Alignments for a candidate for pobA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Phaeobacter inhibens BS107

Align p-hydroxybenzoate hydroxylase; PHBH; PHBHase; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate GFF269 PGA1_c02810 P-hydroxybenzoate hydroxylase PobA

Query= SwissProt::P00438
         (394 letters)



>FitnessBrowser__Phaeo:GFF269
          Length = 408

 Score =  503 bits (1295), Expect = e-147
 Identities = 247/388 (63%), Positives = 295/388 (76%)

Query: 3   TQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVD 62
           TQV I+G GPSGLLL QLLH+AGID ++LERQT DYVLGRIRAGVLE G VDLLR AG  
Sbjct: 21  TQVVIVGGGPSGLLLSQLLHRAGIDTIVLERQTRDYVLGRIRAGVLEHGFVDLLRRAGAS 80

Query: 63  RRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVY 122
            RM RDG+VH G  IA  G+  RIDL   + G+TV VYGQTEVTRDL +AR+A G   ++
Sbjct: 81  ARMDRDGMVHHGFHIAHQGRLDRIDLAGSAKGQTVMVYGQTEVTRDLYDARDAMGGQIIH 140

Query: 123 QAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYP 182
           +AA V LHDL   RP VT+E+ GE  R+D  +I G DGFHG+SR+SIP++ L+ +E+VYP
Sbjct: 141 EAANVALHDLTTARPNVTYEQQGETRRIDTKFIVGADGFHGVSRKSIPSDVLQEYEKVYP 200

Query: 183 FGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFWTE 242
           FGWLG+L+ T P + ELIYA H RGFALCS R+A  SRYY+QVPLT++VEDWSD  FW E
Sbjct: 201 FGWLGVLSQTSPAADELIYARHDRGFALCSMRNAQLSRYYIQVPLTDRVEDWSDAAFWEE 260

Query: 243 LKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLA 302
           LK RLP +VA+ L TG S+EKSIAPLRSFV EPM++G LFLAGDAAHIVPPTGAKGLNLA
Sbjct: 261 LKRRLPEDVAKGLQTGVSIEKSIAPLRSFVAEPMRYGALFLAGDAAHIVPPTGAKGLNLA 320

Query: 303 ASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQR 362
           ASD+  LY  L   ++      L+ YS   L RIWKAERFSWWMT++LHRFPD      R
Sbjct: 321 ASDIHYLYEGLSDHFQRNDDTALDSYSERALARIWKAERFSWWMTNLLHRFPDMSPADLR 380

Query: 363 IQQTELEYYLGSEAGLATIAENYVGLPY 390
           +QQ +L+Y   S+A  A++AENYVGLPY
Sbjct: 381 LQQADLDYLFSSDAAQASLAENYVGLPY 408


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: 511
Number of extensions: 16
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: 408
Length adjustment: 31
Effective length of query: 363
Effective length of database: 377
Effective search space:   136851
Effective search space used:   136851
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 GFF269 PGA1_c02810 (P-hydroxybenzoate hydroxylase PobA)
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.2780.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-206  671.3   0.0   2.4e-206  671.0   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF269  PGA1_c02810 P-hydroxybenzoate hy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF269  PGA1_c02810 P-hydroxybenzoate hydroxylase PobA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.0   0.0  2.4e-206  2.4e-206       3     390 .]      21     408 .]      19     408 .] 1.00

  Alignments for each domain:
  == domain 1  score: 671.0 bits;  conditional E-value: 2.4e-206
                         TIGR02360   3 tqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvheGveiaf 79 
                                       tqv+i+g+GpsGlll+qllh+aGid+++ler++rdyvlgriraGvle+g+vdll++ag++ r+dr+g+vh+G++ia+
  lcl|FitnessBrowser__Phaeo:GFF269  21 TQVVIVGGGPSGLLLSQLLHRAGIDTIVLERQTRDYVLGRIRAGVLEHGFVDLLRRAGASARMDRDGMVHHGFHIAH 97 
                                       9**************************************************************************** PP

                         TIGR02360  80 egekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdgeekrldcdfia 156
                                       +g+  r+dl+  ++g++v+vyGqtevtrdly+ar+a+g+++++ea++v lhdl++ rp+vt+e++ge++r+d  fi+
  lcl|FitnessBrowser__Phaeo:GFF269  98 QGRLDRIDLAGSAKGQTVMVYGQTEVTRDLYDARDAMGGQIIHEAANVALHDLTTARPNVTYEQQGETRRIDTKFIV 174
                                       ***************************************************************************** PP

                         TIGR02360 157 GcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrsryyvqvsltdkved 233
                                       G+dGfhGvsrksip+++l+e+ekvypfGwlG+ls+t p++deliy++++rGfalcs+r++++sryy+qv+ltd+ved
  lcl|FitnessBrowser__Phaeo:GFF269 175 GADGFHGVSRKSIPSDVLQEYEKVYPFGWLGVLSQTSPAADELIYARHDRGFALCSMRNAQLSRYYIQVPLTDRVED 251
                                       ***************************************************************************** PP

                         TIGR02360 234 wsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivpptGakGlnlaasdvayly 310
                                       wsd++fweelkrrl+e++a+ l tg sieksiaplrsfvaepmryG lflaGdaahivpptGakGlnlaasd++yly
  lcl|FitnessBrowser__Phaeo:GFF269 252 WSDAAFWEELKRRLPEDVAKGLQTGVSIEKSIAPLRSFVAEPMRYGALFLAGDAAHIVPPTGAKGLNLAASDIHYLY 328
                                       ***************************************************************************** PP

                         TIGR02360 311 ealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqqaeleylleseaaqktlaenyvG 387
                                       e+l ++++ +d+++l++ys++alar+wkaerfsww+t+llhrfpd +  d ++qqa+l+yl++s+aaq++laenyvG
  lcl|FitnessBrowser__Phaeo:GFF269 329 EGLSDHFQRNDDTALDSYSERALARIWKAERFSWWMTNLLHRFPDMSPADLRLQQADLDYLFSSDAAQASLAENYVG 405
                                       ***************************************************************************** PP

                         TIGR02360 388 lpy 390
                                       lpy
  lcl|FitnessBrowser__Phaeo:GFF269 406 LPY 408
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (408 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: 00:00:00.02
# Mc/sec: 7.54
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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