Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_007474311.1 CMTB2_RS04300 acetate--CoA ligase
Query= SwissProt::P31638
(660 letters)
>NCBI__GCF_000170735.1:WP_007474311.1
Length = 648
Score = 740 bits (1910), Expect = 0.0
Identities = 370/646 (57%), Positives = 468/646 (72%), Gaps = 11/646 (1%)
Query: 13 VFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAPF 72
VF P + A +M Y+ L +E E++YEG W++ A+E + W + F + LD SNAPF
Sbjct: 5 VFYPKKEMFKNPAFKNMCEYKELVEEFEKNYEGTWSKLAKEKITWFEDFKQTLDTSNAPF 64
Query: 73 YKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLKA 132
YKWF G+LN +YNC+DR+L++ +K AI++E D+G +TY EL+ V RFAN LK+
Sbjct: 65 YKWFVGGKLNVTYNCIDRHLED-KKNKAAIIWEGDNGEKRIITYLELYRDVNRFANLLKS 123
Query: 133 LGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALITA 192
LG++KGDRVVIYMPM E AM ACAR+GA HSVVFGGFSA++L++R++D A +ITA
Sbjct: 124 LGVKKGDRVVIYMPMIPEAAYAMLACARIGAIHSVVFGGFSAEALKDRILDAEAKIVITA 183
Query: 193 DEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQPD 252
D R GK LK + D AL G + V VIV R + W EGRD D+ Q D
Sbjct: 184 DGAFRKGKPYMLKPVVDKALE--GVDIVEKVIVVERNNEDINWVEGRDLSYNDLIINQDD 241
Query: 253 TCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTAD 312
C+ E + +E PLF+LYTSGSTGKPKGVQHS GY+LWA +TM+W FDIK +D FWCTAD
Sbjct: 242 KCKCEIMDSEDPLFLLYTSGSTGKPKGVQHSQAGYILWAQLTMEWVFDIKDNDTFWCTAD 301
Query: 313 IGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIK 372
IGW+TGHTYI YGPLAAG T ++FEGV TYP++GR W M+ +KV+ FYTAPTAIR L K
Sbjct: 302 IGWITGHTYIVYGPLAAGGTTLMFEGVLTYPDSGRTWKMVEEYKVNQFYTAPTAIRLLHK 361
Query: 373 AAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHM 432
+ PK+YDLSSLR+LGTVGEPI+P AW WYY+ +G RC IVDT+WQTETGGHM
Sbjct: 362 MGPDE----PKKYDLSSLRILGTVGEPIDPTAWKWYYEVVGGGRCSIVDTWWQTETGGHM 417
Query: 433 ITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDPE 492
I+PLP ATP+ PGS T PLPGI A I+DE G+ +P G+L + +PWP+MIRTIWGDPE
Sbjct: 418 ISPLPAATPIKPGSATFPLPGIFAEIIDEEGNKMPPNEKGLLCITKPWPSMIRTIWGDPE 477
Query: 493 RFRKSYF--PEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALV 550
RF KSYF ++ G +Y +GDG+I D+D GY I GR+DDV+NVSGHR+GT EIE+A+
Sbjct: 478 RFIKSYFSTAKKDGKPVYFSGDGAIYDED-GYIWITGRVDDVINVSGHRLGTAEIEAAIK 536
Query: 551 SNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPK 610
+PLVAE AVVGRPD++ GE+I A+VVLK EE ++I E+ V +EIG IAK
Sbjct: 537 KHPLVAEVAVVGRPDEIKGESIFAYVVLKGEDTIAEE-IEIIQEINAIVKEEIGAIAKVD 595
Query: 611 DIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656
I F LPKTRSGKIMRR+LR++AKGEEI QDTSTLE+P ++E +
Sbjct: 596 TIAFVPGLPKTRSGKIMRRILRAIAKGEEIKQDTSTLEDPKVVEAI 641
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: 1287
Number of extensions: 59
Number of successful extensions: 7
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: 648
Length adjustment: 38
Effective length of query: 622
Effective length of database: 610
Effective search space: 379420
Effective search space used: 379420
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_007474311.1 CMTB2_RS04300 (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.28970.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1012.3 0.5 0 1012.1 0.5 1.0 1 lcl|NCBI__GCF_000170735.1:WP_007474311.1 CMTB2_RS04300 acetate--CoA ligas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000170735.1:WP_007474311.1 CMTB2_RS04300 acetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1012.1 0.5 0 0 2 627 .. 19 642 .. 18 644 .. 0.98
Alignments for each domain:
== domain 1 score: 1012.1 bits; conditional E-value: 0
TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvekr 70
+++ eykel+ee ++++e w+klake+++w+++f+++ld+s++p++kWf++g+lnv+ync+drh+e++
lcl|NCBI__GCF_000170735.1:WP_007474311.1 19 KNMCEYKELVEEFEKNYEGTWSKLAKEKITWFEDFKQTLDTSNAPFYKWFVGGKLNVTYNCIDRHLEDK 87
6789***************************************************************** PP
TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
k+k+aiiwegd+ ++r +tY el+r+v+r+an+lk+lGvkkgdrv+iY+pmipea++amlacaRiGa
lcl|NCBI__GCF_000170735.1:WP_007474311.1 88 KNKAAIIWEGDNG--EKRIITYLELYRDVNRFANLLKSLGVKKGDRVVIYMPMIPEAAYAMLACARIGA 154
***********55..48**************************************************** PP
TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeev 208
+hsvvf+Gfsaeal++Ri daeak+vitad+++R+gk ++lk +vd+ale ++ vekv+vv+r++e++
lcl|NCBI__GCF_000170735.1:WP_007474311.1 155 IHSVVFGGFSAEALKDRILDAEAKIVITADGAFRKGKPYMLKPVVDKALEGVD-IVEKVIVVERNNEDI 222
***************************************************98.7*************6 PP
TIGR02188 209 aewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfd 277
+ w+egrD+ +++l+ +++++c++e +dsedplf+LYtsGstGkPkGv+h+++Gy+l+a+lt+++vfd
lcl|NCBI__GCF_000170735.1:WP_007474311.1 223 N-WVEGRDLSYNDLII-NQDDKCKCEIMDSEDPLFLLYTSGSTGKPKGVQHSQAGYILWAQLTMEWVFD 289
6.**************.5*************************************************** PP
TIGR02188 278 ikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRa 346
ikd+d+fwCtaD+GW+tGh+YivygPLa+G ttl+fegv typd++r w+++e+ykv++fYtaPtaiR+
lcl|NCBI__GCF_000170735.1:WP_007474311.1 290 IKDNDTFWCTADIGWITGHTYIVYGPLAAGGTTLMFEGVLTYPDSGRTWKMVEEYKVNQFYTAPTAIRL 358
********************************************************************* PP
TIGR02188 347 lmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415
l+k+g + +kk+dlsslr+lg+vGepi+p aw+WyyevvG ++c+ivdtwWqtetGg++i+plp+ at+
lcl|NCBI__GCF_000170735.1:WP_007474311.1 359 LHKMGPDEPKKYDLSSLRILGTVGEPIDPTAWKWYYEVVGGGRCSIVDTWWQTETGGHMISPLPA-ATP 426
*****************************************************************.6** PP
TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg....l 480
+kpgsat Pl+Gi ae++deeg+++ ++e+ g+L+i+kpwPsm+rti+gd+erf+++Yf+++k+ +
lcl|NCBI__GCF_000170735.1:WP_007474311.1 427 IKPGSATFPLPGIFAEIIDEEGNKMPPNEK-GLLCITKPWPSMIRTIWGDPERFIKSYFSTAKKdgkpV 494
***************************999.8*****************************9999999* PP
TIGR02188 481 yftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvv 549
yf+GDga d+dGyiwi+GRvDdvinvsGhrlgtaeie+a+ +h+ vae avvg+pdeikge+i+a+vv
lcl|NCBI__GCF_000170735.1:WP_007474311.1 495 YFSGDGAIYDEDGYIWITGRVDDVINVSGHRLGTAEIEAAIKKHPLVAEVAVVGRPDEIKGESIFAYVV 563
********************************************************************* PP
TIGR02188 550 lkegveedee.elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstl 617
lk + + ee e+ +e++++v++eig+iak d+i +v+ lPktRsGkimRR+lr+ia+gee+++d+stl
lcl|NCBI__GCF_000170735.1:WP_007474311.1 564 LKGEDTIAEEiEIIQEINAIVKEEIGAIAKVDTIAFVPGLPKTRSGKIMRRILRAIAKGEEIKQDTSTL 632
**9999888779********************************************************* PP
TIGR02188 618 edpsvveelk 627
edp+vve+++
lcl|NCBI__GCF_000170735.1:WP_007474311.1 633 EDPKVVEAII 642
*******997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (648 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.29
//
[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