RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781050|ref|YP_003065463.1| succinyl-CoA synthetase
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
(300 letters)
>gnl|CDD|180194 PRK05678, PRK05678, succinyl-CoA synthetase subunit alpha;
Validated.
Length = 291
Score = 479 bits (1236), Expect = e-136
Identities = 192/300 (64%), Positives = 231/300 (77%), Gaps = 9/300 (3%)
Query: 1 MSILVDKNTKVLVQGLTGKAGTFHTEQAILYCQTQVVGGIHPKKGSTYWTGGNVNVPVFT 60
MSIL++K+TKV+VQG+TGK GTFHTEQ + Y T +VGG+ P KG T G +PVF
Sbjct: 1 MSILINKDTKVIVQGITGKQGTFHTEQMLAY-GTNIVGGVTPGKGGTTVLG----LPVFN 55
Query: 61 TVAEAKERTAANASVIYVPPSGAGDAIIESIEAEIPLIVCITEGIPVLDMVRVKARLEKS 120
TVAEA E T ANASVIYVPP A DAI+E+I+A I LIVCITEGIPVLDM+ VKA LE+
Sbjct: 56 TVAEAVEATGANASVIYVPPPFAADAILEAIDAGIDLIVCITEGIPVLDMLEVKAYLERK 115
Query: 121 SSRLIGPNCPGILTPDSCKIGIMPGSIFRKGSVGILSRSGTLTYEAVFQTSQEGLGQSTA 180
+RLIGPNCPGI+TP CKIGIMPG I +KG VG++SRSGTLTYEAV Q + G GQST
Sbjct: 116 KTRLIGPNCPGIITPGECKIGIMPGHIHKKGRVGVVSRSGTLTYEAVAQLTDLGFGQSTC 175
Query: 181 VGIGGDPVKGTEFIDVLELFLADEATESIVMVGEIGGSAEEEAAQFLKDEAKRGRKKPIV 240
VGIGGDP+ GT FIDVLE F D TE+IVM+GEIGGSAEEEAA+++K KP+V
Sbjct: 176 VGIGGDPINGTNFIDVLEAFEEDPETEAIVMIGEIGGSAEEEAAEYIKANV----TKPVV 231
Query: 241 GFVAGKTAPPGRTMGHAGAVISGGKGGAEDKINAMKEAGICIAPSPARIGRSLVELLGSL 300
G++AG TAPPG+ MGHAGA+ISGGKG AE+K A++ AG+ +A +P+ IG L E+L L
Sbjct: 232 GYIAGVTAPPGKRMGHAGAIISGGKGTAEEKKEALEAAGVKVARTPSEIGELLKEVLKGL 291
>gnl|CDD|185505 PTZ00187, PTZ00187, succinyl-CoA synthetase alpha subunit;
Provisional.
Length = 317
Score = 427 bits (1101), Expect = e-120
Identities = 184/296 (62%), Positives = 229/296 (77%), Gaps = 7/296 (2%)
Query: 3 ILVDKNTKVLVQGLTGKAGTFHTEQAILYCQTQVVGGIHPKKGSTYWTGGNVNVPVFTTV 62
+ V+KNTKV+ QG+TGK GTFHTEQAI Y T++VGG++PKK T +PVF TV
Sbjct: 24 VWVNKNTKVICQGITGKQGTFHTEQAIEY-GTKMVGGVNPKKAGTTHL--KHGLPVFATV 80
Query: 63 AEAKERTAANASVIYVPPSGAGDAIIESIEAEIPLIVCITEGIPVLDMVRVKARLEKSS- 121
EAK+ T A+ASVIYVPP A AIIE+IEAEIPL+VCITEGIP DMV+VK L +
Sbjct: 81 KEAKKATGADASVIYVPPPHAASAIIEAIEAEIPLVVCITEGIPQHDMVKVKHALLSQNK 140
Query: 122 SRLIGPNCPGILTPDSCKIGIMPGSIFRKGSVGILSRSGTLTYEAVFQTSQEGLGQSTAV 181
+RLIGPNCPGI+ P CKIGIMPG I +KG +GI+SRSGTLTYEAV QT+ GLGQST V
Sbjct: 141 TRLIGPNCPGIIKPGECKIGIMPGHIHKKGKIGIVSRSGTLTYEAVAQTTAVGLGQSTCV 200
Query: 182 GIGGDPVKGTEFIDVLELFLADEATESIVMVGEIGGSAEEEAAQFLKDEAKRGRKKPIVG 241
GIGGDP GT FID L+LFL D TE I+++GEIGG+AEEEAA+++K+ KKP+V
Sbjct: 201 GIGGDPFNGTNFIDCLKLFLNDPETEGIILIGEIGGTAEEEAAEWIKNNPI---KKPVVS 257
Query: 242 FVAGKTAPPGRTMGHAGAVISGGKGGAEDKINAMKEAGICIAPSPARIGRSLVELL 297
F+AG TAPPGR MGHAGA+ISGGKG A KI A++ AG+ + SPA++G++++E++
Sbjct: 258 FIAGITAPPGRRMGHAGAIISGGKGTAPGKIEALEAAGVRVVKSPAQLGKTMLEVM 313
>gnl|CDD|130091 TIGR01019, sucCoAalpha, succinyl-CoA synthetase, alpha subunit.
ATP citrate lyases appear to form an outgroup.
Length = 286
Score = 398 bits (1025), Expect = e-112
Identities = 186/295 (63%), Positives = 223/295 (75%), Gaps = 9/295 (3%)
Query: 3 ILVDKNTKVLVQGLTGKAGTFHTEQAILYCQTQVVGGIHPKKGSTYWTGGNVNVPVFTTV 62
IL+DK+TKV+VQG+TG G+FHTEQ + Y T +VGG+ P KG T G +PVF +V
Sbjct: 1 ILLDKDTKVIVQGITGSQGSFHTEQMLAY-GTNIVGGVTPGKGGTTVLG----LPVFDSV 55
Query: 63 AEAKERTAANASVIYVPPSGAGDAIIESIEAEIPLIVCITEGIPVLDMVRVKARLEKSSS 122
EA E T ANASVI+VP A DAI E+I+A I LIVCITEGIPV DM++VK +E+S +
Sbjct: 56 KEAVEETGANASVIFVPAPFAADAIFEAIDAGIELIVCITEGIPVHDMLKVKRYMEESGT 115
Query: 123 RLIGPNCPGILTPDSCKIGIMPGSIFRKGSVGILSRSGTLTYEAVFQTSQEGLGQSTAVG 182
RLIGPNCPGI+TP CKIGIMPG I + G+VGI+SRSGTLTYEAV Q ++ G GQST VG
Sbjct: 116 RLIGPNCPGIITPGECKIGIMPGHIHKPGNVGIVSRSGTLTYEAVHQLTKAGFGQSTCVG 175
Query: 183 IGGDPVKGTEFIDVLELFLADEATESIVMVGEIGGSAEEEAAQFLKDEAKRGRKKPIVGF 242
IGGDPV GT FIDVLE F D TE+IVM+GEIGGSAEEEAA F+K KP+VGF
Sbjct: 176 IGGDPVNGTSFIDVLEAFEKDPETEAIVMIGEIGGSAEEEAADFIKQNM----SKPVVGF 231
Query: 243 VAGKTAPPGRTMGHAGAVISGGKGGAEDKINAMKEAGICIAPSPARIGRSLVELL 297
+AG TAPPG+ MGHAGA+ISGGKG AE KI A++ AG+ + SP+ IG L E+L
Sbjct: 232 IAGATAPPGKRMGHAGAIISGGKGTAESKIEALEAAGVTVVKSPSDIGELLAEIL 286
>gnl|CDD|177737 PLN00125, PLN00125, Succinyl-CoA ligase [GDP-forming] subunit
alpha.
Length = 300
Score = 366 bits (940), Expect = e-102
Identities = 186/298 (62%), Positives = 233/298 (78%), Gaps = 9/298 (3%)
Query: 2 SILVDKNTKVLVQGLTGKAGTFHTEQAILYCQTQVVGGIHPKKGSTYWTGGNVNVPVFTT 61
++ VDKNT+V+ QG+TGK GTFHTEQAI Y T++VGG+ PKKG T ++ +PVF T
Sbjct: 6 AVFVDKNTRVICQGITGKNGTFHTEQAIEY-GTKMVGGVTPKKGGT----EHLGLPVFNT 60
Query: 62 VAEAKERTAANASVIYVPPSGAGDAIIESIEAEIPLIVCITEGIPVLDMVRVKARL-EKS 120
VAEAK T ANASVIYVPP A AI+E++EAE+ L+VCITEGIP DMVRVKA L +S
Sbjct: 61 VAEAKAETKANASVIYVPPPFAAAAILEAMEAELDLVVCITEGIPQHDMVRVKAALNRQS 120
Query: 121 SSRLIGPNCPGILTPDSCKIGIMPGSIFRKGSVGILSRSGTLTYEAVFQTSQEGLGQSTA 180
+RLIGPNCPGI+ P CKIGIMPG I + G +GI+SRSGTLTYEAVFQT+ GLGQST
Sbjct: 121 KTRLIGPNCPGIIKPGECKIGIMPGYIHKPGRIGIVSRSGTLTYEAVFQTTAVGLGQSTC 180
Query: 181 VGIGGDPVKGTEFIDVLELFLADEATESIVMVGEIGGSAEEEAAQFLKDEAKRGRKKPIV 240
VGIGGDP GT F+D LE F+ D TE I+++GEIGG+AEE+AA F+K + G +KP+V
Sbjct: 181 VGIGGDPFNGTNFVDCLEKFVKDPQTEGIILIGEIGGTAEEDAAAFIK---ESGTEKPVV 237
Query: 241 GFVAGKTAPPGRTMGHAGAVISGGKGGAEDKINAMKEAGICIAPSPARIGRSLVELLG 298
F+AG TAPPGR MGHAGA++SGGKG A+DKI A++EAG+ + SPA+IG +++E+
Sbjct: 238 AFIAGLTAPPGRRMGHAGAIVSGGKGTAQDKIKALREAGVTVVESPAKIGVAMLEVFK 295
>gnl|CDD|178137 PLN02522, PLN02522, ATP citrate (pro-S)-lyase.
Length = 608
Score = 84.9 bits (210), Expect = 2e-17
Identities = 70/260 (26%), Positives = 118/260 (45%), Gaps = 19/260 (7%)
Query: 36 VVGGIHPKKG---STYWTGGNVNVPVFTTVAEA-KERTAANASVIYVPPSGAGDAIIESI 91
V G I+P ++ + +PV ++ A K A+ + + A + +E++
Sbjct: 40 VAGIINPGSEGFQKLFFGQEEIAIPVHGSIEAACKAHPTADVFINFASFRSAAASSMEAL 99
Query: 92 EAE-IPLIVCITEGIPVLDMVRVKARLEKSSSRLIGPNCPGILTPDSCKIGIMPGSI--- 147
+ I ++ I EG+P D ++ A ++ +IGP G + + KIG G++
Sbjct: 100 KQPTIRVVAIIAEGVPESDTKQLIAYARANNKVVIGPATVGGIQAGAFKIGDTAGTLDNI 159
Query: 148 -----FRKGSVGILSRSGTLTYEAVFQTSQEGLGQSTAVGIGGDPVKGTEFIDVLELFLA 202
+R GSVG +S+SG ++ E ++ G + IGGD G+ D + F
Sbjct: 160 IQCKLYRPGSVGFVSKSGGMSNEMYNVIARVTDGIYEGIAIGGDVFPGSTLSDHVLRFNN 219
Query: 203 DEATESIVMVGEIGGSAEEEAAQFLKDEAKRGRKKPIVGFVAGKTA---PPGRTMGHAGA 259
+ IV++GE+GG E + LK KP+V +V+G A GHAGA
Sbjct: 220 IPQIKMIVVLGELGGRDEYSLVEALKQGKV---SKPVVAWVSGTCARLFKSEVQFGHAGA 276
Query: 260 VISGGKGGAEDKINAMKEAG 279
G A+ K A+K+AG
Sbjct: 277 KSGGDMESAQAKNKALKDAG 296
>gnl|CDD|131764 TIGR02717, AcCoA-syn-alpha, acetyl coenzyme A synthetase (ADP
forming), alpha domain. Although technically
reversible, it is believed that this group of
ADP-dependent acetyl-CoA synthetases (ACS) act in the
direction of acetate and ATP production in the organisms
in which it has been characterized. In most species this
protein exists as a fused alpha-beta domain polypeptide.
In Pyrococcus and related species, however the domains
exist as separate polypeptides. This model represents
the alpha (N-terminal) domain. In Pyrococcus and related
species there appears to have been the development of a
paralogous family such that four other proteins are
close relatives. In reference, one of these (along with
its beta-domain partner) was characterized as ACS-II
showing specificity for phenylacetyl-CoA. This model has
been constructed to exclude these non-ACS-I paralogs.
This may result in new, authentic ACS-I sequences
falling below the trusted cutoff.
Length = 447
Score = 67.3 bits (165), Expect = 4e-12
Identities = 53/206 (25%), Positives = 87/206 (42%), Gaps = 19/206 (9%)
Query: 51 GGNVN-VPVFTTVAEAKERTAANASVIYVPPSGAGDAIIESIEAEIPLIVCIT------- 102
G + V + +V E + + +VI VP + E E + V IT
Sbjct: 46 AGEILGVKAYPSVLEIPDPV--DLAVIVVPAKYVPQVVEECGEKGVKGAVVITAGFKEVG 103
Query: 103 -EGIPVLDMVRVKARLEKSSSRLIGPNCPGILTPDSCKIGIMPGSIFRKGSVGILSRSGT 161
EG + + AR K RL+GPNC GI+ ++ +KG + +S+SG
Sbjct: 104 EEGAELEQELVEIAR--KYGMRLLGPNCLGIINTHIKLNATFAPTMPKKGGIAFISQSGA 161
Query: 162 LTYEAVFQTSQEGLGQSTAVGIGGDPVKGTEFIDVLELFLADEATESIVMVGEIGGSAEE 221
L + + G+G S V +G + D+LE D T+ I++ E +
Sbjct: 162 LLTALLDWAEKNGVGFSYFVSLGNKAD--IDESDLLEYLADDPDTKVILLYLE----GIK 215
Query: 222 EAAQFLKDEAKRGRKKPIVGFVAGKT 247
+ +FLK + +KKPIV +G +
Sbjct: 216 DGRKFLKTAREISKKKPIVVLKSGTS 241
>gnl|CDD|180395 PRK06091, PRK06091, membrane protein FdrA; Validated.
Length = 555
Score = 43.5 bits (103), Expect = 7e-05
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 11/88 (12%)
Query: 135 PDSCKIGIMPGS------IFRKGSVGILSRSGTLTYEAVFQTSQEGLGQSTAVGIGG--- 185
PD C ++ G+ + +G++G++ SGT E Q + G G + A+G+GG
Sbjct: 173 PD-CGTAMIAGTPLAFANVMPEGNIGVIGASGTGIQELCSQIALAGEGITHAIGLGGRDL 231
Query: 186 -DPVKGTEFIDVLELFLADEATESIVMV 212
V G + LE+ ADE +E I V
Sbjct: 232 SAEVGGISALTALEMLSADEKSEVIAFV 259
>gnl|CDD|179323 PRK01710, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 458
Score = 31.9 bits (73), Expect = 0.21
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 13 VQGLTGKAGTFHTEQAILYCQTQVVGGIHPKKGSTYWTGGNVNVPVFTTVAEAKE 67
V G+TG G T T ++ + ++G W GGN+ P+F+ + E KE
Sbjct: 119 VFGVTGSDGKTTT--------TTLIYEMLKEEGYKTWVGGNIGTPLFSNIEEIKE 165
>gnl|CDD|173430 PTZ00140, PTZ00140, sexual stage antigen s45/48; Provisional.
Length = 447
Score = 28.2 bits (63), Expect = 2.4
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 118 EKSSSRLIGPNCPGILTPDSC 138
+ L G CP L P C
Sbjct: 332 STKYNHLAGIKCPYKLIPTYC 352
>gnl|CDD|181261 PRK08162, PRK08162, acyl-CoA synthetase; Validated.
Length = 545
Score = 28.4 bits (64), Expect = 2.7
Identities = 14/54 (25%), Positives = 19/54 (35%), Gaps = 19/54 (35%)
Query: 229 DEAKRGRKKPIVGFVAGKTAPPGRTMGHAGAVISGGKGGAEDKINAMKEAGICI 282
E + G P+ VAG A P AVI+ M+E G +
Sbjct: 289 AEWRAGIDHPVHAMVAG--AAP------PAAVIAK-----------MEEIGFDL 323
>gnl|CDD|162232 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast.
This model describes bacterial (and chloroplast)
ribosomal protein L1. The apparent mitochondrial L1 is
sufficiently diverged to be the subject of a separate
model.
Length = 227
Score = 28.0 bits (63), Expect = 3.5
Identities = 26/79 (32%), Positives = 36/79 (45%), Gaps = 15/79 (18%)
Query: 50 TGGNVNVPVFTTVAEAKERTAANASVIYVPPSGAGDAIIESIEAE-IPLIVCITEGIPVL 108
TG V V VF +A+E AA A + D +IE I+ + V I P
Sbjct: 67 TGKTVRVAVFAKGEKAEEAKAAGADYV------GSDDLIEKIKKGWLDFDVVIAT--P-- 116
Query: 109 DMVRVKARLEKSSSRLIGP 127
DM+RV +L R++GP
Sbjct: 117 DMMRVVGKL----GRILGP 131
>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
Length = 230
Score = 27.4 bits (62), Expect = 4.3
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 15/79 (18%)
Query: 50 TGGNVNVPVFTTVAEAKERTAANASVIYVPPSGAGDAIIESIEA-EIPLIVCITEGIPVL 108
TG V V VF +A+E AA A ++ G+ +IE I+ + V I P
Sbjct: 68 TGKTVRVAVFAKGEKAEEAKAAGADIV------GGEDLIEKIKGGWLDFDVVIAT--P-- 117
Query: 109 DMVRVKARLEKSSSRLIGP 127
DM+ +L R++GP
Sbjct: 118 DMMGKVGKL----GRILGP 132
>gnl|CDD|162708 TIGR02109, PQQ_syn_pqqE, coenzyme PQQ biosynthesis protein E. This
model describes coenzyme PQQ biosynthesis protein E, a
gene required for the biosynthesis of
pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is
required for some glucose dehydrogenases and alcohol
dehydrogenases.
Length = 358
Score = 27.4 bits (61), Expect = 4.5
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 61 TVAEAKERTAANASVIYVPP 80
V EA+ER + YV P
Sbjct: 208 IVEEARERLKGGLVIDYVVP 227
>gnl|CDD|129727 TIGR00641, acid_CoA_mut_N, methylmalonyl-CoA mutase N-terminal
domain. Methylmalonyl-CoA mutase (EC 5.4.99.2)
catalyzes a reversible isomerization between
L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an
adenosylcobalamin cofactor. It may be a homodimer, as in
mitochondrion, or a heterodimer with partially
homologous beta chain that does not bind the
adenosylcobalamin cofactor, as in Propionibacterium
freudenreichii. The most similar archaeal sequences are
separate chains, such as AF2215 abd AF2219 of
Archaeoglobus fulgidus, that correspond roughly to the
first 500 and last 130 residues, respectively of known
methylmalonyl-CoA mutases. This model describes the
N-terminal domain subfamily. In a neighbor-joining tree,
AF2215 branches with a bacterial isobutyryl-CoA mutase,
which is also the same length. Scoring between the noise
and trusted cutoffs are the non-catalytic, partially
homologous beta chains from certain heterodimeric
examples of 5.4.99.2.
Length = 528
Score = 26.7 bits (59), Expect = 8.2
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 12/67 (17%)
Query: 186 DPVKGTEFIDVLELFLADEATESIVMVGEIGGSAE-----------EEAAQFLKDEAKRG 234
DP+ G+ +++ L +A+ A + I + E+GG A+ EEAA + G
Sbjct: 369 DPLGGSYYVEWLTDDIAERAWKYIQEIEEMGGMAKAIERGIPKKRIEEAAARTQARIDSG 428
Query: 235 RKKPIVG 241
R +PIVG
Sbjct: 429 R-QPIVG 434
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
0.315 0.135 0.385
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,857,511
Number of extensions: 318557
Number of successful extensions: 505
Number of sequences better than 10.0: 1
Number of HSP's gapped: 484
Number of HSP's successfully gapped: 25
Length of query: 300
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 207
Effective length of database: 3,984,929
Effective search space: 824880303
Effective search space used: 824880303
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 57 (25.7 bits)