Alignments for a candidate for acs in Brevibacterium jeotgali SJ5-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Brevibacterium jeotgali SJ5-8

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_101586946.1 BJEO58_RS01030 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_900169175.1:WP_101586946.1
          Length = 645

 Score =  828 bits (2138), Expect = 0.0
 Identities = 403/648 (62%), Positives = 490/648 (75%), Gaps = 11/648 (1%)

Query: 1   MSESTPEVSSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRL-SWTTPFTEVLDW 59
           M++ T   S++Y PP  FA HAN  A  Y  A+EDRL FWA +A  L  W T FTE LDW
Sbjct: 1   MTDHTESTSTTYAPPEEFAAHANVTAAEYERADEDRLGFWADKARSLLDWETDFTETLDW 60

Query: 60  SGAPFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKA 119
           +  PFA+WF  G LNVA NC+DRHVEAG+GDR+AIH+EGEP GD R +TY++L AEV KA
Sbjct: 61  TNPPFARWFSDGRLNVAANCLDRHVEAGNGDRIAIHFEGEP-GDSRGITYAELTAEVKKA 119

Query: 120 ANALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQA 179
           ANAL  LG+  GDRVAIY+P+IPE VIAMLACARLG  HSVVFGGF++ AL +RI+DA+A
Sbjct: 120 ANALISLGVSQGDRVAIYMPMIPETVIAMLACARLGAPHSVVFGGFSSDALHSRILDAEA 179

Query: 180 KLLITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDLWWHHV 239
           +++ITADG FRRGKPS LK A D A+       VEHV+VV RTG ++ W + RD+ W  +
Sbjct: 180 RVVITADGGFRRGKPSSLKPAVDAAIEK-GGTPVEHVVVVERTGQDVEWFDDRDVAWADL 238

Query: 240 VGSASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSD 299
           +G     HT E F++E+PL++LYTSGTTGKPKGI+HTSGGYLTQ  Y++   FD+KP+ D
Sbjct: 239 MGEQPDEHTAEAFEAENPLYVLYTSGTTGKPKGILHTSGGYLTQATYSVFATFDLKPEKD 298

Query: 300 VFWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPT 359
           VFWCTAD+GWVTGHT+ VYGPL  G T+V+YEGTPDTPD  R + I++KYGVTI YTAPT
Sbjct: 299 VFWCTADVGWVTGHTFIVYGPLSAGATQVIYEGTPDTPDTGRWWDIVQKYGVTILYTAPT 358

Query: 360 LIRMFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETG 419
            IR  MKWG EIP  +DLSSLRLLG+VGEPINPEAW WYR VIG  R P+VDTWWQTETG
Sbjct: 359 AIRTCMKWGDEIPGQYDLSSLRLLGTVGEPINPEAWTWYRSVIGKDRCPVVDTWWQTETG 418

Query: 420 SAMISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSM 479
           + MI+P+PG  A KPGS+  PLPGIS K+VDD G+PL           G LV+D+PWP+M
Sbjct: 419 AHMIAPMPGAMATKPGSSQRPLPGISVKVVDDEGNPL------KNDEPGLLVIDEPWPAM 472

Query: 480 LRGIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAE 539
           LRG++GDP RY  +YWS+F  +G YFAGDGA+ D DG IW LGR+DDVMNVSGHR+ST E
Sbjct: 473 LRGVYGDPERYKDTYWSRF--EGIYFAGDGAKYDEDGDIWFLGRVDDVMNVSGHRLSTTE 530

Query: 540 VESALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYAPHDRTAEELRTEVARVISPIA 599
           +ES+LVAH  VAEAAVVG  D T+ QA+ AF +LR      D   E LR  V   I PIA
Sbjct: 531 IESSLVAHDIVAEAAVVGAADATSGQAVVAFAILRGGVERTDDMEETLRAHVGSDIGPIA 590

Query: 600 RPRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAI 647
           +P+ VH+V ELPKTRSGKI+RRLL+D+AE++ +GD+STL D +V D I
Sbjct: 591 KPKRVHIVDELPKTRSGKIVRRLLKDLAEDKGVGDSSTLADASVMDVI 638


Lambda     K      H
   0.319    0.136    0.433 

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: 1522
Number of extensions: 87
Number of successful extensions: 6
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate WP_101586946.1 BJEO58_RS01030 (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.111990.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-286  937.5   0.0   1.8e-286  937.3   0.0    1.0  1  NCBI__GCF_900169175.1:WP_101586946.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900169175.1:WP_101586946.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  937.3   0.0  1.8e-286  1.8e-286       6     628 ..      24     640 ..      19     641 .. 0.98

  Alignments for each domain:
  == domain 1  score: 937.3 bits;  conditional E-value: 1.8e-286
                             TIGR02188   6 eykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaii 77 
                                             ++ ye+a ed+  fwa++a++ l+w ++f+++ld++++p+++Wf+dg+lnv++nc+drhve+ + d++ai+
  NCBI__GCF_900169175.1:WP_101586946.1  24 VTAAEYERADEDRLGFWADKARSLLDWETDFTETLDWTNPPFARWFSDGRLNVAANCLDRHVEAgNGDRIAIH 96 
                                           55677999***************************************************************** PP

                             TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150
                                           +eg+ +g dsr +tYael++ev ++an+l +lGv +gdrvaiY+pmipe+viamlacaR+Ga hsvvf+Gfs+
  NCBI__GCF_900169175.1:WP_101586946.1  97 FEGE-PG-DSRGITYAELTAEVKKAANALISLGVSQGDRVAIYMPMIPETVIAMLACARLGAPHSVVFGGFSS 167
                                           ****.77.59*************************************************************** PP

                             TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelv 223
                                           +al++Ri daea++vitad+g+R+gk  +lk +vd+a+ek  + ve+v+vv+rtg++v+ w ++rDv+w +l+
  NCBI__GCF_900169175.1:WP_101586946.1 168 DALHSRILDAEARVVITADGGFRRGKPSSLKPAVDAAIEKGGTPVEHVVVVERTGQDVE-WFDDRDVAWADLM 239
                                           *********************************************************66.************* PP

                             TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGWvtG 295
                                            + +++e+++e++++e+pl++LYtsG+tGkPkG+lht+gGyl++a+++v  +fd+k ++d+fwCtaDvGWvtG
  NCBI__GCF_900169175.1:WP_101586946.1 240 GE-QPDEHTAEAFEAENPLYVLYTSGTTGKPKGILHTSGGYLTQATYSVFATFDLKpEKDVFWCTADVGWVTG 311
                                           *6.*****************************************************668************** PP

                             TIGR02188 296 hsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgs 368
                                           h++ivygPL++Gat++++eg+p++pd++r+w++++ky+vti+YtaPtaiR+ mk+g+e++ ++dlsslr+lg+
  NCBI__GCF_900169175.1:WP_101586946.1 312 HTFIVYGPLSAGATQVIYEGTPDTPDTGRWWDIVQKYGVTILYTAPTAIRTCMKWGDEIPGQYDLSSLRLLGT 384
                                           ************************************************************************* PP

                             TIGR02188 369 vGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeve 441
                                           vGepinpeaw+Wy++v+Gk++cp+vdtwWqtetG+++i+p+pg a+++kpgs+++Pl+Gi+++vvd+eg++++
  NCBI__GCF_900169175.1:WP_101586946.1 385 VGEPINPEAWTWYRSVIGKDRCPVVDTWWQTETGAHMIAPMPG-AMATKPGSSQRPLPGISVKVVDDEGNPLK 456
                                           *******************************************.6**************************** PP

                             TIGR02188 442 eeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgt 514
                                           ++e  g+Lvi++pwP+mlr++ygd+er+ +tY+++++g+yf+GDga+ d+dG+iw lGRvDdv+nvsGhrl+t
  NCBI__GCF_900169175.1:WP_101586946.1 457 NDEP-GLLVIDEPWPAMLRGVYGDPERYKDTYWSRFEGIYFAGDGAKYDEDGDIWFLGRVDDVMNVSGHRLST 528
                                           *999.8******************************************************************* PP

                             TIGR02188 515 aeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvvee 587
                                           +eies+lv+h+ vaeaavvg++d + g+a+vaf +l+ gve +++ +e++l+++v + igpiakp+++++v+e
  NCBI__GCF_900169175.1:WP_101586946.1 529 TEIESSLVAHDIVAEAAVVGAADATSGQAVVAFAILRGGVERTDD-MEETLRAHVGSDIGPIAKPKRVHIVDE 600
                                           *****************************************9995.*************************** PP

                             TIGR02188 588 lPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           lPktRsGki+RRll+++ae++  +gd stl+d sv++ +++
  NCBI__GCF_900169175.1:WP_101586946.1 601 LPKTRSGKIVRRLLKDLAEDK-GVGDSSTLADASVMDVISK 640
                                           ******************965.667***********99976 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: 26.50
//
[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 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