Alignments for a candidate for acs in Acidovorax caeni R-24608

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Acidovorax caeni R-24608

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_054257103.1 BN2503_RS13075 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_001298675.1:WP_054257103.1
          Length = 665

 Score = 1043 bits (2697), Expect = 0.0
 Identities = 497/656 (75%), Positives = 571/656 (87%), Gaps = 1/656 (0%)

Query: 2   SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           SAIESV+ E+RVF P E     A I  M+AY+ALC EAE+D+EGFWAR ARE L W++PF
Sbjct: 6   SAIESVLVENRVFPPSEDTVKNARIAGMQAYEALCAEAEKDFEGFWARLARENLQWSRPF 65

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
           T+ LD+SNAPFYKWF DGELNAS NCLDR++     +K AI+FEADDG+VT+VTY+EL  
Sbjct: 66  TQTLDESNAPFYKWFADGELNASANCLDRHIGTPVENKTAIIFEADDGAVTQVTYKELLA 125

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           +V +FAN LKA G++KGDRV+IYMPM++EGVVAMQACAR+GATHSVVFGGFSAK+L ER 
Sbjct: 126 RVGQFANALKARGVQKGDRVLIYMPMTIEGVVAMQACARIGATHSVVFGGFSAKALHERT 185

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDR 241
           +D GAVA+ITA+ Q+RGGK LPLK+I D+ALA+GGC++V+ V+VY RT       EGRD 
Sbjct: 186 IDAGAVAIITANYQLRGGKELPLKSIVDEALAMGGCDSVKTVLVYERTASAWNRVEGRDV 245

Query: 242 WMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDI 301
              +  AGQ   C   PV AEHPLF+LYTSGSTGKPKGVQHSTGGY LWA  TM WTFD+
Sbjct: 246 TFTEALAGQSTECAPVPVGAEHPLFILYTSGSTGKPKGVQHSTGGYTLWARQTMLWTFDL 305

Query: 302 KPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFY 361
           +P D+FWCTADIGW+TGHTY+AYGPLAAGATQVVFEGVPT+P+AGRFW+MI RHKVSIFY
Sbjct: 306 QPSDVFWCTADIGWITGHTYVAYGPLAAGATQVVFEGVPTFPHAGRFWEMIERHKVSIFY 365

Query: 362 TAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVD 421
           TAPTAIRSLIKAA++DEK+HPK ++L+SLR+LG+VGEPINPEAWMWYY+N+G ERCPIVD
Sbjct: 366 TAPTAIRSLIKAADSDEKVHPKNWNLTSLRVLGSVGEPINPEAWMWYYRNVGGERCPIVD 425

Query: 422 TFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWP 481
           TFWQTE GGH+ITPLPGATPLVPGSCTLPLPGI AAIVDETG D+PNG GG+LV+KRPWP
Sbjct: 426 TFWQTENGGHVITPLPGATPLVPGSCTLPLPGIKAAIVDETGKDLPNGAGGMLVIKRPWP 485

Query: 482 AMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMG 541
           +MIRTIWGDPERF+KSYFPEE+GG +YLAGDG++R +D GYF I GRIDDVLNVSGHRMG
Sbjct: 486 SMIRTIWGDPERFKKSYFPEEMGGTIYLAGDGAVRSEDRGYFRITGRIDDVLNVSGHRMG 545

Query: 542 TMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           TMEIESALV+   LVAEAAVVGRPDD+TGEAI AFVVLKR  PTGEEA ++A ELRNWV 
Sbjct: 546 TMEIESALVAKTDLVAEAAVVGRPDDLTGEAIVAFVVLKRPVPTGEEAKQLANELRNWVA 605

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656
           KEIGPIAKPKDIRFG+NLPKTRSGKIMRRLLRSLAKGE ITQDTSTLENP IL+QL
Sbjct: 606 KEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEAITQDTSTLENPTILDQL 661


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: 1487
Number of extensions: 56
Number of successful extensions: 2
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: 665
Length adjustment: 38
Effective length of query: 622
Effective length of database: 627
Effective search space:   389994
Effective search space used:   389994
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_054257103.1 BN2503_RS13075 (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.247481.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-288  944.5   0.0   1.4e-288  944.3   0.0    1.0  1  NCBI__GCF_001298675.1:WP_054257103.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001298675.1:WP_054257103.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  944.3   0.0  1.4e-288  1.4e-288       2     628 ..      31     663 ..      30     664 .. 0.97

  Alignments for each domain:
  == domain 1  score: 944.3 bits;  conditional E-value: 1.4e-288
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdk 73 
                                           a +++y++l++ea++d e fwa+la+e+l+w +pf+++ldes++p++kWf+dgeln+s+nc+drh+ +  ++k
  NCBI__GCF_001298675.1:WP_054257103.1  31 AGMQAYEALCAEAEKDFEGFWARLARENLQWSRPFTQTLDESNAPFYKWFADGELNASANCLDRHIGTpVENK 103
                                           56899***************************************************************99*** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aii+e+d+    + ++tY+ell++v ++an+lk+ Gv+kgdrv iY+pm++e v+am+acaRiGa+hsvvf+
  NCBI__GCF_001298675.1:WP_054257103.1 104 TAIIFEADDGA--VTQVTYKELLARVGQFANALKARGVQKGDRVLIYMPMTIEGVVAMQACARIGATHSVVFG 174
                                           ********664..8*********************************************************** PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfsa+al+eR +da a  +ita+ +lRggk ++lk+ivdeal++  + sv++vlv++rt +   + +egrDv+
  NCBI__GCF_001298675.1:WP_054257103.1 175 GFSAKALHERTIDAGAVAIITANYQLRGGKELPLKSIVDEALAMGGCdSVKTVLVYERTASA-WNRVEGRDVT 246
                                           ********************************************9988*************9.5599****** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           + e+++ ++s+ec+p ++++e+plfiLYtsGstGkPkGv+h+tgGy l+a  t+ ++fd++++d+fwCtaD+G
  NCBI__GCF_001298675.1:WP_054257103.1 247 FTEALA-GQSTECAPVPVGAEHPLFILYTSGSTGKPKGVQHSTGGYTLWARQTMLWTFDLQPSDVFWCTADIG 318
                                           ******.6***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgee....lvkkhdl 360
                                           W+tGh+Y+ ygPLa+Gat+++fegvpt+p+a+rfwe+ie++kv+ifYtaPtaiR+l+k++++    ++k+ +l
  NCBI__GCF_001298675.1:WP_054257103.1 319 WITGHTYVAYGPLAAGATQVVFEGVPTFPHAGRFWEMIERHKVSIFYTAPTAIRSLIKAADSdekvHPKNWNL 391
                                           **********************************************************99542233678899* PP

                             TIGR02188 361 sslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevv 433
                                            slrvlgsvGepinpeaw+Wyy++vG e+cpivdt+Wqte Gg++itplpg at+l pgs+tlPl+Gi+a++v
  NCBI__GCF_001298675.1:WP_054257103.1 392 TSLRVLGSVGEPINPEAWMWYYRNVGGERCPIVDTFWQTENGGHVITPLPG-ATPLVPGSCTLPLPGIKAAIV 463
                                           ***************************************************.6******************** PP

                             TIGR02188 434 deegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDd 503
                                           de+gk++ ++++ g+Lvik+pwPsm+rti+gd+erf ++Yf +  g  +y++GDga+r +d Gy+ i+GR+Dd
  NCBI__GCF_001298675.1:WP_054257103.1 464 DETGKDLPNGAG-GMLVIKRPWPSMIRTIWGDPERFKKSYFPEEMGgtIYLAGDGAVRSEDrGYFRITGRIDD 535
                                           *********999.8***************************9887778**********9998*********** PP

                             TIGR02188 504 vinvsGhrlgtaeiesalvsh.eavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkei 573
                                           v+nvsGhr+gt+eiesalv++ + vaeaavvg+pd+++geaivafvvlk+ v + ee  +l++el+++v+kei
  NCBI__GCF_001298675.1:WP_054257103.1 536 VLNVSGHRMGTMEIESALVAKtDLVAEAAVVGRPDDLTGEAIVAFVVLKRPVPTGEEakQLANELRNWVAKEI 608
                                           *******************872569*************************9987666669************* PP

                             TIGR02188 574 gpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           gpiakp++i++ e+lPktRsGkimRRllr++a+ge +++d+stle+p+++++l +
  NCBI__GCF_001298675.1:WP_054257103.1 609 GPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEAITQDTSTLENPTILDQLAK 663
                                           ***************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (665 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 36.20
//
[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 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