Alignments for a candidate for fadA in Dechloromonas agitata is5

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dechloromonas agitata is5

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_027458119.1 K420_RS0111065 acetyl-CoA C-acyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_000519045.1:WP_027458119.1
          Length = 398

 Score =  350 bits (899), Expect = e-101
 Identities = 194/394 (49%), Positives = 264/394 (67%), Gaps = 7/394 (1%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYE-GNIDDLIIGCATP 59
           ++EA IV+  R PV K K G    VRPDD+ A  +K  + +  G +   I D+I+GCA P
Sbjct: 5   IQEAYIVAATRLPVAK-KGGMFRNVRPDDMLAHAIKSVVAQVPGIDPARIGDVIVGCAMP 63

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           EAEQG+N+AR    LAGLP TVP IT+NR+CSSGLQ++A AA +I LG  D  IA G ES
Sbjct: 64  EAEQGMNVARIGALLAGLPITVPGITINRFCSSGLQAVADAANQIRLGLADVMIAAGTES 123

Query: 120 MSQVP-MMGHVTRPNLAL-AEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           M+ +P +MG+    N A+  ++       MG TAE+VA ++ +SRE+QDAFA+ S+Q A 
Sbjct: 124 MTIMPQIMGNKMAMNPAIFTDENIGIAYGMGLTAEKVANQWQISREEQDAFALASNQKAC 183

Query: 178 KALAEGKFKDEIVP--VEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFS 235
            A+A G FK E  P  +  ++ ++      + ++ V   DEG RP  + + L  LRP F 
Sbjct: 184 AAIAAGHFKAETSPYLIRESLPDLKTGQIKVRERTV-EFDEGPRPDASLEKLGKLRPVFH 242

Query: 236 VDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAI 295
             G+VTAGNSSQ SDGAAAVML+  +      L PL +F SFAVGGV PE+MGIGP+ AI
Sbjct: 243 ARGSVTAGNSSQMSDGAAAVMLVSEKVLKEHNLTPLARFASFAVGGVAPEIMGIGPIAAI 302

Query: 296 PRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTK 355
           P+AL  AG++ +D+   ELNEAFA+Q++ V++ELG+D  K+N  GGAIALGHPLG TG  
Sbjct: 303 PKALAQAGIRQEDLDWIELNEAFAAQSLAVVKELGLDPSKINPLGGAIALGHPLGATGAI 362

Query: 356 LTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
            T +++H ++R   ++G+V+MCIG GMGAAG+FE
Sbjct: 363 RTATIVHGLQRTGGKYGMVSMCIGTGMGAAGIFE 396


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: 440
Number of extensions: 23
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: 398
Length adjustment: 31
Effective length of query: 360
Effective length of database: 367
Effective search space:   132120
Effective search space used:   132120
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_027458119.1 K420_RS0111065 (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.2014364.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-140  454.1   5.2   2.2e-140  453.9   5.2    1.0  1  NCBI__GCF_000519045.1:WP_027458119.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000519045.1:WP_027458119.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.9   5.2  2.2e-140  2.2e-140       1     385 []      10     396 ..      10     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 453.9 bits;  conditional E-value: 2.2e-140
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                           iv+a+R p++k gg +++++++d+la++ik++++++ g+dp++i +vi+G++++++eq +n+aR  al aglp
  NCBI__GCF_000519045.1:WP_027458119.1  10 IVAATRLPVAKKGGMFRNVRPDDMLAHAIKSVVAQVpGIDPARIGDVIVGCAMPEAEQgMNVARIGALLAGLP 82 
                                           8*********88************************************************************* PP

                             TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                            +vp++t+nr+C+SglqAva+aa++i+ G adv++a+G Esm+ +p ++ ++   + +++  +++e+      
  NCBI__GCF_000519045.1:WP_027458119.1  83 ITVPGITINRFCSSGLQAVADAANQIRLGLADVMIAAGTESMTIMPQIMGNK---MAMNPAIFTDEN------ 146
                                           ***********************************************99997...789999999999...... PP

                             TIGR01930 145 vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk............kkvv 205
                                              ++ mg tAe++a++++isReeqD++al+S+qka +Ai++g+fk+e  p+ ++++            +++v
  NCBI__GCF_000519045.1:WP_027458119.1 147 IGIAYGMGLTAEKVANQWQISREEQDAFALASNQKACAAIAAGHFKAETSPYLIRESlpdlktgqikvrERTV 219
                                           5678************************************************99999***********999** PP

                             TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvd 278
                                           + Deg+rp+ +lekL+kL+p+f+   gs vtAgNssq++DGAaa++l+se+v+ke++ltplar+ s+av gv 
  NCBI__GCF_000519045.1:WP_027458119.1 220 EFDEGPRPDASLEKLGKLRPVFHA-RGS-VTAGNSSQMSDGAAAVMLVSEKVLKEHNLTPLARFASFAVGGVA 290
                                           **********************96.8*7.******************************************** PP

                             TIGR01930 279 peemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGar 351
                                           pe+mg+gp+ Ai+kaL++ag++ +d+d++E+nEAFAaq lav+kelg ld++k+N  GGAiAlGHPlGa+Ga+
  NCBI__GCF_000519045.1:WP_027458119.1 291 PEIMGIGPIAAIPKALAQAGIRQEDLDWIELNEAFAAQSLAVVKELG-LDPSKINPLGGAIALGHPLGATGAI 362
                                           ***********************************************.99*********************** PP

                             TIGR01930 352 ivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                            ++t+++ L++ g+kyG++++C+g+G+GaA i+e
  NCBI__GCF_000519045.1:WP_027458119.1 363 RTATIVHGLQRTGGKYGMVSMCIGTGMGAAGIFE 396
                                           *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (398 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.70
//
[ok]

This GapMind analysis is from Apr 09 2024. 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