GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pseudomonas fluorescens GW456-L13

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PfGW456L13_2430 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430
          Length = 403

 Score =  694 bits (1790), Expect = 0.0
 Identities = 348/401 (86%), Positives = 375/401 (93%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           MN+ALIIDAVRTPIGRYAG L+SVRADDLGA+PL+ L+ RHPQ+DW+ VDDVIYGCANQA
Sbjct: 1   MNDALIIDAVRTPIGRYAGVLSSVRADDLGAVPLRELLRRHPQVDWNTVDDVIYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAGLPVSVPGTTLNRLCGSGLDA+G+AARA+R GE GLML GGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPVSVPGTTLNRLCGSGLDAIGTAARAIRSGETGLMLVGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAP VMGK+EQAF R+AE+FDTTIGWRFVN LM++ +GIDSMPETAENVA QFNISRAD
Sbjct: 121 SRAPLVMGKAEQAFSRTAEVFDTTIGWRFVNPLMKKTYGIDSMPETAENVAEQFNISRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFALRSQ +AAAA A+GRLAKEIVAVEI QRKGPAK+VEHDEHPRGDTTLEQLAKLGT
Sbjct: 181 QDAFALRSQQRAAAAQASGRLAKEIVAVEIPQRKGPAKVVEHDEHPRGDTTLEQLAKLGT 240

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFR+GGS+TAGNASGVNDGACALLLAS E A+R GL AR RVV MATAGVEPRIMGIGPV
Sbjct: 241 PFREGGSITAGNASGVNDGACALLLASPEVAKRQGLTARGRVVAMATAGVEPRIMGIGPV 300

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PATRKVLE+  L+LADMDVIELNEAFAAQGLAVLRELGL+D D RVNPNGGAIALGHPLG
Sbjct: 301 PATRKVLEVANLSLADMDVIELNEAFAAQGLAVLRELGLSDTDPRVNPNGGAIALGHPLG 360

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTALHELEER GRYALCTMCIGVGQGIALIIER+
Sbjct: 361 MSGARLVTTALHELEERNGRYALCTMCIGVGQGIALIIERL 401


Lambda     K      H
   0.319    0.134    0.384 

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: 639
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: 401
Length of database: 403
Length adjustment: 31
Effective length of query: 370
Effective length of database: 372
Effective search space:   137640
Effective search space used:   137640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate PfGW456L13_2430 (Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ 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.393030.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.3e-224  731.5   7.9   1.5e-224  731.3   7.9    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430  Acetyl-CoA acetyltransferase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430  Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  731.3   7.9  1.5e-224  1.5e-224       2     400 .]       3     401 ..       2     401 .. 1.00

  Alignments for each domain:
  == domain 1  score: 731.3 bits;  conditional E-value: 1.5e-224
                                               TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGca 56 
                                                             ++ i+da+rtpiGry+G+lssvraddl+avpl++ll+r+p++d++++ddvi+Gca
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430   3 DALIIDAVRTPIGRYAGVLSSVRADDLGAVPLRELLRRHPQVDWNTVDDVIYGCA 57 
                                                             689**************************************************** PP

                                               TIGR02430  57 nqaGednrnvarmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlv 111
                                                             nqaGednrnvarm+allaGlpvsvpgtt+nrlcgsglda+g+aarai++Ge+ l+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430  58 NQAGEDNRNVARMSALLAGLPVSVPGTTLNRLCGSGLDAIGTAARAIRSGETGLM 112
                                                             ******************************************************* PP

                                               TIGR02430 112 iaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnpklkalyGvdsmpeta 166
                                                             + GGvesmsrap v+Gka+ afsr+a+++dttiGwrfvnp +k+ yG+dsmpeta
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 113 LVGGVESMSRAPLVMGKAEQAFSRTAEVFDTTIGWRFVNPLMKKTYGIDSMPETA 167
                                                             ******************************************************* PP

                                               TIGR02430 167 envaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdk 221
                                                             envae+f++sr+dqdafalrsqqr+aaaqa+G +a+eiv vei+q+kG ++vv++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 168 ENVAEQFNISRADQDAFALRSQQRAAAAQASGRLAKEIVAVEIPQRKGPAKVVEH 222
                                                             ******************************************************* PP

                                               TIGR02430 222 dehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhglt 276
                                                             deh+r +ttle+lakl +++re+g++taGnasGvndGa+alllas e +kr+glt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 223 DEHPRGDTTLEQLAKLGTPFREGGSITAGNASGVNDGACALLLASPEVAKRQGLT 277
                                                             ******************************************************* PP

                                               TIGR02430 277 prarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqala 331
                                                             +r+r++a+a+aGvepr+mG+gpvpa++k+l+ a+lsl+d+dvielneafaaq+la
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 278 ARGRVVAMATAGVEPRIMGIGPVPATRKVLEVANLSLADMDVIELNEAFAAQGLA 332
                                                             ******************************************************* PP

                                               TIGR02430 332 vlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlc 386
                                                             vlrelgl+d d rvnpnGGaialGhplG+sGarlv+tal++le+++gryal+t+c
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 333 VLRELGLSDTDPRVNPNGGAIALGHPLGMSGARLVTTALHELEERNGRYALCTMC 387
                                                             ******************************************************* PP

                                               TIGR02430 387 iGvGqGialvierv 400
                                                             iGvGqGial+ier+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 388 IGVGQGIALIIERL 401
                                                             ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (403 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.42
//
[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