Alignments for a candidate for acs in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Derxia gummosa DSM 723

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_028312770.1 H566_RS0119605 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000482785.1:WP_028312770.1
          Length = 655

 Score = 1033 bits (2671), Expect = 0.0
 Identities = 495/660 (75%), Positives = 563/660 (85%), Gaps = 5/660 (0%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           M +IE+ +QE+RVF P E F  QA +  +  Y+AL  EAE D+EGFW R A+E L W  P
Sbjct: 1   MGSIETSLQENRVFEPAEDFVKQARVSGIAGYEALRAEAEADFEGFWGRLAKENLSWKTP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           FTKVLD+SNAPFYKWFEDG +N SYNCLD NLQNGNADKVAI+FEAD G VT+VTYRELH
Sbjct: 61  FTKVLDESNAPFYKWFEDGVMNVSYNCLDVNLQNGNADKVAIIFEADGGEVTKVTYRELH 120

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
            +VC+FANGLK+LG  KG+R +IY+PMS+E VVAMQACARLG  HSVVFGGFSAKS+QER
Sbjct: 121 ARVCQFANGLKSLGYAKGERALIYLPMSIEAVVAMQACARLGIIHSVVFGGFSAKSVQER 180

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           + D GA  +ITADEQ+RGGK +PLK   D+A A+GGCE+VRNVI+Y+RTGG + + EGRD
Sbjct: 181 IADAGASVVITADEQVRGGKNIPLKPAIDEAFAIGGCESVRNVIIYQRTGGNIPFVEGRD 240

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
            W++DV A QP  CE E +SAEHPLF+L+TSGSTGKPKGVQHSTGGYLLWA +++ WTFD
Sbjct: 241 LWLKDVIANQPTECEPEWLSAEHPLFILFTSGSTGKPKGVQHSTGGYLLWAKLSLLWTFD 300

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
           +KP+D+FWCTAD+GWVTGHTYIAYGPLA GAT+VVFEGVPTYP+AGRFW MI  HKVSIF
Sbjct: 301 LKPNDVFWCTADVGWVTGHTYIAYGPLACGATEVVFEGVPTYPDAGRFWKMIQDHKVSIF 360

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIRSLIKA        P +YDLSSLRLLG+VGEPINPEAW+WYY  +G  RCPIV
Sbjct: 361 YTAPTAIRSLIKAGGD----LPTKYDLSSLRLLGSVGEPINPEAWVWYYNVVGGARCPIV 416

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DT+WQTETGGHMITPLPG   L PGSCT PLPGI AAIVDETG DV  GNGG LV+K+PW
Sbjct: 417 DTWWQTETGGHMITPLPGVHGLKPGSCTQPLPGIAAAIVDETGTDVAKGNGGFLVIKKPW 476

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P+MIRTIW DPERF+KSY+P + GGK YLAGDG+  D D GYF IMGRIDDVLNVSGHRM
Sbjct: 477 PSMIRTIWNDPERFKKSYYPADFGGKYYLAGDGANVDLD-GYFWIMGRIDDVLNVSGHRM 535

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTMEIESALV+NPLVAEAAVVGRPDD+TGEAICAFVVLK++ P G EA  IA ELR+WVG
Sbjct: 536 GTMEIESALVANPLVAEAAVVGRPDDLTGEAICAFVVLKQAAPQGAEAQAIAKELRDWVG 595

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQAQ 660
           +EIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRS+AKGEEITQDTSTLENPAIL+QLK ++
Sbjct: 596 REIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEEITQDTSTLENPAILDQLKTSR 655


Lambda     K      H
   0.319    0.136    0.422 

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: 1542
Number of extensions: 68
Number of successful extensions: 3
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: 660
Length of database: 655
Length adjustment: 38
Effective length of query: 622
Effective length of database: 617
Effective search space:   383774
Effective search space used:   383774
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_028312770.1 H566_RS0119605 (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.2603121.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.6e-298  975.3   0.0   6.4e-298  975.2   0.0    1.0  1  NCBI__GCF_000482785.1:WP_028312770.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_028312770.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  975.2   0.0  6.4e-298  6.4e-298       4     628 ..      29     653 ..      26     654 .. 0.97

  Alignments for each domain:
  == domain 1  score: 975.2 bits;  conditional E-value: 6.4e-298
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           +  y++l +ea++d e fw++lake+l+w++pf+kvldes++p++kWfedg +nvsync+d ++++ ++dkva
  NCBI__GCF_000482785.1:WP_028312770.1  29 IAGYEALRAEAEADFEGFWGRLAKENLSWKTPFTKVLDESNAPFYKWFEDGVMNVSYNCLDVNLQNgNADKVA 101
                                           6789********************************************************************* PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           ii+e+d  g ++ k+tY+el+++vc++an lk+lG  kg+r  iYlpm +eav+am+acaR+G++hsvvf+Gf
  NCBI__GCF_000482785.1:WP_028312770.1 102 IIFEAD-GG-EVTKVTYRELHARVCQFANGLKSLGYAKGERALIYLPMSIEAVVAMQACARLGIIHSVVFGGF 172
                                           ******.45.59************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwwe 220
                                           sa++++eRi da a +vitade++Rggk+i+lk ++dea++   + sv++v++++rtg ++  ++egrD+w++
  NCBI__GCF_000482785.1:WP_028312770.1 173 SAKSVQERIADAGASVVITADEQVRGGKNIPLKPAIDEAFAIGGCeSVRNVIIYQRTGGNIP-FVEGRDLWLK 244
                                           ***************************************99988779*************66.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           ++++ ++++ecepe+l++e+plfiL+tsGstGkPkGv+h+tgGyll+a+l+  ++fd+k++d+fwCtaDvGWv
  NCBI__GCF_000482785.1:WP_028312770.1 245 DVIA-NQPTECEPEWLSAEHPLFILFTSGSTGKPKGVQHSTGGYLLWAKLSLLWTFDLKPNDVFWCTADVGWV 316
                                           ****.5******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGh+Yi ygPLa+Gat+++fegvptypda+rfw++i+ +kv+ifYtaPtaiR+l+k+g +l++k+dlsslr+l
  NCBI__GCF_000482785.1:WP_028312770.1 317 TGHTYIAYGPLACGATEVVFEGVPTYPDAGRFWKMIQDHKVSIFYTAPTAIRSLIKAGGDLPTKYDLSSLRLL 389
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaw Wyy+vvG  +cpivdtwWqtetGg++itplpg +  lkpgs+t+Pl+Gi a++vde+g++
  NCBI__GCF_000482785.1:WP_028312770.1 390 GSVGEPINPEAWVWYYNVVGGARCPIVDTWWQTETGGHMITPLPG-VHGLKPGSCTQPLPGIAAAIVDETGTD 461
                                           *********************************************.5************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           v ++++ g+LvikkpwPsm+rti++d+erf ++Y+ +  g  +y++GDga+ d dGy+wi+GR+Ddv+nvsGh
  NCBI__GCF_000482785.1:WP_028312770.1 462 VAKGNG-GFLVIKKPWPSMIRTIWNDPERFKKSYYPADFGgkYYLAGDGANVDLDGYFWIMGRIDDVLNVSGH 533
                                           ***999.8**************************9864434699***************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeigpiakpdk 581
                                           r+gt+eiesalv+++ vaeaavvg+pd+++geai+afvvlk+++ + +e  +++kel+++v +eigpiakp++
  NCBI__GCF_000482785.1:WP_028312770.1 534 RMGTMEIESALVANPLVAEAAVVGRPDDLTGEAICAFVVLKQAAPQGAEaqAIAKELRDWVGREIGPIAKPKD 606
                                           ******************************************9987665559********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           i++ ++lPktRsGkimRRllr+ia+gee+++d+stle+p+++++lk+
  NCBI__GCF_000482785.1:WP_028312770.1 607 IRFGDNLPKTRSGKIMRRLLRSIAKGEEITQDTSTLENPAILDQLKT 653
                                           ********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (655 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: 32.33
//
[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