RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780479|ref|YP_003064892.1| A/G-specific adenine
glycosylase [Candidatus Liberibacter asiaticus str. psy62]
(356 letters)
>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.
Length = 275
Score = 266 bits (683), Expect = 4e-72
Identities = 105/266 (39%), Positives = 150/266 (56%), Gaps = 13/266 (4%)
Query: 9 QSKILDWYDTNHR-VLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQK 67
+L WYD R LPWR + +PY+VW+SE+MLQQT V TV PYF++F+++
Sbjct: 3 SEDLLSWYDKYGRKTLPWRQNK--------TPYRVWLSEVMLQQTQVATVIPYFERFLER 54
Query: 68 WPTIFCLSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIG 127
+PT+ L++A +E+L W GLGYY RARNL K A +V+++ G FP E L LPG+G
Sbjct: 55 FPTVQALANAPQDEVLKLWEGLGYYARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVG 114
Query: 128 DYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPA--PLYHKTIKNYARKITSTSRPG 185
YTA AI++ A N ++D N++R++SR F + + A + + P
Sbjct: 115 RYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGWPGKKKVENRLWTLAESLLPKADPE 174
Query: 186 DFVQAMMDLGALICTSNKPLCPLCPIQKNCLTFSEGKSHLLGINTIKKKRPMRTGAVFIA 245
F QA+MDLGA+ICT KP C LCP+Q CL + +G + K P RT F+
Sbjct: 175 AFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQGTWEEYPVKKPKAAPPERTTY-FLV 233
Query: 246 ITN-DNRILLRKRTNTRLLEGMDELP 270
+ N D +LL +R L G+ P
Sbjct: 234 LQNYDGEVLLEQRPEKGLWGGLYCFP 259
>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional.
Length = 350
Score = 204 bits (522), Expect = 2e-53
Identities = 118/332 (35%), Positives = 176/332 (53%), Gaps = 45/332 (13%)
Query: 12 ILDWYDTNHR-VLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQKWPT 70
+LDWYD R LPW+ KT PYKVW+SE+MLQQT V TV PYF++FM ++PT
Sbjct: 10 VLDWYDKYGRKTLPWQI-DKT-------PYKVWLSEVMLQQTQVATVIPYFERFMARFPT 61
Query: 71 IFCLSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYT 130
+ L++A +E+L W GLGYY RARNL K A + + G FP E + LPG+G T
Sbjct: 62 VTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRST 121
Query: 131 ASAIVAIAF-NHFAVVVDTNIERIISRYFDIIK-PAPLYHKTIKNYARKITSTSRPGD-- 186
A AI++++ HF ++D N++R+++R + + P K ++N +++ P
Sbjct: 122 AGAILSLSLGKHFP-ILDGNVKRVLARCYAVSGWPG---KKEVENRLWQLSEQVTPAVGV 177
Query: 187 --FVQAMMDLGALICTSNKPLCPLCPIQKNCLTFSEGKSHLLGINTIKKKRPMRTGAVFI 244
F QAMMDLGA++CT +KP C LCP+Q C+ ++ L K+ P RTG F+
Sbjct: 178 ERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANHSWALYPGKKPKQTLPERTG-YFL 236
Query: 245 AITNDNRILLRKRTNTRLLEGM---------DELPGSAWSSTKDGNIDTHSAPFTANWIL 295
+ + + + L +R + L G+ +EL W + + D + TA
Sbjct: 237 LLQHGDEVWLEQRPPSGLWGGLFCFPQFADEEEL--RQWLAQRGIAADNLT-QLTA---- 289
Query: 296 CNTITHTFTHFTLTLFVWKTIVPQIVIIPDST 327
HTF+HF L IVP + + T
Sbjct: 290 ---FRHTFSHFHL------DIVPMWLPVSSFT 312
>gnl|CDD|172427 PRK13910, PRK13910, DNA glycosylase MutY; Provisional.
Length = 289
Score = 145 bits (366), Expect = 2e-35
Identities = 92/264 (34%), Positives = 146/264 (55%), Gaps = 22/264 (8%)
Query: 48 MLQQTTVKTV-EPYFKKFMQKWPTIFCLSSAKDEEILSAWAGLGYYTRARNLKKCADIIV 106
M QQT + TV E ++ F++ +PT+ L++A EE+L W GLGYY+RA+NLKK A+I V
Sbjct: 1 MSQQTQINTVVERFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICV 60
Query: 107 KKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPAPL 166
K++ P+ + L KLPGIG YTA+AI+ F + VD NI+R++ R F + +
Sbjct: 61 KEHHSQLPNDYQSLLKLPGIGAYTANAILCFGFREKSACVDANIKRVLLRLFGL--DPNI 118
Query: 167 YHKTIKNYARKITSTSRPGDFVQAMMDLGALICTSNKPLCPLCPIQKNCLTFSEGKSHLL 226
+ K ++ A + + + QA++DLGALIC S KP C +CP+ CL GK++
Sbjct: 119 HAKDLQIKANDFLNLNESFNHNQALIDLGALIC-SPKPKCAICPLNPYCL----GKNNPE 173
Query: 227 GINTIKKKRPMRTGAVFIAITNDNRILLRKRTNTRLLEGMDELPGSAWSSTKDGNIDTHS 286
+T+KKK+ + ++ + N + ++ +L GM P + K+ N++ +
Sbjct: 174 K-HTLKKKQEIVQEERYLGVVIQNNQIALEKIEQKLYLGMHHFP-----NLKE-NLE-YK 225
Query: 287 APFTANWILCNTITHTFTHFTLTL 310
PF I H+ T F L L
Sbjct: 226 LPFLG------AIKHSHTKFKLNL 243
>gnl|CDD|128754 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 = 134 bits (339), Expect = 4e-32
Identities = 43/151 (28%), Positives = 78/151 (51%), Gaps = 3/151 (1%)
Query: 48 MLQQTTVKTVEPYFKKFMQKWPTIFCLSSAKDEEILSAWAGLGYYT-RARNLKKCADIIV 106
+ QQT+ + V ++ +K+PT L++A +EE+ LG+Y +A+ L + A I+V
Sbjct: 1 LSQQTSDEAVNKATERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILV 60
Query: 107 KKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPAPL 166
++Y G P E L KLPG+G TA+A+++ A + VDT++ RI R + K +
Sbjct: 61 EEYGGEVPDDREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKST- 119
Query: 167 YHKTIKNYARKITSTSRPGDFVQAMMDLGAL 197
+ ++ K+ + ++D G
Sbjct: 120 -PEEVEKLLEKLLPKEDWRELNLLLIDFGRT 149
>gnl|CDD|130155 TIGR01083, nth, endonuclease III. This equivalog model identifes
nth 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.
Length = 191
Score = 85.1 bits (211), Expect = 3e-17
Identities = 49/175 (28%), Positives = 85/175 (48%), Gaps = 14/175 (8%)
Query: 38 SPYKVWISEIMLQQTTVKTVEPYFKKFMQKWPTIFCLSSAKDEEILSAWAGLGYY-TRAR 96
+P+++ ++ I+ Q T K+V KK + +PT L+ A EE+ +G Y +A+
Sbjct: 25 NPFELLVATILSAQATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAK 84
Query: 97 NLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNHFAVVVDTNIERI--- 153
N+ I+V++Y G P E L KLPG+G TA+ ++ +AF A+ VDT++ R+
Sbjct: 85 NIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNVAFGIPAIAVDTHVFRVSNR 144
Query: 154 --ISRYFDIIKPAPLYHKTIKNYARKITSTSRPGDFVQAMMDLGALICTSNKPLC 206
+S+ D K ++ K+ ++ G C + KPLC
Sbjct: 145 LGLSKGKDPDK--------VEEELLKLIPREFWTKLHHWLILHGRYTCKARKPLC 191
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 50.4 bits (120), Expect = 8e-07
Identities = 47/189 (24%), Positives = 86/189 (45%), Gaps = 7/189 (3%)
Query: 29 PKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQKWPTIFCLSSAKDEEILSAWAG 88
P TE + SP+++ I+ ++ Q T +V K T + E + +
Sbjct: 20 PTTELN-FSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKT 78
Query: 89 LGYY-TRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNHFAVVVD 147
+G Y ++A N+ K I+++++ G P L+ LPG+G TA+ ++ AF + VD
Sbjct: 79 IGLYNSKAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGWPTIAVD 138
Query: 148 TNIERIISRYFDIIKPAPLYH-KTIKNYARKITSTSRPGDFVQAMMDLGALICTSNKPLC 206
T+I R+ +R + AP + + ++ K+ D ++ G C + KP C
Sbjct: 139 THIFRVCNR----TQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRC 194
Query: 207 PLCPIQKNC 215
C I+ C
Sbjct: 195 GSCIIEDLC 203
>gnl|CDD|128798 smart00525, FES, FES domain. iron-sulpphur binding domain in
DNA-(apurinic or apyrimidinic site) lyase (subfamily of
ENDO3).
Length = 21
Score = 33.3 bits (77), Expect = 0.091
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 198 ICTSNKPLCPLCPIQKNC 215
ICT+ KP C CP++ C
Sbjct: 1 ICTARKPRCDECPLKDLC 18
>gnl|CDD|151111 pfam10576, EndIII_4Fe-2S, Iron-sulfur binding domain of
endonuclease III. Escherichia coli endonuclease III (EC
4.2.99.18) is a DNA repair enzyme that acts both as a
DNA N-glycosylase, removing oxidized pyrimidines from
DNA, and as an apurinic/apyrimidinic (AP) endonuclease,
introducing a single-strand nick at the site from which
the damaged base was removed. Endonuclease III is an
iron-sulfur protein that binds a single 4Fe-4S cluster.
The 4Fe-4S cluster does not seem to be important for
catalytic activity, but is probably involved in the
proper positioning of the enzyme along the DNA strand.
The 4Fe-4S cluster is bound by four cysteines which are
all located in a 17 amino acid region at the C-terminal
end of endonuclease III. A similar region is also
present in the central section of mutY and in the
C-terminus of ORF-10 and of the Micro-coccus UV
endonuclease.
Length = 17
Score = 32.0 bits (74), Expect = 0.25
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 199 CTSNKPLCPLCPIQKNC 215
CT+ KP C CP+ C
Sbjct: 1 CTARKPKCEECPLADLC 17
>gnl|CDD|179200 PRK00994, PRK00994, F420-dependent methylenetetrahydromethanopterin
dehydrogenase; Provisional.
Length = 277
Score = 29.2 bits (66), Expect = 1.8
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 9/61 (14%)
Query: 64 FMQKWPTIFCLSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYEGNFPHKV--EILK 121
FM K + A E++ A A L AR ++K D +++K PH +IL
Sbjct: 216 FMTKEMEKYIPIVASAHEMMRAAAKLAD--EAREIEKANDTVLRK-----PHAKDGKILS 268
Query: 122 K 122
K
Sbjct: 269 K 269
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional.
Length = 244
Score = 28.8 bits (64), Expect = 1.9
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 127 GDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPAPLYHKTIK-------NYARKIT 179
GD T IVA A + FA V + + ++SR+ I+ P + +K YAR
Sbjct: 87 GDLTGH-IVARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMYSALKRDGKPLYEYARAGI 145
Query: 180 STSRP 184
RP
Sbjct: 146 ELDRP 150
>gnl|CDD|128712 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 28.9 bits (65), Expect = 2.3
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 92 YTRARNLKKCADIIVKKYEGNFPHKV 117
Y +AR LKK D I K Y + K
Sbjct: 85 YEKARKLKKHIDKIRKDYTKDLKSKE 110
>gnl|CDD|129520 TIGR00426, TIGR00426, competence protein ComEA helix-hairpin-helix
repeat region. Members of the subfamily recognized by
this model include competence protein ComEA and closely
related proteins from a number of species that exhibit
competence for transformation by exongenous DNA,
including Streptococcus pneumoniae, Bacillus subtilis,
Neisseria meningitidis, and Haemophilus influenzae. This
model represents a region of two tandem copies of a
helix-hairpin-helix domain (pfam00633), each about 30
residues in length. Limited sequence similarity can be
found among some members of this family N-terminal to
the region covered by this model.
Length = 69
Score = 28.0 bits (62), Expect = 3.6
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 9/58 (15%)
Query: 74 LSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYE-GNFPHKVEILKKLPGIGDYT 130
+++A EE+ A G+G LKK I+ + E G F VE LK++PGIG+
Sbjct: 10 INTATAEELQRAMNGVG-------LKKAEAIVSYREEYGPF-KTVEDLKQVPGIGNSL 59
>gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 28.0 bits (63), Expect = 4.0
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 68 WPTIFCLSSAKDEEILSAWAGLGYYTRARNLKKCADIIV 106
W I D S W +Y RA+N K AD+++
Sbjct: 399 WNRI-ASDGESDGGKQSPWFSRCFYQRAKNRAKFADLVI 436
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 27.6 bits (61), Expect = 5.0
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 14 DWYDTNHRVLPWRTSPKT 31
+WY R PW+ P+
Sbjct: 433 EWYSRVRRAAPWKDLPRR 450
>gnl|CDD|163497 TIGR03785, marine_sort_HK, proteobacterial dedicated sortase system
histidine kinase. This histidine kinase protein is
paired with an adjacent response regulator (TIGR03787)
gene. It co-occurs with a variant sortase enzyme
(TIGR03784), usually in the same gene neighborhood, in
proteobacterial species most of which are marine, and
with an LPXTG motif-containing sortase target conserved
protein (TIGR03788). Sortases and LPXTG proteins are far
more common in Gram-positive bacteria, where sortase
systems mediate attachment to the cell wall or
cross-linking of pilin structures. We give this
predicted sensor histidine kinase the gene symbol psdS,
for Proteobacterial Dedicated Sortase system Sensor
histidine kinase.
Length = 703
Score = 27.4 bits (61), Expect = 5.5
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 25 WRTSPKTEKSSLPSPYKVWISE-----IMLQQTT 53
WR SP ++ L + Y +WI ++ +QTT
Sbjct: 361 WRLSPDSKAVILSAAYPIWIDTEVLGAVIAEQTT 394
>gnl|CDD|180664 PRK06705, PRK06705, argininosuccinate lyase; Provisional.
Length = 502
Score = 27.3 bits (60), Expect = 5.7
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 10/69 (14%)
Query: 53 TVKTVEPYFKKFMQKWPTIFCLSSA------KDEEILSAWAGLGYYTRARNLKKCADIIV 106
T ++PY K ++K +FC+ +A +E+ L + Y A + AD++
Sbjct: 328 TEDDLQPYLYKGIEKAIRVFCIMNAVIRTMKVEEDTLKRRS----YKHAITITDFADVLT 383
Query: 107 KKYEGNFPH 115
K Y F H
Sbjct: 384 KNYGIPFRH 392
>gnl|CDD|163580 TIGR03868, F420-O_ABCperi, proposed F420-0 ABC transporter,
periplasmic F420-0 binding protein. This small clade of
ABC-type transporter periplasmic binding protein
components is found as a three gene cassette along with
a permease (TIGR03869) and an ATPase (TIGR03873). The
organisms containing this cassette are all
Actinobacteria and all contain numerous genes requiring
the coenzyme F420. This model was defined based on five
such organisms, four of which are lacking all F420
biosynthetic capability save the final side-chain
polyglutamate attachment step (via the gene cofE:
TIGR01916). In Jonesia denitrificans DSM 20603 and
marine actinobacterium PHSC20C1 this cassette is in an
apparent operon with the cofE gene and, in PHSC20C1,
also with a F420-dependent glucose-6-phosphate
dehydrogenase (TIGR03554). Based on these observations
we propose that this periplasmic binding protein is a
component of an F420-0 (that is, F420 lacking only the
polyglutamate tail) transporter.
Length = 287
Score = 27.1 bits (60), Expect = 6.3
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 305 HFTLTLFVWKTIV---PQIVIIPDSTWHDAQ--------NLANAALPTVMKK 345
H T T W+ +V P ++++ DS W+ A+ N A + L V ++
Sbjct: 206 HDTWTPMSWEAVVDADPDVIVLVDSAWNSAEKKIEVLESNPATSNLTAVQEQ 257
>gnl|CDD|129252 TIGR00148, TIGR00148, UbiD family decarboxylases. Found in
bacteria, archaea, and yeast, with two members in A.
fulgidus. No homologs were detected besides those
classified as orthologs. The member from H. pylori has a
C-terminal extension of just over 100 residues that is
shared in part by the Aquifex aeolicus homolog.
Length = 438
Score = 27.3 bits (61), Expect = 6.9
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 8/95 (8%)
Query: 157 YFDIIKPAPLYH-KTIKNYARK--ITSTSRPGDFVQAMMDLGALICTSNKPLC--PLCPI 211
Y+DI++P P+ K + Y R+ I + PG +G P+ + I
Sbjct: 275 YYDIVRPEPVITVKRM--YHREDPIYHATYPGGPPHEDALMGVPTEPVFYPILRNQVPEI 332
Query: 212 QKNCLTFSEGKSHLLGINTIKKKRPMRTGAVFIAI 246
+ + G LL + +IKK+ P V +A
Sbjct: 333 -IDAVLPEGGCHWLLAVVSIKKRYPGDAKNVIMAA 366
>gnl|CDD|177825 PLN02168, PLN02168, copper ion binding / pectinesterase.
Length = 545
Score = 26.9 bits (59), Expect = 9.1
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 2 PQPEHIIQSKILDWYDTNHRVLPWRTSPKTEKSSLPSP 39
P+P+ I DW+ +H V+ R S SLP+P
Sbjct: 154 PKPDEEYDILIGDWFYADHTVM--RASLDN-GHSLPNP 188
>gnl|CDD|161960 TIGR00615, recR, recombination protein RecR. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 195
Score = 26.9 bits (60), Expect = 9.3
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 108 KYEGNFPHKVEILKKLPGIGDYTASAIVAIAFN 140
+Y +E LKKLPGIG +A +AF+
Sbjct: 1 QYPPPISKLIESLKKLPGIGPKSAQ---RLAFH 30
>gnl|CDD|128574 smart00278, HhH1, Helix-hairpin-helix DNA-binding motif class 1.
Length = 20
Score = 26.5 bits (60), Expect = 9.9
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 118 EILKKLPGIGDYTASAIVA 136
E L K+PGIG TA I+
Sbjct: 1 EELLKVPGIGPKTAEKILE 19
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.321 0.135 0.421
Gapped
Lambda K H
0.267 0.0628 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,877,083
Number of extensions: 368360
Number of successful extensions: 719
Number of sequences better than 10.0: 1
Number of HSP's gapped: 711
Number of HSP's successfully gapped: 26
Length of query: 356
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 262
Effective length of database: 3,963,321
Effective search space: 1038390102
Effective search space used: 1038390102
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 (21.9 bits)
S2: 58 (26.3 bits)