Alignments for a candidate for acs in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Acidovorax sp. GW101-3H11

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Ac3H11_951 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_951
          Length = 664

 Score = 1038 bits (2684), Expect = 0.0
 Identities = 495/659 (75%), Positives = 568/659 (86%), Gaps = 2/659 (0%)

Query: 2   SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           SAIESV+ E+RVF P +     A +  M  Y ALC EA++D+EGFWAR ARE ++WTKPF
Sbjct: 6   SAIESVLVENRVFPPSDAVVKAARVSGMAGYDALCAEADKDFEGFWARLARENVNWTKPF 65

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
            + LD SNAPF+KWF+DGELNAS NCLDR++     +K AIVFEADDG+VTR+TY+EL  
Sbjct: 66  NRTLDTSNAPFFKWFDDGELNASANCLDRHIGTPTENKTAIVFEADDGTVTRITYKELLA 125

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           +V +FAN LKA G+ KGDRV+IYMPM++EGV+AMQACAR+GATHSVVFGGFSAK++QER+
Sbjct: 126 RVSQFANALKAHGVTKGDRVLIYMPMTIEGVIAMQACARIGATHSVVFGGFSAKAVQERI 185

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDR 241
           +D GAVA+ITA+ QMRGGK LPLKAI D+ALA+GGC+ +RNV VY+RT        GRD+
Sbjct: 186 IDAGAVAVITANYQMRGGKELPLKAIIDEALAMGGCDTIRNVFVYQRTATACNMVAGRDK 245

Query: 242 WMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDI 301
              ++ AGQ   C   PV AEHPLF+LYTSGSTGKPKGVQH+TGGYLLWA +TM WTFD+
Sbjct: 246 TFGEMLAGQSTECAPVPVGAEHPLFILYTSGSTGKPKGVQHATGGYLLWAKLTMDWTFDL 305

Query: 302 KPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFY 361
           + DD+FWCTADIGW+TGHTY+AYGPLAAGATQ++FEGVPT+PNAGRFW MI +HK +IFY
Sbjct: 306 RADDVFWCTADIGWITGHTYVAYGPLAAGATQIIFEGVPTFPNAGRFWQMIEKHKCTIFY 365

Query: 362 TAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVD 421
           TAPTAIRSLIKAAE D  +HP + DLSSLR+LG+VGEPINPEAWMWY+KN+G ERCPIVD
Sbjct: 366 TAPTAIRSLIKAAEGDAAVHPARSDLSSLRILGSVGEPINPEAWMWYHKNVGGERCPIVD 425

Query: 422 TFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWP 481
           TFWQTETGGH+ITPLPGATPLVPGSCTLPLPGI AAIVDE G+DV NG GGILV+K+PWP
Sbjct: 426 TFWQTETGGHVITPLPGATPLVPGSCTLPLPGISAAIVDEMGNDVANGAGGILVIKKPWP 485

Query: 482 AMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMG 541
           +MIRTIW DPERF+K+YFPEEL G  YLAGDG++R  D GYF I GRIDDVLNVSGHRMG
Sbjct: 486 SMIRTIWNDPERFKKAYFPEELKG-YYLAGDGAVRSADRGYFRITGRIDDVLNVSGHRMG 544

Query: 542 TMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           TMEIESALVS   LVAEAAVVGRPDD+TGEAICAFVVLKRSRPTGEEA +IA ELRNWV 
Sbjct: 545 TMEIESALVSKTDLVAEAAVVGRPDDVTGEAICAFVVLKRSRPTGEEAKQIANELRNWVA 604

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
           KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRS+AKGE ITQDTSTLENPAIL+QL +A
Sbjct: 605 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEAITQDTSTLENPAILDQLAKA 663


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: 1493
Number of extensions: 73
Number of successful extensions: 4
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: 664
Length adjustment: 38
Effective length of query: 622
Effective length of database: 626
Effective search space:   389372
Effective search space used:   389372
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 Ac3H11_951 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
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.28930.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   5.3e-292  955.6   0.0   6.2e-292  955.4   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951  Acetyl-coenzyme A synthetase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951  Acetyl-coenzyme A synthetase (EC 6.2.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  955.4   0.0  6.2e-292  6.2e-292       4     628 ..      33     662 ..      30     663 .. 0.96

  Alignments for each domain:
  == domain 1  score: 955.4 bits;  conditional E-value: 6.2e-292
                                       TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrh 66 
                                                     +  y +l++ea +d e fwa+la+e+++w+kpf+++ld+s++p+ kWf+dgeln+s+nc+drh
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951  33 MAGYDALCAEADKDFEGFWARLARENVNWTKPFNRTLDTSNAPFFKWFDDGELNASANCLDRH 95 
                                                     67899********************************************************** PP

                                       TIGR02188  67 vek.rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeav 128
                                                     + + +++k+ai++e+d+ +  + ++tY+ell++v+++an+lk++Gv kgdrv iY+pm++e v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951  96 IGTpTENKTAIVFEADDGT--VTRITYKELLARVSQFANALKAHGVTKGDRVLIYMPMTIEGV 156
                                                     ***9************664..89**************************************** PP

                                       TIGR02188 129 iamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealeka 191
                                                     iam+acaRiGa+hsvvf+Gfsa+a++eRi+da a  vita+ ++Rggk ++lk+i+deal++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 157 IAMQACARIGATHSVVFGGFSAKAVQERIIDAGAVAVITANYQMRGGKELPLKAIIDEALAMG 219
                                                     **************************************************************9 PP

                                       TIGR02188 192 ee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGk 253
                                                      + ++++v v++rt +   +++ grD+++ e+++ ++s+ec+p ++++e+plfiLYtsGstGk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 220 GCdTIRNVFVYQRTATA-CNMVAGRDKTFGEMLA-GQSTECAPVPVGAEHPLFILYTSGSTGK 280
                                                     988**************.56**************.6*************************** PP

                                       TIGR02188 254 PkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegv 316
                                                     PkGv+h+tgGyll+a+lt+ ++fd++ +d+fwCtaD+GW+tGh+Y+ ygPLa+Gat+++fegv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 281 PKGVQHATGGYLLWAKLTMDWTFDLRADDVFWCTADIGWITGHTYVAYGPLAAGATQIIFEGV 343
                                                     *************************************************************** PP

                                       TIGR02188 317 ptypdasrfweviekykvtifYtaPtaiRalmklg....eelvkkhdlsslrvlgsvGepinp 375
                                                     pt+p+a+rfw++iek+k tifYtaPtaiR+l+k++      ++++ dlsslr+lgsvGepinp
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 344 PTFPNAGRFWQMIEKHKCTIFYTAPTAIRSLIKAAegdaAVHPARSDLSSLRILGSVGEPINP 406
                                                     ********************************98733223467899***************** PP

                                       TIGR02188 376 eaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
                                                     eaw+Wy+++vG e+cpivdt+WqtetGg++itplpg at+l pgs+tlPl+Gi+a++vde g+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 407 EAWMWYHKNVGGERCPIVDTFWQTETGGHVITPLPG-ATPLVPGSCTLPLPGISAAIVDEMGN 468
                                                     ************************************.6************************* PP

                                       TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfk.klkglyftGDgarrdkd.GyiwilG 499
                                                     +v ++++ g+LvikkpwPsm+rti++d+erf ++Yf  +lkg+y++GDga+r +d Gy+ i+G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 469 DVANGAG-GILVIKKPWPSMIRTIWNDPERFKKAYFPeELKGYYLAGDGAVRSADrGYFRITG 530
                                                     ****999.8***************************626889**********9988******* PP

                                       TIGR02188 500 RvDdvinvsGhrlgtaeiesalvshe.avaeaavvgvpdeikgeaivafvvlkegveedee.. 559
                                                     R+Ddv+nvsGhr+gt+eiesalvs++  vaeaavvg+pd+++geai+afvvlk+++ + ee  
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 531 RIDDVLNVSGHRMGTMEIESALVSKTdLVAEAAVVGRPDDVTGEAICAFVVLKRSRPTGEEak 593
                                                     ***********************975269*************************998776666 PP

                                       TIGR02188 560 elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsv 622
                                                     ++++el+++v+keigpiakp++i++ ++lPktRsGkimRRllr+ia+ge +++d+stle+p++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 594 QIANELRNWVAKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEAITQDTSTLENPAI 656
                                                     9************************************************************** PP

                                       TIGR02188 623 veelke 628
                                                     +++l +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 657 LDQLAK 662
                                                     **9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (664 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.05
//
[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