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 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_011802842.1 PNAP_RS17350 acetyl-CoA C-acyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_000015505.1:WP_011802842.1
          Length = 399

 Score =  346 bits (887), Expect = e-100
 Identities = 195/395 (49%), Positives = 252/395 (63%), Gaps = 8/395 (2%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59
           ++EA IV+  RTP+G++ +G     RPDDL    +K  L +    +   I+D+I GCA P
Sbjct: 5   VQEAYIVAATRTPIGRSHRGFFRNTRPDDLLVSVLKAALAQVPTLDPKAIEDIICGCAIP 64

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           E  QGLN+AR    LAGLP +V  ITVNR+C+SGL +I  AA++I +G  D   A G ES
Sbjct: 65  EGPQGLNIARIGAVLAGLPTSVGGITVNRFCASGLSAIQMAADRIRVGEADVMFAAGTES 124

Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMS----MGHTAEQVAKKYGVSREDQDAFAVRSHQN 175
           MS VPM G+   P+L+ A  A +  +     MG TAE+VA+++ VSR  QD FA  SH  
Sbjct: 125 MSMVPMSGN--SPSLSPAMFANDENVGIAYGMGLTAEKVAQQWKVSRAAQDQFAYESHMK 182

Query: 176 AAKALAEGKFKDEIVPVEVTVTEIG-EDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAF 234
           A KA   G+F  EI PVEVT      E  + +      S DEG RP TT + L+ L+  F
Sbjct: 183 ALKAQQAGEFSAEITPVEVTDRTANLETGEVIATTRTVSLDEGARPDTTLEGLAKLKTPF 242

Query: 235 SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEA 294
           +  G+VTAGNSSQTSDGA A++L   +     GL PL +F S+A  GVPPE+MGIGP+EA
Sbjct: 243 AARGSVTAGNSSQTSDGAGALILASEKAVKEFGLKPLARFVSYAAKGVPPEIMGIGPIEA 302

Query: 295 IPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGT 354
           IP AL+ AGL   DI  FELNEAFA+Q++ VI  LG+D  KVN  GGAIALGHPLG TG 
Sbjct: 303 IPAALRYAGLTQNDIDWFELNEAFAAQSLAVINTLGLDPAKVNPMGGAIALGHPLGATGA 362

Query: 355 KLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
               ++IH + R   ++G+VTMC+G G GAAG+FE
Sbjct: 363 IRAATVIHALHRHQLKYGMVTMCVGMGQGAAGIFE 397


Lambda     K      H
   0.316    0.133    0.377 

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: 402
Number of extensions: 17
Number of successful extensions: 4
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: 391
Length of database: 399
Length adjustment: 31
Effective length of query: 360
Effective length of database: 368
Effective search space:   132480
Effective search space used:   132480
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_011802842.1 PNAP_RS17350 (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.937886.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-143  464.8   4.0   1.2e-143  464.6   4.0    1.0  1  NCBI__GCF_000015505.1:WP_011802842.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015505.1:WP_011802842.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.6   4.0  1.2e-143  1.2e-143       1     385 []      10     397 ..      10     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: 464.6 bits;  conditional E-value: 1.2e-143
                             TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaagl 70 
                                           iv+a+Rtpig + +g +++++++dLl+ v+k++l+++  ldp++i+++i+G+++++g q  niaR  a+ agl
  NCBI__GCF_000015505.1:WP_011802842.1  10 IVAATRTPIGrSHRGFFRNTRPDDLLVSVLKAALAQVpTLDPKAIEDIICGCAIPEGPQgLNIARIGAVLAGL 82 
                                           8**********89************************************************************ PP

                             TIGR01930  71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkd 143
                                           p+sv ++tvnr+CaSgl A+++aa++i++Geadv+ a+G EsmS vp++ ++     sl++  + +++     
  NCBI__GCF_000015505.1:WP_011802842.1  83 PTSVGGITVNRFCASGLSAIQMAADRIRVGEADVMFAAGTESMSMVPMSGNSP----SLSPAMFANDE----- 146
                                           ***********************************************988875....77776666666..... PP

                             TIGR01930 144 lvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk............kkv 204
                                            v  ++ mg tAe++a+++++sR  qD++a++Sh+ka kA+++g+f++ei+pvev ++            +++
  NCBI__GCF_000015505.1:WP_011802842.1 147 NVGIAYGMGLTAEKVAQQWKVSRAAQDQFAYESHMKALKAQQAGEFSAEITPVEVTDRtanletgeviatTRT 219
                                           45678***************************************************99***********999* PP

                             TIGR01930 205 vskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagv 277
                                           vs Deg rp+ttle LakLk+ f+   gs vtAgNssq++DGA+al+l+se+++ke+gl+plar+vs+a  gv
  NCBI__GCF_000015505.1:WP_011802842.1 220 VSLDEGARPDTTLEGLAKLKTPFAA-RGS-VTAGNSSQTSDGAGALILASEKAVKEFGLKPLARFVSYAAKGV 290
                                           ***********************96.8*7.******************************************* PP

                             TIGR01930 278 dpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGa 350
                                           +pe+mg+gp++Ai++aL+ agl+ +did++E+nEAFAaq lav++ lg ld++kvN  GGAiAlGHPlGa+Ga
  NCBI__GCF_000015505.1:WP_011802842.1 291 PPEIMGIGPIEAIPAALRYAGLTQNDIDWFELNEAFAAQSLAVINTLG-LDPAKVNPMGGAIALGHPLGATGA 362
                                           ************************************************.99********************** PP

                             TIGR01930 351 rivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           +  +t++++L++++ kyG++t+Cvg+GqGaA i+e
  NCBI__GCF_000015505.1:WP_011802842.1 363 IRAATVIHALHRHQLKYGMVTMCVGMGQGAAGIFE 397
                                           ********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (399 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: 00:00:00.01
# Mc/sec: 13.73
//
[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