Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011766145.1 AZO_RS12180 acetate--CoA ligase
Query= SwissProt::P31638
(660 letters)
>NCBI__GCF_000061505.1:WP_011766145.1
Length = 654
Score = 1061 bits (2745), Expect = 0.0
Identities = 500/649 (77%), Positives = 571/649 (87%)
Query: 9 QEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQS 68
Q+ R++NP E AA+ MEAY ALC EAE+DYEG+WAR+AREL+ W KPFT+VLD+S
Sbjct: 5 QQVRIYNPSEEVVKNAAVSGMEAYWALCKEAEQDYEGYWARNARELIDWKKPFTQVLDES 64
Query: 69 NAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFAN 128
NAPF+KWF DG+LN SYNCLDRN++ G DKVA++FEAD G VTRVTY++L G+VC+FAN
Sbjct: 65 NAPFFKWFADGQLNVSYNCLDRNVEKGLGDKVALIFEADSGEVTRVTYKDLLGRVCKFAN 124
Query: 129 GLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVA 188
L+A GI+KGDRVVIY+PMS+EGVVAMQACAR+GATHS+VFGGFSA++L++R+ D GAVA
Sbjct: 125 ALRASGIKKGDRVVIYLPMSIEGVVAMQACARIGATHSIVFGGFSAQALRDRINDAGAVA 184
Query: 189 LITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSA 248
LIT+D Q RGGKALPLK IAD+AL+LGGCE ++NV V +RTG VA+ GRD W DV A
Sbjct: 185 LITSDGQFRGGKALPLKPIADEALSLGGCETIKNVFVVKRTGADVAFVAGRDVWYHDVVA 244
Query: 249 GQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFW 308
Q D CE E V AEHPLF+LYTSGSTGKPKGVQHSTGGYLL A++TMK+TFDIKP D+FW
Sbjct: 245 SQSDVCEPEWVDAEHPLFLLYTSGSTGKPKGVQHSTGGYLLHAILTMKYTFDIKPSDVFW 304
Query: 309 CTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIR 368
CTADIGWVTGHTYI YGPLA G+T++VFEGVPTYP+AGRFW MI HKV+IFYTAPTAIR
Sbjct: 305 CTADIGWVTGHTYITYGPLACGSTEIVFEGVPTYPDAGRFWKMIQDHKVNIFYTAPTAIR 364
Query: 369 SLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTET 428
SLIKAA+ + +HPK YDLSSLR+LG+VGEPINP AW WYY+N+G RCPIVDTFWQTET
Sbjct: 365 SLIKAADNNPTVHPKNYDLSSLRILGSVGEPINPAAWEWYYENVGGGRCPIVDTFWQTET 424
Query: 429 GGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIW 488
GGHMITPLPGATPLVPGSCTLP PGI AA+VDETG +VPNG GGILVVKRPWP+MIRTIW
Sbjct: 425 GGHMITPLPGATPLVPGSCTLPFPGIQAAVVDETGTEVPNGQGGILVVKRPWPSMIRTIW 484
Query: 489 GDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESA 548
GDPERF+KSY+P++ GKLYLAGDG+IRDK+TGYFTI GRIDDVLNVSGHRMGTMEIESA
Sbjct: 485 GDPERFKKSYYPDDFKGKLYLAGDGAIRDKETGYFTITGRIDDVLNVSGHRMGTMEIESA 544
Query: 549 LVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAK 608
LV++ VAEAAVVGRPDD+TGEAI AFVVLK +RPTGE A + EL+NWVG EIGPIAK
Sbjct: 545 LVAHEKVAEAAVVGRPDDLTGEAIVAFVVLKGARPTGEAAAAVVKELQNWVGHEIGPIAK 604
Query: 609 PKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657
PKDIRFG+NLPKTRSGKIMRRLLR LAKGEEITQDTSTLENPAILEQLK
Sbjct: 605 PKDIRFGENLPKTRSGKIMRRLLRQLAKGEEITQDTSTLENPAILEQLK 653
Lambda K H
0.319 0.136 0.422
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1528
Number of extensions: 63
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 660
Length of database: 654
Length adjustment: 38
Effective length of query: 622
Effective length of database: 616
Effective search space: 383152
Effective search space used: 383152
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 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate WP_011766145.1 AZO_RS12180 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR02188.hmm
# target sequence database: /tmp/gapView.14303.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02188 [M=629]
Accession: TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.9e-299 980.2 0.0 2.2e-299 980.0 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011766145.1 AZO_RS12180 acetate--CoA ligase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011766145.1 AZO_RS12180 acetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 980.0 0.0 2.2e-299 2.2e-299 3 627 .. 24 653 .. 22 654 .] 0.97
Alignments for each domain:
== domain 1 score: 980.0 bits; conditional E-value: 2.2e-299
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70
+e+y +l++ea++d+e +wa++a+e ++w+kpf++vldes++p+ kWf+dg+lnvsync+dr+vek
lcl|NCBI__GCF_000061505.1:WP_011766145.1 24 GMEAYWALCKEAEQDYEGYWARNARELIDWKKPFTQVLDESNAPFFKWFADGQLNVSYNCLDRNVEKgL 92
6899***************************************************************99 PP
TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
dkva+i+e+d +g ++ ++tY++ll +vc++an+l++ G+kkgdrv+iYlpm +e v+am+acaRiGa
lcl|NCBI__GCF_000061505.1:WP_011766145.1 93 GDKVALIFEAD-SG-EVTRVTYKDLLGRVCKFANALRASGIKKGDRVVIYLPMSIEGVVAMQACARIGA 159
***********.55.49**************************************************** PP
TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgee 207
+hs+vf+Gfsa+al++Ri+da a +it+d+++Rggk+++lk i+deal+ + ++++v vvkrtg++
lcl|NCBI__GCF_000061505.1:WP_011766145.1 160 THSIVFGGFSAQALRDRINDAGAVALITSDGQFRGGKALPLKPIADEALSLGGCeTIKNVFVVKRTGAD 228
*************************************************9988879************* PP
TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
va ++ grDvw++++v++ +s+ cepe++d+e+plf+LYtsGstGkPkGv+h+tgGyll+a lt+ky+f
lcl|NCBI__GCF_000061505.1:WP_011766145.1 229 VA-FVAGRDVWYHDVVAS-QSDVCEPEWVDAEHPLFLLYTSGSTGKPKGVQHSTGGYLLHAILTMKYTF 295
77.**************6.************************************************** PP
TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345
dik++d+fwCtaD+GWvtGh+Yi ygPLa+G t+++fegvptypda+rfw++i+ +kv+ifYtaPtaiR
lcl|NCBI__GCF_000061505.1:WP_011766145.1 296 DIKPSDVFWCTADIGWVTGHTYITYGPLACGSTEIVFEGVPTYPDAGRFWKMIQDHKVNIFYTAPTAIR 364
********************************************************************* PP
TIGR02188 346 almklgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplp 410
+l+k++++ ++k++dlsslr+lgsvGepinp aweWyye+vG ++cpivdt+WqtetGg++itplp
lcl|NCBI__GCF_000061505.1:WP_011766145.1 365 SLIKAADNnptvHPKNYDLSSLRILGSVGEPINPAAWEWYYENVGGGRCPIVDTFWQTETGGHMITPLP 433
*****987333357899**************************************************** PP
TIGR02188 411 gvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfk.klk 478
g at+l pgs+tlP++Gi+a+vvde+g+ev ++++ g+Lv+k+pwPsm+rti+gd+erf ++Y+ ++k
lcl|NCBI__GCF_000061505.1:WP_011766145.1 434 G-ATPLVPGSCTLPFPGIQAAVVDETGTEVPNGQG-GILVVKRPWPSMIRTIWGDPERFKKSYYPdDFK 500
*.6*****************************999.8*************************9962577 PP
TIGR02188 479 g.lyftGDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaiv 545
g ly++GDga rdk+ Gy++i+GR+Ddv+nvsGhr+gt+eiesalv+he+vaeaavvg+pd+++geaiv
lcl|NCBI__GCF_000061505.1:WP_011766145.1 501 GkLYLAGDGAIRDKEtGYFTITGRIDDVLNVSGHRMGTMEIESALVAHEKVAEAAVVGRPDDLTGEAIV 569
679**********988***************************************************** PP
TIGR02188 546 afvvlkegveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellg 612
afvvlk ++ + e ++ kel+++v +eigpiakp++i++ e+lPktRsGkimRRllr++a+gee+++
lcl|NCBI__GCF_000061505.1:WP_011766145.1 570 AFVVLKGARPTGEAaaAVVKELQNWVGHEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRQLAKGEEITQ 638
******998876655689*************************************************** PP
TIGR02188 613 dvstledpsvveelk 627
d+stle+p+++e+lk
lcl|NCBI__GCF_000061505.1:WP_011766145.1 639 DTSTLENPAILEQLK 653
************986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (654 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.93
//
[ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory