GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 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 TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.24208.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-226  737.6  10.8   2.1e-226  737.4  10.8    1.0  1  lcl|FitnessBrowser__WCS417:GFF1320  PS417_06710 beta-ketoadipyl CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1320  PS417_06710 beta-ketoadipyl CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.4  10.8  2.1e-226  2.1e-226       1     400 []       2     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 737.4 bits;  conditional E-value: 2.1e-226
                           TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaG 75 
                                         ++v+i+dairtpiGr+gG+ls+vraddlaa+p+kal++rnps+d++a+d+v+lGcanqaGednrnvarma+llaG
  lcl|FitnessBrowser__WCS417:GFF1320   2 RDVFICDAIRTPIGRFGGGLSTVRADDLAALPIKALIERNPSVDWTAVDEVFLGCANQAGEDNRNVARMALLLAG 76 
                                         689************************************************************************ PP

                           TIGR02430  76 lpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvn 150
                                         lp+s+pg+t+nrlc+sg+da+g+a+rai++Ge +l iaGGvesmsrapfv+Gkad+afsr+ kledttiGwrf+n
  lcl|FitnessBrowser__WCS417:GFF1320  77 LPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAPFVMGKADAAFSRTMKLEDTTIGWRFIN 151
                                         *************************************************************************** PP

                           TIGR02430 151 pklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehl 225
                                         p +ka+yGvd+mp+ta+nva+++ vsr+dqdafalrsqqrtaaaqa+Gffaeeivpv++++kkG etvv++deh+
  lcl|FitnessBrowser__WCS417:GFF1320 152 PLMKAQYGVDAMPQTADNVADDYHVSRADQDAFALRSQQRTAAAQAAGFFAEEIVPVRVAHKKG-ETVVEQDEHP 225
                                         ****************************************************************.899******* PP

                           TIGR02430 226 raettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvp 300
                                         ra+ttleal+klk+v+ +d+tvtaGnasGvndGaaal+las+eavk+hglt+rar+l++asaGv+prvmG+gpvp
  lcl|FitnessBrowser__WCS417:GFF1320 226 RADTTLEALTKLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASAGVAPRVMGIGPVP 300
                                         *************************************************************************** PP

                           TIGR02430 301 avkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqlek 375
                                         av+kl++r+gl++ d+dvielneafa+q+lavlrelg+add+ +vnpnGGaialGhplG+sGarlvltal+qlek
  lcl|FitnessBrowser__WCS417:GFF1320 301 AVRKLVERLGLAVTDFDVIELNEAFASQGLAVLRELGIADDAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEK 375
                                         *************************************************************************** PP

                           TIGR02430 376 sggryalatlciGvGqGialvierv 400
                                         +gg  +lat+c+GvGqG+al+ier+
  lcl|FitnessBrowser__WCS417:GFF1320 376 TGGSKGLATMCVGVGQGLALAIERI 400
                                         ************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.17
//
[ok]

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

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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