GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pobA in Pseudomonas fluorescens FW300-N2C3

Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate AO356_05295 AO356_05295 4-hydroxybenzoate 3-monooxygenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2914
         (396 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05295
          Length = 396

 Score =  775 bits (2000), Expect = 0.0
 Identities = 383/396 (96%), Positives = 389/396 (98%)

Query: 1   MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLR 60
           MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTP+YVL RIRAGVLEQGMVELLR
Sbjct: 1   MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPDYVLGRIRAGVLEQGMVELLR 60

Query: 61  QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120
           QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG
Sbjct: 61  QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120

Query: 121 ARTLYLASNAQPHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180
           ARTLYLASNAQPHDMQT+ PFVTFEHEG+T RLDCDYIAGCDGFHGVARQSIPAEKLKVF
Sbjct: 121 ARTLYLASNAQPHDMQTEHPFVTFEHEGQTLRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180

Query: 181 ERVYPFGWLGVLADTPPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240
           ERVYPFGWLGVLADTPPVHEELVYARH RGFALCSMRSKTRTRYYLQVPAEEQVADWPDE
Sbjct: 181 ERVYPFGWLGVLADTPPVHEELVYARHARGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240

Query: 241 RFWGELKNRLPADLAAALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300
           RFW ELKNRLP DLA ALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK
Sbjct: 241 RFWHELKNRLPTDLAEALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300

Query: 301 GLNLAASDVSTLFNILLKVYRDGRVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDDDA 360
           GLNLAASDVSTLFNILLKVYRDGRV+LLE+YSAICLRRVWKAERFSWWMTSMLHRFDDDA
Sbjct: 301 GLNLAASDVSTLFNILLKVYRDGRVDLLEQYSAICLRRVWKAERFSWWMTSMLHRFDDDA 360

Query: 361 FNQRISEAELEYFVDSEAGRKTIAENYVGLPYEAIE 396
           FNQRISEAELEYF+DSEAGRKTIAENYVGLPYEAIE
Sbjct: 361 FNQRISEAELEYFLDSEAGRKTIAENYVGLPYEAIE 396


Lambda     K      H
   0.321    0.137    0.415 

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: 681
Number of extensions: 12
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: 396
Length of database: 396
Length adjustment: 31
Effective length of query: 365
Effective length of database: 365
Effective search space:   133225
Effective search space used:   133225
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate AO356_05295 AO356_05295 (4-hydroxybenzoate 3-monooxygenase)
to HMM TIGR02360 (pobA: 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2))

# 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/TIGR02360.hmm
# target sequence database:        /tmp/gapView.820947.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02360  [M=390]
Accession:   TIGR02360
Description: pbenz_hydroxyl: 4-hydroxybenzoate 3-monooxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                   -----------
   1.9e-209  681.2   0.0   2.2e-209  681.0   0.0    1.0  1  FitnessBrowser__pseudo5_N2C3_1:AO356_05295  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo5_N2C3_1:AO356_05295  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  681.0   0.0  2.2e-209  2.2e-209       1     390 []       4     392 ..       4     392 .. 1.00

  Alignments for each domain:
  == domain 1  score: 681.0 bits;  conditional E-value: 2.2e-209
                                   TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldr 67 
                                                 +ktqvaiigaGpsGlllgqllh+aGid+viler+++dyvlgriraGvleqg+v+ll++agv++r+d+
  FitnessBrowser__pseudo5_N2C3_1:AO356_05295   4 LKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPDYVLGRIRAGVLEQGMVELLRQAGVGQRMDA 70 
                                                 69***************************************************************** PP

                                   TIGR02360  68 eglvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdles 134
                                                 egl+h+G+e+  ++++v++dlk ltggk+v+vyGqtevtrdl+ areaag++t+y a + ++hd+++
  FitnessBrowser__pseudo5_N2C3_1:AO356_05295  71 EGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAGARTLYLASNAQPHDMQT 137
                                                 ******************************************************************* PP

                                   TIGR02360 135 drpkvtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliy 201
                                                 ++p vtfe++g++ rldcd+iaGcdGfhGv+r+sipaeklk+fe+vypfGwlG+l++tppv++el+y
  FitnessBrowser__pseudo5_N2C3_1:AO356_05295 138 EHPFVTFEHEGQTLRLDCDYIAGCDGFHGVARQSIPAEKLKVFERVYPFGWLGVLADTPPVHEELVY 204
                                                 ******************************************************************* PP

                                   TIGR02360 202 snserGfalcslrsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiapl 268
                                                 ++++rGfalcs+rs+tr+ryy+qv+ +++v dw+d+rfw+elk+rl+++ ae lvtgpsieksiapl
  FitnessBrowser__pseudo5_N2C3_1:AO356_05295 205 ARHARGFALCSMRSKTRTRYYLQVPAEEQVADWPDERFWHELKNRLPTDLAEALVTGPSIEKSIAPL 271
                                                 ******************************************************************* PP

                                   TIGR02360 269 rsfvaepmryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykekdsaglerysakalar 335
                                                 rsfv+epm+yGr+fl+GdaahivpptGakGlnlaasdv++l++ ll+ y++++ + le+ysa +l+r
  FitnessBrowser__pseudo5_N2C3_1:AO356_05295 272 RSFVVEPMQYGRMFLVGDAAHIVPPTGAKGLNLAASDVSTLFNILLKVYRDGRVDLLEQYSAICLRR 338
                                                 ******************************************************************* PP

                                   TIGR02360 336 vwkaerfswwltsllhrfpdedefdkkiqqaeleylleseaaqktlaenyvGlpy 390
                                                 vwkaerfsww+ts+lhrf+d d+f+++i +aeley+l+sea++kt+aenyvGlpy
  FitnessBrowser__pseudo5_N2C3_1:AO356_05295 339 VWKAERFSWWMTSMLHRFDD-DAFNQRISEAELEYFLDSEAGRKTIAENYVGLPY 392
                                                 ******************76.79*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (396 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: 00:00:00.00
# Mc/sec: 17.77
//
[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