Alignments for a candidate for acs in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Dechlorosoma suillum PS

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Dsui_2003 Dsui_2003 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__PS:Dsui_2003
          Length = 658

 Score = 1028 bits (2659), Expect = 0.0
 Identities = 498/660 (75%), Positives = 565/660 (85%), Gaps = 5/660 (0%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           MS IESV+ E+RVF P E    +A I  M AY+ALC EAE DY G+W R A+E + W +P
Sbjct: 1   MSQIESVLVENRVFPPSEEVVKRATISGMAAYEALCKEAETDYTGYWGRLAKEHVVWKQP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           FT VLD+SNAPFYKWF DG+LN SYNCLD+N++ G  DKVAI+FEAD G+V++VTY+EL 
Sbjct: 61  FTSVLDESNAPFYKWFADGKLNVSYNCLDKNVEAGLGDKVAIIFEADGGAVSKVTYKELL 120

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
            +V +FAN LKA GI+KGDRV+IY+PMS+EG+VAMQACAR+GA HSVVFGGFSAKSL+ER
Sbjct: 121 SRVAKFANALKAKGIKKGDRVIIYLPMSIEGIVAMQACARIGAIHSVVFGGFSAKSLEER 180

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEA-VRNVIVYRRTGGKVAWTEGR 239
           ++D GAVA+ITADEQ RGGK +PLK   D+AL L G  + V+ VIV +RTGG      GR
Sbjct: 181 ILDAGAVAVITADEQTRGGKNIPLKPAVDEALTLVGANSPVKTVIVAKRTGGACNMVAGR 240

Query: 240 DRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTF 299
           D W  D  AGQ D CE E V AEHPLF+LYTSGSTGKPKGVQHS+GGYLL A +TMKWTF
Sbjct: 241 DVWWTDAEAGQSDICEPEWVEAEHPLFLLYTSGSTGKPKGVQHSSGGYLLHAALTMKWTF 300

Query: 300 DIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSI 359
           DIKPDD+FWCTADIGWVTGHTYI YGPLA GAT++VFEGVPT+P+AGRFW MI  HKVSI
Sbjct: 301 DIKPDDVFWCTADIGWVTGHTYITYGPLACGATEIVFEGVPTFPDAGRFWKMIQDHKVSI 360

Query: 360 FYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPI 419
           FYTAPTAIRSLIKA  AD    PK+YDL+SLRLLG+VGEPINPEAWMWYY  IG  RCPI
Sbjct: 361 FYTAPTAIRSLIKAG-ADL---PKKYDLTSLRLLGSVGEPINPEAWMWYYNEIGGGRCPI 416

Query: 420 VDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRP 479
           VDTFWQTETGGHMITPLPG TPLVPGSCTLP PGI AAIVDETGH++  G GG LVVK+P
Sbjct: 417 VDTFWQTETGGHMITPLPGVTPLVPGSCTLPFPGIQAAIVDETGHELEWGKGGFLVVKKP 476

Query: 480 WPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHR 539
           WP+MIRTIWGDPERF+KSY+PE+LGG+LYLAGDG++R+  TG FTI GRIDDVLNVSGHR
Sbjct: 477 WPSMIRTIWGDPERFKKSYYPEDLGGRLYLAGDGAVRNAKTGNFTITGRIDDVLNVSGHR 536

Query: 540 MGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWV 599
           MGTMEIESALV+NPLVAEAAVVGRPDD+TGEAICAFVVLK SRP+GE+A ++  EL++WV
Sbjct: 537 MGTMEIESALVANPLVAEAAVVGRPDDLTGEAICAFVVLKGSRPSGEDAKRVIKELQDWV 596

Query: 600 GKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
           GKEIGPIAKPKDIRFG+NLPKTRSGKIMRRLLRSLAKGEE+TQD STLENPAILEQLKQA
Sbjct: 597 GKEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEEVTQDVSTLENPAILEQLKQA 656


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: 1552
Number of extensions: 80
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: 658
Length adjustment: 38
Effective length of query: 622
Effective length of database: 620
Effective search space:   385640
Effective search space used:   385640
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 Dsui_2003 Dsui_2003 (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.16587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.8e-297  971.4   0.0     1e-296  971.2   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_2003  Dsui_2003 acetate--CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2003  Dsui_2003 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  971.2   0.0    1e-296    1e-296       3     628 ..      28     655 ..      26     656 .. 0.97

  Alignments for each domain:
  == domain 1  score: 971.2 bits;  conditional E-value: 1e-296
                         TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiw 78 
                                        + +y++l++ea++d++ +w++lake++ w++pf++vldes++p++kWf+dg+lnvsync+d++ve+   dkvaii+
  lcl|FitnessBrowser__PS:Dsui_2003  28 GMAAYEALCKEAETDYTGYWGRLAKEHVVWKQPFTSVLDESNAPFYKWFADGKLNVSYNCLDKNVEAgLGDKVAIIF 104
                                       6789***************************************************************99******** PP

                         TIGR02188  79 egdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealae 155
                                       e+d  g  + k+tY+ell++v+++an+lk+ G+kkgdrv+iYlpm +e ++am+acaRiGa+hsvvf+Gfsa++l+e
  lcl|FitnessBrowser__PS:Dsui_2003 105 EAD-GG-AVSKVTYKELLSRVAKFANALKAKGIKKGDRVIIYLPMSIEGIVAMQACARIGAIHSVVFGGFSAKSLEE 179
                                       ***.44.48******************************************************************** PP

                         TIGR02188 156 RivdaeaklvitadeglRggkvielkkivdealekaee..svekvlvvkrtgeevaewkegrDvwweelvekeasae 230
                                       Ri da a  vitade++Rggk+i+lk +vdeal+ + +   v++v+v krtg    +++ grDvww ++ + ++s+ 
  lcl|FitnessBrowser__PS:Dsui_2003 180 RILDAGAVAVITADEQTRGGKNIPLKPAVDEALTLVGAnsPVKTVIVAKRTGGA-CNMVAGRDVWWTDAEA-GQSDI 254
                                       *********************************98776568*************.55************99.6**** PP

                         TIGR02188 231 cepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanG 307
                                       cepe++++e+plf+LYtsGstGkPkGv+h++gGyll+aalt+k++fdik++d+fwCtaD+GWvtGh+Yi ygPLa+G
  lcl|FitnessBrowser__PS:Dsui_2003 255 CEPEWVEAEHPLFLLYTSGSTGKPKGVQHSSGGYLLHAALTMKWTFDIKPDDVFWCTADIGWVTGHTYITYGPLACG 331
                                       ***************************************************************************** PP

                         TIGR02188 308 attllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyev 384
                                       at+++fegvpt+pda+rfw++i+ +kv+ifYtaPtaiR+l+k+g +l+kk+dl slr+lgsvGepinpeaw+Wyy++
  lcl|FitnessBrowser__PS:Dsui_2003 332 ATEIVFEGVPTFPDAGRFWKMIQDHKVSIFYTAPTAIRSLIKAGADLPKKYDLTSLRLLGSVGEPINPEAWMWYYNE 408
                                       ***************************************************************************** PP

                         TIGR02188 385 vGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrt 461
                                       +G ++cpivdt+WqtetGg++itplpg +t+l pgs+tlP++Gi+a++vde+g+e+e +++ g+Lv+kkpwPsm+rt
  lcl|FitnessBrowser__PS:Dsui_2003 409 IGGGRCPIVDTFWQTETGGHMITPLPG-VTPLVPGSCTLPFPGIQAAIVDETGHELEWGKG-GFLVVKKPWPSMIRT 483
                                       ***************************.5*****************************999.8************** PP

                         TIGR02188 462 iygdeerfvetYfkklkg..lyftGDgarrd.kdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgv 535
                                       i+gd+erf ++Y+ +  g  ly++GDga+r+ k G ++i+GR+Ddv+nvsGhr+gt+eiesalv+++ vaeaavvg+
  lcl|FitnessBrowser__PS:Dsui_2003 484 IWGDPERFKKSYYPEDLGgrLYLAGDGAVRNaKTGNFTITGRIDDVLNVSGHRMGTMEIESALVANPLVAEAAVVGR 560
                                       *************9876668********987256******************************************* PP

                         TIGR02188 536 pdeikgeaivafvvlkegveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeel 610
                                       pd+++geai+afvvlk ++ + e+  ++ kel+++v keigpiakp++i++ e+lPktRsGkimRRllr++a+gee+
  lcl|FitnessBrowser__PS:Dsui_2003 561 PDDLTGEAICAFVVLKGSRPSGEDakRVIKELQDWVGKEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEEV 637
                                       ****************99875554449************************************************** PP

                         TIGR02188 611 lgdvstledpsvveelke 628
                                       ++dvstle+p+++e+lk+
  lcl|FitnessBrowser__PS:Dsui_2003 638 TQDVSTLENPAILEQLKQ 655
                                       ***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (658 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.94
//
[ok]

This GapMind analysis is from Sep 17 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