RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780625|ref|YP_003065038.1| formamidopyrimidine-DNA
glycosylase [Candidatus Liberibacter asiaticus str. psy62]
(289 letters)
>gnl|CDD|179222 PRK01103, PRK01103, formamidopyrimidine/5-formyluracil/
5-hydroxymethyluracil DNA glycosylase; Validated.
Length = 274
Score = 375 bits (965), Expect = e-105
Identities = 125/289 (43%), Positives = 169/289 (58%), Gaps = 16/289 (5%)
Query: 1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYL 60
MPELPEVE +RR L + T+T + + R LR+ P F+ G+ I+ V RR KYL
Sbjct: 1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYL 60
Query: 61 LIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPR 120
L++L+ ++I HLGMSGS + P K H+HV L + T + YNDPR
Sbjct: 61 LLDLDDGGTLISHLGMSGSLRL-LPEDTPPEK---HDHVDFVLDDGT-----VLRYNDPR 111
Query: 121 RFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGI 180
RFG M L +P L LGPEP ++F+ YL + KK + +K ALL+Q +V G+
Sbjct: 112 RFGAMLLTPKGDLEAHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIKPALLDQTVVVGV 171
Query: 181 GNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYV 240
GNIY EAL+RA + P R SL + + +L+ I+ VL +AI+ GG++LRDYV
Sbjct: 172 GNIYADEALFRAGIHPERPAGSL-----SRAEAE-RLVDAIKAVLAEAIEQGGTTLRDYV 225
Query: 241 HIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
+ DG GYFQ + VYG+ GEPC CG I +I Q GRSTF+C CQK
Sbjct: 226 NADGKPGYFQQSLQVYGREGEPC-RRCGTPIEKIKQGGRSTFFCPRCQK 273
>gnl|CDD|161937 TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fpg). All
proteins in the FPG family with known functions are
FAPY-DNA glycosylases that function in base excision
repair. Homologous to endonuclease VIII (nei). This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University).
Length = 272
Score = 267 bits (684), Expect = 3e-72
Identities = 110/289 (38%), Positives = 151/289 (52%), Gaps = 19/289 (6%)
Query: 2 PELPEVEIIRRNLMMVMKNMTVTDICLH--RKNLRFDFPHHFSAATRGKKIIDVSRRAKY 59
PELPEVE +RR L ++ T+ + + LR P G+ I+ + RR KY
Sbjct: 1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLRPAGPEDLQKRLLGQTILSIQRRGKY 60
Query: 60 LLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDP 119
LL EL+ ++ HL M G + +E A P +H+HV + T + Y+DP
Sbjct: 61 LLFELDDGA-LVSHLRMEGKYRLE----AVPDAPEKHDHVDFLFDDGT-----ELRYHDP 110
Query: 120 RRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAG 179
RRFG L + P L LGPEP F A YL + K +K ALL+Q++VAG
Sbjct: 111 RRFGTWLLFDRGQVENVPLLAKLGPEPLSEDFTAEYLFEKLAKSKRKIKTALLDQRLVAG 170
Query: 180 IGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDY 239
IGNIY E L+RA + P R SL + ++ L + I++VL AI+ GG+++RDY
Sbjct: 171 IGNIYADEVLFRAGIHPERLANSL-----SKEEC-ELLHRAIKEVLRKAIEMGGTTIRDY 224
Query: 240 VHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288
+ DG GYFQ VYG+ GEPC CG I +I GR T +C CQ
Sbjct: 225 SNSDGHNGYFQQELQVYGRKGEPC-RRCGTPIEKIKVGGRGTHFCPQCQ 272
>gnl|CDD|184831 PRK14811, PRK14811, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 269
Score = 208 bits (530), Expect = 2e-54
Identities = 109/298 (36%), Positives = 155/298 (52%), Gaps = 44/298 (14%)
Query: 1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHF--SAATRGKKIIDVSRRAK 58
MPELPEVE RR L ++ T+ + +H P + + G++++ +SRR K
Sbjct: 1 MPELPEVETTRRKLEPLLLGQTIQQV-VHDD------PARYRNTELAEGRRVLGLSRRGK 53
Query: 59 YLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYND 118
YLL+ L +L +IVHLGM+G F +E H VT+ L T + + D
Sbjct: 54 YLLLHLPHDLELIVHLGMTGGFRLEPG---------PHTRVTLELPGRT------LYFTD 98
Query: 119 PRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSN---LKNALLNQK 175
PRRFG +V + P L +GPEP + F +F + + +K LL+QK
Sbjct: 99 PRRFGKWWVVRAGDYREIPLLARMGPEPLSDDFT----EPEFVRALATARPVKPWLLSQK 154
Query: 176 IVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDI--LYKLIQEIQKVLIDAIDAGG 233
VAG+GNIY E+LWRA++ P R SL + LY+ I+E V+ +A++AGG
Sbjct: 155 PVAGVGNIYADESLWRARIHPARPATSL-----KAPEARRLYRAIRE---VMAEAVEAGG 206
Query: 234 SSLRD--YVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
S+L D Y DG G FQ +VYG+ G+PC CG I +IV GR T +C CQ
Sbjct: 207 STLSDGSYRQPDGEPGGFQFQHAVYGREGQPC-PRCGTPIEKIVVGGRGTHFCPQCQP 263
>gnl|CDD|173271 PRK14810, PRK14810, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 272
Score = 187 bits (476), Expect = 3e-48
Identities = 107/294 (36%), Positives = 155/294 (52%), Gaps = 27/294 (9%)
Query: 1 MPELPEVEIIRRNLMMVMKNMTVTDICLHR-KNLRFDFPHHFSAATRGKKIIDVSRRAKY 59
MPELPEVE + R L + + R P +A G+KI+ V R K+
Sbjct: 1 MPELPEVETVARGLAPRAAGRRIATAEFRNLRIPRKGDPDLMAARLAGRKILSVKRVGKH 60
Query: 60 LLIELEG----NLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVI 115
++ +LEG I+HLGM+G ++ +P+H H ++L++ +
Sbjct: 61 IVADLEGPGEPRGQWIIHLGMTGKLLL----GGPDTPSPKHTHAVLTLSSG-----KELR 111
Query: 116 YNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQK 175
+ D R+FG ++ E K GPEP + SF F + + +K+ALLNQ
Sbjct: 112 FVDSRQFGCIEYSEAFPK----RFARPGPEPLEISFED--FAALFRGRKTRIKSALLNQT 165
Query: 176 IVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSS 235
++ G+GNIY EAL+RA + P R SL ++ L KL I +VL +AI+ GGSS
Sbjct: 166 LLRGVGNIYADEALFRAGIRPQRLASSL------SRERLRKLHDAIGEVLREAIELGGSS 219
Query: 236 LRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
+ DYV +G G+FQ + VY +TGEPCL NC IRR+V AGRS+ YC +CQK
Sbjct: 220 VSDYVDAEGRSGFFQLSHRVYQRTGEPCL-NCKTPIRRVVVAGRSSHYCPHCQK 272
>gnl|CDD|184410 PRK13945, PRK13945, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 282
Score = 185 bits (471), Expect = 1e-47
Identities = 105/299 (35%), Positives = 145/299 (48%), Gaps = 27/299 (9%)
Query: 1 MPELPEVEIIRRNLMMVMKNMTVTD--ICLHRKNLRFDF-PHHFSAATRGKKIIDVSRRA 57
MPELPEVE +RR L ++ N + + L R + F +G I RR
Sbjct: 1 MPELPEVETVRRGLEQLLLNFIIKGVEVLLER-TIASPGGVEEFIKGLKGSLIGQWQRRG 59
Query: 58 KYLLIEL-----EGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKY 112
KYLL L E + VHL M+G F+ S P H + L N ++
Sbjct: 60 KYLLASLKKEGSENAGWLGVHLRMTGQFLWVEQS------TPPCKHTRVRLFFEKN-QEL 112
Query: 113 RVIYNDPRRFGFMDLV--ETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNA 170
R + D R FG M V S + L+ LGPEP F+ YL + K+ ++K A
Sbjct: 113 RFV--DIRSFGQMWWVPPGVSPESIITGLQKLGPEPFSPEFSVEYLKKKLKKRTRSIKTA 170
Query: 171 LLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAID 230
LL+Q IVAGIGNIY E+L++A + P L + L +L + I +VL +I
Sbjct: 171 LLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQ------LERLREAIIEVLKTSIG 224
Query: 231 AGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
AGG++ D+ ++G G + VY +TG+PC CG I RI AGRST +C CQK
Sbjct: 225 AGGTTFSDFRDLEGVNGNYGGQAWVYRRTGKPCR-KCGTPIERIKLAGRSTHWCPNCQK 282
>gnl|CDD|115485 pfam06831, H2TH, Formamidopyrimidine-DNA glycosylase H2TH domain.
Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA
repair enzyme that excises oxidized purines from damaged
DNA. This family is the central domain containing the
DNA-binding helix-two turn-helix domain.
Length = 93
Score = 88.9 bits (221), Expect = 1e-18
Identities = 39/99 (39%), Positives = 53/99 (53%), Gaps = 6/99 (6%)
Query: 142 LGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTR 201
LGP+P F A + KK +K ALL+Q++VAGIGNIY E L+RA + P R
Sbjct: 1 LGPDPLSEPFTADEFAERLAKKKRPIKTALLDQRVVAGIGNIYADEVLFRAGIHPERPAS 60
Query: 202 SLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYV 240
SL + K+ L I+ VL AI+ GG +R +
Sbjct: 61 SL-----SKKECEA-LHTVIKDVLQKAIEMGGGGIRTFS 93
>gnl|CDD|182467 PRK10445, PRK10445, endonuclease VIII; Provisional.
Length = 263
Score = 72.0 bits (177), Expect = 2e-13
Identities = 74/306 (24%), Positives = 125/306 (40%), Gaps = 60/306 (19%)
Query: 1 MPELPEVEIIRR---NLMMVMKNMTVTDICLHRKNLRFDFPH--HFSAATRGKKIIDVSR 55
MPE PE IRR NL +K +TD+ F FP + + G+++ +
Sbjct: 1 MPEGPE---IRRAADNLEAAIKGKPLTDV-------WFAFPQLKPYESQLIGQRVTHIET 50
Query: 56 RAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHV-TISLTNNTNTKKYRV 114
R K LL L++ H + G + + T + PQ V + L K +
Sbjct: 51 RGKALLTHFSNGLTLYSHNQLYGVWRVVDTG-----EEPQTTRVLRVRLQTA---DKTIL 102
Query: 115 IYN--DPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAI-----YLTHQFHKKNSNL 167
+Y+ D ++++ +P L+ +GP+ D + L+ +F +
Sbjct: 103 LYSASD------IEMLTPEQLTTHPFLQRVGPDVLDPNLTPEQVKERLLSPRFRNRQ--F 154
Query: 168 KNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLID 227
LL+Q +AG+GN E LW+A L+P K KD+ + + L+D
Sbjct: 155 SGLLLDQAFLAGLGNYLRVEILWQAGLTPQHK----------AKDLNEAQLDALAHALLD 204
Query: 228 ----AIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFY 283
+ G D G++ F+ F V+ + GE C CG +I + + R ++
Sbjct: 205 IPRLSYATRG--QVDENKHHGAL--FR--FKVFHRDGEACE-RCGGIIEKTTLSSRPFYW 257
Query: 284 CTYCQK 289
C CQK
Sbjct: 258 CPGCQK 263
>gnl|CDD|148438 pfam06827, zf-FPG_IleRS, Zinc finger found in FPG and IleRS. This
zinc binding domain is found at the C-terminus of
isoleucyl tRNA synthetase and the enzyme
Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.
Length = 30
Score = 40.8 bits (96), Expect = 4e-04
Identities = 15/30 (50%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 260 GEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
GE C C I ++ Q GRSTF C CQK
Sbjct: 1 GEKCP-RCWTYIEKVGQGGRSTFLCPRCQK 29
>gnl|CDD|177837 PLN02182, PLN02182, cytidine deaminase.
Length = 339
Score = 28.1 bits (62), Expect = 3.1
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 251 NAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTF 282
N ++ G GE C +C + + + A ++F
Sbjct: 185 NCLTLSGPAGEICSLDCSHLKCKALAAANNSF 216
>gnl|CDD|182057 PRK09741, PRK09741, hypothetical protein; Provisional.
Length = 148
Score = 27.8 bits (62), Expect = 3.9
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 190 WRAKLSPIRKTRSLIQNN 207
+R + P R+ RSL QN
Sbjct: 29 FRIIIKPWREKRSLSQNA 46
>gnl|CDD|184095 PRK13504, PRK13504, sulfite reductase subunit beta; Provisional.
Length = 569
Score = 27.1 bits (61), Expect = 5.8
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 200 TRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGG 233
TR Q +G K L +IQ I VL+D + A G
Sbjct: 111 TRQTFQFHGILKKNLKPVIQTINSVLLDTLAACG 144
>gnl|CDD|184892 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 26.4 bits (58), Expect = 8.7
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 10/54 (18%)
Query: 201 RSLIQNNGTPKDILYKLIQEIQKVLI--DAIDAG--------GSSLRDYVHIDG 244
++L + K+I+ K I I++VL+ + + GS+LR+ I+G
Sbjct: 671 KALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEG 724
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
0.323 0.138 0.413
Gapped
Lambda K H
0.267 0.0731 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,736,910
Number of extensions: 296473
Number of successful extensions: 587
Number of sequences better than 10.0: 1
Number of HSP's gapped: 560
Number of HSP's successfully gapped: 17
Length of query: 289
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 197
Effective length of database: 4,006,537
Effective search space: 789287789
Effective search space used: 789287789
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: 57 (25.7 bits)