Alignments for a candidate for fadA in Sphingopyxis indica DS15

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sphingopyxis indica DS15

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_089216969.1 CHB69_RS16130 acetyl-CoA C-acyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_900188185.1:WP_089216969.1
          Length = 393

 Score =  328 bits (840), Expect = 2e-94
 Identities = 180/392 (45%), Positives = 251/392 (64%), Gaps = 2/392 (0%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60
           M++AVIVS ARTP+ KA +GS        LGA  VK  ++RAG   G IDD++ G A  +
Sbjct: 1   MRDAVIVSTARTPLTKAARGSFNNTPSPTLGAFSVKAAVERAGLEGGEIDDVVFGAAMQQ 60

Query: 61  AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120
             Q  N+AR I   AGLP TVP ++++R CSSGL +IA AA++I++   D  +AGG ES+
Sbjct: 61  GSQSPNVARLIALRAGLPVTVPGMSIDRQCSSGLMTIATAAKQIIVDRQDICVAGGVESI 120

Query: 121 SQVPMMGHV-TRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179
           S+V   G V   P+  L     + YM M  TAE VAK+Y + RE QD ++++S Q  A A
Sbjct: 121 SKVSGSGKVFIEPDAELLAMHKDTYMPMIGTAEVVAKRYNIGREAQDEYSLQSQQRTAAA 180

Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPME-KQFVFSQDEGVRPQTTADILSTLRPAFSVDG 238
            A GKF DEI+P + T+  + ++ K +  K     +DE  RP TT + L++L+P      
Sbjct: 181 QAAGKFADEIIPCKATMAIVDKETKEVSYKDVTADRDECNRPDTTLEGLASLKPVMGEGH 240

Query: 239 TVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRA 298
           T+TAGN+SQ SDG++A ++M+ + A+  GL PL ++   AV G  P+ MGIGPV AIP+ 
Sbjct: 241 TITAGNASQLSDGSSACVVMEAKVAEKRGLQPLGRYVGMAVAGTEPDEMGIGPVFAIPKL 300

Query: 299 LKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTL 358
           L+   L++ DIGL+ELNEAFA Q +    +LGI  E +NVNGG+I++GHP G TG +   
Sbjct: 301 LERFELKMDDIGLWELNEAFAVQVLYCRDKLGIPNELLNVNGGSISIGHPFGMTGARCVG 360

Query: 359 SLIHEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390
             + E KRR  ++ VVTMCIGGG GAAG+FE+
Sbjct: 361 HALIEGKRRGVKYAVVTMCIGGGQGAAGLFEV 392


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: 14
Number of successful extensions: 3
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: 393
Length adjustment: 31
Effective length of query: 360
Effective length of database: 362
Effective search space:   130320
Effective search space used:   130320
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_089216969.1 CHB69_RS16130 (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.3792947.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.9e-131  422.3   1.9     1e-130  422.1   1.9    1.0  1  NCBI__GCF_900188185.1:WP_089216969.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188185.1:WP_089216969.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.1   1.9    1e-130    1e-130       1     385 []       6     391 ..       6     391 .. 0.95

  Alignments for each domain:
  == domain 1  score: 422.1 bits;  conditional E-value: 1e-130
                             TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                           iv+++Rtp + +++gs++++++ +L+a  +k+++eragl+  +id+v++G+++q+g+q  n+aR +al+aglp
  NCBI__GCF_900188185.1:WP_089216969.1   6 IVSTARTPLTkAARGSFNNTPSPTLGAFSVKAAVERAGLEGGEIDDVVFGAAMQQGSQsPNVARLIALRAGLP 78 
                                           89********988************************************************************ PP

                             TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                            +vp+++++r+C+Sgl ++a+aa++i + ++d++vaGGvEs+S+v  + k      + + +   +++      
  NCBI__GCF_900188185.1:WP_089216969.1  79 VTVPGMSIDRQCSSGLMTIATAAKQIIVDRQDICVAGGVESISKVSGSGKV---FIEPDAELLAMHK------ 142
                                           *********************************************754443...3344444455555...... PP

                             TIGR01930 145 vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk............kkvv 205
                                            +t ++m+ tAe +ak+y+i Re qDey+l+S+q++a+A+++gkf+dei+p++   +            +++ 
  NCBI__GCF_900188185.1:WP_089216969.1 143 -DTYMPMIGTAEVVAKRYNIGREAQDEYSLQSQQRTAAAQAAGKFADEIIPCKATMAivdketkevsykDVTA 214
                                           .789***********************************************99988899999******99999 PP

                             TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvd 278
                                           ++De+ rp+ttle La+Lkp+    +g+t+tAgN+sql+DG++a ++m+ +va++ gl+pl+r+v++avag +
  NCBI__GCF_900188185.1:WP_089216969.1 215 DRDECNRPDTTLEGLASLKPVMG--EGHTITAGNASQLSDGSSACVVMEAKVAEKRGLQPLGRYVGMAVAGTE 285
                                           **********************8..4789******************************************** PP

                             TIGR01930 279 peemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGar 351
                                           p+emg+gpv Ai+k+L++ +l+++di l+E+nEAFA+qvl+++++lg + +e +NvnGG+i++GHP+G++Gar
  NCBI__GCF_900188185.1:WP_089216969.1 286 PDEMGIGPVFAIPKLLERFELKMDDIGLWELNEAFAVQVLYCRDKLG-IPNELLNVNGGSISIGHPFGMTGAR 357
                                           ***********************************************.889********************** PP

                             TIGR01930 352 ivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           +v + l e k+rg+ky+++t+C+ggGqGaA ++e
  NCBI__GCF_900188185.1:WP_089216969.1 358 CVGHALIEGKRRGVKYAVVTMCIGGGQGAAGLFE 391
                                           ******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 26.90
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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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