Alignments for a candidate for acs in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Trichormus variabilis ATCC 29413

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011318049.1 AVA_RS06110 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000204075.1:WP_011318049.1
          Length = 657

 Score =  746 bits (1926), Expect = 0.0
 Identities = 373/659 (56%), Positives = 478/659 (72%), Gaps = 13/659 (1%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           IES++QE R+F+P   F+  A I S+E YQ L D+A+ D + FWA  A   LHW + +  
Sbjct: 6   IESILQEKRLFHPSAEFSQNAQIKSLEDYQRLYDKAKADPQKFWAELAETELHWFQKWDT 65

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
           VLD   APF KWF  G++N SYNCLDR+L     +K A+++E + G    +TY +LH +V
Sbjct: 66  VLDWQ-APFAKWFVGGKINISYNCLDRHLTTWRKNKAALIWEGEPGDSRTLTYAQLHREV 124

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
           C+FAN LK LG++KGDRV IYMPM  E  +AM ACAR+GA HSVVFGGFSA++L++RL+D
Sbjct: 125 CQFANVLKQLGVQKGDRVGIYMPMIPEAAIAMLACARIGAPHSVVFGGFSAEALRDRLID 184

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWT-EGRDRW 242
             A  ++TAD   R    +PLK   D ALA G   +V NV+V +RTG  +     GRD W
Sbjct: 185 AQAKVVVTADGGWRKDAIVPLKEQVDKALADGAVPSVENVLVVKRTGQDIYMQLGGRDHW 244

Query: 243 MEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIK 302
             D+  G    C AEP+ +E  LFVLYTSGSTGKPKGV H+TGGY L+  MT KW FD++
Sbjct: 245 WHDLQKGASADCPAEPMDSEDLLFVLYTSGSTGKPKGVVHTTGGYNLYTHMTTKWIFDLQ 304

Query: 303 PDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYT 362
             D++WCTAD+GW+TGH+YI YGPL+ GAT +++EG P   N G FWD+I ++ V+IFYT
Sbjct: 305 DTDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCFWDVIEKYGVNIFYT 364

Query: 363 APTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDT 422
           APTAIR+ IK  E     HP   +LSSLRLLGTVGEPINPEAWMWY+K IG +RCPIVDT
Sbjct: 365 APTAIRAFIKMGEH----HPNARNLSSLRLLGTVGEPINPEAWMWYHKVIGGDRCPIVDT 420

Query: 423 FWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPA 482
           +WQTETGG MITPLPGA    PGS TLP PGI+A IVD  G+ VP   GG L V+ PWP 
Sbjct: 421 WWQTETGGIMITPLPGAISTKPGSATLPFPGILADIVDLDGNTVPQNEGGYLAVRYPWPG 480

Query: 483 MIRTIWGDPERFRKSYF---PEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHR 539
           M+RT++GDPERFR++Y+   P + G   Y AGDG+ +D+D GYF +MGR+DDVLNVSGHR
Sbjct: 481 MMRTVYGDPERFRRTYWEHIPPKDGNYTYFAGDGARKDED-GYFWVMGRVDDVLNVSGHR 539

Query: 540 MGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWV 599
           +GTME+ESALVS+P VAEAAVVG+PDD+ GE + AFV L+ +    ++  K+   L+  V
Sbjct: 540 LGTMEVESALVSHPAVAEAAVVGKPDDLKGEEVVAFVTLEGTYQASDDLSKV---LKQHV 596

Query: 600 GKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658
            +EIG IA+P +IRF D LPKTRSGKIMRRLLR+LA G+E++ DTSTLE+ ++L++L++
Sbjct: 597 VQEIGAIARPGEIRFTDALPKTRSGKIMRRLLRNLAAGQEVSGDTSTLEDRSVLDKLRE 655


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: 1408
Number of extensions: 73
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: 657
Length adjustment: 38
Effective length of query: 622
Effective length of database: 619
Effective search space:   385018
Effective search space used:   385018
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_011318049.1 AVA_RS06110 (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.19932.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 1026.6   0.0          0 1026.4   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011318049.1  AVA_RS06110 acetate--CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011318049.1  AVA_RS06110 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1026.4   0.0         0         0       2     628 ..      29     655 ..      28     656 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1026.4 bits;  conditional E-value: 0
                                 TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek. 69 
                                               ++le+y++ly++a++dp+kfwa+la++el+w++++++vld++ +p++kWf++g++n+sync+drh+++ 
  lcl|NCBI__GCF_000204075.1:WP_011318049.1  29 KSLEDYQRLYDKAKADPQKFWAELAETELHWFQKWDTVLDWQ-APFAKWFVGGKINISYNCLDRHLTTw 96 
                                               6899*************************************9.78************************ PP

                                 TIGR02188  70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138
                                               rk+k+a+iweg+ +g dsr+ltYa+l+revc++anvlk+lGv+kgdrv iY+pmipea+iamlacaRiG
  lcl|NCBI__GCF_000204075.1:WP_011318049.1  97 RKNKAALIWEGE-PG-DSRTLTYAQLHREVCQFANVLKQLGVQKGDRVGIYMPMIPEAAIAMLACARIG 163
                                               ************.77.59*************************************************** PP

                                 TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtge 206
                                               a hsvvf+Gfsaeal++R++da+ak+v+tad+g+R++ +++lk++vd+al++    sve+vlvvkrtg+
  lcl|NCBI__GCF_000204075.1:WP_011318049.1 164 APHSVVFGGFSAEALRDRLIDAQAKVVVTADGGWRKDAIVPLKEQVDKALADGAVpSVENVLVVKRTGQ 232
                                               ***************************************************99989************* PP

                                 TIGR02188 207 evaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyv 275
                                               ++     grD+ww++l + +asa+c++e++dsed+lf+LYtsGstGkPkGv+httgGy l++++t+k++
  lcl|NCBI__GCF_000204075.1:WP_011318049.1 233 DIYMQLGGRDHWWHDLQK-GASADCPAEPMDSEDLLFVLYTSGSTGKPKGVVHTTGGYNLYTHMTTKWI 300
                                               *998889**********9.6************************************************* PP

                                 TIGR02188 276 fdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtai 344
                                               fd++d+d++wCtaDvGW+tGhsYivygPL+nGattl++eg+p+ +++++fw+vieky+v+ifYtaPtai
  lcl|NCBI__GCF_000204075.1:WP_011318049.1 301 FDLQDTDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCFWDVIEKYGVNIFYTAPTAI 369
                                               ********************************************************************* PP

                                 TIGR02188 345 RalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgva 413
                                               Ra++k+ge+++++++lsslr+lg+vGepinpeaw+Wy++v+G ++cpivdtwWqtetGgi+itplpg a
  lcl|NCBI__GCF_000204075.1:WP_011318049.1 370 RAFIKMGEHHPNARNLSSLRLLGTVGEPINPEAWMWYHKVIGGDRCPIVDTWWQTETGGIMITPLPG-A 437
                                               *******************************************************************.6 PP

                                 TIGR02188 414 telkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg... 479
                                               +++kpgsatlP++Gi a++vd +g++v ++e+ g+L+++ pwP+m+rt+ygd+erf +tY+++++    
  lcl|NCBI__GCF_000204075.1:WP_011318049.1 438 ISTKPGSATLPFPGILADIVDLDGNTVPQNEG-GYLAVRYPWPGMMRTVYGDPERFRRTYWEHIPPkdg 505
                                               *****************************999.8*****************************987788 PP

                                 TIGR02188 480 ..lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaiva 546
                                                 +yf+GDgar+d+dGy+w++GRvDdv+nvsGhrlgt+e+esalvsh+avaeaavvg+pd++kge +va
  lcl|NCBI__GCF_000204075.1:WP_011318049.1 506 nyTYFAGDGARKDEDGYFWVMGRVDDVLNVSGHRLGTMEVESALVSHPAVAEAAVVGKPDDLKGEEVVA 574
                                               989****************************************************************** PP

                                 TIGR02188 547 fvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvs 615
                                               fv+l+ +++++++ l+k lk++v +eig+ia+p +i+++++lPktRsGkimRRllr++a+g+e+ gd+s
  lcl|NCBI__GCF_000204075.1:WP_011318049.1 575 FVTLEGTYQASDD-LSKVLKQHVVQEIGAIARPGEIRFTDALPKTRSGKIMRRLLRNLAAGQEVSGDTS 642
                                               **********995.******************************************************* PP

                                 TIGR02188 616 tledpsvveelke 628
                                               tled+sv+++l+e
  lcl|NCBI__GCF_000204075.1:WP_011318049.1 643 TLEDRSVLDKLRE 655
                                               *********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (657 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: 12.55
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources