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)