Alignments for a candidate for PAH in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for PAH in Shewanella loihica PV-4

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate 5208934 Shew_1435 phenylalanine 4-monooxygenase (RefSeq)

Query= reanno::MR1:200831
         (271 letters)



>FitnessBrowser__PV4:5208934
          Length = 277

 Score =  385 bits (990), Expect = e-112
 Identities = 192/258 (74%), Positives = 208/258 (80%), Gaps = 1/258 (0%)

Query: 11  YVARSADDSGYIHYPQEEHDIWRQLYARQAVNLPGRACKEYLQGLDALAMPKDRIPQLAE 70
           Y AR  D  G I YP  EH+IW+ LY RQ  NLP  AC  YL+GL+ LA+P DRIPQL E
Sbjct: 19  YQARLPDSQGVIQYPDNEHEIWQALYDRQKGNLPHYACDAYLKGLEDLALPADRIPQLGE 78

Query: 71  IDKVLMATTGWKTADVPALISFGRFFELLANKEFPVATFIRRKEEFDYLQEPDIFHEIFG 130
           ID VL   TGWKTA VPALISF +FF+LLAN+EFPVATFIR KEEFDYLQEPDIFHEIFG
Sbjct: 79  IDAVLQQATGWKTAAVPALISFEKFFQLLANQEFPVATFIRSKEEFDYLQEPDIFHEIFG 138

Query: 131 HCPLLTNPSFAHFSHMYGQLGLNASKEDRVFLARLYWFTVEFGLLKPQEGELCIYGGGIL 190
           HCPLLTNPSFA FSH YG+LGL ASKE+RVFLARLYWFTVEFGL++    EL IYGGGIL
Sbjct: 139 HCPLLTNPSFARFSHEYGKLGLAASKEERVFLARLYWFTVEFGLIRQTNDELKIYGGGIL 198

Query: 191 SSPGETLYAMESQVPERKPFDLLDVLRTPYRIDIMQPIYYVIEHIDVLDEIAKMDIMAYV 250
           SSPGETLYAM S  P  KPFDLLD+LRTPYRIDIMQPIYY I+ ID LDEI KMDIM  V
Sbjct: 199 SSPGETLYAM-SDTPVVKPFDLLDILRTPYRIDIMQPIYYAIDSIDYLDEIVKMDIMGAV 257

Query: 251 AKARQLGLFAPKYPPKAK 268
            KARQLGL AP + PK+K
Sbjct: 258 TKARQLGLHAPMFEPKSK 275


Lambda     K      H
   0.323    0.140    0.430 

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: 303
Number of extensions: 9
Number of successful extensions: 2
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: 271
Length of database: 277
Length adjustment: 25
Effective length of query: 246
Effective length of database: 252
Effective search space:    61992
Effective search space used:    61992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)

Align candidate 5208934 Shew_1435 (phenylalanine 4-monooxygenase (RefSeq))
to HMM TIGR01267 (phhA: phenylalanine-4-hydroxylase (EC 1.14.16.1))

# 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/TIGR01267.hmm
# target sequence database:        /tmp/gapView.23856.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01267  [M=248]
Accession:   TIGR01267
Description: Phe4hydrox_mono: phenylalanine-4-hydroxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   4.2e-103  329.9   0.0   4.9e-103  329.7   0.0    1.0  1  lcl|FitnessBrowser__PV4:5208934  Shew_1435 phenylalanine 4-monoox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208934  Shew_1435 phenylalanine 4-monooxygenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.7   0.0  4.9e-103  4.9e-103       2     247 ..      23     268 ..      22     269 .. 0.98

  Alignments for each domain:
  == domain 1  score: 329.7 bits;  conditional E-value: 4.9e-103
                        TIGR01267   2 ftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwkivavpglipa 79 
                                       +++q+ ++y+++eh++w++l+drq   l+  acd yl+G+e l l+adrip+l e++ +l+++tGwk +avp+li +
  lcl|FitnessBrowser__PV4:5208934  23 LPDSQGVIQYPDNEHEIWQALYDRQKGNLPHYACDAYLKGLEDLALPADRIPQLGEIDAVLQQATGWKTAAVPALISF 100
                                      57899************************************************************************* PP

                        TIGR01267  80 dvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvkakalgaallarlywytv 157
                                      + ff++lan++fpv+tf+r +ee+dylqepd+fh++fGh+pll+np fa f + yGk+g+ a+++++++larlyw+tv
  lcl|FitnessBrowser__PV4:5208934 101 EKFFQLLANQEFPVATFIRSKEEFDYLQEPDIFHEIFGHCPLLTNPSFARFSHEYGKLGLAASKEERVFLARLYWFTV 178
                                      ****************************************************************************** PP

                        TIGR01267 158 efGlvetaag.lriyGaGilsskkelvyaleskeplrvafdllevmrtryridklqkayfvlpslkrlfdaaqedfea 234
                                      efGl++++++ l+iyG+Gilss+ e++ya  s+ p  ++fdll+++rt+yrid++q++y+ ++s++ l ++++ d++ 
  lcl|FitnessBrowser__PV4:5208934 179 EFGLIRQTNDeLKIYGGGILSSPGETLYA-MSDTPVVKPFDLLDILRTPYRIDIMQPIYYAIDSIDYLDEIVKMDIMG 255
                                      *****766555******************.89********************************************** PP

                        TIGR01267 235 lvaeakdlkaldp 247
                                       v++a++l++++p
  lcl|FitnessBrowser__PV4:5208934 256 AVTKARQLGLHAP 268
                                      ********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (277 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: 00:00:00.00
# Mc/sec: 7.41
//
[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