Alignments for a candidate for acs in Archaeoglobus veneficus SNP6

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Archaeoglobus veneficus SNP6

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_013683035.1 ARCVE_RS01620 acetate--CoA ligase

Query= BRENDA::A0B8F1
         (659 letters)



>NCBI__GCF_000194625.1:WP_013683035.1
          Length = 657

 Score =  771 bits (1990), Expect = 0.0
 Identities = 360/646 (55%), Positives = 475/646 (73%), Gaps = 4/646 (0%)

Query: 10  LQEETRIFNTPQWIIEYSNSYQWMKKKGFKTEKEMREWCAQNYLDFWDEMAQTYADWFKP 69
           + EE ++  +   + E        ++K +  +  + +   ++++ FWDE+A+T  +WF+P
Sbjct: 1   MSEEPKVIESLLKVEETYEPPADFREKAWVKDDSVYKKAEEDFISFWDEIAKTEIEWFEP 60

Query: 70  YTQILE-WNPPYAKWFLGGKCNVAHNAVDRHAKSWRRNKVAYYFVGEPVGDTKTITYYQL 128
           Y ++L+  N P+ KWF+GGK N+ +N +DRH KSWR+NK A  + GEP  D + ITYY+L
Sbjct: 61  YEKVLDDSNAPFYKWFIGGKINITYNCLDRHVKSWRKNKAAIIWQGEPEEDKRVITYYEL 120

Query: 129 YQAVNKMANGLKSLGVKKGDRVSIYLPMIPELPITMLACAKIGAIHSVVFSGFSAGGLQS 188
           Y+ V + AN LK LGVKKGDRV+IY+ M+PELP+ MLACA+IGAIHSVVF GFSA  L+ 
Sbjct: 121 YRRVCRFANALKKLGVKKGDRVTIYMGMVPELPVAMLACARIGAIHSVVFGGFSASALRD 180

Query: 189 RVTDAEAKVVVTSDGFYRRGKPLPLKPNVDEAVQNAPSVEKVVVVKRVGLDVPMKEGRDI 248
           R+ DA+AKVV+T DGFYRRGK +  K  VDEA+++APSV+ VVV+KR+G ++ M+E RDI
Sbjct: 181 RINDAQAKVVITMDGFYRRGKVVETKRIVDEALEDAPSVQNVVVLKRIGNEINMEEDRDI 240

Query: 249 WYHDLVKDQPAECYTEELDPEDRLFILYTSGTTGKPKGIEHAHGGFCVGPAYTTAWALDV 308
           W+HDL      EC  E +D E  LFILYTSGTTGKPKG+ H HGG+ VG   TT W  D+
Sbjct: 241 WWHDLQYGVTPECEPEVVDSEHPLFILYTSGTTGKPKGVLHVHGGYNVGTHITTKWIFDL 300

Query: 309 HEEDVYWCTADCGWITGHSYVVYGPLCLGATSILYEGAPDYPDIGRWWSIIEEYGVSVFY 368
            ++D+YWCTAD GWITGHSY+VYGPL  GAT ++YEGAPDYP   RWWSIIE YGV+VFY
Sbjct: 301 KDDDIYWCTADIGWITGHSYIVYGPLSNGATVLMYEGAPDYPQPDRWWSIIERYGVTVFY 360

Query: 369 TAPTAIRMFMKAGDQWPKKYNLKSIRILASVGEPLNPEAYVWFRNNIGGGQAPIIDTWWQ 428
           TAPTAIR FM+ G++WPKK++L S+R+L +VGEP+NPEA+ W+   IG  + PI+DTWWQ
Sbjct: 361 TAPTAIRFFMRLGEEWPKKHDLSSLRLLGTVGEPINPEAWKWYYKYIGNEKCPIVDTWWQ 420

Query: 429 TETGCHVIAPLP-MTPEKPGSVAFPLPGFNTDIYDEDGNSVPLGYGGNIVQKTPWPSMLR 487
           TETG  +I+PLP +T  KPGS   P PG   DIYDEDGN VP   GG +V   PWPSMLR
Sbjct: 421 TETGMILISPLPGVTKLKPGSATLPFPGVVADIYDEDGNPVPPNTGGKLVITRPWPSMLR 480

Query: 488 AFFRDPERYMKEYWQMYWDIKPGTYLAGDKATRDKDGYWWIQGRIDDVLKVAGHRISNAE 547
             + DP+RY+++YW  Y D     Y  GD A RD+DGY+WI GRIDDVL V+GHRI  AE
Sbjct: 481 TLWGDPDRYVRQYWSAYKD--KLVYFTGDGARRDEDGYFWIIGRIDDVLNVSGHRIGTAE 538

Query: 548 VESAAVSHPAVAEAAVIGKPDEVKGEVIVAFIILKEGVQESEDLKKDIAKHVRSVLGPVA 607
           +ESA V+H AV+EAAVIGKP EVKGEV VAF++LK G + + +LKK++   VR  +GP+A
Sbjct: 539 LESALVAHKAVSEAAVIGKPHEVKGEVPVAFVVLKAGYEPTPELKKELKNWVRKEIGPIA 598

Query: 608 YPEIVYFVKDVPKTRSGKIMRRVIKAKALGKPVGDISALANPESVE 653
            PE ++F++ +PKTRSGKIMRR+++A   G+ +GD++ L +  +VE
Sbjct: 599 VPEEIHFLEKLPKTRSGKIMRRILRAIEKGEAIGDVTTLEDETAVE 644


Lambda     K      H
   0.318    0.137    0.438 

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: 1482
Number of extensions: 71
Number of successful extensions: 4
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: 659
Length of database: 657
Length adjustment: 38
Effective length of query: 621
Effective length of database: 619
Effective search space:   384399
Effective search space used:   384399
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_013683035.1 ARCVE_RS01620 (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.2569437.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 1027.3   0.4          0 1027.0   0.4    1.0  1  NCBI__GCF_000194625.1:WP_013683035.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000194625.1:WP_013683035.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1027.0   0.4         0         0       8     628 ..      33     648 ..      27     649 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1027.0 bits;  conditional E-value: 0
                             TIGR02188   8 kelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwe 79 
                                            ++y++a+ed  +fw++ ak+e+ew++p+ekvld+s++p++kWf +g++n++ync+drhv++ rk+k+aiiw 
  NCBI__GCF_000194625.1:WP_013683035.1  33 DSVYKKAEEDFISFWDEIAKTEIEWFEPYEKVLDDSNAPFYKWFIGGKINITYNCLDRHVKSwRKNKAAIIWQ 105
                                           5789********************************************************************* PP

                             TIGR02188  80 gdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152
                                           g+ ++ed+r +tY+el+r+vcr+an+lk+lGvkkgdrv+iY+ m+pe+ +amlacaRiGa+hsvvf+Gfsa+a
  NCBI__GCF_000194625.1:WP_013683035.1 106 GE-PEEDKRVITYYELYRRVCRFANALKKLGVKKGDRVTIYMGMVPELPVAMLACARIGAIHSVVFGGFSASA 177
                                           **.6668****************************************************************** PP

                             TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvek 225
                                           l++Ri+da+ak+vit d+ +R+gkv+e+k+ivdeale+a+ sv++v+v+kr+g+e++ ++e+rD+ww++l   
  NCBI__GCF_000194625.1:WP_013683035.1 178 LRDRINDAQAKVVITMDGFYRRGKVVETKRIVDEALEDAP-SVQNVVVLKRIGNEIN-MEEDRDIWWHDLQY- 247
                                           ***************************************9.7*************66.*************9. PP

                             TIGR02188 226 easaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298
                                           +++ ecepe +dse+plfiLYtsG+tGkPkGvlh  gGy + +++t+k++fd+kd+di+wCtaD+GW+tGhsY
  NCBI__GCF_000194625.1:WP_013683035.1 248 GVTPECEPEVVDSEHPLFILYTSGTTGKPKGVLHVHGGYNVGTHITTKWIFDLKDDDIYWCTADIGWITGHSY 320
                                           6************************************************************************ PP

                             TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGe 371
                                           ivygPL+nGat l++eg+p+yp+++r+w++ie+y+vt+fYtaPtaiR +m+lgee++kkhdlsslr+lg+vGe
  NCBI__GCF_000194625.1:WP_013683035.1 321 IVYGPLSNGATVLMYEGAPDYPQPDRWWSIIERYGVTVFYTAPTAIRFFMRLGEEWPKKHDLSSLRLLGTVGE 393
                                           ************************************************************************* PP

                             TIGR02188 372 pinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeee 444
                                           pinpeaw+Wyy+++G+ekcpivdtwWqtetG ili+plpg +t+lkpgsatlP++G+ a++ de+g++v +++
  NCBI__GCF_000194625.1:WP_013683035.1 394 PINPEAWKWYYKYIGNEKCPIVDTWWQTETGMILISPLPG-VTKLKPGSATLPFPGVVADIYDEDGNPVPPNT 465
                                           ****************************************.5*****************************99 PP

                             TIGR02188 445 eggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgta 515
                                           + g Lvi++pwPsmlrt++gd++r+v++Y++++k+  +yftGDgarrd+dGy+wi+GR+Ddv+nvsGhr+gta
  NCBI__GCF_000194625.1:WP_013683035.1 466 G-GKLVITRPWPSMLRTLWGDPDRYVRQYWSAYKDklVYFTGDGARRDEDGYFWIIGRIDDVLNVSGHRIGTA 537
                                           9.8******************************99899*********************************** PP

                             TIGR02188 516 eiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveel 588
                                           e+esalv+h+av+eaav+g+p+e+kge+ vafvvlk+g+e++ e l+kelk++vrkeigpia p++i++ e+l
  NCBI__GCF_000194625.1:WP_013683035.1 538 ELESALVAHKAVSEAAVIGKPHEVKGEVPVAFVVLKAGYEPTPE-LKKELKNWVRKEIGPIAVPEEIHFLEKL 609
                                           *******************************************5.**************************** PP

                             TIGR02188 589 PktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           PktRsGkimRR+lr+i +ge  +gdv+tled+++vee k+
  NCBI__GCF_000194625.1:WP_013683035.1 610 PKTRSGKIMRRILRAIEKGEA-IGDVTTLEDETAVEEAKK 648
                                           ****************99875.56************9887 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 22.37
//
[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