GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pseudomonas fluorescens FW300-N1B4

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate Pf1N1B4_3234 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234
          Length = 400

 Score =  704 bits (1816), Expect = 0.0
 Identities = 355/400 (88%), Positives = 381/400 (95%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           MRDV+ICDAIRTPIGRFGG L+ VRADDLAAVP+KAL+  NP+V W  VDEVF GCANQA
Sbjct: 1   MRDVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMARNPSVDWSAVDEVFLGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMALLLAGLPE+IPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPETIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVMGKA++ +SRNMKLEDTTIGWRFINPLMK+QYGVD+MP+TADNVADDY++SRAD
Sbjct: 121 SRAPFVMGKADAAFSRNMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYRISRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QDAFALRSQQ+ AAAQAAGFFAEEIV VRIAHKKGE++V +DEH R +TTLE L KLKPV
Sbjct: 181 QDAFALRSQQRTAAAQAAGFFAEEIVEVRIAHKKGESVVTQDEHPRADTTLETLAKLKPV 240

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
           NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLT RA+VLGM+S GVAPRVMGIGPVP
Sbjct: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARAKVLGMSSAGVAPRVMGIGPVP 300

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           AVRKLTERLG+AVSDFDVIELNEAFASQGLAVLRELG+ADD+ QVNPNGGAIALGHPLGM
Sbjct: 301 AVRKLTERLGLAVSDFDVIELNEAFASQGLAVLRELGLADDSAQVNPNGGAIALGHPLGM 360

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLVLTALHQLEK+GG+KGLATMCVGVGQGLALAIERV
Sbjct: 361 SGARLVLTALHQLEKTGGKKGLATMCVGVGQGLALAIERV 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: 633
Number of extensions: 14
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 Pf1N1B4_3234 (Beta-ketoadipyl CoA thiolase (EC 2.3.1.-))
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.25100.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.5e-226  737.2  12.2   2.8e-226  737.0  12.2    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234  Beta-ketoadipyl CoA thiolase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234  Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.0  12.2  2.8e-226  2.8e-226       1     400 []       2     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 737.0 bits;  conditional E-value: 2.8e-226
                                      TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednr 64 
                                                    ++vyi+dairtpiGr+gG+ls+vraddlaavp+kal+arnps+d++a+d+v+lGcanqaGednr
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234   2 RDVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMARNPSVDWSAVDEVFLGCANQAGEDNR 65 
                                                    689************************************************************* PP

                                      TIGR02430  65 nvarmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGk 128
                                                    nvarma+llaGlp+++pg+t+nrlc+sg+da+g+a+rai++Ge +l iaGGvesmsrapfv+Gk
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234  66 NVARMALLLAGLPETIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAPFVMGK 129
                                                    **************************************************************** PP

                                      TIGR02430 129 adsafsrsakledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrta 192
                                                    ad+afsr+ kledttiGwrf+np +ka+yGvd+mp+ta+nva+++++sr+dqdafalrsqqrta
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234 130 ADAAFSRNMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYRISRADQDAFALRSQQRTA 193
                                                    **************************************************************** PP

                                      TIGR02430 193 aaqakGffaeeivpveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvn 256
                                                    aaqa+Gffaeeiv+v+i++kkG e+vv +deh+ra+ttle+laklk+v+ +d+tvtaGnasGvn
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234 194 AAQAAGFFAEEIVEVRIAHKKG-ESVVTQDEHPRADTTLETLAKLKPVNGPDKTVTAGNASGVN 256
                                                    **********************.78999************************************ PP

                                      TIGR02430 257 dGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvie 320
                                                    dGaaal+las+eavk+hglt+ra++l+++saGv+prvmG+gpvpav+kl +r+gl+++d+dvie
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234 257 DGAAALILASAEAVKKHGLTARAKVLGMSSAGVAPRVMGIGPVPAVRKLTERLGLAVSDFDVIE 320
                                                    **************************************************************** PP

                                      TIGR02430 321 lneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalat 384
                                                    lneafa+q+lavlrelgladd+a+vnpnGGaialGhplG+sGarlvltal+qlek+gg+ +lat
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234 321 LNEAFASQGLAVLRELGLADDSAQVNPNGGAIALGHPLGMSGARLVLTALHQLEKTGGKKGLAT 384
                                                    **************************************************************** PP

                                      TIGR02430 385 lciGvGqGialvierv 400
                                                    +c+GvGqG+al+ierv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234 385 MCVGVGQGLALAIERV 400
                                                    ***************8 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: 11.54
//
[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:

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