLRRESLRVRIGIHTGEVVVGNTGGYTVVG-------SAV 161
Query: 184 KVASKLTS 191
A++L S
Sbjct: 162 NQAARLES 169
>gnl|CDD|226540 COG4054, McrB, Methyl coenzyme M reductase, beta subunit [Coenzyme
metabolism].
Length = 447
Score = 29.4 bits (66), Expect = 4.4
Identities = 11/37 (29%), Positives = 25/37 (67%), Gaps = 3/37 (8%)
Query: 66 EQQDALLAQVKRMLRLSEADERNVR---DFKRIVRQV 99
E +A+ +VK+M+++SE D+ +V+ K+++ Q+
Sbjct: 83 ENAEAIAEKVKKMVQVSEDDDTSVKLINGGKQLLVQL 119
>gnl|CDD|217539 pfam03407, Nucleotid_trans, Nucleotide-diphospho-sugar transferase.
Proteins in this family have been been predicted to be
nucleotide-diphospho-sugar transferases.
Length = 208
Score = 28.4 bits (64), Expect = 5.0
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 314 QLSQINGFGPF-TRNNVLVCIGFYHVIPTDSETIRHLKQVHAR 355
+S N G + GF++V PT + +I K+ R
Sbjct: 94 IISSDNYDGTTADGLKNWLNGGFFYVRPT-NRSIALFKKWAER 135
>gnl|CDD|188317 TIGR03415, ABC_choXWV_ATP, choline ABC transporter, ATP-binding
protein. Members of this protein family are the
ATP-binding subunit of a three-protein transporter. This
family belongs, more broadly, to the family of proline
and glycine-betaine transporters, but members have been
identified by direct characterization and by
bioinformatic means as choline transporters. Many
species have several closely-related members of this
family, probably with variable abilities to act
additionally on related quaternary amines [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 382
Score = 28.6 bits (64), Expect = 6.6
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 10/53 (18%)
Query: 315 LSQINGFGPFTRNNVLVCIGFYHVIPT--DSETIRHLKQVHARNCTSKTVQMI 365
L +NG P +R +VLV G V D+ T+R L+ V M+
Sbjct: 67 LRAVNGLNPVSRGSVLVKDGDGSVDVANCDAATLRRLRT--------HRVSMV 111
>gnl|CDD|227184 COG4847, COG4847, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 103
Score = 27.1 bits (60), Expect = 6.6
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 167 IPQTPAGKESKR--RQKVSKVASKLTSRIAE 195
I ++ KES R RQ+V K+A LT +I E
Sbjct: 72 IAESEEAKESIRQVRQEVEKLAGDLTKKIEE 102
>gnl|CDD|227137 COG4800, COG4800, Predicted transcriptional regulator with an HTH
domain [Transcription].
Length = 170
Score = 28.0 bits (62), Expect = 6.8
Identities = 8/34 (23%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 391 KRFGKLSEMPYSD-YKLITASNMGIKNIRKVKRT 423
F K + +P S YK++ S+ + ++ +T
Sbjct: 33 SEFAKRANIPLSTLYKILKGSDPRYDTLTRIFKT 66
>gnl|CDD|214928 smart00944, Pro-kuma_activ, Pro-kumamolisin, activation domain.
This domain is found at the N-terminus of peptidases
belonging to MEROPS peptidase family S53 (sedolisin,
clan SB). The domain adopts a ferredoxin-like fold,
with an alpha+beta sandwich. Cleavage of the domain
results in activation of the peptidase.
Length = 136
Score = 27.6 bits (62), Expect = 7.5
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 30 PSVSVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNV 89
P+ +V VTI Q++ L V+ S P + + + S AD V
Sbjct: 8 PNETVSVTIALKQRNLAQLEQLVQ---EVSDPGSPNYGKFLSPEEFASLFGPSPADVNAV 64
Query: 90 RDF 92
+
Sbjct: 65 LAW 67
>gnl|CDD|146261 pfam03528, Rabaptin, Rabaptin.
Length = 106
Score = 27.2 bits (60), Expect = 8.2
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 40 QPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVK-RMLRLSEADERNVRDFKRIVRQ 98
Q Q++ SL+ ++ + SG E Q LL Q + + ++ EA+ER V+ +R +RQ
Sbjct: 21 QEQEEVASLQAIMKETVSG------YETQWNLLQQERLQWIQYQEAEEREVKKLQRRLRQ 74
Query: 99 VAQEEGEESQ 108
+E+ E
Sbjct: 75 ANEEDQLEKT 84
>gnl|CDD|224781 COG1868, FliM, Flagellar motor switch protein [Cell motility and
secretion].
Length = 332
Score = 28.0 bits (63), Expect = 9.7
Identities = 20/43 (46%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 63 LSQEQQDALLAQVKRMLR-LSEADERNVR--DFKRIVRQVAQE 102
LSQE+ DALL+ V + L E DER V+ DFKR R ++
Sbjct: 5 LSQEEIDALLSGVSEGVEELKEEDERKVKPYDFKRPDRFSKEQ 47
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 0.388
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,034,980
Number of extensions: 1983331
Number of successful extensions: 1886
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1883
Number of HSP's successfully gapped: 31
Length of query: 426
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 326
Effective length of database: 6,502,202
Effective search space: 2119717852
Effective search space used: 2119717852
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: 60 (26.8 bits)