Alignments for a candidate for acs in Methylomonas methanica MC09

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methylomonas methanica MC09

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_013819039.1 METME_RS12080 acetate--CoA ligase

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



>NCBI__GCF_000214665.1:WP_013819039.1
          Length = 645

 Score =  862 bits (2227), Expect = 0.0
 Identities = 416/643 (64%), Positives = 491/643 (76%), Gaps = 5/643 (0%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTS 59
           MS   +YPV+PE+AA    D A Y+ +YQQS+ +P+GFW EQA++ LDW +P+  V +  
Sbjct: 1   MSEHHIYPVKPEIAAMAHIDAARYQRLYQQSINDPEGFWAEQARQFLDWAQPWQQVMKCD 60

Query: 60  FDDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCK 119
           F     DI WF  G LNVS NCLDRHL  RGDQ+AIIWEGD P     +TYRELH EVCK
Sbjct: 61  FPTG--DIHWFMGGKLNVSVNCLDRHLDTRGDQVAIIWEGDHPDYDDTLTYRELHSEVCK 118

Query: 120 FANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCK 179
           FAN L+ Q V +GD V IY+PMI EA V +LACTRIGA+HS+VFGGFS +AL  RI+D  
Sbjct: 119 FANVLKAQGVKKGDRVCIYLPMISEAAVVILACTRIGAVHSIVFGGFSADALRDRILDAD 178

Query: 180 SKVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYED 239
            + +I ADE  R GK +P K N D A    +  ++  +IV K T   I W + RD+ Y +
Sbjct: 179 CRYLICADESFRGGKIVPAKINADKAAA--QCPNLHTIIVIKHTGHTIPWTEGRDVCYRE 236

Query: 240 LMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGE 299
            M  A   C P+ M AE+ LFILYTSGSTG+PKGV HTT GYLLYAA+TH+ VFDY+ G+
Sbjct: 237 AMANASDDCPPEIMDAEDPLFILYTSGSTGQPKGVMHTTGGYLLYAAMTHKYVFDYQDGD 296

Query: 300 VYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPT 359
           VYWCTAD+GW+TGHSY++YGPL NGATTL+FEGVP YP   R  +V+DKH+V+I YTAPT
Sbjct: 297 VYWCTADIGWITGHSYVLYGPLCNGATTLMFEGVPTYPAADRFWQVVDKHQVNIFYTAPT 356

Query: 360 AIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETG 419
           AIRA+MA G   V   + SSLR+LGSVGEPINPEAW+WYY  VG+ RCPIVDTWWQTETG
Sbjct: 357 AIRALMAQGDDYVTRTNRSSLRILGSVGEPINPEAWEWYYHVVGEARCPIVDTWWQTETG 416

Query: 420 GVLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYG 479
           G+LI+PLPGAT LKPGSAT PFFG+ PALVDN G L+EG AEGNLVI  SWPGQ R++YG
Sbjct: 417 GILITPLPGATDLKPGSATLPFFGIKPALVDNDGRLLEGVAEGNLVITASWPGQMRSVYG 476

Query: 480 DHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 539
           DHDRF++TYFK F G+YF GDGARRDE GYYWITGRVDDV+NVSGHR+GTAEIESA+V H
Sbjct: 477 DHDRFIETYFKKFPGLYFAGDGARRDEQGYYWITGRVDDVINVSGHRLGTAEIESALVLH 536

Query: 540 PKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWA 599
             VAEAAVVG PH IKGQGIY YVTLNAG E ++ L+ +LK  +++EI  IA PD IQWA
Sbjct: 537 HDVAEAAVVGFPHAIKGQGIYAYVTLNAGVEPTDELKKQLKELIKEEISAIALPDFIQWA 596

Query: 600 PGLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           PGLPKTRSGKIMRRILRKIA  +   LGD STLADP VV  L+
Sbjct: 597 PGLPKTRSGKIMRRILRKIAANDISSLGDTSTLADPAVVDDLL 639


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: 1432
Number of extensions: 67
Number of successful extensions: 3
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: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
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_013819039.1 METME_RS12080 (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.2335295.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 1024.8   0.0          0 1024.5   0.0    1.0  1  NCBI__GCF_000214665.1:WP_013819039.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214665.1:WP_013819039.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1024.5   0.0         0         0       4     627 ..      21     639 ..      18     641 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1024.5 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                           + +y++ly+++i+dpe fwa++a++ l+w++p+++v+++++++ +++Wf +g+lnvs+nc+drh+ +r d+va
  NCBI__GCF_000214665.1:WP_013819039.1  21 AARYQRLYQQSINDPEGFWAEQARQFLDWAQPWQQVMKCDFPTgDIHWFMGGKLNVSVNCLDRHLDTRGDQVA 93 
                                           678***************************************99***************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           iiwegd+++    +ltY+el++evc++anvlk++Gvkkgdrv+iYlpmi ea++++lac+RiGavhs+vf+Gf
  NCBI__GCF_000214665.1:WP_013819039.1  94 IIWEGDHPDY-DDTLTYRELHSEVCKFANVLKAQGVKKGDRVCIYLPMISEAAVVILACTRIGAVHSIVFGGF 165
                                           ******9997.99************************************************************ PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           sa+al++Ri da+++++i+ade++Rggk+++ k ++d+a ++++ ++++++v+k+tg+ +  w+egrDv ++e
  NCBI__GCF_000214665.1:WP_013819039.1 166 SADALRDRILDADCRYLICADESFRGGKIVPAKINADKAAAQCP-NLHTIIVIKHTGHTIP-WTEGRDVCYRE 236
                                           *******************************************9.6*************66.*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                           +++ +as++c+pe +d+edplfiLYtsGstG+PkGv+httgGyll+aa+t+kyvfd++d+d++wCtaD+GW+t
  NCBI__GCF_000214665.1:WP_013819039.1 237 AMA-NASDDCPPEIMDAEDPLFILYTSGSTGQPKGVMHTTGGYLLYAAMTHKYVFDYQDGDVYWCTADIGWIT 308
                                           ***.5******************************************************************** PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           GhsY++ygPL+nGattl+fegvptyp a+rfw+v++k++v+ifYtaPtaiRalm++g++ v+++++sslr+lg
  NCBI__GCF_000214665.1:WP_013819039.1 309 GHSYVLYGPLCNGATTLMFEGVPTYPAADRFWQVVDKHQVNIFYTAPTAIRALMAQGDDYVTRTNRSSLRILG 381
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           svGepinpeaweWyy+vvG+ +cpivdtwWqtetGgilitplpg at+lkpgsatlP+fGi++++vd++g+ +
  NCBI__GCF_000214665.1:WP_013819039.1 382 SVGEPINPEAWEWYYHVVGEARCPIVDTWWQTETGGILITPLPG-ATDLKPGSATLPFFGIKPALVDNDGRLL 453
                                           ********************************************.6*************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                           e  +e g Lvi+ +wP+++r++ygd++rf+etYfkk++glyf+GDgarrd++Gy+wi+GRvDdvinvsGhrlg
  NCBI__GCF_000214665.1:WP_013819039.1 454 EGVAE-GNLVITASWPGQMRSVYGDHDRFIETYFKKFPGLYFAGDGARRDEQGYYWITGRVDDVINVSGHRLG 525
                                           98777.79***************************************************************** PP

                             TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
                                           taeiesalv h++vaeaavvg+p+ ikg+ i+a+v+l++gve+++e l+k+lk+l+++ei++ia pd i++++
  NCBI__GCF_000214665.1:WP_013819039.1 526 TAEIESALVLHHDVAEAAVVGFPHAIKGQGIYAYVTLNAGVEPTDE-LKKQLKELIKEEISAIALPDFIQWAP 597
                                           *********************************************5.************************** PP

                             TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                            lPktRsGkimRR+lrkia+++ ++lgd+stl+dp+vv++l 
  NCBI__GCF_000214665.1:WP_013819039.1 598 GLPKTRSGKIMRRILRKIAANDiSSLGDTSTLADPAVVDDLL 639
                                           **************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (645 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: 31.19
//
[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