Alignments for a candidate for acs in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Klebsiella variicola At-22

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_008807262.1 KVAR_RS23800 acetate--CoA ligase

Query= SwissProt::Q8ZKF6
         (652 letters)



>NCBI__GCF_000025465.1:WP_008807262.1
          Length = 652

 Score = 1264 bits (3271), Expect = 0.0
 Identities = 603/652 (92%), Positives = 624/652 (95%)

Query: 1   MSQTHKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSF 60
           MSQ HKH IPANIA+RCLINPEQY+ +Y+QSI DPDTFWGEQGKILDWI PY +VKNTSF
Sbjct: 1   MSQIHKHPIPANIAERCLINPEQYKAQYQQSITDPDTFWGEQGKILDWIRPYTRVKNTSF 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRF 120
           APGN+SIKWYEDGTLNLAANCLDRHL E GD+TAIIWEGDD SQSKHI+YRELH DVCRF
Sbjct: 61  APGNISIKWYEDGTLNLAANCLDRHLAERGDQTAIIWEGDDASQSKHITYRELHADVCRF 120

Query: 121 ANTLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSS 180
           AN LLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGA+HSVIFGGFSPEAVAGRIIDSSS
Sbjct: 121 ANVLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAIHSVIFGGFSPEAVAGRIIDSSS 180

Query: 181 RLVITADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDL 240
           RLVITADEG+RAGR+IPLKKNVDDALKNPNV S+EHV+VLKRTG  IDWQEGRDLWW DL
Sbjct: 181 RLVITADEGLRAGRAIPLKKNVDDALKNPNVNSIEHVVVLKRTGGKIDWQEGRDLWWSDL 240

Query: 241 IEKASPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDI 300
           +  AS EH+P  MNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDI
Sbjct: 241 MANASAEHRPVEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDI 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTA 360
           YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKH+V+ILYTAPTA
Sbjct: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHKVSILYTAPTA 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGG 420
           IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIG EKCPV+DTWWQTETGG
Sbjct: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVMDTWWQTETGG 420

Query: 421 FMITPLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGD 480
           FMITPLPGAIELKAGSATRPFFGVQP LVDNEG P +GATEGNL I DSWPGQARTLFGD
Sbjct: 421 FMITPLPGAIELKAGSATRPFFGVQPVLVDNEGLPLDGATEGNLAIADSWPGQARTLFGD 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALV+HP
Sbjct: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVSHP 540

Query: 541 KIAEAAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
           KIAEAAVVGIPH IKGQAIYAYVTLNHGEEP+PELYAEVRNWVRKEIGPLATPDVLHWTD
Sbjct: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPTPELYAEVRNWVRKEIGPLATPDVLHWTD 600

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652
           SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAI MPS
Sbjct: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAITMPS 652


Lambda     K      H
   0.317    0.135    0.423 

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: 1700
Number of extensions: 55
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 WP_008807262.1 KVAR_RS23800 (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.2988136.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 1030.0   0.0          0 1029.8   0.0    1.0  1  NCBI__GCF_000025465.1:WP_008807262.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_008807262.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1029.8   0.0         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1029.8 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 
                                           + e+yk+ y+++i+dp++fw++++k  l+w++p+++v+++s++p   ++kW+edg+ln+++nc+drh+++r d
  NCBI__GCF_000025465.1:WP_008807262.1  20 NPEQYKAQYQQSITDPDTFWGEQGK-ILDWIRPYTRVKNTSFAPgniSIKWYEDGTLNLAANCLDRHLAERGD 91 
                                           679**********************.6****************99899************************* PP

                             TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145
                                           ++aiiwegd++++ s+++tY+el+++vcr+anvl +lG+kkgd vaiY+pm+pea++amlacaRiGa+hsv+f
  NCBI__GCF_000025465.1:WP_008807262.1  92 QTAIIWEGDDASQ-SKHITYRELHADVCRFANVLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAIHSVIF 163
                                           *********9996.*********************************************************** PP

                             TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDv 217
                                           +Gfs+ea+a Ri+d++++lvitadeglR g++i+lkk+vd+al++ +  s+e+v+v+krtg ++  w+egrD+
  NCBI__GCF_000025465.1:WP_008807262.1 164 GGFSPEAVAGRIIDSSSRLVITADEGLRAGRAIPLKKNVDDALKNPNVnSIEHVVVLKRTGGKID-WQEGRDL 235
                                           *********************************************9988**************66.******* PP

                             TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290
                                           ww++l++ +asae++p ++++edplfiLYtsGstGkPkGvlhttgGyl++aa+t+kyvfd++++di+wCtaDv
  NCBI__GCF_000025465.1:WP_008807262.1 236 WWSDLMA-NASAEHRPVEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADV 307
                                           *******.5**************************************************************** PP

                             TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363
                                           GWvtGhsY++ygPLa+Gattl+fegvp++p+++r+++v++k+kv+i+YtaPtaiRalm++g+++++ +d+ssl
  NCBI__GCF_000025465.1:WP_008807262.1 308 GWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHKVSILYTAPTAIRALMAEGDKAIEGTDRSSL 380
                                           ************************************************************************* PP

                             TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436
                                           r+lgsvGepinpeaweWy++++G+ekcp++dtwWqtetGg++itplpg a+elk+gsat+P+fG+++++vd+e
  NCBI__GCF_000025465.1:WP_008807262.1 381 RILGSVGEPINPEAWEWYWKKIGNEKCPVMDTWWQTETGGFMITPLPG-AIELKAGSATRPFFGVQPVLVDNE 452
                                           ************************************************.6*********************** PP

                             TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           g +++  +e g L+i ++wP+++rt++gd+erf +tYf+++k++yf+GDgarrd+dGy+wi+GRvDdv+nvsG
  NCBI__GCF_000025465.1:WP_008807262.1 453 GLPLDGATE-GNLAIADSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSG 524
                                           *****8777.79************************************************************* PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582
                                           hrlgtaeiesalvsh+++aeaavvg+p++ikg+ai+a+v+l++g+e++ e l +e++++vrkeigp+a+pd +
  NCBI__GCF_000025465.1:WP_008807262.1 525 HRLGTAEIESALVSHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPTPE-LYAEVRNWVRKEIGPLATPDVL 596
                                           *************************************************5.********************** PP

                             TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++++lPktRsGkimRR+lrkia+g+ ++lgd+stl+dp vve+l e
  NCBI__GCF_000025465.1:WP_008807262.1 597 HWTDSLPKTRSGKIMRRILRKIAAGDtSNLGDTSTLADPGVVEKLLE 643
                                           **************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.27
//
[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