Alignments for a candidate for acs in Williamsia sterculiae CPCC 203464

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Williamsia sterculiae CPCC 203464

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_076478630.1 BW971_RS08810 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_900156495.1:WP_076478630.1
          Length = 657

 Score =  910 bits (2352), Expect = 0.0
 Identities = 447/647 (69%), Positives = 512/647 (79%), Gaps = 12/647 (1%)

Query: 7   EVSSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSGAPFAK 66
           E   S+PP   FA+ ANA AELY  A+ DRL FWA+QA  L W T FT+VLDWS APFAK
Sbjct: 14  EAGQSFPPSRDFADQANAGAELYTRADADRLEFWAEQARALDWDTDFTDVLDWSNAPFAK 73

Query: 67  WFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAANALTDL 126
           WFVGG+LNVA NCVDRHV AG+GDRVAIHW GEP GD R +TYS LL +VS+AAN    +
Sbjct: 74  WFVGGKLNVAVNCVDRHVAAGNGDRVAIHWVGEP-GDHRDITYSQLLGDVSRAANYFDSI 132

Query: 127 GLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKLLITAD 186
           GL  GDRVAIY+P++PEA++ MLACARLG+ HSVVF GF++ AL++R+ DA+AKL++T D
Sbjct: 133 GLRPGDRVAIYMPMVPEAIVTMLACARLGLTHSVVFAGFSSTALRSRVDDAEAKLVVTTD 192

Query: 187 GQFRRGKPSPLKAAADEALAAIPDC--SVEHVLVVRRTGI--EMAWSEGRDLWWHHVVGS 242
           GQ+RRGKP+PLKA  DEAL    D   SV+ VLVVRRT    E+ W  GRD+WW   V  
Sbjct: 193 GQYRRGKPAPLKANVDEALGTGDDAAVSVQTVLVVRRTNHDPELNWVSGRDVWWDDTVAE 252

Query: 243 ASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDVFW 302
           AS  H P+ FDSE PLFLLYTSGTTGKPKGI+HTSGGYLTQ  YT   +FD K   DVFW
Sbjct: 253 ASDHHEPDAFDSEQPLFLLYTSGTTGKPKGILHTSGGYLTQVRYTFHNVFDHKEGRDVFW 312

Query: 303 CTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTLIR 362
           C ADIGWVTGH+Y VYGPL NG TEV+YEGTP++P+ HRHF+IIE+YGV+IYY APTLIR
Sbjct: 313 CGADIGWVTGHSYLVYGPLSNGATEVVYEGTPNSPNEHRHFEIIERYGVSIYYIAPTLIR 372

Query: 363 MFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGSAM 422
            FMKWGREIPD+HDLSSLRLLGSVGEPINPEAWRWYR+VIG    P+VDTWWQTETG+ M
Sbjct: 373 TFMKWGREIPDAHDLSSLRLLGSVGEPINPEAWRWYREVIGHDSCPIVDTWWQTETGAIM 432

Query: 423 ISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLRG 482
           ISPLPG+  AKPGSAM PLPGISA IVDD   P+      A    GYLVLD+PWPSMLRG
Sbjct: 433 ISPLPGVTDAKPGSAMRPLPGISATIVDDDAAPV------AAGEQGYLVLDKPWPSMLRG 486

Query: 483 IWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVES 542
           IWGD  R+  +YWS+F+D+G+YFAGDGAR D D A+WVLGRIDDVMNVSGHRIST+EVES
Sbjct: 487 IWGDDQRFIDTYWSRFADQGWYFAGDGARYDDDHALWVLGRIDDVMNVSGHRISTSEVES 546

Query: 543 ALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYA-PHDRTAEELRTEVARVISPIARP 601
           ALV H  VAEAAV+G  D TT Q I AFV+LR       D    ELR +VA+ ISPIA+P
Sbjct: 547 ALVNHHSVAEAAVIGAADATTGQGIVAFVILRGGVEDTGDTLIAELRDQVAKDISPIAKP 606

Query: 602 RDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAIR 648
           R+V VVPELPKTRSGKIMRRLL+DVAE RELGDTSTL+DPTVF+ IR
Sbjct: 607 REVLVVPELPKTRSGKIMRRLLKDVAEGRELGDTSTLVDPTVFEEIR 653


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: 1537
Number of extensions: 93
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: 657
Length adjustment: 38
Effective length of query: 613
Effective length of database: 619
Effective search space:   379447
Effective search space used:   379447
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_076478630.1 BW971_RS08810 (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.1355379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-285  932.9   0.0   4.5e-285  932.7   0.0    1.0  1  NCBI__GCF_900156495.1:WP_076478630.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900156495.1:WP_076478630.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  932.7   0.0  4.5e-285  4.5e-285       4     627 ..      29     653 ..      26     655 .. 0.97

  Alignments for each domain:
  == domain 1  score: 932.7 bits;  conditional E-value: 4.5e-285
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           +++ +ely++a +d+ +fwa++a+  l+w+++f+ vld+s++p++kWf++g+lnv++ncvdrhv++ + d+va
  NCBI__GCF_900156495.1:WP_076478630.1  29 ANAGAELYTRADADRLEFWAEQAR-ALDWDTDFTDVLDWSNAPFAKWFVGGKLNVAVNCVDRHVAAgNGDRVA 100
                                           5667899*****************.6****************************************9****** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           i+w g+ +g d+r +tY++ll +v+r+an + ++G++ gdrvaiY+pm+pea+++mlacaR+G +hsvvfaGf
  NCBI__GCF_900156495.1:WP_076478630.1 101 IHWVGE-PG-DHRDITYSQLLGDVSRAANYFDSIGLRPGDRVAIYMPMVPEAIVTMLACARLGLTHSVVFAGF 171
                                           *****9.77.59************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgee.vaewkegrDv 217
                                           s+ al++R+ daeaklv+t+d+++R+gk  +lk++vdeal + ++   sv++vlvv+rt+++   +w++grDv
  NCBI__GCF_900156495.1:WP_076478630.1 172 SSTALRSRVDDAEAKLVVTTDGQYRRGKPAPLKANVDEALGTGDDaavSVQTVLVVRRTNHDpELNWVSGRDV 244
                                           ****************************************987766679**********9752568******* PP

                             TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikd.edifwCtaD 289
                                           ww+++v++ as+++ep+++dse+plf+LYtsG+tGkPkG+lht+gGyl+++ +t++ vfd+k+  d+fwC aD
  NCBI__GCF_900156495.1:WP_076478630.1 245 WWDDTVAE-ASDHHEPDAFDSEQPLFLLYTSGTTGKPKGILHTSGGYLTQVRYTFHNVFDHKEgRDVFWCGAD 316
                                           *******6.*****************************************************636******** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           +GWvtGhsY+vygPL+nGat++++eg+p+ p+++r++e+ie+y+v+i+Y aPt+iR++mk+g+e++++hdlss
  NCBI__GCF_900156495.1:WP_076478630.1 317 IGWVTGHSYLVYGPLSNGATEVVYEGTPNSPNEHRHFEIIERYGVSIYYIAPTLIRTFMKWGREIPDAHDLSS 389
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lr+lgsvGepinpeaw+Wy+ev+G+++cpivdtwWqtetG+i+i+plpg +t++kpgsa++Pl+Gi+a++vd+
  NCBI__GCF_900156495.1:WP_076478630.1 390 LRLLGSVGEPINPEAWRWYREVIGHDSCPIVDTWWQTETGAIMISPLPG-VTDAKPGSAMRPLPGISATIVDD 461
                                           *************************************************.5********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvin 506
                                           ++ +v ++e+ g+Lv++kpwPsmlr+i+gd++rf++tY++++ +   yf+GDgar d+d  +w+lGR+Ddv+n
  NCBI__GCF_900156495.1:WP_076478630.1 462 DAAPVAAGEQ-GYLVLDKPWPSMLRGIWGDDQRFIDTYWSRFADqgWYFAGDGARYDDDHALWVLGRIDDVMN 533
                                           *******999.8******************************87779************************** PP

                             TIGR02188 507 vsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakp 579
                                           vsGhr++t+e+esalv+h++vaeaav+g++d ++g+ ivafv+l+ gve + ++l +el+++v+k i+piakp
  NCBI__GCF_900156495.1:WP_076478630.1 534 VSGHRISTSEVESALVNHHSVAEAAVIGAADATTGQGIVAFVILRGGVEDTGDTLIAELRDQVAKDISPIAKP 606
                                           *************************************************9999******************** PP

                             TIGR02188 580 dkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           +++lvv+elPktRsGkimRRll+++aeg+el gd+stl dp+v+ee++
  NCBI__GCF_900156495.1:WP_076478630.1 607 REVLVVPELPKTRSGKIMRRLLKDVAEGREL-GDTSTLVDPTVFEEIR 653
                                           ***************************9875.6************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (657 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: 19.44
//
[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 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