Alignments for a candidate for acs in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Hydrogenophaga taeniospiralis NBRC 102512

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_068175567.1 HTA01S_RS22665 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_001592305.1:WP_068175567.1
          Length = 664

 Score = 1054 bits (2725), Expect = 0.0
 Identities = 509/658 (77%), Positives = 570/658 (86%), Gaps = 2/658 (0%)

Query: 2   SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           ++IES + E+RVF P E     A I  M+AY ALC EAE D+EGFW R ARE L W KPF
Sbjct: 6   TSIESTLVENRVFEPTEATVKAARISGMDAYNALCAEAEDDFEGFWVRRARETLTWHKPF 65

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
           TK LD+SNAPF+KWFEDGELNASYNCLDR++     +K AI+FEAD G VT+VTY+EL G
Sbjct: 66  TKTLDESNAPFFKWFEDGELNASYNCLDRHMGTPVENKTAIIFEADGGEVTKVTYKELLG 125

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           KV +FAN LKA G++KGDRVVIYMPM++EGVVAMQACAR+GATHSVVFGGFSAK+LQER+
Sbjct: 126 KVSQFANALKARGVKKGDRVVIYMPMTIEGVVAMQACARIGATHSVVFGGFSAKALQERI 185

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDR 241
            D GAVA+ITA+ Q+RGGK LPLKAI D+ +A+GGCE +++VIV++RT   V    GRD 
Sbjct: 186 QDAGAVAVITANYQLRGGKELPLKAIVDEGIAMGGCECIKDVIVFQRTPTAVNMVAGRDS 245

Query: 242 WMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDI 301
           +M DV AGQ   C AE V AEHPLFVLYTSGSTGKPKGVQHSTGGYLLWA +TM+WTFD+
Sbjct: 246 FMHDVMAGQSTDCPAEMVGAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWASLTMQWTFDL 305

Query: 302 KPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFY 361
           +  D+FWCTADIGW+TGHTY+AYGPLAAGATQ+VFEGVPTYPNAGRFW MI RHK +IFY
Sbjct: 306 QDKDIFWCTADIGWITGHTYVAYGPLAAGATQIVFEGVPTYPNAGRFWQMIERHKCTIFY 365

Query: 362 TAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVD 421
           TAPTAIRSLIKAAE DEK+HP + DLSSLR+LG+VGEPINPEAWMWYYK++G ERCPIVD
Sbjct: 366 TAPTAIRSLIKAAEGDEKVHPARSDLSSLRILGSVGEPINPEAWMWYYKHVGGERCPIVD 425

Query: 422 TFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWP 481
           TFWQTETGGHMI+PLPGATPLVPGSCTLPLPGI AAIVDE G DVPNG+GGILVVKRPWP
Sbjct: 426 TFWQTETGGHMISPLPGATPLVPGSCTLPLPGITAAIVDEAGMDVPNGSGGILVVKRPWP 485

Query: 482 AMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMG 541
           +MIRTIWGDPERF+KSYFPEEL G  YLAGDG++R  D GYF I GRIDDVLNVSGHRMG
Sbjct: 486 SMIRTIWGDPERFKKSYFPEELKG-YYLAGDGAVRSADRGYFRITGRIDDVLNVSGHRMG 544

Query: 542 TMEIESALV-SNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           TMEIESALV    LVAEAAVVGRPDD+TGEAI AFVVLKRSRPTG+EA  IA  LR+WVG
Sbjct: 545 TMEIESALVGKTDLVAEAAVVGRPDDLTGEAIVAFVVLKRSRPTGDEAKAIAKVLRDWVG 604

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658
           KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRS+AKGE ITQDTSTLENPAIL+QL +
Sbjct: 605 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEAITQDTSTLENPAILDQLSE 662


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: 1517
Number of extensions: 74
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: 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 WP_068175567.1 HTA01S_RS22665 (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.31155.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-293  961.1   0.0   1.3e-293  960.9   0.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068175567.1  HTA01S_RS22665 acetate--CoA liga


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068175567.1  HTA01S_RS22665 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  960.9   0.0  1.3e-293  1.3e-293       2     628 ..      31     662 ..      30     663 .. 0.96

  Alignments for each domain:
  == domain 1  score: 960.9 bits;  conditional E-value: 1.3e-293
                                 TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek. 69 
                                               + +++y++l++ea++d e fw + a+e+l+w+kpf+k+ldes++p+ kWfedgeln+sync+drh+ + 
  lcl|NCBI__GCF_001592305.1:WP_068175567.1  31 SGMDAYNALCAEAEDDFEGFWVRRARETLTWHKPFTKTLDESNAPFFKWFEDGELNASYNCLDRHMGTp 99 
                                               5789****************************************************************9 PP

                                 TIGR02188  70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138
                                                ++k+aii+e+d  g ++ k+tY+ell +v+++an+lk+ Gvkkgdrv+iY+pm++e v+am+acaRiG
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 100 VENKTAIIFEAD-GG-EVTKVTYKELLGKVSQFANALKARGVKKGDRVVIYMPMTIEGVVAMQACARIG 166
                                               9***********.45.59*************************************************** PP

                                 TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtge 206
                                               a+hsvvf+Gfsa+al+eRi+da a  vita+ +lRggk ++lk+ivde +++  +  +++v+v++rt +
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 167 ATHSVVFGGFSAKALQERIQDAGAVAVITANYQLRGGKELPLKAIVDEGIAMGGCeCIKDVIVFQRTPT 235
                                               *************************************************99988878************ PP

                                 TIGR02188 207 evaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyv 275
                                                v+ ++ grD  ++++++ ++s++c++e +++e+plf+LYtsGstGkPkGv+h+tgGyll+a+lt++++
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 236 AVN-MVAGRDSFMHDVMA-GQSTDCPAEMVGAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWASLTMQWT 302
                                               *66.**************.6************************************************* PP

                                 TIGR02188 276 fdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtai 344
                                               fd++d+difwCtaD+GW+tGh+Y+ ygPLa+Gat+++fegvptyp+a+rfw++ie++k tifYtaPtai
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 303 FDLQDKDIFWCTADIGWITGHTYVAYGPLAAGATQIVFEGVPTYPNAGRFWQMIERHKCTIFYTAPTAI 371
                                               ********************************************************************* PP

                                 TIGR02188 345 Ralmklg..ee..lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitpl 409
                                               R+l+k++  +e  ++++ dlsslr+lgsvGepinpeaw+Wyy++vG e+cpivdt+WqtetGg++i+pl
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 372 RSLIKAAegDEkvHPARSDLSSLRILGSVGEPINPEAWMWYYKHVGGERCPIVDTFWQTETGGHMISPL 440
                                               ****98633442266799*************************************************** PP

                                 TIGR02188 410 pgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfk.kl 477
                                               pg at+l pgs+tlPl+Gi+a++vde g +v ++++ g+Lv+k+pwPsm+rti+gd+erf ++Yf  +l
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 441 PG-ATPLVPGSCTLPLPGITAAIVDEAGMDVPNGSG-GILVVKRPWPSMIRTIWGDPERFKKSYFPeEL 507
                                               **.6*****************************999.8***************************6268 PP

                                 TIGR02188 478 kglyftGDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsh.eavaeaavvgvpdeikgeai 544
                                               kg+y++GDga+r +d Gy+ i+GR+Ddv+nvsGhr+gt+eiesalv + + vaeaavvg+pd+++geai
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 508 KGYYLAGDGAVRSADrGYFRITGRIDDVLNVSGHRMGTMEIESALVGKtDLVAEAAVVGRPDDLTGEAI 576
                                               89**********9988******************************762679***************** PP

                                 TIGR02188 545 vafvvlkegveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeell 611
                                               vafvvlk+++ + +e  +++k l+++v keigpiakp++i++ ++lPktRsGkimRRllr+ia+ge ++
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 577 VAFVVLKRSRPTGDEakAIAKVLRDWVGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEAIT 645
                                               *********9987776689************************************************** PP

                                 TIGR02188 612 gdvstledpsvveelke 628
                                               +d+stle+p+++++l+e
  lcl|NCBI__GCF_001592305.1:WP_068175567.1 646 QDTSTLENPAILDQLSE 662
                                               **************986 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: 10.87
//
[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 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