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.17680.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.88
//
[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:

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:

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:

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:

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