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 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_011802183.1 PNAP_RS14005 acetyl-CoA C-acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>NCBI__GCF_000015505.1:WP_011802183.1
          Length = 392

 Score =  594 bits (1531), Expect = e-174
 Identities = 296/392 (75%), Positives = 334/392 (85%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M ++VIVSA RTAVGKFGGSLAKIPA ELGA VIKA L R+G+  EQ+ EVIMGQVL AG
Sbjct: 1   MEEIVIVSAGRTAVGKFGGSLAKIPATELGAAVIKAVLARSGLNAEQIGEVIMGQVLAAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
           +GQNPARQ+ +KAG P  +P +TIN VCGSGLKAVMLAA A+  GD+EIV+AGGQENMSA
Sbjct: 61  AGQNPARQSVLKAGFPQGIPGLTINAVCGSGLKAVMLAAQAVATGDSEIVIAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           +PHVL GSRDG RMGD K+VDTMIVDGLWDVYNQYHMGITAENVAK+Y I REAQD  A+
Sbjct: 121 SPHVLNGSRDGQRMGDWKMVDTMIVDGLWDVYNQYHMGITAENVAKKYNINREAQDALAL 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
            SQ KA AAQ AGKF +EI+P+ IPQ+KGDP+ F  DEF+ +  + + ++GL+PAFDKAG
Sbjct: 181 ASQTKAAAAQDAGKFKDEIIPISIPQKKGDPLVFSADEFINRKTSAEGLAGLRPAFDKAG 240

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
            VTA NASGLNDGAAAV+VM+A KA  LGLTPLA I SYA AG+DP  MGMGPVPAS +A
Sbjct: 241 GVTAGNASGLNDGAAAVMVMTAKKAAALGLTPLARIASYATAGLDPAYMGMGPVPASTKA 300

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L RA W  QDLDL+EINEAFAAQA AV+Q+MGWDTSKVNVNGGAIAIGHPIGASGCRILV
Sbjct: 301 LQRAGWNAQDLDLLEINEAFAAQACAVNQEMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM RRDAKKG+ASLCIGGGMGVAL +ER
Sbjct: 361 TLLHEMVRRDAKKGIASLCIGGGMGVALTLER 392


Lambda     K      H
   0.315    0.131    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: 540
Number of extensions: 18
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: 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_011802183.1 PNAP_RS14005 (acetyl-CoA C-acetyltransferase)
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.18591.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-149  483.4  11.7   2.7e-149  483.2  11.7    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011802183.1  PNAP_RS14005 acetyl-CoA C-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011802183.1  PNAP_RS14005 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.2  11.7  2.7e-149  2.7e-149       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 483.2 bits;  conditional E-value: 2.7e-149
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               iv+a Rt++gk+ggsl++++a +L+aavik++l+r+gl++e+i evi+G+vl ag+++n+aR+ +l+ag
  lcl|NCBI__GCF_000015505.1:WP_011802183.1   6 IVSAGRTAVGKFGGSLAKIPATELGAAVIKAVLARSGLNAEQIGEVIMGQVLAAGAGQNPARQSVLKAG 74 
                                               89******************************************************************* PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               +p+ +p+lt+n vC+Sgl+Av+laaq++++G+ ++v+aGG E+mS +p++l+ s  r++ ++g+ k+ d
  lcl|NCBI__GCF_000015505.1:WP_011802183.1  75 FPQGIPGLTINAVCGSGLKAVMLAAQAVATGDSEIVIAGGQENMSASPHVLNGS--RDGQRMGDWKMVD 141
                                               ****************************************************98..8************ PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201
                                               +++ d+   v+++++mg+tAen+akky+i+Re qD++al+S++kaa+A+++gkfkdei+p+++++k   
  lcl|NCBI__GCF_000015505.1:WP_011802183.1 142 TMIVDGlwdVYNQYHMGITAENVAKKYNINREAQDALALASQTKAAAAQDAGKFKDEIIPISIPQKkgd 210
                                               *****9***99*****************************************************999*9 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                               + v+s De i ++t++e La+L+paf++ +g  vtAgN+s+lnDGAaa+++m+ ++a++lgltplari 
  lcl|NCBI__GCF_000015505.1:WP_011802183.1 211 PLVFSADEFINRKTSAEGLAGLRPAFDK-AGG-VTAGNASGLNDGAAAVMVMTAKKAAALGLTPLARIA 277
                                               9*************************96.785.************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               s+a+ag+dp++mg+gpvpA++kaL++ag++++d+dl EinEAFAaq+ av++e+g  d++kvNvnGGAi
  lcl|NCBI__GCF_000015505.1:WP_011802183.1 278 SYATAGLDPAYMGMGPVPASTKALQRAGWNAQDLDLLEINEAFAAQACAVNQEMG-WDTSKVNVNGGAI 345
                                               *******************************************************.88*********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               A+GHP+GasG+ri++tll+e+ +r++k G+a+lC+ggG+G+A+ le
  lcl|NCBI__GCF_000015505.1:WP_011802183.1 346 AIGHPIGASGCRILVTLLHEMVRRDAKKGIASLCIGGGMGVALTLE 391
                                               ******************************************9886 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.10
//
[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