Alignments for a candidate for fadA in Geobacter metallireducens GS-15

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Geobacter metallireducens GS-15

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_011365969.1 GMET_RS11145 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-13468
         (393 letters)



>NCBI__GCF_000012925.1:WP_011365969.1
          Length = 392

 Score =  404 bits (1039), Expect = e-117
 Identities = 213/392 (54%), Positives = 275/392 (70%), Gaps = 2/392 (0%)

Query: 1   MREVVIVSAVRTAIGSFGGTLKDVSAVDLGAIVIKEAVKRAGIKPEQVDEVIFGNVIQAG 60
           M E VIV A RTAIG F G LKDVSAVDLG   ++ A+K+AGI PE V+EV+ G + +AG
Sbjct: 1   MEEAVIVGAARTAIGDFMGALKDVSAVDLGIAAVQGALKKAGIGPELVEEVVGGMIYKAG 60

Query: 61  VGQSLARQSAVYAGLPVEVPAFTVNKLCGSGLRTVSLAASLISNGDADTIVVGGSENMSA 120
              + ARQ  +  G+P+E  A TV +LCGS +R + +A+  I  G     V  G E+MS 
Sbjct: 61  AKGNPARQVQLKTGIPLEGAATTVEQLCGSAMRALEIASQQILLGKTSVGVAVGMESMSQ 120

Query: 121 SPYLIPKARFGYRMGEAKIYDAMLHDGLIDSFNNYHMGITAENIAEKWGITREDQDKFAL 180
           +PYL+  AR G R+G   I D +LHD LID+F+  HMGITAEN+AEK+GI+RE+QD  AL
Sbjct: 121 APYLLLNARQGLRLGSDSIEDHLLHDALIDAFSGTHMGITAENLAEKYGISREEQDDLAL 180

Query: 181 ASQQKAEAAIKAGKFKDEIVPVTVKMKKKEVVFDTDEDPRFGTTIETLAKLKPAFKRDGT 240
            S Q+A AA ++GKF+ EIVPV VK +K  +V DTDE PR   + E LA L+PAFK+D  
Sbjct: 181 LSHQRAVAAAESGKFRAEIVPVEVKSRKGTIVIDTDEHPRADMSREKLAALRPAFKKD-- 238

Query: 241 GTVTAGNSSGINDSSAALILMSADKAKELGVKPMAKYVDFASAGLDPAIMGYGPYYATKK 300
           GTVTAGN+S IND +AAL+LM+A +A+ELGV P+A+    AS G+ P IMG GP YA  K
Sbjct: 239 GTVTAGNASSINDGAAALVLMTARRARELGVSPIARIRATASFGVAPEIMGIGPAYAIPK 298

Query: 301 VLAKTNLTIKDFDLIEANEAFAAQSIAVARDLEFDMSKVNVNGGAIALGHPVGCSGARIL 360
            L   +L +KD D  E NEAFAAQ +AV R+L  D+S+VN NG  IALGHPVGC+G RI+
Sbjct: 299 ALKYADLQMKDIDYFEINEAFAAQFLAVNRELNIDLSRVNANGSGIALGHPVGCTGIRII 358

Query: 361 VTLLHEMQKRDAKKGLATLCIGGGQGTAVVVE 392
           VT+L EM++R  + G+A+LC+GGG   A V+E
Sbjct: 359 VTMLEEMKRRQGRYGVASLCVGGGPAMATVIE 390


Lambda     K      H
   0.316    0.133    0.369 

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: 425
Number of extensions: 12
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: 393
Length of database: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_011365969.1 GMET_RS11145 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.10680.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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-140  454.9   7.0   1.2e-140  454.8   7.0    1.0  1  lcl|NCBI__GCF_000012925.1:WP_011365969.1  GMET_RS11145 acetyl-CoA C-acyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012925.1:WP_011365969.1  GMET_RS11145 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.8   7.0  1.2e-140  1.2e-140       1     385 []       6     390 ..       6     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 454.8 bits;  conditional E-value: 1.2e-140
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               iv+a+Rt+ig + g+lk++sa+dL+ a+++++l++ag+ pe ++ev+ G+  +ag++ n+aR++ l++g
  lcl|NCBI__GCF_000012925.1:WP_011365969.1   6 IVGAARTAIGDFMGALKDVSAVDLGIAAVQGALKKAGIGPELVEEVVGGMIYKAGAKGNPARQVQLKTG 74 
                                               89******************************************************************* PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               +p + +a+tv+++C+S+++A+++a q+i  G+ +v va G+EsmS++p+ll ++  r++l+lg+ + ed
  lcl|NCBI__GCF_000012925.1:WP_011365969.1  75 IPLEGAATTVEQLCGSAMRALEIASQQILLGKTSVGVAVGMESMSQAPYLLLNA--RQGLRLGSDSIED 141
                                               ****************************************************98..8************ PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               +ll+d+   + ++ +mg+tAenla+kygisReeqD++al Shq+a +A e+gkf +eivpvevk +  +
  lcl|NCBI__GCF_000012925.1:WP_011365969.1 142 HLLHDAlidAFSGTHMGITAENLAEKYGISREEQDDLALLSHQRAVAAAESGKFRAEIVPVEVKSRkgT 210
                                               *********999****************************************************99999 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                                v+++De++r++++ ekLa L+pafk+ +g tvtAgN+s++nDGAaal+lm+ ++a+elg++p+ari++
  lcl|NCBI__GCF_000012925.1:WP_011365969.1 211 IVIDTDEHPRADMSREKLAALRPAFKK-DG-TVTAGNASSINDGAAALVLMTARRARELGVSPIARIRA 277
                                               99***********************95.9*.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a  gv pe+mg+gp++Ai+kaLk a+l+++did++EinEAFAaq+lav++el+ +dl++vN nG+ iA
  lcl|NCBI__GCF_000012925.1:WP_011365969.1 278 TASFGVAPEIMGIGPAYAIPKALKYADLQMKDIDYFEINEAFAAQFLAVNRELN-IDLSRVNANGSGIA 345
                                               ******************************************************.88************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               lGHP+G++G ri++t+l+e+k+r+++yG+a+lCvggG ++A+++e
  lcl|NCBI__GCF_000012925.1:WP_011365969.1 346 LGHPVGCTGIRIIVTMLEEMKRRQGRYGVASLCVGGGPAMATVIE 390
                                               *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 00:00:00.02
# Mc/sec: 7.13
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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