Alignments for a candidate for pobA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Cupriavidus basilensis 4G11

Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate RR42_RS21940 RR42_RS21940 4-hydroxybenzoate 3-monooxygenase

Query= reanno::Cup4G11:RR42_RS21940
         (389 letters)



>FitnessBrowser__Cup4G11:RR42_RS21940
          Length = 389

 Score =  779 bits (2011), Expect = 0.0
 Identities = 389/389 (100%), Positives = 389/389 (100%)

Query: 1   MRTQVAIIGAGPAGLLLGQLLAKAGIDAVIVEQRSPDYILGRIRAGILESVTADALERAG 60
           MRTQVAIIGAGPAGLLLGQLLAKAGIDAVIVEQRSPDYILGRIRAGILESVTADALERAG
Sbjct: 1   MRTQVAIIGAGPAGLLLGQLLAKAGIDAVIVEQRSPDYILGRIRAGILESVTADALERAG 60

Query: 61  VAQRLQHDGLVHHGIELSYGGERHRIDFHALIGRSVTVYGQTEVTRDLMAARQAGNAVTI 120
           VAQRLQHDGLVHHGIELSYGGERHRIDFHALIGRSVTVYGQTEVTRDLMAARQAGNAVTI
Sbjct: 61  VAQRLQHDGLVHHGIELSYGGERHRIDFHALIGRSVTVYGQTEVTRDLMAARQAGNAVTI 120

Query: 121 YDAQDVSVHDFDTATPMVRYRKGGQQYELRCDFIAGCDGFHGVTRRSVPEPSRRIFERVY 180
           YDAQDVSVHDFDTATPMVRYRKGGQQYELRCDFIAGCDGFHGVTRRSVPEPSRRIFERVY
Sbjct: 121 YDAQDVSVHDFDTATPMVRYRKGGQQYELRCDFIAGCDGFHGVTRRSVPEPSRRIFERVY 180

Query: 181 PFGWLGVLADTPPVANELIYASHERGFALCSMRSLTRSRYYVQVSADERVEDWSDQRFWD 240
           PFGWLGVLADTPPVANELIYASHERGFALCSMRSLTRSRYYVQVSADERVEDWSDQRFWD
Sbjct: 181 PFGWLGVLADTPPVANELIYASHERGFALCSMRSLTRSRYYVQVSADERVEDWSDQRFWD 240

Query: 241 ELRSRLDTSAAEALVTGASIEKSIAPLRSFVCEPMRFGNLFLAGDAAHIVPPTGAKGLNL 300
           ELRSRLDTSAAEALVTGASIEKSIAPLRSFVCEPMRFGNLFLAGDAAHIVPPTGAKGLNL
Sbjct: 241 ELRSRLDTSAAEALVTGASIEKSIAPLRSFVCEPMRFGNLFLAGDAAHIVPPTGAKGLNL 300

Query: 301 AASDVLYLADGLIARYLRDDASELDAYSQKCLRRVWKAERFSWWMTSLLHRFPDADDFAL 360
           AASDVLYLADGLIARYLRDDASELDAYSQKCLRRVWKAERFSWWMTSLLHRFPDADDFAL
Sbjct: 301 AASDVLYLADGLIARYLRDDASELDAYSQKCLRRVWKAERFSWWMTSLLHRFPDADDFAL 360

Query: 361 RIQQAELDYLAGSRAAQMSLAENYVGLPY 389
           RIQQAELDYLAGSRAAQMSLAENYVGLPY
Sbjct: 361 RIQQAELDYLAGSRAAQMSLAENYVGLPY 389


Lambda     K      H
   0.323    0.137    0.414 

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: 623
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: 389
Length of database: 389
Length adjustment: 30
Effective length of query: 359
Effective length of database: 359
Effective search space:   128881
Effective search space used:   128881
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 RR42_RS21940 RR42_RS21940 (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.32356.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-203  662.1   0.0   1.4e-203  661.9   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS21940  RR42_RS21940 4-hydroxybenzoate 3


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS21940  RR42_RS21940 4-hydroxybenzoate 3-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  661.9   0.0  1.4e-203  1.4e-203       1     390 []       1     389 []       1     389 [] 1.00

  Alignments for each domain:
  == domain 1  score: 661.9 bits;  conditional E-value: 1.4e-203
                                 TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreg 69 
                                               m+tqvaiigaGp+Glllgqll kaGidavi+e++s+dy+lgriraG+le++t+d le+agv++rl+++g
  lcl|FitnessBrowser__Cup4G11:RR42_RS21940   1 MRTQVAIIGAGPAGLLLGQLLAKAGIDAVIVEQRSPDYILGRIRAGILESVTADALERAGVAQRLQHDG 69 
                                               9******************************************************************** PP

                                 TIGR02360  70 lvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpk 138
                                               lvh+G+e+++ ge++r+d+++l g +sv+vyGqtevtrdl+ ar+a ++ t+y+a++v +hd+++ +p 
  lcl|FitnessBrowser__Cup4G11:RR42_RS21940  70 LVHHGIELSYGGERHRIDFHALIG-RSVTVYGQTEVTRDLMAARQAGNAVTIYDAQDVSVHDFDTATPM 137
                                               **********************99.******************************************** PP

                                 TIGR02360 139 vtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserG 207
                                               v ++k g++++l cdfiaGcdGfhGv+r+s+p+  ++ fe+vypfGwlG+l++tppv++eliy+ +erG
  lcl|FitnessBrowser__Cup4G11:RR42_RS21940 138 VRYRKGGQQYELRCDFIAGCDGFHGVTRRSVPEPSRRIFERVYPFGWLGVLADTPPVANELIYASHERG 206
                                               ********************************************************************* PP

                                 TIGR02360 208 falcslrsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepm 276
                                               falcs+rs trsryyvqvs +++vedwsd+rfw+el++rld+ aae lvtg sieksiaplrsfv+epm
  lcl|FitnessBrowser__Cup4G11:RR42_RS21940 207 FALCSMRSLTRSRYYVQVSADERVEDWSDQRFWDELRSRLDTSAAEALVTGASIEKSIAPLRSFVCEPM 275
                                               ********************************************************************* PP

                                 TIGR02360 277 ryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfsww 345
                                               r+G lflaGdaahivpptGakGlnlaasdv yl ++l+++y   d++ l++ys+k+l+rvwkaerfsww
  lcl|FitnessBrowser__Cup4G11:RR42_RS21940 276 RFGNLFLAGDAAHIVPPTGAKGLNLAASDVLYLADGLIARYLRDDASELDAYSQKCLRRVWKAERFSWW 344
                                               ********************************************************************* PP

                                 TIGR02360 346 ltsllhrfpdedefdkkiqqaeleylleseaaqktlaenyvGlpy 390
                                               +tsllhrfpd d+f  +iqqael+yl++s+aaq +laenyvGlpy
  lcl|FitnessBrowser__Cup4G11:RR42_RS21940 345 MTSLLHRFPDADDFALRIQQAELDYLAGSRAAQMSLAENYVGLPY 389
                                               ********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (389 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: 00:00:00.02
# Mc/sec: 7.50
//
[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