Alignments for a candidate for pobA in Polaromonas naphthalenivorans CJ2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Polaromonas naphthalenivorans CJ2

Align p-hydroxybenzoate hydroxylase; PHBH; PHBHase; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate WP_011801292.1 PNAP_RS09520 4-hydroxybenzoate 3-monooxygenase

Query= SwissProt::P00438
         (394 letters)



>NCBI__GCF_000015505.1:WP_011801292.1
          Length = 394

 Score =  534 bits (1375), Expect = e-156
 Identities = 252/389 (64%), Positives = 308/389 (79%)

Query: 1   MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAG 60
           M+TQVAIIGAGPSGLLLGQLLHKAGID +ILERQT DYVLGRIRAG+LEQ  +DL+ EAG
Sbjct: 1   MRTQVAIIGAGPSGLLLGQLLHKAGIDAIILERQTGDYVLGRIRAGILEQVCIDLMDEAG 60

Query: 61  VDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATT 120
           V  RM ++GLVH G E+ + G+R RID+ +L+GGK V VYGQTE+TRDLM+AR A G  T
Sbjct: 61  VGERMHKEGLVHGGFEMLYNGKRHRIDMNKLTGGKNVMVYGQTELTRDLMDARAAAGLPT 120

Query: 121 VYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERV 180
           VY+A  V +HD    +P VT+E+DG++  ++CD+IAGCDGFHG+ R S P   +  FE+V
Sbjct: 121 VYEATHVAVHDFDTAKPRVTYEKDGQKFEIECDFIAGCDGFHGVCRASAPRSAITEFEKV 180

Query: 181 YPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFW 240
           YPFGWLGLL+DTPPV  ELIY N PRGFALCSQRS TRSRYY+QVPLT+++E+W+DE FW
Sbjct: 181 YPFGWLGLLSDTPPVHDELIYVNSPRGFALCSQRSKTRSRYYLQVPLTDRIEEWTDEAFW 240

Query: 241 TELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLN 300
            EL+ RL  E  EKL+TGPS+EKSIAPLRSF+ EP++ GR+FLAGDA HIVPPTGAKGLN
Sbjct: 241 QELRLRLDDEGREKLITGPSIEKSIAPLRSFITEPLRFGRMFLAGDAGHIVPPTGAKGLN 300

Query: 301 LAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFS 360
           LAA+DV  L   +++ Y++     ++ YS  CL+RIWK ERFSWW T ++HRFPD  A  
Sbjct: 301 LAATDVKYLSSAIIEFYQDKTEAGIDNYSERCLKRIWKGERFSWWFTQLMHRFPDDGAIV 360

Query: 361 QRIQQTELEYYLGSEAGLATIAENYVGLP 389
            + QQ EL+Y L SEAG  +IAENYVGLP
Sbjct: 361 AKFQQAELDYLLNSEAGSRSIAENYVGLP 389


Lambda     K      H
   0.321    0.138    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: 555
Number of extensions: 17
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 WP_011801292.1 PNAP_RS09520 (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.845304.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.6e-209  679.1   0.0   9.7e-209  678.9   0.0    1.0  1  NCBI__GCF_000015505.1:WP_011801292.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015505.1:WP_011801292.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  678.9   0.0  9.7e-209  9.7e-209       1     390 []       1     390 [.       1     390 [. 1.00

  Alignments for each domain:
  == domain 1  score: 678.9 bits;  conditional E-value: 9.7e-209
                             TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvhe 73 
                                           m+tqvaiigaGpsGlllgqllhkaGida+iler++ dyvlgriraG+leq+ +dl++eagv+er+++eglvh 
  NCBI__GCF_000015505.1:WP_011801292.1   1 MRTQVAIIGAGPSGLLLGQLLHKAGIDAIILERQTGDYVLGRIRAGILEQVCIDLMDEAGVGERMHKEGLVHG 73 
                                           9************************************************************************ PP

                             TIGR02360  74 GveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdge 146
                                           G+e+ ++g+++r+d++kltggk+v+vyGqte+trdl++ar aagl tvyea +v +hd+++ +p+vt+ekdg+
  NCBI__GCF_000015505.1:WP_011801292.1  74 GFEMLYNGKRHRIDMNKLTGGKNVMVYGQTELTRDLMDARAAAGLPTVYEATHVAVHDFDTAKPRVTYEKDGQ 146
                                           ************************************************************************* PP

                             TIGR02360 147 ekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrs 219
                                           + +++cdfiaGcdGfhGv+r+s p++++ efekvypfGwlG+ls+tppv+deliy+ns rGfalcs+rs+trs
  NCBI__GCF_000015505.1:WP_011801292.1 147 KFEIECDFIAGCDGFHGVCRASAPRSAITEFEKVYPFGWLGLLSDTPPVHDELIYVNSPRGFALCSQRSKTRS 219
                                           ************************************************************************* PP

                             TIGR02360 220 ryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivp 292
                                           ryy+qv+ltd++e+w+d++fw+el+ rld+e  ekl+tgpsieksiaplrsf++ep+r+Gr+flaGda hivp
  NCBI__GCF_000015505.1:WP_011801292.1 220 RYYLQVPLTDRIEEWTDEAFWQELRLRLDDEGREKLITGPSIEKSIAPLRSFITEPLRFGRMFLAGDAGHIVP 292
                                           ************************************************************************* PP

                             TIGR02360 293 ptGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqq 365
                                           ptGakGlnlaa+dv+yl++a++e+y++k +ag+++ys+++l+r+wk erfsww+t+l+hrfpd+ ++ +k+qq
  NCBI__GCF_000015505.1:WP_011801292.1 293 PTGAKGLNLAATDVKYLSSAIIEFYQDKTEAGIDNYSERCLKRIWKGERFSWWFTQLMHRFPDDGAIVAKFQQ 365
                                           ************************************************************************* PP

                             TIGR02360 366 aeleylleseaaqktlaenyvGlpy 390
                                           ael+yll+sea+ +++aenyvGlp+
  NCBI__GCF_000015505.1:WP_011801292.1 366 AELDYLLNSEAGSRSIAENYVGLPL 390
                                           ***********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (394 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: 15.27
//
[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:

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 2024 update 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