GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas simiae WCS417

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF1320 PS417_06710 beta-ketoadipyl CoA thiolase

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__WCS417:GFF1320
          Length = 400

 Score =  717 bits (1852), Expect = 0.0
 Identities = 363/400 (90%), Positives = 383/400 (95%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           MRDVFICDAIRTPIGRFGG L+ VRADDLAA+P+KALIE NP+V W  VDEVF GCANQA
Sbjct: 1   MRDVFICDAIRTPIGRFGGGLSTVRADDLAALPIKALIERNPSVDWTAVDEVFLGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVMGKA++ +SR MKLEDTTIGWRFINPLMK+QYGVD+MP+TADNVADDY VSRAD
Sbjct: 121 SRAPFVMGKADAAFSRTMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYHVSRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QDAFALRSQQ+ AAAQAAGFFAEEIVPVR+AHKKGET+VE+DEH R +TTLEALTKLKPV
Sbjct: 181 QDAFALRSQQRTAAAQAAGFFAEEIVPVRVAHKKGETVVEQDEHPRADTTLEALTKLKPV 240

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
           NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLT RARVLGMAS GVAPRVMGIGPVP
Sbjct: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASAGVAPRVMGIGPVP 300

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           AVRKL ERLG+AV+DFDVIELNEAFASQGLAVLRELG+ADDAPQVNPNGGAIALGHPLGM
Sbjct: 301 AVRKLVERLGLAVTDFDVIELNEAFASQGLAVLRELGIADDAPQVNPNGGAIALGHPLGM 360

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLVLTALHQLEK+GG KGLATMCVGVGQGLALAIER+
Sbjct: 361 SGARLVLTALHQLEKTGGSKGLATMCVGVGQGLALAIERI 400


Lambda     K      H
   0.318    0.134    0.383 

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: 655
Number of extensions: 16
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF1320 PS417_06710 (beta-ketoadipyl CoA thiolase)
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.3320527.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   7.5e-138  445.5   4.4   8.5e-138  445.4   4.4    1.0  1  FitnessBrowser__WCS417:GFF1320  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF1320  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.4   4.4  8.5e-138  8.5e-138       1     385 []       6     398 ..       6     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 445.4 bits;  conditional E-value: 8.5e-138
                       TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglpesvpal 77 
                                     i da+Rtpig++gg l++++a+dL+a  ik+l+er+  +d  ++dev lG++ qage+  n+aR+a+l aglpes+p++
  FitnessBrowser__WCS417:GFF1320   6 ICDAIRTPIGRFGGGLSTVRADDLAALPIKALIERNpSVDWTAVDEVFLGCANQAGEDnRNVARMALLLAGLPESIPGV 84 
                                     789*******************************************************9******************** PP

                       TIGR01930  78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl..........vk 146
                                     t+nr+CaSg++A+ +a ++i++Ge+++++aGGvEsmSr+p+++ ++ +   +  +++kled+++  +          ++
  FitnessBrowser__WCS417:GFF1320  85 TLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAPFVMGKADA---AFSRTMKLEDTTI--GwrfinplmkaQY 158
                                     *****************************************9999743...3333444444332..1335677789877 PP

                       TIGR01930 147 tklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakL 223
                                        +m +tA+n+a++y++sR +qD++alrS+q++a+A+++g+f++eivpv+v +k  ++vv++De++r++ttle+L kL
  FitnessBrowser__WCS417:GFF1320 159 GVDAMPQTADNVADDYHVSRADQDAFALRSQQRTAAAQAAGFFAEEIVPVRVAHKkgETVVEQDEHPRADTTLEALTKL 237
                                     7889************************************************9999999******************** PP

                       TIGR01930 224 kpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsis 302
                                     kp+  + +  tvtAgN+s++nDGAaal+l+s e++k++glt  ar+ ++a agv p++mg+gpvpA++k++++ gl ++
  FitnessBrowser__WCS417:GFF1320 238 KPVNGP-DK-TVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASAGVAPRVMGIGPVPAVRKLVERLGLAVT 314
                                     ****95.77.7******************************************************************** PP

                       TIGR01930 303 didlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGa 380
                                     d+d++E+nEAFA+q lav +elg  d   +vN nGGAiAlGHPlG+sGar+vlt l++L++ g+  Glat+Cvg GqG 
  FitnessBrowser__WCS417:GFF1320 315 DFDVIELNEAFASQGLAVLRELGIADdAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKTGGSKGLATMCVGVGQGL 393
                                     ***********************866789************************************************** PP

                       TIGR01930 381 Avile 385
                                     A+ +e
  FitnessBrowser__WCS417:GFF1320 394 ALAIE 398
                                     *9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (400 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: 26.69
//
[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:

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:

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:

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:

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