Alignments for a candidate for acs in Thermithiobacillus tepidarius DSM 3134

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Thermithiobacillus tepidarius DSM 3134

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_028989221.1 G579_RS0104490 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000423825.1:WP_028989221.1
          Length = 652

 Score =  809 bits (2089), Expect = 0.0
 Identities = 409/654 (62%), Positives = 488/654 (74%), Gaps = 10/654 (1%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           +ES++ E RVF   E FA QA + S E Y ALC  AE D  GFW   AR+ L W KPFT+
Sbjct: 6   LESILTEARVFPVHEDFARQANLNS-EQYAALCRRAEEDPSGFWGDLARQELAWDKPFTQ 64

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
           VLD S APFY+WF DGELN + NCLDR+L +   +K A+++E +DG V   TY +LH +V
Sbjct: 65  VLDDSRAPFYRWFADGELNVAANCLDRHLSSPTRNKAALIWEGEDGEVRTFTYGQLHREV 124

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
            RFAN LK LGI  GDRV IYMPM  E  VAM ACARLGA HSVVFGGFSA++L++R+ D
Sbjct: 125 SRFANVLKKLGITTGDRVAIYMPMVPEAAVAMLACARLGAIHSVVFGGFSAEALKDRIED 184

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
             A  LITAD   R G+ + LK  AD AL   G  +V  V+V RRTG +V   +GRD W 
Sbjct: 185 TQAKLLITADGGFRAGRVVHLKQHADQALMRDG-HSVDKVVVLRRTGQEVDMLDGRDLWW 243

Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
            ++       C A  V+AEHPLFVLYTSGSTGKPKG+ HS+GGYLLW+ +TM+W FDIKP
Sbjct: 244 HELMQDAEPQCPAVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFDIKP 303

Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
           +D++WCTADIGWVTGHTY  YGPLA GAT ++FEGVPTYP+AGRFW MI RH VS+FYTA
Sbjct: 304 EDVYWCTADIGWVTGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVFYTA 363

Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
           PTA+R+L+K  E      P +YDLSSLRLLGTVGEPINPEAWMWYY+ IG ERCP+VDT+
Sbjct: 364 PTAVRALMKLGEE----WPGKYDLSSLRLLGTVGEPINPEAWMWYYRVIGKERCPVVDTW 419

Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGN-GGILVVKRPWPA 482
           WQTETGGH+I PLPG TPL PGSCT PLPGI   IVDE G  V     GG LVVKRPWP 
Sbjct: 420 WQTETGGHLIAPLPGVTPLKPGSCTRPLPGIFPDIVDEEGDPVQGTEAGGYLVVKRPWPG 479

Query: 483 MIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGT 542
           M+RT+WG+  R+ ++Y+  +   + Y+AGD + RD D GY+ IMGRIDDVLNVSGHR+GT
Sbjct: 480 MLRTVWGNDARYLETYW-AKFQNRYYVAGDSAHRDAD-GYYWIMGRIDDVLNVSGHRLGT 537

Query: 543 MEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKE 602
           MEIESALVS+P VAEAAVVGRP ++ GEAI AFV+L++S    ++  ++   LR  V + 
Sbjct: 538 MEIESALVSHPAVAEAAVVGRPHEIKGEAITAFVILRQSH-VQDDRDRLTEALRQHVSEA 596

Query: 603 IGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656
           IGPIAKP DIRF DNLPKTRSGKIMRRLLR++A+GEEITQDTSTLEN   + QL
Sbjct: 597 IGPIAKPDDIRFTDNLPKTRSGKIMRRLLRAIARGEEITQDTSTLENEETVRQL 650


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: 1406
Number of extensions: 78
Number of successful extensions: 9
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: 652
Length adjustment: 38
Effective length of query: 622
Effective length of database: 614
Effective search space:   381908
Effective search space used:   381908
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_028989221.1 G579_RS0104490 (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.38042.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1025.6   0.0          0 1025.4   0.0    1.0  1  NCBI__GCF_000423825.1:WP_028989221.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000423825.1:WP_028989221.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1025.4   0.0         0         0       3     626 ..      29     650 ..      27     652 .] 0.98

  Alignments for each domain:
  == domain 1  score: 1025.4 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 
                                           + e+y++l+++a+edp+ fw++la++el+w+kpf++vld+s +p+++Wf+dgelnv++nc+drh+++ +++k+
  NCBI__GCF_000423825.1:WP_028989221.1  29 NSEQYAALCRRAEEDPSGFWGDLARQELAWDKPFTQVLDDSRAPFYRWFADGELNVAANCLDRHLSSpTRNKA 101
                                           6799***************************************************************9***** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           a+iweg++   ++r++tY +l+rev+r+anvlk+lG+  gdrvaiY+pm+pea++amlacaR+Ga+hsvvf+G
  NCBI__GCF_000423825.1:WP_028989221.1 102 ALIWEGEDG--EVRTFTYGQLHREVSRFANVLKKLGITTGDRVAIYMPMVPEAAVAMLACARLGAIHSVVFGG 172
                                           *******55..49************************************************************ PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fsaeal++Ri+d++akl+itad+g+R g+v++lk+ +d+al +  +sv+kv+v++rtg+ev  + +grD+ww+
  NCBI__GCF_000423825.1:WP_028989221.1 173 FSAEALKDRIEDTQAKLLITADGGFRAGRVVHLKQHADQALMRDGHSVDKVVVLRRTGQEVD-MLDGRDLWWH 244
                                           ************************************************************66.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           el+++ a+ +c++ ++++e+plf+LYtsGstGkPkG++h++gGyll+ alt+++vfdik+ed++wCtaD+GWv
  NCBI__GCF_000423825.1:WP_028989221.1 245 ELMQD-AEPQCPAVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFDIKPEDVYWCTADIGWV 316
                                           ****7.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGh+Y +ygPLa+Gat llfegvptypda+rfw++ie+++v++fYtaPta+Ralmklgee++ k+dlsslr+l
  NCBI__GCF_000423825.1:WP_028989221.1 317 TGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVFYTAPTAVRALMKLGEEWPGKYDLSSLRLL 389
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           g+vGepinpeaw+Wyy+v+Gke+cp+vdtwWqtetGg+li+plpg +t+lkpgs+t+Pl+Gi +++vdeeg++
  NCBI__GCF_000423825.1:WP_028989221.1 390 GTVGEPINPEAWMWYYRVIGKERCPVVDTWWQTETGGHLIAPLPG-VTPLKPGSCTRPLPGIFPDIVDEEGDP 461
                                           *********************************************.5************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGDgarrdkdGyiwilGRvDdvinvsGhr 511
                                           v+ +e gg+Lv+k+pwP+mlrt++g++ r+ etY+ k+++ +y +GD+a+rd+dGy+wi+GR+Ddv+nvsGhr
  NCBI__GCF_000423825.1:WP_028989221.1 462 VQGTEAGGYLVVKRPWPGMLRTVWGNDARYLETYWAKFQNrYYVAGDSAHRDADGYYWIMGRIDDVLNVSGHR 534
                                           **88888*******************************997999***************************** PP

                             TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee.elekelkklvrkeigpiakpdkil 583
                                           lgt+eiesalvsh+avaeaavvg+p+eikgeai+afv+l++++ +d++ +l++ l+++v++ igpiakpd+i+
  NCBI__GCF_000423825.1:WP_028989221.1 535 LGTMEIESALVSHPAVAEAAVVGRPHEIKGEAITAFVILRQSHVQDDRdRLTEALRQHVSEAIGPIAKPDDIR 607
                                           ****************************************9877666549*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaegeellgdvstledpsvveel 626
                                           ++++lPktRsGkimRRllr+ia+gee+++d+stle+++ v +l
  NCBI__GCF_000423825.1:WP_028989221.1 608 FTDNLPKTRSGKIMRRLLRAIARGEEITQDTSTLENEETVRQL 650
                                           **************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (652 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: 35.71
//
[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