RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781031|ref|YP_003065444.1| exsB protein [Candidatus
Liberibacter asiaticus str. psy62]
(240 letters)
>3bl5_A Queuosine biosynthesis protein QUEC; PREQ1 biosynthesis, RNA
modification, tRNA, hydrolase; 2.95A {Bacillus subtilis}
Length = 219
Score = 207 bits (527), Expect = 2e-54
Identities = 98/226 (43%), Positives = 150/226 (66%), Gaps = 22/226 (9%)
Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
A+++FSGGQDS+TCL WAL F+ VET++F Y QR+ E+E + +K
Sbjct: 6 AIVVFSGGQDSTTCLLWALKEFEEVETVTFHYNQRHSQEVEVAKSIAEK----------- 54
Query: 71 LG-EDHILPLAILGDISHSSLTK-NVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGI 128
LG ++H+L +++L ++ ++LT+ ++ ++++D LP+TFVPGRN++FL FA+ LAY++G
Sbjct: 55 LGVKNHLLDMSLLNQLAPNALTRNDIEIEVKDGELPSTFVPGRNLVFLSFASILAYQIGA 114
Query: 129 TNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIG 188
+I+ GVCETD+SGYPDCR + +++ +NL ME +HTPLMWL K ETWKLA ++G
Sbjct: 115 RHIITGVCETDFSGYPDCRDEFVKSCNVTVNLAMEKPFVIHTPLMWLNKAETWKLADELG 174
Query: 189 GQDLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKGWMEF 234
++ + + TCY G GC CPAC+LR KG+ E+
Sbjct: 175 ---ALDFVKNNTLTCYNG------IIADGCGECPACHLRSKGYEEY 211
>2pg3_A Queuosine biosynthesis protein QUEC; YP_049261.1, hypothetical
protein, structural genomics; 2.40A {Pectobacterium
atrosepticum SCRI1043} SCOP: c.26.2.1
Length = 232
Score = 150 bits (378), Expect = 3e-37
Identities = 86/227 (37%), Positives = 124/227 (54%), Gaps = 14/227 (6%)
Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
A+++FSGGQDS+TCL AL +D V ++FDYGQR++ E+E + +K+ K
Sbjct: 5 AVVVFSGGQDSTTCLIQALQDYDDVHCITFDYGQRHRAEIEVAQELSQKLGAAAHKVL-- 62
Query: 71 LGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITN 130
D L + +PNTFVPGRNI+FL A+ AY++G
Sbjct: 63 ---DVGLLNELATSSLTRDSIPVPDYDANAQGIPNTFVPGRNILFLTLASIYAYQVGAEA 119
Query: 131 IVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIGGQ 190
++ GVCETD+SGYPDCR + ++A+ AI LG+ + TPLMWL K ETW LA
Sbjct: 120 VITGVCETDFSGYPDCRDEFVKALNQAIVLGIARDIRFETPLMWLNKAETWALADYYQQ- 178
Query: 191 DLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKGWMEFKEK 237
++ + + TCY G + G GC C AC+LR G ++++
Sbjct: 179 --LDTVRYHTLTCYNGIK------GDGCGQCAACHLRANGLAQYQKD 217
>2c5s_A THII, probable thiamine biosynthesis protein THII; RNA-binding
protein, RNA binding protein, tRNA modification,
4-thiouridine synthase; HET: AMP; 2.5A {Bacillus
anthracis} SCOP: c.26.2.6 d.308.1.1
Length = 413
Score = 52.0 bits (124), Expect = 1e-07
Identities = 30/198 (15%), Positives = 58/198 (29%), Gaps = 25/198 (12%)
Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
++L SGG DS + R VE + F ++ + +
Sbjct: 190 VMVLLSGGIDSPVAAYLTMKRGVSVEAVHFHSPP----------FTSERAKQKVIDLAQE 239
Query: 71 LGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITN 130
L + + T+ ++ + R ++ +A
Sbjct: 240 LTKYCKRV-----TLHLVPFTEVQKTINKEIPSSYSMTVMRRMMM-RITERIAEERNALA 293
Query: 131 IVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIGGQ 190
I G D++ I N + PL+ + K E K+A++IG
Sbjct: 294 ITTGESLGQ---VASQTLDSMHTINEVTNYPV------IRPLITMDKLEIIKIAEEIGTY 344
Query: 191 DLVNLILEESHTCYLGKR 208
D+ E+ T +
Sbjct: 345 DISIRPYEDCCTVFTPAS 362
>3k32_A Uncharacterized protein MJ0690; predicted subunit of tRNA
methyltransferase, methanocaldococcus jannaschii DSM ,
PSI- 2; 2.50A {Methanocaldococcus jannaschii}
Length = 203
Score = 48.5 bits (115), Expect = 1e-06
Identities = 26/177 (14%), Positives = 47/177 (26%), Gaps = 32/177 (18%)
Query: 12 LLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDSL 71
+LFSGG+DSS ++ ++G +L
Sbjct: 10 HVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGF----------- 58
Query: 72 GEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITNI 131
+ ++ + + K M I+ PG I ++ + +
Sbjct: 59 -KHKVI------TLDRKIVEKAADMIIEHKY------PGPAIQYVHKTVLEILADEYSIL 105
Query: 132 VIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIG 188
G D +L M ++ TPLM LA +
Sbjct: 106 ADGTRRDDRVPKLSYSEIQ--------SLEMRKNIQYITPLMGFGYKTLRHLASEFF 154
>1k92_A Argininosuccinate synthase, argininosuccinate; N-type ATP
pyrophosphatase, ligase; 1.60A {Escherichia coli} SCOP:
c.26.2.1 d.210.1.1 PDB: 1k97_A* 1kp2_A* 1kp3_A*
Length = 455
Score = 36.0 bits (83), Expect = 0.008
Identities = 10/39 (25%), Positives = 19/39 (48%)
Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELE 51
+ FSGG D+S L W + + + GQ ++ + +
Sbjct: 15 IAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYD 53
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 31.5 bits (71), Expect = 0.16
Identities = 41/224 (18%), Positives = 63/224 (28%), Gaps = 107/224 (47%)
Query: 8 APSALLLFSGGQDS--------STCLSWA-LDRFDRVET----------------LSFDY 42
PS L +DS S LS + L + ++V+ +S
Sbjct: 320 PPSIL------EDSLENNEGVPSPMLSISNLTQ-EQVQDYVNKTNSHLPAGKQVEISLVN 372
Query: 43 GQRNKV------ELECRLCVR-KKIVELMPKWKDSLGED--HI-------------LPLA 80
G +N V L L + +K K G D I LP
Sbjct: 373 GAKNLVVSGPPQSL-YGLNLTLRKA-------KAPSGLDQSRIPFSERKLKFSNRFLP-- 422
Query: 81 ILGDIS---HSSLTKNVAMKI-QDNNLPNTFVPGRNIIFLVFAATLAYRLGITNIVIGVC 136
++ HS L + I +D + N+ F A + I V
Sbjct: 423 ----VASPFHSHLLVPASDLINKD-------LVKNNVSFN--AKDIQ---------IPVY 460
Query: 137 ETDYSGYPDCR-------HDTIRAI-------ETAINLGMESHV 166
+T + G D R + I ET +H+
Sbjct: 461 DT-FDG-SDLRVLSGSISERIVDCIIRLPVKWETTTQFKA-THI 501
>1vl2_A Argininosuccinate synthase; TM1780, structural genomics, JCSG,
protein structure initiative, PSI, joint center for
structural genomics; 1.65A {Thermotoga maritima} SCOP:
c.26.2.1 d.210.1.1
Length = 421
Score = 31.1 bits (70), Expect = 0.26
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVE 49
L +SGG D+S L W ++ V + GQ++
Sbjct: 19 LAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFV 55
>2ntx_A EMB|CAB41934.1, prone8; dimer, guanine nucleotide exchange
factor, signaling protein; HET: MSE; 2.20A {Arabidopsis
thaliana} PDB: 2nty_A* 2wbl_A
Length = 365
Score = 30.9 bits (70), Expect = 0.27
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 34 RVETLSFDYGQRNKVELECRLCVRKKIVELMPKW 67
+++ + D R K E++ L V IVE +P
Sbjct: 57 KLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQ 90
>2dpl_A GMP synthetase, GMP synthase [glutamine-hydrolyzing] subunit B;
structural genomics, NPPSFA; 1.43A {Pyrococcus
horikoshii OT3} PDB: 2z0c_A 3a4i_A
Length = 308
Score = 30.9 bits (69), Expect = 0.28
Identities = 31/180 (17%), Positives = 62/180 (34%), Gaps = 25/180 (13%)
Query: 10 SALLLFSGGQDSSTCLSWALDRF-DRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWK 68
A++ SGG DSST A DR+ + + G K E E + + + +
Sbjct: 22 KAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYV 81
Query: 69 DSLGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGI 128
D+ + + V +++ + +A ++G
Sbjct: 82 DAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEE--------------------VAKKIGA 121
Query: 129 TNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIG 188
++ G D+ I++ L + ++ + PL L K E +LA+ +G
Sbjct: 122 EYLIQGTIAPDWIES----QGKIKSHHNVGGLPEKLNLKLIEPLRDLYKDEVRELAKFLG 177
>2nz2_A Argininosuccinate synthase; amino-acid biosynthesis, aspartate,
citrulline, structural genomics, structural genomics
consortium, SGC, ligase; HET: CIR; 2.40A {Homo sapiens}
Length = 413
Score = 29.9 bits (67), Expect = 0.47
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVE 49
L +SGG D+S L W ++ V + GQ+ E
Sbjct: 10 LAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFE 46
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.0 bits (66), Expect = 0.49
Identities = 7/22 (31%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 5 IKKAPSALLLFSGGQDSSTCLS 26
+KK ++L L++ DS+ L+
Sbjct: 22 LKKLQASLKLYA--DDSAPALA 41
Score = 28.4 bits (62), Expect = 1.5
Identities = 8/18 (44%), Positives = 9/18 (50%), Gaps = 2/18 (11%)
Query: 216 YGCNSCPACYLRQKGWME 233
Y +S PA L K ME
Sbjct: 32 YADDSAPA--LAIKATME 47
>1kor_A Argininosuccinate synthetase; ligase, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; HET: ANP ARG; 1.95A {Thermus thermophilus}
SCOP: c.26.2.1 d.210.1.1 PDB: 1j1z_A* 1j21_A* 1kh1_A
1kh2_A* 1kh3_A* 1j20_A*
Length = 400
Score = 29.8 bits (67), Expect = 0.58
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 13 LLFSGGQDSSTCLSWALDRFD-RVETLSFDYGQRNKVE 49
L +SGG D+S L W + + V + D GQ +VE
Sbjct: 5 LAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVE 42
>3fiu_A NH(3)-dependent NAD(+) synthetase; rossman fold, adenine
nucleotide alpha hydrolase-like, ATP- binding, ligase,
nucleotide-binding; HET: AMP; 1.85A {Francisella
tularensis subsp}
Length = 249
Score = 29.6 bits (65), Expect = 0.75
Identities = 10/49 (20%), Positives = 17/49 (34%)
Query: 7 KAPSALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLC 55
A ++ SGG DS+ S A+ L +++ L
Sbjct: 28 PAEGFVIGLSGGIDSAVAASLAVKTGLPTTALILPSDNNQHQDMQDALE 76
>2r79_A Periplasmic binding protein; heme transport, transport protein;
HET: HEM; 2.40A {Pseudomonas aeruginosa}
Length = 283
Score = 28.8 bits (63), Expect = 1.1
Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 5/75 (6%)
Query: 108 VPGRNIIFLVFAAT-LAYRLGITNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHV 166
+P R + + + LG + ++GV S +P + ++ L E +
Sbjct: 1 LPQR-WVSAGGSLSEWVVALGGESKLVGV--DTTSQHPQ-ALKQLPSVGYQRQLAAEGVL 56
Query: 167 TVHTPLMWLKKYETW 181
+ ++ +
Sbjct: 57 ALRPDILIGTEEMGP 71
>1jyk_A LICC protein, CTP:phosphocholine cytidylytransferase; 3D structure,
CTP:phosphocholine cytidylyltransferase; 1.50A
{Streptococcus pneumoniae} SCOP: c.68.1.13 PDB: 1jyl_A*
Length = 254
Score = 27.9 bits (61), Expect = 1.8
Identities = 11/119 (9%), Positives = 29/119 (24%)
Query: 96 MKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITNIVIGVCETDYSGYPDCRHDTIRAIE 155
++ N P V + + GI +I+I V +R +
Sbjct: 39 LRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVF 98
Query: 156 TAINLGMESHVTVHTPLMWLKKYETWKLAQDIGGQDLVNLILEESHTCYLGKRDKRYEW 214
+ +++ L + N + ++ + +
Sbjct: 99 NDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWF 157
>3a2k_A TRNA(Ile)-lysidine synthase; ligase, pseudo-knot, ligase/RNA
complex; 3.65A {Geobacillus kaustophilus}
Length = 464
Score = 27.7 bits (60), Expect = 2.5
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 2 NDIIKKAPSALLLFSGGQDSSTCLSWALDRFDR----VETLSFDYGQRNK-----VELEC 52
+ ++ + + ++ SGG DS L L D V D+ R + +E
Sbjct: 12 HQLLSEGAAVIVGVSGGPDSLALLHVFLSLRDEWKLQVIAAHVDHMFRGRESEEEMEFVK 71
Query: 53 RLCVRKKI 60
R CV ++I
Sbjct: 72 RFCVERRI 79
>2gm3_A Unknown protein; AT3G01520, putative ethylene-responsive protein,
USP domain, nucleotide binding domain, AMP, protein
structure initiative; HET: MSE AMP; 2.46A {Arabidopsis
thaliana} SCOP: c.26.2.4
Length = 175
Score = 27.2 bits (59), Expect = 3.1
Identities = 9/46 (19%), Positives = 19/46 (41%)
Query: 129 TNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMW 174
T +++ V + YP+ RA E + + S+ + L+
Sbjct: 6 TKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLL 51
>2vld_A NUCS, UPF0286 protein pyrab01260; endonuclease, hydrolase; 2.60A
{Pyrococcus abyssi}
Length = 251
Score = 26.7 bits (59), Expect = 4.3
Identities = 6/23 (26%), Positives = 9/23 (39%)
Query: 120 ATLAYRLGITNIVIGVCETDYSG 142
LA + G + C+ Y G
Sbjct: 19 LDLAEKHGGVVTIFARCKVHYEG 41
>2phn_A F420-0:gamma-glutamyl ligase; coenzyme F420 biosynthesis, amide
bond forming enzyme, metal dependent, NEW fold, GDP
binding MCSG; HET: GDP; 1.35A {Archaeoglobus fulgidus
dsm 4304} SCOP: d.340.1.1 PDB: 2g9i_A
Length = 254
Score = 26.7 bits (59), Expect = 4.6
Identities = 7/42 (16%), Positives = 13/42 (30%), Gaps = 4/42 (9%)
Query: 121 TLAYRLGITNIVIGVCE----TDYSGYPDCRHDTIRAIETAI 158
+R G+ IG+ D+ G D + +
Sbjct: 156 GRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECV 197
>2e18_A NH(3)-dependent NAD(+) synthetase; ligase, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 2.10A {Pyrococcus horikoshii OT3}
Length = 257
Score = 26.1 bits (56), Expect = 8.4
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 4/71 (5%)
Query: 3 DIIKK--APSALLLFSGGQDSSTCLSWALDRF--DRVETLSFDYGQRNKVELECRLCVRK 58
+ I++ ++ SGG DS+T A ++V L Y + VE + +
Sbjct: 15 EFIREKGNNGVVIGISGGVDSATVAYLATKALGKEKVLGLIMPYFENKDVEDAKLVAEKL 74
Query: 59 KIVELMPKWKD 69
I + K
Sbjct: 75 GIGYKVINIKP 85
>3dpi_A NAD+ synthetase; ssgcid, decode, structural genomics, PSI,
protein structure initiative; 2.20A {Burkholderia
pseudomallei 1710B}
Length = 285
Score = 26.0 bits (56), Expect = 8.4
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 1 MNDIIKKA--PSALLLFSGGQDSSTCLSWALDRFDRVETLSFDY 42
+ D ++ A + +L SGG DSST A +R+ +D
Sbjct: 37 VADYLRTAGLRACVLGISGGIDSSTAGRLAQLAVERLRASGYDA 80
>2gw6_A TRNA-splicing endonuclease subunit SEN15; SEN15_human, tRNA
endonuclease, structural genomics, PSI, protein
structure initiative; NMR {Homo sapiens} SCOP: c.52.2.1
Length = 123
Score = 26.0 bits (57), Expect = 8.5
Identities = 9/62 (14%), Positives = 26/62 (41%)
Query: 45 RNKVELECRLCVRKKIVELMPKWKDSLGEDHILPLAILGDISHSSLTKNVAMKIQDNNLP 104
++ E+ C +++ L+ + G ++P I +SH+ + + + + P
Sbjct: 40 KSWHEVNCVGLPELQLICLVGTEIEGEGLQTVVPTPITASLSHNRIREILKASRKLQGDP 99
Query: 105 NT 106
+
Sbjct: 100 DL 101
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.322 0.138 0.438
Gapped
Lambda K H
0.267 0.0544 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,150,595
Number of extensions: 96386
Number of successful extensions: 286
Number of sequences better than 10.0: 1
Number of HSP's gapped: 281
Number of HSP's successfully gapped: 29
Length of query: 240
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 150
Effective length of database: 3,511,270
Effective search space: 526690500
Effective search space used: 526690500
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: 55 (25.4 bits)