Alignments for a candidate for acs in Pandoraea thiooxydans ATSB16

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pandoraea thiooxydans ATSB16

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_047213862.1 PATSB16_RS09165 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_001931675.1:WP_047213862.1
          Length = 660

 Score = 1061 bits (2743), Expect = 0.0
 Identities = 500/656 (76%), Positives = 570/656 (86%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           M+  E+++ +  +F PPE FA+ AAIP M AY+ L  EAERDYEGFWAR ARE L W KP
Sbjct: 1   MTVAEALLDKQEIFPPPEAFAAAAAIPGMAAYRTLMAEAERDYEGFWARLARETLSWKKP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           F KVLD++ APFYKWFEDG LNASYN LDR+++ G+ ++VAI+FEAD+G+VTRVTYR+L 
Sbjct: 61  FAKVLDETAAPFYKWFEDGRLNASYNSLDRHVEAGHGNRVAIIFEADNGAVTRVTYRDLL 120

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
            +VCRFAN LK  GI+KGDRVVIYMPMS+EG+ AMQACAR+GATHSVVFGGFS+K+L ER
Sbjct: 121 LQVCRFANALKKRGIKKGDRVVIYMPMSIEGIAAMQACARIGATHSVVFGGFSSKALHER 180

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           +VDVGAVA+ITADEQ+RGGK LPLK I D+ALA+ GC+AV++VIVYRRTGG + W  GRD
Sbjct: 181 IVDVGAVAVITADEQVRGGKVLPLKQIVDEALAMEGCDAVQSVIVYRRTGGNIPWVAGRD 240

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
            WM +++ G+ D+CE E VSAEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA  TMKWTFD
Sbjct: 241 LWMHELTRGESDSCEPEWVSAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAAQTMKWTFD 300

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
            KP D+FWCTADIGWVTGH+YIAYGPL  G TQVVFEGVPTYPNAGRFW+MIARH+VS+F
Sbjct: 301 WKPGDIFWCTADIGWVTGHSYIAYGPLVLGGTQVVFEGVPTYPNAGRFWEMIARHRVSVF 360

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIRSL+K +E D    P  YDLSSLRLLGTVGEPI+P+ W WYY  +G  RCP+V
Sbjct: 361 YTAPTAIRSLVKTSELDPNTRPTAYDLSSLRLLGTVGEPISPQTWRWYYDQVGGGRCPVV 420

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DT+WQTETGGHMI P+PGATPLVPGSCTLPLPGIMAAIVDETG + PNG GG+LV+KRPW
Sbjct: 421 DTWWQTETGGHMIAPMPGATPLVPGSCTLPLPGIMAAIVDETGQEEPNGQGGLLVIKRPW 480

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           PAM+RT+WGDPERFRKSYFPEELGG LYLAGDG+ RDKDTGYFTI GRIDDVLNVSGHR+
Sbjct: 481 PAMLRTVWGDPERFRKSYFPEELGGHLYLAGDGATRDKDTGYFTITGRIDDVLNVSGHRL 540

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTMEIESALV+NPLVAEAAVV RPD++TGEAI AFVVLKR  P   +A ++A ELR WVG
Sbjct: 541 GTMEIESALVANPLVAEAAVVSRPDELTGEAIVAFVVLKRQGPGDGDARQLADELRAWVG 600

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656
           KEIGPIAKPKDIRFG+NLPKTRSGKIMRRLLRS+AK E ITQD STLENPAIL QL
Sbjct: 601 KEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSIAKEEGITQDVSTLENPAILSQL 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: 1582
Number of extensions: 66
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: 660
Length adjustment: 38
Effective length of query: 622
Effective length of database: 622
Effective search space:   386884
Effective search space used:   386884
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_047213862.1 PATSB16_RS09165 (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.3187516.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-295  967.8   0.0   1.2e-295  967.6   0.0    1.0  1  NCBI__GCF_001931675.1:WP_047213862.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001931675.1:WP_047213862.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  967.6   0.0  1.2e-295  1.2e-295       4     627 ..      29     657 ..      26     659 .. 0.97

  Alignments for each domain:
  == domain 1  score: 967.6 bits;  conditional E-value: 1.2e-295
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           + +y++l++ea++d+e fwa+la+e+l+w+kpf kvlde+ +p++kWfedg+ln+syn++drhve+ + ++va
  NCBI__GCF_001931675.1:WP_047213862.1  29 MAAYRTLMAEAERDYEGFWARLARETLSWKKPFAKVLDETAAPFYKWFEDGRLNASYNSLDRHVEAgHGNRVA 101
                                           679********************************************************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           ii+e+d+    + ++tY++ll +vcr+an+lk+ G+kkgdrv+iY+pm +e ++am+acaRiGa+hsvvf+Gf
  NCBI__GCF_001931675.1:WP_047213862.1 102 IIFEADNGA--VTRVTYRDLLLQVCRFANALKKRGIKKGDRVVIYMPMSIEGIAAMQACARIGATHSVVFGGF 172
                                           ******554..89************************************************************ PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwwe 220
                                           s++al+eRivd+ a  vitade++Rggkv++lk+ivdeal+++ + +v++v+v++rtg ++  w+ grD+w++
  NCBI__GCF_001931675.1:WP_047213862.1 173 SSKALHERIVDVGAVAVITADEQVRGGKVLPLKQIVDEALAMEGCdAVQSVIVYRRTGGNIP-WVAGRDLWMH 244
                                           *****************************************999989*************66.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           el++ ++s++cepe++++e+plfiLYtsGstGkPkGv+h+tgGyll+aa t+k++fd k++difwCtaD+GWv
  NCBI__GCF_001931675.1:WP_047213862.1 245 ELTR-GESDSCEPEWVSAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAAQTMKWTFDWKPGDIFWCTADIGWV 316
                                           ****.6******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklg....eelvkkhdlss 362
                                           tGhsYi ygPL+ G t+++fegvptyp+a+rfwe+i +++v++fYtaPtaiR+l+k++    +  ++++dlss
  NCBI__GCF_001931675.1:WP_047213862.1 317 TGHSYIAYGPLVLGGTQVVFEGVPTYPNAGRFWEMIARHRVSVFYTAPTAIRSLVKTSeldpNTRPTAYDLSS 389
                                           ********************************************************984444677899***** PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lr+lg+vGepi p++w+Wyy++vG ++cp+vdtwWqtetGg++i+p+pg at+l pgs+tlPl+Gi+a++vde
  NCBI__GCF_001931675.1:WP_047213862.1 390 LRLLGTVGEPISPQTWRWYYDQVGGGRCPVVDTWWQTETGGHMIAPMPG-ATPLVPGSCTLPLPGIMAAIVDE 461
                                           *************************************************.6********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDdvi 505
                                           +g+e  ++++ g+Lvik+pwP+mlrt++gd+erf ++Yf +  g  ly++GDga+rdkd Gy++i+GR+Ddv+
  NCBI__GCF_001931675.1:WP_047213862.1 462 TGQEEPNGQG-GLLVIKRPWPAMLRTVWGDPERFRKSYFPEELGghLYLAGDGATRDKDtGYFTITGRIDDVL 533
                                           ****999999.8***************************9876668************99************* PP

                             TIGR02188 506 nvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeigpi 576
                                           nvsGhrlgt+eiesalv+++ vaeaavv++pde++geaivafvvlk++   d +  +l++el+++v keigpi
  NCBI__GCF_001931675.1:WP_047213862.1 534 NVSGHRLGTMEIESALVANPLVAEAAVVSRPDELTGEAIVAFVVLKRQGPGDGDarQLADELRAWVGKEIGPI 606
                                           **********************************************99876554559**************** PP

                             TIGR02188 577 akpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           akp++i++ e+lPktRsGkimRRllr+ia++e +++dvstle+p+++ +l 
  NCBI__GCF_001931675.1:WP_047213862.1 607 AKPKDIRFGENLPKTRSGKIMRRLLRSIAKEEGITQDVSTLENPAILSQLG 657
                                           ***********************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (660 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: 25.86
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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