Alignments for a candidate for pobA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Pseudomonas fluorescens FW300-N2E2

Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate Pf6N2E2_2914 P-hydroxybenzoate hydroxylase (EC 1.14.13.2)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914
          Length = 396

 Score =  800 bits (2065), Expect = 0.0
 Identities = 396/396 (100%), Positives = 396/396 (100%)

Query: 1   MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLR 60
           MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLR
Sbjct: 1   MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLR 60

Query: 61  QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120
           QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG
Sbjct: 61  QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120

Query: 121 ARTLYLASNAQPHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180
           ARTLYLASNAQPHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVF
Sbjct: 121 ARTLYLASNAQPHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180

Query: 181 ERVYPFGWLGVLADTPPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240
           ERVYPFGWLGVLADTPPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDE
Sbjct: 181 ERVYPFGWLGVLADTPPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240

Query: 241 RFWGELKNRLPADLAAALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300
           RFWGELKNRLPADLAAALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK
Sbjct: 241 RFWGELKNRLPADLAAALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300

Query: 301 GLNLAASDVSTLFNILLKVYRDGRVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDDDA 360
           GLNLAASDVSTLFNILLKVYRDGRVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDDDA
Sbjct: 301 GLNLAASDVSTLFNILLKVYRDGRVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDDDA 360

Query: 361 FNQRISEAELEYFVDSEAGRKTIAENYVGLPYEAIE 396
           FNQRISEAELEYFVDSEAGRKTIAENYVGLPYEAIE
Sbjct: 361 FNQRISEAELEYFVDSEAGRKTIAENYVGLPYEAIE 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: 692
Number of extensions: 9
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 Pf6N2E2_2914 (P-hydroxybenzoate hydroxylase (EC 1.14.13.2))
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.7863.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-207  674.6   0.0   2.2e-207  674.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914  P-hydroxybenzoate hydroxylase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914  P-hydroxybenzoate hydroxylase (EC 1.14.13.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.4   0.0  2.2e-207  2.2e-207       1     390 []       4     392 ..       4     392 .. 1.00

  Alignments for each domain:
  == domain 1  score: 674.4 bits;  conditional E-value: 2.2e-207
                                      TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvder 64 
                                                    +ktqvaiigaGpsGlllgqllh+aGid+viler++++yvl+riraGvleqg+v+ll++agv++r
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914   4 LKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLRQAGVGQR 67 
                                                    69************************************************************** PP

                                      TIGR02360  65 ldreglvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevr 128
                                                    +d+egl+h+G+e+  ++++v++dlk ltggk+v+vyGqtevtrdl+ areaag++t+y a + +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914  68 MDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAGARTLYLASNAQ 131
                                                    **************************************************************** PP

                                      TIGR02360 129 lhdlesdrpkvtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilset 192
                                                    +hd+++++p vtfe++ge+ rldcd+iaGcdGfhGv+r+sipaeklk+fe+vypfGwlG+l++t
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914 132 PHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVFERVYPFGWLGVLADT 195
                                                    **************************************************************** PP

                                      TIGR02360 193 ppvsdeliysnserGfalcslrsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklv 256
                                                    ppv++el+y+++ rGfalcs+rs+tr+ryy+qv+ +++v dw+d+rfw elk+rl+ + a+ lv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914 196 PPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDERFWGELKNRLPADLAAALV 259
                                                    **************************************************************** PP

                                      TIGR02360 257 tgpsieksiaplrsfvaepmryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykek 320
                                                    tgpsieksiaplrsfv+epm+yGr+fl+GdaahivpptGakGlnlaasdv++l++ ll+ y+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914 260 TGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAKGLNLAASDVSTLFNILLKVYRDG 323
                                                    **************************************************************** PP

                                      TIGR02360 321 dsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqqaeleylleseaaqktlaen 384
                                                    + + le+ysa +l+rvwkaerfsww+ts+lhrf+d d+f+++i +aeley+++sea++kt+aen
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914 324 RVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDD-DAFNQRISEAELEYFVDSEAGRKTIAEN 386
                                                    *********************************76.79************************** PP

                                      TIGR02360 385 yvGlpy 390
                                                    yvGlpy
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2914 387 YVGLPY 392
                                                    *****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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.44
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources