Alignments for a candidate for acs in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Escherichia coli BW25113

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 18097 b4069 acetyl-coenzyme A synthetase (NCBI)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Keio:18097
          Length = 652

 Score = 1347 bits (3487), Expect = 0.0
 Identities = 652/652 (100%), Positives = 652/652 (100%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF
Sbjct: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
           APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF
Sbjct: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS
Sbjct: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
           RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL
Sbjct: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
           VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI
Sbjct: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA
Sbjct: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG
Sbjct: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480
           FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD
Sbjct: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP
Sbjct: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540

Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
           KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD
Sbjct: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652
           SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS
Sbjct: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652


Lambda     K      H
   0.317    0.135    0.421 

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: 1730
Number of extensions: 45
Number of successful extensions: 1
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: 652
Length of database: 652
Length adjustment: 38
Effective length of query: 614
Effective length of database: 614
Effective search space:   376996
Effective search space used:   376996
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 18097 b4069 (acetyl-coenzyme A synthetase (NCBI))
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.5466.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 1039.2   0.0          0 1038.9   0.0    1.0  1  lcl|FitnessBrowser__Keio:18097  b4069 acetyl-coenzyme A syntheta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18097  b4069 acetyl-coenzyme A synthetase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1038.9   0.0         0         0       3     628 ..      20     643 ..      18     644 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1038.9 bits;  conditional E-value: 0
                       TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaiiw 78 
                                     + ++y+++y+++i+ p++fw++++k  l+w+kp++kv+++s++p   ++kW+edg+ln+++nc+drh++++ d++aiiw
  lcl|FitnessBrowser__Keio:18097  20 NPQQYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTSFAPgnvSIKWYEDGTLNLAANCLDRHLQENGDRTAIIW 97 
                                     6799*********************.6***************999899******************************* PP

                       TIGR02188  79 egdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRi 157
                                     egd++++ s++++Y+el+r+vcr+an+l elG+kkgd vaiY+pm+pea++amlacaRiGavhsv+f+Gfs+ea+a Ri
  lcl|FitnessBrowser__Keio:18097  98 EGDDASQ-SKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRI 175
                                     ***9996.*********************************************************************** PP

                       TIGR02188 158 vdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepek 235
                                     +d++++lvit+deg+R g++i+lkk+vd+al++ +  sve+v+v+krtg ++  w+egrD+ww++lve+ as+++++e+
  lcl|FitnessBrowser__Keio:18097 176 IDSNSRLVITSDEGVRAGRSIPLKKNVDDALKNPNVtSVEHVVVLKRTGGKID-WQEGRDLWWHDLVEQ-ASDQHQAEE 252
                                     *********************************9988**************66.**************6.********* PP

                       TIGR02188 236 ldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfe 314
                                     +++edplfiLYtsGstGkPkGvlhttgGyl++aalt+kyvfd++++di+wCtaDvGWvtGhsY++ygPLa+Gattl+fe
  lcl|FitnessBrowser__Keio:18097 253 MNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLACGATTLMFE 331
                                     ******************************************************************************* PP

                       TIGR02188 315 gvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpiv 393
                                     gvp++p+++r+++v++k++v+i+YtaPtaiRalm++g+++++ +d+sslr+lgsvGepinpeaweWy++++G+ekcp+v
  lcl|FitnessBrowser__Keio:18097 332 GVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVV 410
                                     ******************************************************************************* PP

                       TIGR02188 394 dtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvet 472
                                     dtwWqtetGg++itplpg atelk+gsat+P+fG+++++vd+eg+++e  +e g Lvi+++wP+++rt++gd+erf +t
  lcl|FitnessBrowser__Keio:18097 411 DTWWQTETGGFMITPLPG-ATELKAGSATRPFFGVQPALVDNEGNPLEGATE-GSLVITDSWPGQARTLFGDHERFEQT 487
                                     ******************.6****************************8888.89************************ PP

                       TIGR02188 473 YfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
                                     Yf+++k++yf+GDgarrd+dGy+wi+GRvDdv+nvsGhrlgtaeiesalv+h+++aeaavvg+p++ikg+ai+a+v+l+
  lcl|FitnessBrowser__Keio:18097 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYAYVTLN 566
                                     ******************************************************************************* PP

                       TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                     +g+e++ e l +e++++vrkeigp+a+pd ++++++lPktRsGkimRR+lrkia+g+ ++lgd+stl+dp vve+l e
  lcl|FitnessBrowser__Keio:18097 567 HGEEPSPE-LYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDtSNLGDTSTLADPGVVEKLLE 643
                                     *******5.************************************************99***************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (652 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.84
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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