Alignments for a candidate for fadA in Amphritea japonica JAMM 1866

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Amphritea japonica JAMM 1866

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_019620367.1 G329_RS0102470 beta-ketothiolase BktB

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_000381785.1:WP_019620367.1
          Length = 394

 Score =  478 bits (1229), Expect = e-139
 Identities = 249/392 (63%), Positives = 290/392 (73%), Gaps = 1/392 (0%)

Query: 3   REVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEP 62
           REVVV+SGVRTAIG FGGSLK   P EL    V EA++R+  + +D GH VFGNVI TE 
Sbjct: 4   REVVVLSGVRTAIGGFGGSLKSQTPCELATTCVSEAVSRSGAAAEDFGHSVFGNVIHTER 63

Query: 63  RDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSR 122
           RDMYLGRVAAVNGG+    P +T+NRLCGSGLQAI+SA Q I LG  D A+ GG+E MS+
Sbjct: 64  RDMYLGRVAAVNGGLPHETPGVTINRLCGSGLQAIISATQQIELGVCDAAVAGGSEVMSK 123

Query: 123 APYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALE 182
           + Y  P AR+G RMGD  +VD M+GAL  PF   HMG+TAEN+A ++ +SR  QD  A+ 
Sbjct: 124 SQYWMPTARFGQRMGDGAIVDAMVGALTCPFDDTHMGITAENIADKWQVSREDQDALAVM 183

Query: 183 SHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGT 242
           SH  A  AI  G FK+QIVP+  K RKG   FDTDEH+R+  T  DM KLRP F K +G+
Sbjct: 184 SHNNAERAITEGRFKEQIVPIELKSRKGVTVFDTDEHLRYGCTTADMEKLRPAF-KRDGS 242

Query: 243 VTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIAL 302
           VTAGNASGLNDAAAAV +M    AE +GLKP+ARLV Y  AGV+PK MGIGPVPA +  L
Sbjct: 243 VTAGNASGLNDAAAAVTLMAAETAEAKGLKPMARLVGYSFAGVEPKYMGIGPVPAVRKLL 302

Query: 303 ERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVK 362
             A L + D+DV E NEAFAAQA AV + L L   KVN NGSGISLGHPIGATGA+ITVK
Sbjct: 303 ADAELSIGDIDVWEVNEAFAAQALAVCRDLELPLEKVNVNGSGISLGHPIGATGAIITVK 362

Query: 363 ALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           ALHEL R  GRYA+VTMCIGGGQGIAA+FER+
Sbjct: 363 ALHELQRSGGRYAVVTMCIGGGQGIAALFERV 394


Lambda     K      H
   0.318    0.134    0.381 

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: 466
Number of extensions: 16
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_019620367.1 G329_RS0102470 (beta-ketothiolase BktB)
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.1399686.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-135  438.1   3.0   1.6e-135  437.9   3.0    1.0  1  NCBI__GCF_000381785.1:WP_019620367.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381785.1:WP_019620367.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.9   3.0  1.6e-135  1.6e-135       1     385 []       8     392 ..       8     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 437.9 bits;  conditional E-value: 1.6e-135
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpe 72 
                                           ++++vRt+ig +ggslk+ ++ +L+++ ++e++ r+g  +e+  + ++Gnv+++ +  + ++R aa++ glp+
  NCBI__GCF_000381785.1:WP_019620367.1   8 VLSGVRTAIGGFGGSLKSQTPCELATTCVSEAVSRSGAAAEDFGHSVFGNVIHTERRdMYLGRVAAVNGGLPH 80 
                                           689*******99*******************************************999*************** PP

                             TIGR01930  73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl. 144
                                           ++p++t+nr+C+SglqA+++a q+i+ G +d++vaGG E mS++ ++++ +  r + ++g+    d+++  l 
  NCBI__GCF_000381785.1:WP_019620367.1  81 ETPGVTINRLCGSGLQAIISATQQIELGVCDAAVAGGSEVMSKSQYWMPTA--RFGQRMGDGAIVDAMVGALt 151
                                           *************************************************98..89999999999998888889 PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            + ++ +mg+tAen+a+k+++sRe+qD++a+ Sh++a++Ai eg+fk++ivp+e+k +   +v+++De++r +
  NCBI__GCF_000381785.1:WP_019620367.1 152 cPFDDTHMGITAENIADKWQVSREDQDALAVMSHNNAERAITEGRFKEQIVPIELKSRkgVTVFDTDEHLRYG 224
                                           999*****************************************************999999*********** PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                            t +++ kL+pafk+ +gs vtAgN+s+lnD+Aaa+ lm  e+a+++gl+p+ar+v++++agv+p++mg+gpv
  NCBI__GCF_000381785.1:WP_019620367.1 225 CTTADMEKLRPAFKR-DGS-VTAGNASGLNDAAAAVTLMAAETAEAKGLKPMARLVGYSFAGVEPKYMGIGPV 295
                                           *************96.9*7.***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           pA++k+L+ a+lsi did++E+nEAFAaq+lav ++l+ l lekvNvnG+ i+lGHP+Ga+Ga+i+++ l+eL
  NCBI__GCF_000381785.1:WP_019620367.1 296 PAVRKLLADAELSIGDIDVWEVNEAFAAQALAVCRDLE-LPLEKVNVNGSGISLGHPIGATGAIITVKALHEL 367
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           ++ g++y+++t+C+ggGqG+A+++e
  NCBI__GCF_000381785.1:WP_019620367.1 368 QRSGGRYAVVTMCIGGGQGIAALFE 392
                                           **********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.88
//
[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