Alignments for a candidate for acs in Nocardioides daejeonensis MJ31

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Nocardioides daejeonensis MJ31

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_110207905.1 DNK54_RS14895 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_003194585.1:WP_110207905.1
          Length = 644

 Score =  835 bits (2156), Expect = 0.0
 Identities = 403/638 (63%), Positives = 486/638 (76%), Gaps = 10/638 (1%)

Query: 12  YPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSGAPFAKWFVGG 71
           +PPP   A  AN   E Y  AE DR  FWA+QA RL W   +  VLDW   PFAKWF GG
Sbjct: 7   FPPPEALAAAANVTEEAYARAEADREGFWAEQAERLDWGQKWDRVLDWDNPPFAKWFTGG 66

Query: 72  ELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAANALTDLGLVAG 131
            +N A NCVDRHV AG G++VAIHW GEP  D R +TY+ L  EV++AANALT+LG+  G
Sbjct: 67  TINAAVNCVDRHVTAGRGEKVAIHWVGEPEDDTRDITYAQLQDEVNRAANALTELGVAKG 126

Query: 132 DRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKLLITADGQFRR 191
           DRVAIYLP+IPEAV+ MLACARLG  H+VVFGGF+A AL +RIVD  A++++TADG +RR
Sbjct: 127 DRVAIYLPMIPEAVVTMLACARLGAPHTVVFGGFSADALASRIVDCGARVVVTADGGYRR 186

Query: 192 GKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDLWWHHVVGSASPAHTPEP 251
           G PS LK A DEA+A   D  VEHV+VV+RTG E+A+ E RDLWWH ++G  SP H  E 
Sbjct: 187 GAPSALKPAVDEAVAKA-DGLVEHVVVVQRTGQEVAFDETRDLWWHELMGRQSPQHDAEL 245

Query: 252 FDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDVFWCTADIGWVT 311
            D+EHPL+++YTSGTTGKPKGI+HT+GGYL    Y+   +FD+K D+DV+WCTADIGWVT
Sbjct: 246 HDAEHPLYVMYTSGTTGKPKGILHTTGGYLVGTAYSHWAVFDLKADTDVYWCTADIGWVT 305

Query: 312 GHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTLIRMFMKWGREI 371
           GH+Y VYGPL NG T+VLYEGTPD+P + R ++IIEKYGVTI+YTAPT IR FMKWG +I
Sbjct: 306 GHSYLVYGPLANGATQVLYEGTPDSPHKGRWWEIIEKYGVTIFYTAPTAIRTFMKWGNDI 365

Query: 372 PDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGSAMISPLPGIAA 431
           P   DLSS+R+LGSVGEPINPEA+ WYR  IGG R P+VDTWWQTETG  MI+P+PG+  
Sbjct: 366 PAKFDLSSIRVLGSVGEPINPEAYVWYRSTIGGDRAPVVDTWWQTETGQIMITPMPGVTH 425

Query: 432 AKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLRGIWGDPARYW 491
           AKPGSAM PLPGI A +V+D G+ +P  +       GYL++ +PWP+MLR +WGD  RY 
Sbjct: 426 AKPGSAMRPLPGIVADVVNDEGESVPDGS------GGYLIIREPWPAMLRTVWGDDERYK 479

Query: 492 HSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVESALVAHSGVA 551
            +YWS++   G YFAGDGA+ D DG IWVLGR+DDVMNVSGHR+ST E+ESALV+H  VA
Sbjct: 480 DTYWSRW--PGVYFAGDGAKKDEDGDIWVLGRVDDVMNVSGHRLSTTEIESALVSHPKVA 537

Query: 552 EAAVVGVTDETTTQAICAFVVLRANYAP-HDRTAEELRTEVARVISPIARPRDVHVVPEL 610
           EAAVVG TDETT QA+CAFV+LR +     D    ELR  VA+ I  IA+PR V +VPEL
Sbjct: 538 EAAVVGATDETTGQAVCAFVILRESAGDGGDEIVAELRNHVAKEIGAIAKPRQVMIVPEL 597

Query: 611 PKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAIR 648
           PKTRSGKIMRRLLRDVAENRE+GD +TL D +V   I+
Sbjct: 598 PKTRSGKIMRRLLRDVAENREIGDVTTLADSSVMSLIQ 635


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: 1506
Number of extensions: 65
Number of successful extensions: 5
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: 644
Length adjustment: 38
Effective length of query: 613
Effective length of database: 606
Effective search space:   371478
Effective search space used:   371478
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_110207905.1 DNK54_RS14895 (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.3711669.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-296  970.0   1.5   2.6e-296  969.8   1.5    1.0  1  NCBI__GCF_003194585.1:WP_110207905.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003194585.1:WP_110207905.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  969.8   1.5  2.6e-296  2.6e-296       5     627 ..      18     635 ..      14     637 .. 0.98

  Alignments for each domain:
  == domain 1  score: 969.8 bits;  conditional E-value: 2.6e-296
                             TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvai 76 
                                           +  +e y++a++d+e fwa++a+ +l+w +++++vld++++p++kWf++g++n+++ncvdrhv++ r +kvai
  NCBI__GCF_003194585.1:WP_110207905.1  18 NVTEEAYARAEADREGFWAEQAE-RLDWGQKWDRVLDWDNPPFAKWFTGGTINAAVNCVDRHVTAgRGEKVAI 89 
                                           5678999***************9.5****************************************9******* PP

                             TIGR02188  77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfs 149
                                           +w g+ +++d+r +tYa+l++ev+r+an+l+elGv kgdrvaiYlpmipeav++mlacaR+Ga h+vvf+Gfs
  NCBI__GCF_003194585.1:WP_110207905.1  90 HWVGE-PEDDTRDITYAQLQDEVNRAANALTELGVAKGDRVAIYLPMIPEAVVTMLACARLGAPHTVVFGGFS 161
                                           *****.5568*************************************************************** PP

                             TIGR02188 150 aealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweel 222
                                           a+ala+Rivd+ a++v+tad+g+R+g   +lk +vdea++ka+  ve+v+vv+rtg+eva ++e rD+ww+el
  NCBI__GCF_003194585.1:WP_110207905.1 162 ADALASRIVDCGARVVVTADGGYRRGAPSALKPAVDEAVAKADGLVEHVVVVQRTGQEVA-FDETRDLWWHEL 233
                                           **********************************************************77.************ PP

                             TIGR02188 223 vekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGWvt 294
                                           + + +s ++++e  d+e+pl+++YtsG+tGkPkG+lhttgGyl+ +a+++  vfd+k d+d++wCtaD+GWvt
  NCBI__GCF_003194585.1:WP_110207905.1 234 MGR-QSPQHDAELHDAEHPLYVMYTSGTTGKPKGILHTTGGYLVGTAYSHWAVFDLKaDTDVYWCTADIGWVT 305
                                           **6.****************************************************9899************* PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           GhsY+vygPLanGat++l+eg+p+ p+++r+we+ieky+vtifYtaPtaiR++mk+g+++++k dlss+rvlg
  NCBI__GCF_003194585.1:WP_110207905.1 306 GHSYLVYGPLANGATQVLYEGTPDSPHKGRWWEIIEKYGVTIFYTAPTAIRTFMKWGNDIPAKFDLSSIRVLG 378
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           svGepinpea+ Wy++++G +++p+vdtwWqtetG i+itp+pg +t++kpgsa++Pl+Gi a+vv++eg++v
  NCBI__GCF_003194585.1:WP_110207905.1 379 SVGEPINPEAYVWYRSTIGGDRAPVVDTWWQTETGQIMITPMPG-VTHAKPGSAMRPLPGIVADVVNDEGESV 450
                                           ********************************************.5*************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                            ++++ g+L+i++pwP+mlrt++gd+er+ +tY+++ +g+yf+GDga++d+dG+iw+lGRvDdv+nvsGhrl+
  NCBI__GCF_003194585.1:WP_110207905.1 451 PDGSG-GYLIIREPWPAMLRTVWGDDERYKDTYWSRWPGVYFAGDGAKKDEDGDIWVLGRVDDVMNVSGHRLS 522
                                           *9999.8****************************************************************** PP

                             TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
                                           t+eiesalvsh++vaeaavvg++de++g+a++afv+l+e++    +e+ +el+++v+keig+iakp+++++v+
  NCBI__GCF_003194585.1:WP_110207905.1 523 TTEIESALVSHPKVAEAAVVGATDETTGQAVCAFVILRESAGDGGDEIVAELRNHVAKEIGAIAKPRQVMIVP 595
                                           ******************************************99999************************** PP

                             TIGR02188 587 elPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           elPktRsGkimRRllr++ae++e+ gdv+tl+d+sv+  ++
  NCBI__GCF_003194585.1:WP_110207905.1 596 ELPKTRSGKIMRRLLRDVAENREI-GDVTTLADSSVMSLIQ 635
                                           ********************8876.5**********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (644 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: 26.49
//
[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