RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780628|ref|YP_003065041.1| coproporphyrinogen III oxidase
[Candidatus Liberibacter asiaticus str. psy62]
(395 letters)
>1olt_A Oxygen-independent coproporphyrinogen III oxidase; heme
biosynthesis, decarboxylase, radical SAM enzyme, 4Fe- 4S
cluster; HET: SAM; 2.07A {Escherichia coli} SCOP:
c.1.28.2
Length = 457
Score = 276 bits (707), Expect = 5e-75
Identities = 90/404 (22%), Positives = 168/404 (41%), Gaps = 21/404 (5%)
Query: 5 SAYENNMTGQGSNSLGVYVHWPFCVKKCPYCDFNSHVRRYKVGQENFIQSFLTEMQWMRQ 64
A+ + L +YVH PFC K C +C N V R + + ++ + E+
Sbjct: 39 QAFLQAVARYPERPLSLYVHIPFCHKLCYFCGCNKIVTRQQHKADQYLDALEQEIVHRAP 98
Query: 65 LTGPRSISSIFFGGGTPSLIEPQNIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQG 124
L R +S + +GGGTP+ + I+ ++ + +N+ +++ EI+IE +P +E++
Sbjct: 99 LFAGRHVSQLHWGGGTPTYLNKAQISRLMKLLRENFQFNADAEISIEVDPREIELDVLDH 158
Query: 125 YRKAGVNRISLGVQSLEEQSLRFLGRNHNASEAIAAIHLARNI-FPRMSFDLIYALPKQT 183
R G NR+S+GVQ ++ R + R + A ++ AR I F + DLIY LPKQT
Sbjct: 159 LRAEGFNRLSMGVQDFNKEVQRLVNREQDEEFIFALLNHAREIGFTSTNIDLIYGLPKQT 218
Query: 184 MTQWEMELQRALSYAVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVAVDLYNLTQSIT 243
+ L+R D LS++ T+F K D LPS +D+ T +
Sbjct: 219 PESFAFTLKRVAELNPDRLSVFNYAHL-PTIFAAQRKIKDADLPSPQQKLDILQETIAFL 277
Query: 244 SAHGLHAY----------EISNHSFLGAESLHNLNYWRYGDYIGIGPGAHSRVKVGSHRV 293
+ G E++ G + Y GD +G G + +G
Sbjct: 278 TQSGYQFIGMDHFARPDDELAVAQREGVLHRNFQGYTTQGDTDLLGMGVSAISMIGDCY- 336
Query: 294 AISIEKHPESWLKMVRKNGHAVVEKEFLSSEQQADEFLMMGLRLREGISVKDWEMLAGRN 353
+K + + + V + G+A+ L+ + ++ L + E
Sbjct: 337 -AQNQKELKQYYQQVDEQGNALWRGIALTRDDCIRRDVIKSLICNFRLDYSPIEQQWDLL 395
Query: 354 L------DIECERNLQRQGFIERVQFSRLRCTQRGMTMLDSVIA 391
D++ L + G ++ + ++ T +G ++ ++
Sbjct: 396 FADYFAEDLKLLAPLAKDGLVDVDE-KGIQVTAKGRLLIRNICM 438
>3iix_A Biotin synthetase, putative; adoMet radical, SAM radical, adoMet
cleavage, Fe4S4 cluster, HYDE, hydrogenase, maturation,
beta barrel; HET: OTY CSO 5AD CPS; 1.25A {Thermotoga
maritima} PDB: 3ciw_A* 3iiz_A* 3cix_A*
Length = 348
Score = 43.4 bits (101), Expect = 9e-05
Identities = 28/193 (14%), Positives = 56/193 (29%), Gaps = 12/193 (6%)
Query: 28 CVKKCPYCDFNSHVRRYKVGQENFIQSFLTEMQWMRQLTGPRSISSIFFGGGTPSLIEPQ 87
C K C YC + E+ +L +I G P
Sbjct: 63 CRKNCLYCGLRRD-----NKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYXMPD 117
Query: 88 NIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGYRKAGVNRISLGVQSLEEQSLRF 147
I+ I+ I K + + ++ +++AG +R L ++ R
Sbjct: 118 VISDIVKEIKKMGVAVTL-------SLGEWPREYYEKWKEAGADRYLLRHETANPVLHRK 170
Query: 148 LGRNHNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRALSYAVDHLSLYQL 207
L + + + + + + + LP QT+ +L + D + +
Sbjct: 171 LRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMVGIGPF 230
Query: 208 TIEKGTLFYKMHK 220
T K
Sbjct: 231 IPHPDTPLANEKK 243
>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 = 42.6 bits (100), Expect = 1e-04
Identities = 55/297 (18%), Positives = 88/297 (29%), Gaps = 121/297 (40%)
Query: 49 ENFIQSFLTEMQ---WM--R-QLTGPR-SIS------SIFFGGGTPS------------- 82
E+F S + ++ R P S+ S+ G PS
Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQV 349
Query: 83 --LIE------PQN----IALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGY----R 126
+ P I+L+ +G AKN VS P S+ G R
Sbjct: 350 QDYVNKTNSHLPAGKQVEISLV-NG-AKNLVVS--------GPPQSL-----YGLNLTLR 394
Query: 127 KAGV------NRISLGVQSLEEQSLRFLGRNHNASEAIAAIHLARNIFPRMSFDLIYALP 180
KA +RI + L+ S RFL +A+ P F
Sbjct: 395 KAKAPSGLDQSRIPFSERKLK-FSNRFL--------PVAS--------P---FHSHL--- 431
Query: 181 KQTMTQWEMELQRALSYAVDHLSLYQLTIEKGTLFYKM---H-KDG-DLVLPSENVAVDL 235
L A L ++ + ++ DG DL + S ++
Sbjct: 432 ----------LVPASDLINKDLVKNNVSFNAKDI--QIPVYDTFDGSDLRVLSGSI---S 476
Query: 236 YNLTQSITSAHGLHAYEISNHSFLGAESLHNLNYWRYGDYIGIGPGAHSRVKVGSHR 292
+ I + +E + ++ H L D+ GPG S + V +HR
Sbjct: 477 ERIVDCIIRLP-VK-WETT----TQFKATHIL------DF---GPGGASGLGVLTHR 518
Score = 39.9 bits (93), Expect = 9e-04
Identities = 65/378 (17%), Positives = 118/378 (31%), Gaps = 139/378 (36%)
Query: 59 MQWMRQLTGPRSISSIFFGGGTP-SLIEPQNIALILDGIAK--NWTVSSNVEITIEANPS 115
++W L P + + P S P LI G+ + ++ V++ + + P
Sbjct: 216 LEW---LENPSNTPDKDYLLSIPISC--P----LI--GVIQLAHYVVTAKL---LGFTPG 261
Query: 116 SVEVN-NFQGYRKAGVNRISLGV------------QSLEEQSLR------FLG-RNHNAS 155
E+ +G G S G+ +S + F+G R + A
Sbjct: 262 --ELRSYLKG--ATGH---SQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEA- 313
Query: 156 EAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRA-----LSYAVDHLSLYQL--T 208
+P S LP ++ + +E LS + +L+ Q+
Sbjct: 314 ------------YPNTS------LP-PSILEDSLENNEGVPSPMLS--ISNLTQEQVQDY 352
Query: 209 IEKGTLFYKMHKDGDLVLPSEN-VAVDLYNLTQSITSAHGLHAYEISNHSFLGAESLHNL 267
+ K H LP+ V + L N +++ + G +SL+ L
Sbjct: 353 VNK---TNS-H------LPAGKQVEISLVNGAKNLVVS-GP------------PQSLYGL 389
Query: 268 NYW-RYGDYIGIGPGA-HSRV-----KVG-SHR-VAISIEKHPESWLKMVRKNGHAVVEK 318
N R G SR+ K+ S+R + ++ H L ++ K
Sbjct: 390 NLTLR---KAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFH-SHLLVPAS----DLINK 441
Query: 319 EFLSSEQQADEFLMMGLRLREGISVKDWEMLAGRNLDIECERNLQ--------RQGFIER 370
+ + ++ I V D G +L R L
Sbjct: 442 DL-----VKNNVSFNAKDIQ--IPVYDTF--DGSDL-----RVLSGSISERIVDCIIRLP 487
Query: 371 VQFSRLRCTQRGMT-MLD 387
V++ TQ T +LD
Sbjct: 488 VKWE--TTTQFKATHILD 503
Score = 33.4 bits (76), Expect = 0.10
Identities = 36/210 (17%), Positives = 55/210 (26%), Gaps = 96/210 (45%)
Query: 35 CDFNSHVRRYKVGQE-------------NFIQSFLTEMQWMRQLTGPRSISSIFFGGGTP 81
N +R+ K F FL P ++S F +
Sbjct: 387 YGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFL-----------P--VASPFH---SH 430
Query: 82 SLIEPQNIALILDGIAKNWTVSSNVEITIEANPSSVEV-NNFQGYRKAGVNRISLGVQSL 140
L+ LI + KN ++ A + V + F G
Sbjct: 431 LLVPAS--DLINKDLVKN-------NVSFNAKDIQIPVYDTFDG---------------- 465
Query: 141 EEQSLRFLGRNHNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRALSYAVD 200
LR S +I R+ D I LP +WE +
Sbjct: 466 --SDLR------VLSG---------SISERI-VDCIIRLP----VKWE----TTTQFKAT 499
Query: 201 HLSLYQLT--------IEKGTLFYKMHKDG 222
H+ L + G L ++ KDG
Sbjct: 500 HI----LDFGPGGASGL--GVLTHRN-KDG 522
Score = 30.3 bits (68), Expect = 0.80
Identities = 44/223 (19%), Positives = 87/223 (39%), Gaps = 48/223 (21%)
Query: 178 ALPKQTMTQWEMELQRALSYAVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVAVDLYN 237
A+ +T+ +++ ++ +H + Y EKG L L L + DL +
Sbjct: 1690 AMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKS 1749
Query: 238 L----TQSITSAHGLHAYE--ISNHSFLGAESLHNLNYWR-----------------YGD 274
+ + H L Y S + ESL + ++R YG
Sbjct: 1750 KGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYG- 1808
Query: 275 YIGIGPGAHSRVKVGSHRVAISIEKHPESWL--KMVRKNGHAVVEKEFLSSEQQADEFLM 332
I I PG RVA S + ++ ++ ++ G V E ++ + +++
Sbjct: 1809 MIAINPG----------RVAASFSQEALQYVVERVGKRTGWLV---EIVNYNVENQQYVA 1855
Query: 333 MG-LRLREGIS-VKDWEMLAGRNLD-IECERNLQRQGFIERVQ 372
G LR + ++ V ++ L + +D IE +++L +E V+
Sbjct: 1856 AGDLRALDTVTNVLNFIKL--QKIDIIELQKSLS----LEEVE 1892
>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 = 31.1 bits (69), Expect = 0.49
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 19/46 (41%)
Query: 141 EEQSLRFLGRNHNASEAIAAIHL-ARNIFPRMSFDLIYALP-KQTM 184
E+Q+L+ L AS + L A + P AL K TM
Sbjct: 18 EKQALKKL----QAS-----LKLYADDSAP--------ALAIKATM 46
>2gzs_A IROE protein; enterobactin, salmochelin, DFP, hydrolase, catalytic
DYAD; HET: DFP; 1.40A {Escherichia coli} SCOP: c.69.1.38
PDB: 2gzr_A*
Length = 278
Score = 30.7 bits (68), Expect = 0.58
Identities = 10/133 (7%), Positives = 28/133 (21%), Gaps = 4/133 (3%)
Query: 152 HNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRALSYAVDHLSLYQLTIEK 211
++ + + + S+ + + L I +
Sbjct: 147 GHSYGGLFVLDSWLSSSYFRSYYSASPSLGRGYDALLSRVTAVEPLQFCTKHLA---IME 203
Query: 212 GTLFYKMHKDGDLVLPSENVAVDLYNLTQSITSAHGLHAYEISNHSFLGAESLHNLNYWR 271
G+ +++ V + + + H + S
Sbjct: 204 GSATQGDNRETHAVGVLSK-IHTTLTILKDKGVNAVFWDFPNLGHGPMFNASFRQALLDI 262
Query: 272 YGDYIGIGPGAHS 284
G+ G H
Sbjct: 263 SGENANYTAGCHE 275
>3lyw_A YBBR family protein; structural genomics, PSI-2, protein structure
initiative, northeast structural genomics consortium,
NESG; 1.90A {Desulfitobacterium hafniense} PDB: 2kpu_A
Length = 90
Score = 28.4 bits (63), Expect = 3.3
Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 8/61 (13%)
Query: 88 NIALILDGIAKNWTVSS---NVEITIEANPSSVEVNNFQGY-----RKAGVNRISLGVQS 139
++LI N + + +V + E S+ VN Y + G + + V+
Sbjct: 6 TLSLIAKNTPANSMIMTKLPSVRVKTEGYNPSINVNELFAYVDLSGSEPGEHDYEVKVEP 65
Query: 140 L 140
+
Sbjct: 66 I 66
>1z3i_X Similar to RAD54-like; recombination ATPase helicase,
recombination/DNA binding complex; 3.00A {Danio rerio}
SCOP: c.37.1.19 c.37.1.19
Length = 644
Score = 26.9 bits (58), Expect = 7.8
Identities = 21/240 (8%), Positives = 58/240 (24%), Gaps = 10/240 (4%)
Query: 156 EAIAAIHLARNIFPRMSFDLIYAL---PKQTMTQWEMELQRALSYAVDHLSLYQLTIEKG 212
+ I I P ++ + P + W E+ + L V +++ + ++
Sbjct: 95 QCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEI 154
Query: 213 TLFYKMHKDGDLVLPSENVAVDLYNLTQSITSAHGLHAYEISNHSFLGAESLHNLNYWRY 272
+ + + Y + + E N
Sbjct: 155 DSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICD----EGHRLKNSDNQ 210
Query: 273 GDYIGIGPGAHSRVKVGSHRVAISIEKHPESWLKM---VRKNGHAVVEKEFLSSEQQADE 329
A RV + + + ++ + + ++ + + D
Sbjct: 211 TYLALNSMNAQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDA 270
Query: 330 FLMMGLRLREGISVKDWEMLAGRNLDIECERNLQRQGFIERVQFSRLRCTQRGMTMLDSV 389
R +++ + R L L + ++ Q T +
Sbjct: 271 DASDKDRAAGEQKLQELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLF 330
>3en9_A Glycoprotease, O-sialoglycoprotein endopeptidase/protein kinase;
endopeptidase activity, protein kinase activity; HET:
TBR; 2.67A {Methanocaldococcus jannaschii} PDB: 3enh_A*
2vwb_A*
Length = 540
Score = 26.8 bits (59), Expect = 8.0
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 229 ENVAVDLYNLTQSITSAHGLHAYEISNH 256
E+ AVDL +++ S H EI
Sbjct: 483 EDKAVDLIVFKKAVLSTHHEKFDEIWER 510
>1r30_A Biotin synthase; SAM radical protein, TIM barrel, FES cluster,
transferase; HET: SAM DTB; 3.40A {Escherichia coli}
SCOP: c.1.28.1
Length = 369
Score = 26.7 bits (58), Expect = 9.1
Identities = 15/116 (12%), Positives = 36/116 (31%), Gaps = 10/116 (8%)
Query: 28 CVKKCPYCDFNSHVRRYKVGQENF-IQSFLTEMQWMRQLTGPRSISSIFFGGGTPSLIEP 86
C + C YC + RYK G E + ++ R+ S
Sbjct: 76 CPEDCKYCPQS---SRYKTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKN--PHE 130
Query: 87 QNIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGYRKAGVNRISLGVQSLEE 142
+++ + + + + ++ + Q AG++ + + + E
Sbjct: 131 RDMPYLEQMVQGVK----AMGLEACMTLGTLSESQAQRLANAGLDYYNHNLDTSPE 182
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double
chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces
cerevisiae}
Length = 800
Score = 26.7 bits (58), Expect = 9.3
Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 15/91 (16%)
Query: 110 IEANPSSVEVNNFQGYRKAGVNRISLGVQSLEEQSLRF-------LGRNHNASEAIAAIH 162
+ P ++ + ++ G+N ++ L + LG+ I+ +
Sbjct: 225 LSVQPPFIKGGELRDFQLTGINWMA----FLWSKGDNGILADEMGLGKTVQTVAFISWLI 280
Query: 163 LARNIFPRMSFDLIYALPKQTMTQWEMELQR 193
AR +I P TM W ++
Sbjct: 281 FARRQNGPH---IIVV-PLSTMPAWLDTFEK 307
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
0.320 0.134 0.401
Gapped
Lambda K H
0.267 0.0479 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,395,744
Number of extensions: 155235
Number of successful extensions: 432
Number of sequences better than 10.0: 1
Number of HSP's gapped: 427
Number of HSP's successfully gapped: 17
Length of query: 395
Length of database: 5,693,230
Length adjustment: 94
Effective length of query: 301
Effective length of database: 3,414,294
Effective search space: 1027702494
Effective search space used: 1027702494
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 (21.8 bits)
S2: 58 (26.7 bits)