Alignments for a candidate for acs in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Thiothrix lacustris DSM 21227

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_028489625.1 Q394_RS0112815 acetate--CoA ligase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>NCBI__GCF_000621325.1:WP_028489625.1
          Length = 648

 Score =  865 bits (2236), Expect = 0.0
 Identities = 423/645 (65%), Positives = 492/645 (76%), Gaps = 4/645 (0%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTS 59
           MS    YPV  E AA    +   Y +MY QS+ +PD FW EQA++ L W + +  V+  S
Sbjct: 1   MSDVKTYPVPAEFAAQANINAEQYASMYAQSINDPDTFWGEQAEQYLTWFQKWDKVQDWS 60

Query: 60  FDDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCK 119
           FD   + I WF  GTLNVSYNCLDRHL  RGDQ+AIIWEGD+P+E R ITYRELH EV K
Sbjct: 61  FDQDDLHINWFTGGTLNVSYNCLDRHLDTRGDQVAIIWEGDNPNEDRKITYRELHAEVSK 120

Query: 120 FANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCK 179
            AN L+ + V RGD V++Y+PMIPEA VAMLACTRIGAIHS+VFGGFSP+AL  RI D +
Sbjct: 121 LANVLKARGVKRGDRVSLYLPMIPEAAVAMLACTRIGAIHSIVFGGFSPDALRDRIQDSE 180

Query: 180 SKVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYED 239
             VVIT+D+ +R GKK+PLK N D A+   +  S+   IV +R    +KWN  RD+WY +
Sbjct: 181 CGVVITSDQSMRGGKKVPLKGNADKAMD--QCPSVHTCIVVQRGGDPVKWNDSRDVWYHE 238

Query: 240 LMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGE 299
            +  A   C  + M A++ LFILYTSGSTGKPKGV HTT GYLL AA+TH+ VFDYK GE
Sbjct: 239 AIAAADAECPAEPMEADDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTHKTVFDYKDGE 298

Query: 300 VYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPT 359
           VYWCTADVGWVTGHSYIVYGPLANGAT+L+FEG+P YPD  R  +V DKH V+  YTAPT
Sbjct: 299 VYWCTADVGWVTGHSYIVYGPLANGATSLMFEGIPTYPDAGRFWQVCDKHNVATFYTAPT 358

Query: 360 AIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETG 419
           AIR +M +G   VE A  SSLRLLGSVGEPINPEAW+WY++ VGK RCPIVDTWWQTETG
Sbjct: 359 AIRMLMGAGDQFVEKAQLSSLRLLGSVGEPINPEAWEWYHRVVGKNRCPIVDTWWQTETG 418

Query: 420 GVLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEG-AAEGNLVILDSWPGQARTLY 478
             +++PLPGAT LKPGSAT PFFGV P L+D+ GN +EG  A GNL I   WP   R+LY
Sbjct: 419 AHMLTPLPGATPLKPGSATHPFFGVEPCLLDDQGNEVEGNPAVGNLAIKRPWPSMMRSLY 478

Query: 479 GDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVA 538
           GDH RF + YF  F G YFTGDGARRDEDGYYWITGRVDDVLN+SGHR+GTAEIESA+V 
Sbjct: 479 GDHKRFYEAYFAMFKGYYFTGDGARRDEDGYYWITGRVDDVLNISGHRLGTAEIESALVL 538

Query: 539 HPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQW 598
           HPKVAEAAVVG PH++ GQGIY YVTL AGEE ++ L+ EL   VRKEIGPIA  ++IQW
Sbjct: 539 HPKVAEAAVVGYPHELTGQGIYAYVTLMAGEEGTDDLKNELNTLVRKEIGPIAKINIIQW 598

Query: 599 APGLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           +PGLPKTRSGKIMRRILRKIA  E DGLGD STLADP VV +LI+
Sbjct: 599 SPGLPKTRSGKIMRRILRKIAANEIDGLGDTSTLADPSVVDNLID 643


Lambda     K      H
   0.318    0.135    0.418 

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: 1437
Number of extensions: 77
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: 651
Length of database: 648
Length adjustment: 38
Effective length of query: 613
Effective length of database: 610
Effective search space:   373930
Effective search space used:   373930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_028489625.1 Q394_RS0112815 (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.590711.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 1042.6   0.0          0 1042.4   0.0    1.0  1  NCBI__GCF_000621325.1:WP_028489625.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000621325.1:WP_028489625.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1042.4   0.0         0         0       3     627 ..      20     642 ..      18     644 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1042.4 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 
                                           ++e+y+++y+++i+dp++fw+++a++ l+w+++++kv+d+s+++   +++Wf++g+lnvsync+drh+ +r d
  NCBI__GCF_000621325.1:WP_028489625.1  20 NAEQYASMYAQSINDPDTFWGEQAEQYLTWFQKWDKVQDWSFDQddlHINWFTGGTLNVSYNCLDRHLDTRGD 92 
                                           789**************************************9988889************************* PP

                             TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145
                                           +vaiiwegd+++e  rk+tY+el++ev++lanvlk+ Gvk+gdrv++Ylpmipea++amlac+RiGa+hs+vf
  NCBI__GCF_000621325.1:WP_028489625.1  93 QVAIIWEGDNPNE-DRKITYRELHAEVSKLANVLKARGVKRGDRVSLYLPMIPEAAVAMLACTRIGAIHSIVF 164
                                           **********996.9********************************************************** PP

                             TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvw 218
                                           +Gfs++al++Ri+d+e+ +vit+d+++Rggk+++lk ++d+a+++++ sv++++vv+r g++v+ w+++rDvw
  NCBI__GCF_000621325.1:WP_028489625.1 165 GGFSPDALRDRIQDSECGVVITSDQSMRGGKKVPLKGNADKAMDQCP-SVHTCIVVQRGGDPVK-WNDSRDVW 235
                                           **********************************************9.7*************66.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           ++e+++  a+aec++e+++++dplfiLYtsGstGkPkGvlhttgGyll+aa+t+k+vfd+kd++++wCtaDvG
  NCBI__GCF_000621325.1:WP_028489625.1 236 YHEAIAA-ADAECPAEPMEADDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTHKTVFDYKDGEVYWCTADVG 307
                                           ******5.***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           WvtGhsYivygPLanGat+l+feg+ptypda+rfw+v++k++v++fYtaPtaiR+lm +g+++v+k +lsslr
  NCBI__GCF_000621325.1:WP_028489625.1 308 WVTGHSYIVYGPLANGATSLMFEGIPTYPDAGRFWQVCDKHNVATFYTAPTAIRMLMGAGDQFVEKAQLSSLR 380
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           +lgsvGepinpeaweWy++vvGk++cpivdtwWqtetG++++tplpg at+lkpgsat+P+fG+e+ ++d++g
  NCBI__GCF_000621325.1:WP_028489625.1 381 LLGSVGEPINPEAWEWYHRVVGKNRCPIVDTWWQTETGAHMLTPLPG-ATPLKPGSATHPFFGVEPCLLDDQG 452
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           +eve +   g L+ik+pwPsm+r++ygd++rf e+Yf  +kg+yftGDgarrd+dGy+wi+GRvDdv+n+sGh
  NCBI__GCF_000621325.1:WP_028489625.1 453 NEVEGNPAVGNLAIKRPWPSMMRSLYGDHKRFYEAYFAMFKGYYFTGDGARRDEDGYYWITGRVDDVLNISGH 525
                                           ****888889*************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           rlgtaeiesalv h++vaeaavvg+p+e++g+ i+a+v+l++g+e ++ +l++el++lvrkeigpiak + i+
  NCBI__GCF_000621325.1:WP_028489625.1 526 RLGTAEIESALVLHPKVAEAAVVGYPHELTGQGIYAYVTLMAGEEGTD-DLKNELNTLVRKEIGPIAKINIIQ 597
                                           *********************************************999.5*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           + + lPktRsGkimRR+lrkia++e + lgd+stl+dpsvv++l+
  NCBI__GCF_000621325.1:WP_028489625.1 598 WSPGLPKTRSGKIMRRILRKIAANEiDGLGDTSTLADPSVVDNLI 642
                                           ******************************************987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 22.22
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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