Alignments for a candidate for acs in Thiohalospira halophila HL 3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Thiohalospira halophila HL 3

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_093426890.1 BM272_RS00970 acetate--CoA ligase

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



>NCBI__GCF_900112605.1:WP_093426890.1
          Length = 646

 Score =  861 bits (2225), Expect = 0.0
 Identities = 418/648 (64%), Positives = 498/648 (76%), Gaps = 4/648 (0%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTS 59
           MS   +YPV   VAA     +A Y+AMY++SV +P+GFW EQA R LDW + + T    S
Sbjct: 1   MSEHKVYPVPESVAARAHVTQAEYEAMYRRSVDDPEGFWAEQADRFLDWFEKWDTTLDWS 60

Query: 60  FDDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCK 119
           F+   V ++WF  G LNV++NC+DRHLAE  ++ A+IWEGD+P + ++IT+RELHE+V +
Sbjct: 61  FEGD-VHVEWFKGGKLNVAHNCIDRHLAEHAEKTALIWEGDEPDQDQHITFRELHEQVSR 119

Query: 120 FANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCK 179
             N L+ + V +GD V +YMPMIPEAV AMLAC RIGA+HSVVFGGFSPEAL  RI D +
Sbjct: 120 LGNVLKERGVSKGDRVCLYMPMIPEAVYAMLACARIGAVHSVVFGGFSPEALKDRIQDAE 179

Query: 180 SKVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYED 239
           + VVITADEGVR G+K+ LKAN D A+   +  S+  V+  +RT G+I WN  RD+WY +
Sbjct: 180 ASVVITADEGVRGGRKVGLKANTDKAVD--QCPSVHTVLTVRRTGGDIGWNDSRDVWYHE 237

Query: 240 LMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGE 299
            ++ A   C  + M AE+ LFILYTSGSTGKPKGV HTT GYLLYAA+T    FD +P +
Sbjct: 238 AVEAASADCPAEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLYAAITTWYTFDLQPDD 297

Query: 300 VYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPT 359
           VYWCTADVGW+TGHSY+VYGPLAN  T+++FEGVP+YPD +R  +V+DKH+VS+ YTAPT
Sbjct: 298 VYWCTADVGWITGHSYLVYGPLANATTSVVFEGVPSYPDASRFWEVVDKHQVSVFYTAPT 357

Query: 360 AIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETG 419
           AIRA+M  G   V   D SSLR+LG+VGEPINPEAW+WYY  VGKE+CPIVDTWWQTETG
Sbjct: 358 AIRALMREGDEPVTKTDRSSLRILGTVGEPINPEAWEWYYHVVGKEQCPIVDTWWQTETG 417

Query: 420 GVLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYG 479
           G LI+PLPGAT LKPGSATRPFFG+VPAL+D  G+++EG  EG LVI   WPGQ RT+YG
Sbjct: 418 GHLITPLPGATELKPGSATRPFFGIVPALMDTDGHVVEGEGEGALVITRPWPGQMRTIYG 477

Query: 480 DHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 539
           +H RFV+TYF  F G YF+GDGARRD +G YWITGR+DDVLNVSGHRMGTAEIESA+V H
Sbjct: 478 NHQRFVETYFSAFKGCYFSGDGARRDGNGDYWITGRMDDVLNVSGHRMGTAEIESALVLH 537

Query: 540 PKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWA 599
             VAEAAVVG PHD+KGQGIY YV L    E S+ALR EL N VR EIGPIASPD IQWA
Sbjct: 538 DAVAEAAVVGYPHDVKGQGIYAYVILVKDAEPSDALRKELVNLVRSEIGPIASPDAIQWA 597

Query: 600 PGLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKT 647
           PGLPKTRSGKIMRRILRKIA  E D LGD STLADP VV  LI    T
Sbjct: 598 PGLPKTRSGKIMRRILRKIAANELDSLGDTSTLADPAVVDELINNRVT 645


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: 1445
Number of extensions: 73
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: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space:   372704
Effective search space used:   372704
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_093426890.1 BM272_RS00970 (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.362720.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 1026.7   0.0          0 1026.5   0.0    1.0  1  NCBI__GCF_900112605.1:WP_093426890.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093426890.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1026.5   0.0         0         0       4     628 ..      21     641 ..      18     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1026.5 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                           + ey+++y+++++dpe fwa++a + l+w+++++++ld+s+e   +v+Wf++g+lnv+ nc+drh++++++k+
  NCBI__GCF_900112605.1:WP_093426890.1  21 QAEYEAMYRRSVDDPEGFWAEQADRFLDWFEKWDTTLDWSFEGdvHVEWFKGGKLNVAHNCIDRHLAEHAEKT 93 
                                           679**************************************987899************************** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           a+iwegde+++  +++t++el+++v+rl nvlke Gv kgdrv++Y+pmipeav+amlacaRiGavhsvvf+G
  NCBI__GCF_900112605.1:WP_093426890.1  94 ALIWEGDEPDQ-DQHITFRELHEQVSRLGNVLKERGVSKGDRVCLYMPMIPEAVYAMLACARIGAVHSVVFGG 165
                                           *********97.99*********************************************************** PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fs+eal++Ri+daea +vitadeg+Rgg+++ lk+++d+a+++++ sv++vl v+rtg ++  w+++rDvw++
  NCBI__GCF_900112605.1:WP_093426890.1 166 FSPEALKDRIQDAEASVVITADEGVRGGRKVGLKANTDKAVDQCP-SVHTVLTVRRTGGDIG-WNDSRDVWYH 236
                                           ********************************************9.7*************77.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           e+ve  asa+c++e++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+ y+fd++++d++wCtaDvGW+
  NCBI__GCF_900112605.1:WP_093426890.1 237 EAVEA-ASADCPAEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLYAAITTWYTFDLQPDDVYWCTADVGWI 308
                                           ****5.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsY+vygPLan  t+++fegvp+ypdasrfwev++k++v++fYtaPtaiRalm++g+e v+k+d+sslr+l
  NCBI__GCF_900112605.1:WP_093426890.1 309 TGHSYLVYGPLANATTSVVFEGVPSYPDASRFWEVVDKHQVSVFYTAPTAIRALMREGDEPVTKTDRSSLRIL 381
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           g+vGepinpeaweWyy+vvGke+cpivdtwWqtetGg+litplpg atelkpgsat+P+fGi ++++d++g+ 
  NCBI__GCF_900112605.1:WP_093426890.1 382 GTVGEPINPEAWEWYYHVVGKEQCPIVDTWWQTETGGHLITPLPG-ATELKPGSATRPFFGIVPALMDTDGHV 453
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ve e e g+Lvi++pwP+++rtiyg+++rfvetYf+++kg+yf+GDgarrd +G++wi+GR+Ddv+nvsGhr+
  NCBI__GCF_900112605.1:WP_093426890.1 454 VEGEGE-GALVITRPWPGQMRTIYGNHQRFVETYFSAFKGCYFSGDGARRDGNGDYWITGRMDDVLNVSGHRM 525
                                           *98777.8***************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtaeiesalv h+avaeaavvg+p+++kg+ i+a+v+l + +e+++ +l+kel +lvr+eigpia+pd i+++
  NCBI__GCF_900112605.1:WP_093426890.1 526 GTAEIESALVLHDAVAEAAVVGYPHDVKGQGIYAYVILVKDAEPSD-ALRKELVNLVRSEIGPIASPDAIQWA 597
                                           **********************************************.5************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           + lPktRsGkimRR+lrkia++e ++lgd+stl+dp+vv+el++
  NCBI__GCF_900112605.1:WP_093426890.1 598 PGLPKTRSGKIMRRILRKIAANElDSLGDTSTLADPAVVDELIN 641
                                           *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (646 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: 22.26
//
[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