Alignments for a candidate for pobA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Pseudomonas putida KT2440

Align p-hydroxybenzoate hydroxylase (EC 1.14.13.2) (characterized)
to candidate PP_3537 PP_3537 p-hydroxybenzoate hydroxylase

Query= metacyc::MONOMER-11506
         (395 letters)



>FitnessBrowser__Putida:PP_3537
          Length = 395

 Score =  751 bits (1940), Expect = 0.0
 Identities = 368/394 (93%), Positives = 380/394 (96%)

Query: 1   MKTQVAIIGAGPSGLLLGQLLHNAGIETVIVERQTPEYVLGRIRAGVLEQGTVDLLREAG 60
           MKTQVAIIGAGPSGLLLGQLLH AGI+ +IVERQT EYVLGRIRAGVLEQGTVDLLREAG
Sbjct: 1   MKTQVAIIGAGPSGLLLGQLLHKAGIDNIIVERQTAEYVLGRIRAGVLEQGTVDLLREAG 60

Query: 61  VSARMDREGLVHEGVELLVGGRRQRLDLKALTGGKTVMVYGQTEVTRDLMQAREASGAPI 120
           V+ RMDREGLVHEGVELLVGGRRQRLDLKALTGGKTVMVYGQTEVTRDLMQAREASGAPI
Sbjct: 61  VAERMDREGLVHEGVELLVGGRRQRLDLKALTGGKTVMVYGQTEVTRDLMQAREASGAPI 120

Query: 121 IYAANNVQPHELKGERPYLTFEKDGQAHRLECDYIAGCDGFHGVSRQSIPEGVLKQYERV 180
           IY+A NVQPHELKGE+PYLTFEKDG+  R++CDYIAGCDGFHG+SRQSIPEGVLKQYERV
Sbjct: 121 IYSAANVQPHELKGEKPYLTFEKDGRVQRIDCDYIAGCDGFHGISRQSIPEGVLKQYERV 180

Query: 181 YPFGWLGLLSDTPPVNHELIYAHHERGFALCSQRSQTRSRYYLQVPLDDKVEAWSDERFW 240
           YPFGWLGLLSDTPPVNHELIYAHHERGFALCSQRSQTRSRYYLQVPL D+VE WSDERFW
Sbjct: 181 YPFGWLGLLSDTPPVNHELIYAHHERGFALCSQRSQTRSRYYLQVPLQDRVEEWSDERFW 240

Query: 241 DELKARLPAEVAADLVTGPALEKSIAPLRSLVVEPMQYGHLFLVGDAAHIVPPTGAKGLN 300
           DELKARLPAEVAADLVTGPALEKSIAPLRSLVVEPMQYGHLFLVGDAAHIVPPTGAKGLN
Sbjct: 241 DELKARLPAEVAADLVTGPALEKSIAPLRSLVVEPMQYGHLFLVGDAAHIVPPTGAKGLN 300

Query: 301 LAASDVNYLYRILVKVYGEGRTDLLQQYSPLALRRVWKGERFSWFMTQLLHDFGSHKDAW 360
           LAASDVNYLYRILVKVY EGR DLL QYSPLALRRVWKGERFSWFMTQLLHDFGSHKDAW
Sbjct: 301 LAASDVNYLYRILVKVYHEGRVDLLAQYSPLALRRVWKGERFSWFMTQLLHDFGSHKDAW 360

Query: 361 DQKMQEADREYFLNSPAGLLNIAENYVGLPYEAV 394
           DQKMQEADREYFL SPAGL+NIAENYVGLP+E V
Sbjct: 361 DQKMQEADREYFLTSPAGLVNIAENYVGLPFEEV 394


Lambda     K      H
   0.320    0.138    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: 726
Number of extensions: 21
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
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 PP_3537 PP_3537 (p-hydroxybenzoate hydroxylase)
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.24428.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.2e-206  671.1   0.0   2.5e-206  671.0   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3537  PP_3537 p-hydroxybenzoate hydrox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3537  PP_3537 p-hydroxybenzoate hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.0   0.0  2.5e-206  2.5e-206       1     390 []       1     391 [.       1     391 [. 0.99

  Alignments for each domain:
  == domain 1  score: 671.0 bits;  conditional E-value: 2.5e-206
                           TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvheGv 75 
                                         mktqvaiigaGpsGlllgqllhkaGid++i+er++++yvlgriraGvleqgtvdll+eagv+er+dreglvheGv
  lcl|FitnessBrowser__Putida:PP_3537   1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNIIVERQTAEYVLGRIRAGVLEQGTVDLLREAGVAERMDREGLVHEGV 75 
                                         9************************************************************************** PP

                           TIGR02360  76 eiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdgeekrl 150
                                         e+ + g+++r+dlk+ltggk+v+vyGqtevtrdl++area g+ ++y a++v++h+l++++p++tfekdg+ +r+
  lcl|FitnessBrowser__Putida:PP_3537  76 ELLVGGRRQRLDLKALTGGKTVMVYGQTEVTRDLMQAREASGAPIIYSAANVQPHELKGEKPYLTFEKDGRVQRI 150
                                         *************************************************************************** PP

                           TIGR02360 151 dcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrsryyvqv 225
                                         dcd+iaGcdGfhG+sr+sip+ +lk++e+vypfGwlG+ls+tppv++eliy+++erGfalcs+rs+trsryy+qv
  lcl|FitnessBrowser__Putida:PP_3537 151 DCDYIAGCDGFHGISRQSIPEGVLKQYERVYPFGWLGLLSDTPPVNHELIYAHHERGFALCSQRSQTRSRYYLQV 225
                                         *************************************************************************** PP

                           TIGR02360 226 sltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivpptGakGln 300
                                         +l+d+ve+wsd+rfw+elk+rl+ e+a+ lvtgp++eksiaplrs+v+epm+yG+lfl+GdaahivpptGakGln
  lcl|FitnessBrowser__Putida:PP_3537 226 PLQDRVEEWSDERFWDELKARLPAEVAADLVTGPALEKSIAPLRSLVVEPMQYGHLFLVGDAAHIVPPTGAKGLN 300
                                         *************************************************************************** PP

                           TIGR02360 301 laasdvaylyealleaykekdsaglerysakalarvwkaerfswwltsllhrf.pdedefdkkiqqaeleylles 374
                                         laasdv+yly+ l++ y+e++ + l +ys  al+rvwk erfsw++t+llh f  ++d++d+k+q+a+ ey+l+s
  lcl|FitnessBrowser__Putida:PP_3537 301 LAASDVNYLYRILVKVYHEGRVDLLAQYSPLALRRVWKGERFSWFMTQLLHDFgSHKDAWDQKMQEADREYFLTS 375
                                         *****************************************************447899**************** PP

                           TIGR02360 375 eaaqktlaenyvGlpy 390
                                          a++  +aenyvGlp+
  lcl|FitnessBrowser__Putida:PP_3537 376 PAGLVNIAENYVGLPF 391
                                         ***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (395 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: 7.89
//
[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