Alignments for a candidate for fadA in Polaromonas naphthalenivorans CJ2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Polaromonas naphthalenivorans CJ2

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_011800568.1 PNAP_RS05805 acetyl-CoA C-acyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_000015505.1:WP_011800568.1
          Length = 394

 Score =  610 bits (1573), Expect = e-179
 Identities = 306/394 (77%), Positives = 343/394 (87%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           MTREVVVVSGVRTAIGTFGGSLKD  P EL ALVVRE+LARA V G DVGHVVFG+V+ T
Sbjct: 1   MTREVVVVSGVRTAIGTFGGSLKDTPPTELAALVVRESLARAGVEGKDVGHVVFGHVVNT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           E +DMYL RVAAVNGG     PA  VNRLCGSGLQAI+SA+Q+ILLGD D+AIGGGAE+M
Sbjct: 61  EAKDMYLSRVAAVNGGCAEGTPAFNVNRLCGSGLQAIISASQSILLGDADIAIGGGAENM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SR PY + A R+GARMGD  ++DM++GALHDPFH IHMGVTAEN+A +Y ISR +QD  A
Sbjct: 121 SRGPYASLATRFGARMGDTKMIDMVVGALHDPFHTIHMGVTAENIAAKYGISREEQDALA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           ++SH RA  AI+AGYFK+QIVPV+ K RKG+V +DTDEH R + T+ DM KL+PVFVKEN
Sbjct: 181 VQSHNRAQKAIEAGYFKEQIVPVMLKSRKGEVAYDTDEHFRPNCTMADMAKLKPVFVKEN 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASG+NDAAAAVV+ME   AE RGLKPLARLV+Y HAGVDPK MGIGPVPAT++
Sbjct: 241 GTVTAGNASGINDAAAAVVLMEAGVAEARGLKPLARLVAYAHAGVDPKYMGIGPVPATQL 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           AL++AGL VSDLDVIEANEAFAAQACAVT+ LGLDPAKVNPNGSGISLGHPIGATGALIT
Sbjct: 301 ALKKAGLTVSDLDVIEANEAFAAQACAVTRDLGLDPAKVNPNGSGISLGHPIGATGALIT 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           VKALHEL R+ GRYALVTMCIGGGQGIAAIFERI
Sbjct: 361 VKALHELQRIGGRYALVTMCIGGGQGIAAIFERI 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: 574
Number of extensions: 10
Number of successful extensions: 1
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_011800568.1 PNAP_RS05805 (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.11086.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-141  455.7   7.4   7.2e-141  455.5   7.4    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011800568.1  PNAP_RS05805 acetyl-CoA C-acyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011800568.1  PNAP_RS05805 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.5   7.4  7.2e-141  7.2e-141       1     385 []       7     392 ..       7     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 455.5 bits;  conditional E-value: 7.2e-141
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 
                                               +v++vRt+ig++ggslk++++ +L+a v++e l+rag++ +++ +v++G+v+++ ++ + + R aa++ 
  lcl|NCBI__GCF_000015505.1:WP_011800568.1   7 VVSGVRTAIGTFGGSLKDTPPTELAALVVRESLARAGVEGKDVGHVVFGHVVNTEAKdMYLSRVAAVNG 75 
                                               79***************************************************99999*********** PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               g+ e +pa++vnr+C+SglqA+++a q+i  G+ad+++ GG+E+mSr p+ + a   r ++++g++k+ 
  lcl|NCBI__GCF_000015505.1:WP_011800568.1  76 GCAEGTPAFNVNRLCGSGLQAIISASQSILLGDADIAIGGGAENMSRGPYASLAT--RFGARMGDTKMI 142
                                               **************************************************99997..89********** PP

                                 TIGR01930 138 dqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               d+++  l  + + ++mg+tAen+a+kygisReeqD++a++Sh++a+kAie+g+fk++ivpv +k +  +
  lcl|NCBI__GCF_000015505.1:WP_011800568.1 143 DMVVGALhdPFHTIHMGVTAENIAAKYGISREEQDALAVQSHNRAQKAIEAGYFKEQIVPVMLKSRkgE 211
                                               *88888899999***************************************************999999 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               + +++De+ rpn t++++akLkp+f +++g tvtAgN+s++nD+Aaa++lm+  va++ gl+plar+v+
  lcl|NCBI__GCF_000015505.1:WP_011800568.1 212 VAYDTDEHFRPNCTMADMAKLKPVFVKENG-TVTAGNASGINDAAAAVVLMEAGVAEARGLKPLARLVA 279
                                               99****************************.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+agvdp++mg+gpvpA++ aLkkagl++sd+d++E nEAFAaq+ av+++lg ld++kvN nG+ i+
  lcl|NCBI__GCF_000015505.1:WP_011800568.1 280 YAHAGVDPKYMGIGPVPATQLALKKAGLTVSDLDVIEANEAFAAQACAVTRDLG-LDPAKVNPNGSGIS 347
                                               ******************************************************.99************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               lGHP+Ga+Ga i+++ l+eL++ g++y+l+t+C+ggGqG+A+i+e
  lcl|NCBI__GCF_000015505.1:WP_011800568.1 348 LGHPIGATGALITVKALHELQRIGGRYALVTMCIGGGQGIAAIFE 392
                                               *******************************************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.26
//
[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