Alignments for a candidate for acs in Nocardioides dokdonensis FR1436

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Nocardioides dokdonensis FR1436

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_068107934.1 I601_RS07695 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_001653335.1:WP_068107934.1
          Length = 661

 Score =  842 bits (2175), Expect = 0.0
 Identities = 415/642 (64%), Positives = 491/642 (76%), Gaps = 13/642 (2%)

Query: 12  YPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSGAPFAKWFVGG 71
           + PPA  A +AN  AE Y  A  D  AFWA+QA RL+W TP+  VL+W   PFAKWF GG
Sbjct: 16  FEPPAELAANANVTAEAYDAAAADPEAFWAEQAGRLTWATPWDRVLNWDDPPFAKWFEGG 75

Query: 72  ELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAANALTDLGLVAG 131
            LN AYNCVDRHVEAG GD+VA H+ GEPV D R +TY++L   V +AAN L DLG+  G
Sbjct: 76  RLNAAYNCVDRHVEAGRGDKVAFHFVGEPVDDTRDITYAELQDLVCQAANTLIDLGVQTG 135

Query: 132 DRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKLLITADGQFRR 191
           DRVAIY+P+IPEAV+AMLACAR+G  H+VVFGGF++ AL +R+ D QAK+++TADG +RR
Sbjct: 136 DRVAIYMPMIPEAVVAMLACARIGAPHTVVFGGFSSDALASRLEDCQAKVVVTADGGYRR 195

Query: 192 GKPSPLKAAADEAL--AAIPDCSVEHVLVVRRTGIEM---AWSEGRDLWWHHVVGSASPA 246
           G PS LK A DEA   AA    +VE VLVVRRTG ++   +W +  D+WWH  V  AS  
Sbjct: 196 GAPSALKPAVDEARVKAAGLGHTVEKVLVVRRTGQDLGADSWDDAVDVWWHESVDRASTE 255

Query: 247 HTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDVFWCTAD 306
           H  E FD+EHPL+++YTSGTTGKPKGI+HT+GGYLT   YT   +FD+KPD DVFWCTAD
Sbjct: 256 HAHEAFDAEHPLYVMYTSGTTGKPKGILHTTGGYLTGAAYTHWAVFDIKPD-DVFWCTAD 314

Query: 307 IGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTLIRMFMK 366
           IGWVTGH+Y VYGPL NGVT+VLYEGTPD+P++ R +QIIE+ GVTI YTAPT IR FMK
Sbjct: 315 IGWVTGHSYIVYGPLANGVTQVLYEGTPDSPEKGRWWQIIEQQGVTILYTAPTAIRSFMK 374

Query: 367 WGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGSAMISPL 426
            GREIPD HDLSSLRLLGSVGEPINPEA+ WYR VIGG RTP+VDTWWQTETG  +ISPL
Sbjct: 375 QGREIPDRHDLSSLRLLGSVGEPINPEAYVWYRHVIGGDRTPVVDTWWQTETGQILISPL 434

Query: 427 PGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLRGIWGD 486
           PG+ A KPGSAM P+PGISA +VD+ G       E A+   GYLVL +PWP+MLR IWGD
Sbjct: 435 PGVTAGKPGSAMVPIPGISAAVVDEEG------REVAKGGGGYLVLTKPWPAMLRTIWGD 488

Query: 487 PARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVESALVA 546
             RY  +YW++F   GYYFAGDGA++D DG +WVLGR+DDVMNVSGHR+ST E+ESALV+
Sbjct: 489 DERYKETYWARFEKLGYYFAGDGAKLDDDGDLWVLGRVDDVMNVSGHRLSTTEIESALVS 548

Query: 547 HSGVAEAAVVGVTDETTTQAICAFVVLRANYAPHDR-TAEELRTEVARVISPIARPRDVH 605
           H  VAEAAVVG  DE T QA+CAFV+LR           EELR  V + I PIA+PR + 
Sbjct: 549 HPKVAEAAVVGAQDEDTGQAVCAFVILRDEAGDGGADIVEELRAHVRKEIGPIAKPRQIM 608

Query: 606 VVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAI 647
           +VPELPKTRSGKIMRRLLRDVAENRE+GD +TL D +V D I
Sbjct: 609 IVPELPKTRSGKIMRRLLRDVAENREVGDVTTLADSSVMDLI 650


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: 1562
Number of extensions: 83
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: 661
Length adjustment: 38
Effective length of query: 613
Effective length of database: 623
Effective search space:   381899
Effective search space used:   381899
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_068107934.1 I601_RS07695 (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.1392951.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-291  952.9   0.1   4.1e-291  952.7   0.1    1.0  1  NCBI__GCF_001653335.1:WP_068107934.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001653335.1:WP_068107934.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  952.7   0.1  4.1e-291  4.1e-291       4     627 ..      26     651 ..      23     653 .. 0.97

  Alignments for each domain:
  == domain 1  score: 952.7 bits;  conditional E-value: 4.1e-291
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           ++  +e y+ a++dpe+fwa++a  +l+w++p+++vl+++ +p++kWfe+g+ln++yncvdrhve+ r dkva
  NCBI__GCF_001653335.1:WP_068107934.1  26 ANVTAEAYDAAAADPEAFWAEQAG-RLTWATPWDRVLNWDDPPFAKWFEGGRLNAAYNCVDRHVEAgRGDKVA 97 
                                           56678999****************.5*********************************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                            ++ g+ + +d+r +tYael++ vc++an+l +lGv+ gdrvaiY+pmipeav+amlacaRiGa h+vvf+Gf
  NCBI__GCF_001653335.1:WP_068107934.1  98 FHFVGE-PVDDTRDITYAELQDLVCQAANTLIDLGVQTGDRVAIYMPMIPEAVVAMLACARIGAPHTVVFGGF 169
                                           ******.5568************************************************************** PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeev..aewkegrD 216
                                           s++ala+R++d++ak+v+tad+g+R+g   +lk +vdea  ka     +vekvlvv+rtg+++   +w++  D
  NCBI__GCF_001653335.1:WP_068107934.1 170 SSDALASRLEDCQAKVVVTADGGYRRGAPSALKPAVDEARVKAAGlghTVEKVLVVRRTGQDLgaDSWDDAVD 242
                                           ***************************************766654467************9863368****** PP

                             TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           vww+e v++ as+e++ e++d+e+pl+++YtsG+tGkPkG+lhttgGyl+ aa+t+  vfdik++d+fwCtaD
  NCBI__GCF_001653335.1:WP_068107934.1 243 VWWHESVDR-ASTEHAHEAFDAEHPLYVMYTSGTTGKPKGILHTTGGYLTGAAYTHWAVFDIKPDDVFWCTAD 314
                                           ********6.*************************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           +GWvtGhsYivygPLanG+t++l+eg+p+ p+++r+w++ie+ +vti+YtaPtaiR++mk+g+e++++hdlss
  NCBI__GCF_001653335.1:WP_068107934.1 315 IGWVTGHSYIVYGPLANGVTQVLYEGTPDSPEKGRWWQIIEQQGVTILYTAPTAIRSFMKQGREIPDRHDLSS 387
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lr+lgsvGepinpea+ Wy++v+G +++p+vdtwWqtetG ili+plpg +t+ kpgsa++P++Gi+a+vvde
  NCBI__GCF_001653335.1:WP_068107934.1 388 LRLLGSVGEPINPEAYVWYRHVIGGDRTPVVDTWWQTETGQILISPLPG-VTAGKPGSAMVPIPGISAAVVDE 459
                                           *************************************************.5********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvin 506
                                           eg+ev ++ + g+Lv++kpwP+mlrti+gd+er+ etY+ ++++  +yf+GDga+ d+dG++w+lGRvDdv+n
  NCBI__GCF_001653335.1:WP_068107934.1 460 EGREVAKGGG-GYLVLTKPWPAMLRTIWGDDERYKETYWARFEKlgYYFAGDGAKLDDDGDLWVLGRVDDVMN 531
                                           ******9988.8*******************************999*************************** PP

                             TIGR02188 507 vsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakp 579
                                           vsGhrl+t+eiesalvsh++vaeaavvg++de +g+a++afv+l++++     ++ +el+++vrkeigpiakp
  NCBI__GCF_001653335.1:WP_068107934.1 532 VSGHRLSTTEIESALVSHPKVAEAAVVGAQDEDTGQAVCAFVILRDEAGDGGADIVEELRAHVRKEIGPIAKP 604
                                           ************************************************999999******************* PP

                             TIGR02188 580 dkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           ++i++v+elPktRsGkimRRllr++ae++e+ gdv+tl+d+sv++ ++
  NCBI__GCF_001653335.1:WP_068107934.1 605 RQIMIVPELPKTRSGKIMRRLLRDVAENREV-GDVTTLADSSVMDLIS 651
                                           ***************************8876.5**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (661 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: 00:00:00.02
# Mc/sec: 18.29
//
[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