Alignments for a candidate for acs in Methanococcus maripaludis C5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methanococcus maripaludis C5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_011869271.1 MMARC5_RS07750 acetate--CoA ligase

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_000016125.1:WP_011869271.1
          Length = 636

 Score =  721 bits (1861), Expect = 0.0
 Identities = 351/645 (54%), Positives = 458/645 (71%), Gaps = 14/645 (2%)

Query: 22  KWRSKYTPIDAYFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRL 81
           K   KY  ++ Y +  ++ +E+ E FW   AK LEW K WD VL+  NPP+ KWF  G L
Sbjct: 2   KTGDKYILLEKYSEMQQKALEDPEKFWGEQAKCLEWDKTWDNVLEW-NPPYAKWFKSGSL 60

Query: 82  NLSYLAVDRHVKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNF 141
           N SY  VDRH+K  R+NK AI  E E             LTYY+LYRE+N+ A +L +N 
Sbjct: 61  NASYNCVDRHIKGNRRNKAAIICEKEDGSCG-------ILTYYELYREINKFANVL-ENL 112

Query: 142 GVKKGDKITLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITAD 201
           GV+KGD +T+Y+PM+ E  I MLA  RIG I +VVFSGFS+DALA+RINDS+S+I++T +
Sbjct: 113 GVEKGDVVTIYMPMMTEAIIAMLACSRIGVIHNVVFSGFSSDALADRINDSKSKILVTTN 172

Query: 202 GFWRRGRVVRLKEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNA 261
             +RRG+ + LK+++D AL     ++ V+ + R G+++  +  G++Y+W++LM G    +
Sbjct: 173 LLYRRGKEIELKKILDKALLNCNSIKHVVYVKR-GIEEFNLVSGKEYFWDELMGGA--KS 229

Query: 262 YIEPEPVESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTAD 321
           Y+EP PVES+HP FILYTSGTTG PKG+VH TGG+  +   TM W + + + D+FWCTAD
Sbjct: 230 YVEPVPVESDHPLFILYTSGTTGSPKGVVHSTGGYLTYATKTMDWTWGLNEMDVFWCTAD 289

Query: 322 IGWVTGHSYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMR 381
           IGW+TGH+YVV GPL +GAT V+YEGA DYP+PDR W I+E +GVT+ YT+PTAIRM M 
Sbjct: 290 IGWITGHTYVVYGPLSLGATIVLYEGAIDYPEPDRLWGIVENHGVTLLYTAPTAIRMLMM 349

Query: 382 YGEEWPRKHDLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHA 441
           YGE+W   HDLSTLR++ SVGEPINP AW+W Y+V+G EK      +W TETGG +I  A
Sbjct: 350 YGEKWVNTHDLSTLRLLGSVGEPINPRAWKWYYKVIGKEKCPICDCYWQTETGGHMIYPA 409

Query: 442 PGLYLVPMKPGTNGPPLPGFEVDVVDENGNPAPPGVKGYLVIKKPWPGMLHGIWGDPERY 501
            G+  VP+KPG+   P  G +VDVVD  GNP    +KG L+IK+PWPGML G+W + ERY
Sbjct: 410 IGIQSVPLKPGSATFPGIGIDVDVVDNEGNPVEANIKGNLIIKRPWPGMLAGLWNNDERY 469

Query: 502 IKTYWSRFPGMFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAE 561
              YW RF   F   DYAIKD+DGYIWVLGR+DEV+ V+GHR+GT ELE  L+S+  VAE
Sbjct: 470 RAAYWDRFKNNFSTSDYAIKDQDGYIWVLGRSDEVLNVSGHRIGTAELEHELVSNKMVAE 529

Query: 562 SAVVGVPDAIKGEVPIAFVVLKQGV--APSDELRKELREHVRRTIGPIAEPAQIFFVTKL 619
           SAVVG PD +KGEVP+AFV+L +     PS+E++  L  H+R T+GPI  PA IFFV KL
Sbjct: 530 SAVVGKPDDVKGEVPVAFVILNERYRELPSNEVKATLIRHIRDTVGPIGTPAMIFFVNKL 589

Query: 620 PKTRSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYEEIK 664
           PKTRSGKIMRR+LK +  G  +GDVTTLED TS+E+ K+  E+ K
Sbjct: 590 PKTRSGKIMRRILKKLIIGEEIGDVTTLEDNTSLEDVKKELEDFK 634


Lambda     K      H
   0.319    0.138    0.440 

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: 1383
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: 670
Length of database: 636
Length adjustment: 38
Effective length of query: 632
Effective length of database: 598
Effective search space:   377936
Effective search space used:   377936
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_011869271.1 MMARC5_RS07750 (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.4192137.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-268  878.1   0.1   1.8e-268  877.9   0.1    1.0  1  NCBI__GCF_000016125.1:WP_011869271.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016125.1:WP_011869271.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  877.9   0.1  1.8e-268  1.8e-268       4     628 ..      10     628 ..       7     629 .. 0.98

  Alignments for each domain:
  == domain 1  score: 877.9 bits;  conditional E-value: 1.8e-268
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           le+y+e+ ++a edpekfw+++ak  lew+k +++vl+++ +p +kWf+ g+ln+syncvdrh++  r++k+a
  NCBI__GCF_000016125.1:WP_011869271.1  10 LEKYSEMQQKALEDPEKFWGEQAK-CLEWDKTWDNVLEWN-PPYAKWFKSGSLNASYNCVDRHIKGnRRNKAA 80 
                                           689*********************.6*************9.88**********************989***** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           ii e ++ +     ltY+el+re++++anvl++lGv+kgd v+iY+pm++ea+iamlac+RiG++h+vvf+Gf
  NCBI__GCF_000016125.1:WP_011869271.1  81 IICEKEDGS--CGILTYYELYREINKFANVLENLGVEKGDVVTIYMPMMTEAIIAMLACSRIGVIHNVVFSGF 151
                                           ******665..79************************************************************ PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           s++ala+Ri+d+++k+++t++  +R+gk ielkki d+al +++ s+++v+ vkr  ee  ++++g+++ w+e
  NCBI__GCF_000016125.1:WP_011869271.1 152 SSDALADRINDSKSKILVTTNLLYRRGKEIELKKILDKALLNCN-SIKHVVYVKRGIEE-FNLVSGKEYFWDE 222
                                           *******************************************8.8*********9999.56*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                           l+  +a++++ep +++s++plfiLYtsG+tG PkGv+h+tgGyl++a+ t+ +++ +++ d+fwCtaD+GW+t
  NCBI__GCF_000016125.1:WP_011869271.1 223 LMG-GAKSYVEPVPVESDHPLFILYTSGTTGSPKGVVHSTGGYLTYATKTMDWTWGLNEMDVFWCTADIGWIT 294
                                           ***.6******************************************************************** PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           Gh+Y+vygPL+ Gat +l+eg+ +yp+++r+w ++e ++vt +YtaPtaiR+lm +ge++v+ hdls+lr+lg
  NCBI__GCF_000016125.1:WP_011869271.1 295 GHTYVVYGPLSLGATIVLYEGAIDYPEPDRLWGIVENHGVTLLYTAPTAIRMLMMYGEKWVNTHDLSTLRLLG 367
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgv.atelkpgsatlPlfGieaevvdeegke 439
                                           svGepinp aw+Wyy+v+Gkekcpi+d +WqtetGg++i p  g+  ++lkpgsat P +Gi+++vvd+eg++
  NCBI__GCF_000016125.1:WP_011869271.1 368 SVGEPINPRAWKWYYKVIGKEKCPICDCYWQTETGGHMIYPAIGIqSVPLKPGSATFPGIGIDVDVVDNEGNP 440
                                           ********************************************9899************************* PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ve++ + g L+ik+pwP+ml ++++++er+  +Y++++k+ + t D+a +d+dGyiw+lGR D+v+nvsGhr+
  NCBI__GCF_000016125.1:WP_011869271.1 441 VEANIK-GNLIIKRPWPGMLAGLWNNDERYRAAYWDRFKNNFSTSDYAIKDQDGYIWVLGRSDEVLNVSGHRI 512
                                           **9999.8***************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegvee.deeelekelkklvrkeigpiakpdkilv 584
                                           gtae+e  lvs+++vae+avvg+pd++kge+ vafv+l+e ++e  ++e++++l++++r+++gpi +p+ i++
  NCBI__GCF_000016125.1:WP_011869271.1 513 GTAELEHELVSNKMVAESAVVGKPDDVKGEVPVAFVILNERYRElPSNEVKATLIRHIRDTVGPIGTPAMIFF 585
                                           ***************************************9987513448************************ PP

                             TIGR02188 585 veelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           v++lPktRsGkimRR+l+k++ gee+  dv+tled++ +e++k+
  NCBI__GCF_000016125.1:WP_011869271.1 586 VNKLPKTRSGKIMRRILKKLIIGEEIG-DVTTLEDNTSLEDVKK 628
                                           **********************98865.************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (636 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 35.96
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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