RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780676|ref|YP_003065089.1| lipoyl synthase [Candidatus
Liberibacter asiaticus str. psy62]
(329 letters)
>gnl|CDD|30668 COG0320, LipA, Lipoate synthase [Coenzyme metabolism].
Length = 306
Score = 486 bits (1253), Expect = e-138
Identities = 179/302 (59%), Positives = 217/302 (71%)
Query: 21 AERLRHPEKIHKPDTEKMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIGE 80
+ R P K +P+ E ++KP+W++V+AP S Y+E ILR L TVCEEA CPNIGE
Sbjct: 5 DKMARIPVKNVRPNEELLRKPEWLKVKAPTGSRYQEIKEILRKNGLHTVCEEASCPNIGE 64
Query: 81 CWNKNHATFMILGAICTRACTFCNVATGKPQPLDPQEPENISWAVRSMKLSHVVITSVDR 140
CW++ ATFMILG ICTR C FC+V TG+P PLDP EPE ++ AV+ M L +VVITSVDR
Sbjct: 65 CWSRGTATFMILGDICTRRCRFCDVKTGRPNPLDPDEPERVAEAVKDMGLKYVVITSVDR 124
Query: 141 DDLDDGGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVA 200
DDL DGGAQHFAE I AIRE P TTIEVLTPDF ALE V A PDVFNHN+ETV
Sbjct: 125 DDLPDGGAQHFAECIRAIRELNPQTTIEVLTPDFRGNDDALEIVADAGPDVFNHNVETVP 184
Query: 201 SNYLMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDF 260
Y VRPGA Y SL LL+R KEL P I TKSG+M+GLGET E++++MDDLR+A VD
Sbjct: 185 RLYPRVRPGATYERSLSLLERAKELGPDIPTKSGLMVGLGETDEEVIEVMDDLRSAGVDI 244
Query: 261 LTMGQYLQPTRKHHKVESFVTPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLRLK 320
LT+GQYLQP+RKH V+ +VTP++F E +A GFL V++ PL RSSYHA + F +
Sbjct: 245 LTIGQYLQPSRKHLPVQRYVTPEEFDELEEVAEEMGFLHVASGPLVRSSYHADEQFAEAE 304
Query: 321 NN 322
Sbjct: 305 VK 306
>gnl|CDD|37883 KOG2672, KOG2672, KOG2672, Lipoate synthase [Coenzyme transport and
metabolism].
Length = 360
Score = 312 bits (800), Expect = 9e-86
Identities = 140/290 (48%), Positives = 185/290 (63%), Gaps = 7/290 (2%)
Query: 36 EKMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIGECWN-----KNHATFM 90
E+++ P W++ + P+ Y + LR L TVCEEA CPNIGECW AT M
Sbjct: 56 ERLRLPPWLKTKIPLGENYNKIKKDLRELKLHTVCEEARCPNIGECWGGGDKSTATATIM 115
Query: 91 ILGAICTRACTFCNVATGK-PQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDDGGAQ 149
++G CTR C FC+V T + P PLDP EPEN + A+ S L ++V+TSVDRDDL DGGA
Sbjct: 116 LMGDTCTRGCRFCSVKTSRNPPPLDPNEPENTAEAIASWGLDYIVLTSVDRDDLPDGGAN 175
Query: 150 HFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYLMVR-P 208
H A+ + I+E AP +E LTPDF A+EKV + DV+ HN+ETV VR P
Sbjct: 176 HIAKTVQKIKEKAPEILVECLTPDFRGDLKAVEKVAKSGLDVYAHNVETVEELTPFVRDP 235
Query: 209 GARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDFLTMGQYLQ 268
A Y SL +L+ KE+ P + TK+ IMLGLGET EI Q + DLR ADVD +T GQY+Q
Sbjct: 236 RANYRQSLSVLKHAKEVKPGLITKTSIMLGLGETDEEIKQTLKDLRAADVDVVTFGQYMQ 295
Query: 269 PTRKHHKVESFVTPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLR 318
PT++H KV+ +VTP+ F ++ GFL V++ PL RSSY AG+ F++
Sbjct: 296 PTKRHLKVKEYVTPEKFDYWKEYGEELGFLYVASGPLVRSSYKAGEYFIK 345
>gnl|CDD|146602 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyse diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 79.1 bits (195), Expect = 1e-15
Identities = 33/169 (19%), Positives = 65/169 (38%), Gaps = 9/169 (5%)
Query: 90 MILGAICTRACTFCNV----ATGKPQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD 145
+I+ C CT+C A GK + L P+E + + + + V++T + L D
Sbjct: 1 IIITPGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELARLGVEVVILTGGEPLLLPD 60
Query: 146 GGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYL- 204
E I + T L LE++ A D + +L++ L
Sbjct: 61 LVELLERL---LKLEELEGIRITLETNGTLLDEELLEELKEAGLDRVSISLQSGDDEVLK 117
Query: 205 MVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDL 253
++ G + L L+ ++E + I+ GE ++ + ++ L
Sbjct: 118 IINRGHTFEEVLEALELLREAG-IPVVVDNIVGLPGENDEDLEETLELL 165
>gnl|CDD|30848 COG0502, BioB, Biotin synthase and related enzymes [Coenzyme
metabolism].
Length = 335
Score = 57.6 bits (139), Expect = 5e-09
Identities = 42/168 (25%), Positives = 66/168 (39%), Gaps = 13/168 (7%)
Query: 96 CTRACTFCNVATGKPQPLDPQ---EPENISWAVRSMK---LSHVVITSVDRDDLDDGGAQ 149
C C +C+ + + + E E I A + K + + + R D
Sbjct: 61 CPEDCAYCSQSARYKTGVKARKLMEVEEILEAAKKAKAAGATRFCMGAAGRGPGRD---- 116
Query: 150 HFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYLMVRPG 209
EV+ AI+ +EV + EK+ A D +NHNLET Y +
Sbjct: 117 -MEEVVEAIKAVKEELGLEVCASLGMLTEEQAEKLADAGVDRYNHNLETSPEFYENIITT 175
Query: 210 ARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTAD 257
Y L L+ V+E I SG ++GLGET + +L+ +L
Sbjct: 176 RTYEDRLNTLENVREAG--IEVCSGGIVGLGETVEDRAELLLELANLP 221
>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
family generate radicals by combining a 4Fe-4S cluster
and S-adenosylmethionine (SAM) in close proximity. They
are characterized by a conserved CxxxCxxC motif, which
coordinates the conserved iron-sulfur cluster.
Mechanistically, they share the transfer of a single
electron from the iron-sulfur cluster to SAM, which
leads to its reductive cleavage to methionine and a
5'-deoxyadenosyl radical, which, in turn, abstracts a
hydrogen from the appropriately positioned carbon atom.
Depending on the enzyme, SAM is consumed during this
process or it is restored and reused. Radical SAM
enzymes catalyze steps in metabolism, DNA repair, the
biosynthesis of vitamins and coenzymes, and the
biosynthesis of many antibiotics. Examples are biotin
synthase (BioB), lipoyl synthase (LipA), pyruvate
formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
reductase (ARR), and MoaA, an enzyme of the
biosynthesis of molybdopterin..
Length = 204
Score = 56.2 bits (135), Expect = 1e-08
Identities = 32/186 (17%), Positives = 72/186 (38%), Gaps = 15/186 (8%)
Query: 90 MILGAICTRACTFCNVATGK----PQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD 145
+ L C C FC+ K P + +E +I + + V++T +
Sbjct: 1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYP- 59
Query: 146 GGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETV--ASNY 203
AE++ +++ P I + T L L+++ D +L++
Sbjct: 60 ----ELAELLRRLKKELPGFEISIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVAD 115
Query: 204 LMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLG-ETRNEILQLMDDLRTAD-VDFL 261
+ G + L L+ ++E + + +++GLG E + L+ ++ L D +
Sbjct: 116 KIRGSGESFKERLEALKELREAG--LGLSTTLLVGLGDEDEEDDLEELELLAEFRSPDRV 173
Query: 262 TMGQYL 267
++ + L
Sbjct: 174 SLFRLL 179
>gnl|CDD|31260 COG1060, ThiH, Thiamine biosynthesis enzyme ThiH and related
uncharacterized enzymes [Coenzyme metabolism / General
function prediction only].
Length = 370
Score = 41.0 bits (96), Expect = 4e-04
Identities = 44/221 (19%), Positives = 80/221 (36%), Gaps = 39/221 (17%)
Query: 95 ICTRACTFCNVATGKPQP----LDPQEPENISWAVRSMKLSHVVITSVDRDDLDDGGAQH 150
IC CTFC P L P+E ++ V+I + +L ++
Sbjct: 68 ICVNDCTFCAFYRKPGDPKAYTLSPEEILEEVREAVKRGITEVLIVGGEHPELS---LEY 124
Query: 151 FAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVF----NHNLETV---ASNY 203
+ E+ I+E P I L+ + A E +S + +V L+++ +
Sbjct: 125 YEELFRTIKEEFPDLHIHALSAGEIL-FLAREGGLSYE-EVLKRLKEAGLDSMPGGGAEI 182
Query: 204 LM--VR-----PGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTA 256
L VR P L + +R L I T + ++LG ETR + + ++ +R
Sbjct: 183 LSEEVRKIHCPPKKSPEEWLEIHERAHRLG--IPTTATMLLGHVETREDRIDHLEHIR-- 238
Query: 257 DVDFLTMGQYLQPTRKHHKVESFVTPQDFKSYETIAYSKGF 297
LQ + + F+ P F+ ++
Sbjct: 239 ---------DLQ--DETGGFQEFI-PLRFRPENGPLPAEVV 267
>gnl|CDD|35762 KOG0542, KOG0542, KOG0542, Predicted exonuclease [Replication,
recombination and repair].
Length = 280
Score = 30.3 bits (68), Expect = 0.85
Identities = 10/43 (23%), Positives = 16/43 (37%)
Query: 37 KMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIG 79
++ P + + YK YN N+T + E G G
Sbjct: 177 NIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEHYGLQFEG 219
>gnl|CDD|30966 COG0621, MiaB, 2-methylthioadenine synthetase [Translation,
ribosomal structure and biogenesis].
Length = 437
Score = 29.4 bits (66), Expect = 1.4
Identities = 40/186 (21%), Positives = 78/186 (41%), Gaps = 20/186 (10%)
Query: 96 CTRACTFCNV--ATGKPQPLDPQEPENISWAVRSMKLS---HVVITSVD----RDDLDDG 146
C + CTFC + A GK + PE+I V+ + +V+T D DL G
Sbjct: 154 CNKFCTFCIIPYARGK---ERSRPPEDILKEVKRLVAQGVKEIVLTGQDVNAYGKDLGGG 210
Query: 147 GAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNH---NLETVASNY 203
+ A+++ + + I + L L + ++ P V H +++ +
Sbjct: 211 KP-NLADLLRELSKIPGIERIRFGSSHPLEFTDDLIEAIAETPKVCPHLHLPVQSGSDRI 269
Query: 204 L--MVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGL-GETRNEILQLMDDLRTADVDF 260
L M R + L ++++++ P I + I++G GET + + +D + D
Sbjct: 270 LKRMKRGYTVEEY-LEIIEKLRAARPDIAISTDIIVGFPGETEEDFEETLDLVEEVRFDR 328
Query: 261 LTMGQY 266
L + +Y
Sbjct: 329 LHVFKY 334
>gnl|CDD|73367 cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP
synthase)/TenI. TMP synthase catalyzes an important step
in the thiamine biosynthesis pathway, the substitution
of the pyrophosphate of 2-methyl-4-amino-5-
hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-
(beta-hydroxyethyl) thiazole phosphate to yield thiamine
phosphate. TenI is a enzymatically inactive regulatory
protein involved in the regulation of several
extracellular enzymes. This superfamily also contains
other enzymatically inactive proteins with unknown
functions..
Length = 196
Score = 29.4 bits (66), Expect = 1.6
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 109 KPQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD---GGAQHFAEVISAI 158
KP P E + +++ V I + ++ + GA A VISAI
Sbjct: 130 KPGAGPPLGLELLREIAELVEIPVVAIGGITPENAAEVLAAGADGVA-VISAI 181
>gnl|CDD|32379 COG2197, CitB, Response regulator containing a CheY-like receiver
domain and an HTH DNA-binding domain [Signal
transduction mechanisms / Transcription].
Length = 211
Score = 29.2 bits (65), Expect = 1.9
Identities = 19/102 (18%), Positives = 38/102 (37%), Gaps = 6/102 (5%)
Query: 152 AEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNH---NLETVASNYLMVRP 208
E + +R P + VLT P + + + A D + + E + V
Sbjct: 62 LEALKQLRARGPDIKVVVLTAHD--DPAYVIRALRAGADGYLLKDASPEELVEAIRAVAA 119
Query: 209 GARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLM 250
G Y + +++ L P ++ + L E+L+L+
Sbjct: 120 GGTYLPP-DIARKLAGLLPSSSAEAPLAELLTPRELEVLRLL 160
>gnl|CDD|38111 KOG2900, KOG2900, KOG2900, Biotin synthase [Coenzyme transport and
metabolism].
Length = 380
Score = 28.5 bits (63), Expect = 2.8
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 192 FNHNLETVASNYLMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMD 251
+NHNL+T Y V Y L+ ++ V+E I SG +LGLGE+ ++ + L+
Sbjct: 193 YNHNLDTSREYYSKVITTRTYDDRLQTIKNVREAG--IKVCSGGILGLGESEDDRIGLIH 250
Query: 252 DLRT 255
L T
Sbjct: 251 TLAT 254
>gnl|CDD|176152 cd08463, PBP2_DntR_like_4, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator similar to DntR, which is involved in the
catabolism of dinitrotoluene; contains the type 2
periplasmic binding fold. This CD includes an
uncharacterized LysR-type transcriptional regulator
similar to DntR, NahR, and LinR, which are involved in
the degradation of aromatic compounds. The transcription
of the genes encoding enzymes involved in such
degradation is regulated and expression of these enzymes
is enhanced by inducers, which are either an
intermediate in the metabolic pathway or compounds to be
degraded. This substrate-binding domain shows
significant homology to the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 203
Score = 27.7 bits (62), Expect = 4.3
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 147 GAQHFAEVISAIRESAPSTTIEV--LTPDFLRKPHALE 182
A E+++ R AP +E+ L PDF AL
Sbjct: 11 NALFLPELVARFRREAPGARLEIHPLGPDF-DYERALA 47
>gnl|CDD|39700 KOG4500, KOG4500, KOG4500, Rho/Rac GTPase guanine nucleotide
exchange factor smgGDS/Vimar [Signal transduction
mechanisms].
Length = 604
Score = 27.4 bits (60), Expect = 5.8
Identities = 16/49 (32%), Positives = 23/49 (46%)
Query: 216 LRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDFLTMG 264
L L +R+ ELD L+ T M L + L R+ D + +TMG
Sbjct: 287 LNLFKRIAELDVLLLTGDESMQKLHADPQFLDFLESWFRSDDSNLITMG 335
>gnl|CDD|30911 COG0565, LasT, rRNA methylase [Translation, ribosomal structure and
biogenesis].
Length = 242
Score = 26.7 bits (59), Expect = 7.9
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 114 DPQEPENISWAVRSMK---LSHVVITSVDRDDLDD---GGAQHFAEVISAIR 159
+P P NI R+MK LS + + + R LD+ A +++ +
Sbjct: 11 EPSHPGNIGSVARAMKNFGLSELRLVN-PRAGLDEEARALAAGARDILENAK 61
>gnl|CDD|30059 cd01316, CAD_DHOase, The eukaryotic CAD protein is a trifunctional
enzyme of carbamoylphosphate synthetase-aspartate
transcarbamoylase-dihydroorotase, which catalyzes the
first three steps of de novo pyrimidine nucleotide
biosynthesis. Dihydroorotase (DHOase) catalyzes the
third step, the reversible interconversion of carbamoyl
aspartate to dihydroorotate..
Length = 344
Score = 26.8 bits (59), Expect = 8.2
Identities = 12/48 (25%), Positives = 18/48 (37%)
Query: 281 TPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLRLKNNRRQHLH 328
+DF S A + GF MV A P T S +++ +
Sbjct: 22 HKEDFASGTKAALAGGFTMVRAMPNTNPSIVDVASLKLVQSLAQAKAR 69
>gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 26.9 bits (59), Expect = 8.3
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 1/48 (2%)
Query: 123 WAVRSMKLSHVVITSVDRDDLDDGGAQHFAEVISAIRESAPSTTIEVL 170
+ K V+ VDR DLDD + F + + L
Sbjct: 296 LLLELPKNPKVLFV-VDRKDLDDQTSDEFQSFGKVAFNDPKAESTSEL 342
>gnl|CDD|36773 KOG1560, KOG1560, KOG1560, Translation initiation factor 3, subunit
h (eIF-3h) [Translation, ribosomal structure and
biogenesis].
Length = 339
Score = 26.5 bits (58), Expect = 9.8
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 20/81 (24%)
Query: 241 ETRNEILQLMDDLRTADVDFLTMGQYLQPTRKHHKVESFVTPQDFKS------------- 287
+ L ++ LR ++D L +G Y V SF++P +S
Sbjct: 79 ARQAYQLAMLRRLRYVNIDHLHVGWYQS-----AYVGSFLSPALVESQYAYQKAIPESVV 133
Query: 288 --YETIAYSKGFLMVSASPLT 306
Y+ I S+G L + A LT
Sbjct: 134 LIYDPIKSSQGTLSLRAYRLT 154
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.134 0.402
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,063,824
Number of extensions: 211833
Number of successful extensions: 458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 453
Number of HSP's successfully gapped: 23
Length of query: 329
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 235
Effective length of database: 4,232,491
Effective search space: 994635385
Effective search space used: 994635385
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 (26.3 bits)