Alignments for a candidate for fadA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudomonas simiae WCS417

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate GFF3753 PS417_19210 acetyl-CoA acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__WCS417:GFF3753
          Length = 394

 Score =  341 bits (875), Expect = 2e-98
 Identities = 189/395 (47%), Positives = 247/395 (62%), Gaps = 10/395 (2%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60
           M+E VIV   RT + K+ +G     RPDD+ A CV   L R G     ++D I+G  + E
Sbjct: 1   MREVVIVDSVRTGLAKSFRGKFNQTRPDDMAAHCVNALLTRNGIDPATVEDCIVGAGSNE 60

Query: 61  AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120
             QG N+ RN+  L+ L      +T+NR+CSSGLQ+IA AA +I  G  D  +AGG ES+
Sbjct: 61  GAQGYNIGRNVAVLSQLGTGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESI 120

Query: 121 SQVPMMGHVTRPNLA---LAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           S    +  V   NL    L E+ P  Y  MG TAE VA++Y VSRE+QD +A++S Q  A
Sbjct: 121 SLT--LKSVNTDNLINPLLKEQVPGLYFPMGQTAEIVARRYSVSREEQDMYALQSQQRTA 178

Query: 178 KALAEGKFKDEIVPVEVTVTEIGEDHKPMEKQF---VFSQDEGVRPQTTADILSTLRPAF 234
           +A A+G F DEIVP+ V      ED    E Q    V  +D+  RP TT   L  L+P F
Sbjct: 179 QAQADGLFDDEIVPMAVKYKV--EDKNTGEAQVLDGVVDRDDCNRPDTTLASLQGLKPVF 236

Query: 235 SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEA 294
           + DG+VTAGNSSQ SDGA+  ++M  EKA ALGL P   FR F V G  P+ MGIGPV +
Sbjct: 237 AEDGSVTAGNSSQLSDGASMTLVMSLEKALALGLKPKAFFRGFTVAGCEPDEMGIGPVFS 296

Query: 295 IPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGT 354
           +P+ LK  GLQ+ DI L+ELNEAFASQ +     L ID  K NVNGG+I++GHP G TG+
Sbjct: 297 VPKLLKAKGLQVADIDLWELNEAFASQCLYARNRLEIDNAKYNVNGGSISIGHPFGMTGS 356

Query: 355 KLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           +    L+ E++RRN ++G+VTMC+GGGMGA G+FE
Sbjct: 357 RQVGHLVRELQRRNLRYGIVTMCVGGGMGATGLFE 391


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: 412
Number of extensions: 16
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: 394
Length adjustment: 31
Effective length of query: 360
Effective length of database: 363
Effective search space:   130680
Effective search space used:   130680
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 GFF3753 PS417_19210 (acetyl-CoA 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.29892.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-135  438.0   0.2   1.7e-135  437.8   0.2    1.0  1  lcl|FitnessBrowser__WCS417:GFF3753  PS417_19210 acetyl-CoA acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3753  PS417_19210 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.8   0.2  1.7e-135  1.7e-135       1     385 []       6     391 ..       6     391 .. 0.97

  Alignments for each domain:
  == domain 1  score: 437.8 bits;  conditional E-value: 1.7e-135
                           TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpes 73 
                                         ivd vRt  + +++g +++++++d++a+ +++ll r+g+dp+ +++ i+G+  ++g+q  ni+R++a+ ++l++ 
  lcl|FitnessBrowser__WCS417:GFF3753   6 IVDSVRTGLAkSFRGKFNQTRPDDMAAHCVNALLTRNGIDPATVEDCIVGAGSNEGAQgYNIGRNVAVLSQLGTG 80 
                                         8*********99*************************************************************** PP

                           TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdlvktk 148
                                         ++++t+nr+C+SglqA+a+aa++i++G  d++vaGGvEs+S +  +++ +   + +++  +++            
  lcl|FitnessBrowser__WCS417:GFF3753  81 TAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESISLTLKSVNTD---NLINPLLKEQVP-------GLY 145
                                         *******************************************9888875...788885555544.......778 PP

                           TIGR01930 149 lsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk............kkvvskDegi 211
                                         ++mg+tAe +a++y++sReeqD yal+S+q++a+A+++g f+deivp+ vk k            + vv++D++ 
  lcl|FitnessBrowser__WCS417:GFF3753 146 FPMGQTAEIVARRYSVSREEQDMYALQSQQRTAQAQADGLFDDEIVPMAVKYKvedkntgeaqvlDGVVDRDDCN 220
                                         9************************************************99999999*****9999999****** PP

                           TIGR01930 212 rpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgp 286
                                         rp+ttl++L++Lkp+f+e +gs vtAgNssql+DGA+++l+ms e+a +lgl+p+a +++++vag++p+emg+gp
  lcl|FitnessBrowser__WCS417:GFF3753 221 RPDTTLASLQGLKPVFAE-DGS-VTAGNSSQLSDGASMTLVMSLEKALALGLKPKAFFRGFTVAGCEPDEMGIGP 293
                                         ****************96.9*7.**************************************************** PP

                           TIGR01930 287 vpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLk 361
                                         v +++k+Lk  gl++ didl+E+nEAFA+q+l++++ l+ +d++k+NvnGG+i++GHP+G++G+r v +l++eL+
  lcl|FitnessBrowser__WCS417:GFF3753 294 VFSVPKLLKAKGLQVADIDLWELNEAFASQCLYARNRLE-IDNAKYNVNGGSISIGHPFGMTGSRQVGHLVRELQ 367
                                         ***************************************.88********************************* PP

                           TIGR01930 362 ergkkyGlatlCvggGqGaAvile 385
                                         +r+ +yG++t+CvggG+Ga+ ++e
  lcl|FitnessBrowser__WCS417:GFF3753 368 RRNLRYGIVTMCVGGGMGATGLFE 391
                                         ******************998876 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.72
//
[ok]

This GapMind analysis is from Sep 17 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