Alignments for a candidate for PAH in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for PAH in Acidovorax sp. GW101-3H11

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate Ac3H11_1847 Phenylalanine-4-hydroxylase (EC 1.14.16.1)

Query= reanno::acidovorax_3H11:Ac3H11_1847
         (290 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1847
          Length = 290

 Score =  590 bits (1520), Expect = e-173
 Identities = 290/290 (100%), Positives = 290/290 (100%)

Query: 1   VRKVMAAKEKKMGQAPVVYGQSTRPPRGDYSRANADYTCPQDYAAYTDADHDTYRRLYER 60
           VRKVMAAKEKKMGQAPVVYGQSTRPPRGDYSRANADYTCPQDYAAYTDADHDTYRRLYER
Sbjct: 1   VRKVMAAKEKKMGQAPVVYGQSTRPPRGDYSRANADYTCPQDYAAYTDADHDTYRRLYER 60

Query: 61  QRALLPGLASQAFIDALPSLGASDQIPRFEEVNERLYKATGWELVGVPGLIPEVPFFTLL 120
           QRALLPGLASQAFIDALPSLGASDQIPRFEEVNERLYKATGWELVGVPGLIPEVPFFTLL
Sbjct: 61  QRALLPGLASQAFIDALPSLGASDQIPRFEEVNERLYKATGWELVGVPGLIPEVPFFTLL 120

Query: 121 ANRQFPVTDWIRKPEEFEYIVEPDIFHDLFGHVPLLFNPVFADYVQRYGQGGLKAQGLGS 180
           ANRQFPVTDWIRKPEEFEYIVEPDIFHDLFGHVPLLFNPVFADYVQRYGQGGLKAQGLGS
Sbjct: 121 ANRQFPVTDWIRKPEEFEYIVEPDIFHDLFGHVPLLFNPVFADYVQRYGQGGLKAQGLGS 180

Query: 181 CEMLSRLYWYTIEFGLIREAGELRAYGAGILSSSGELAYSVQSPEPQRIPLALERTMRTR 240
           CEMLSRLYWYTIEFGLIREAGELRAYGAGILSSSGELAYSVQSPEPQRIPLALERTMRTR
Sbjct: 181 CEMLSRLYWYTIEFGLIREAGELRAYGAGILSSSGELAYSVQSPEPQRIPLALERTMRTR 240

Query: 241 YKIDTYQQTYFVIDSFEQLFEMTAADFAPIYERLRGLPEFAADEREAVAA 290
           YKIDTYQQTYFVIDSFEQLFEMTAADFAPIYERLRGLPEFAADEREAVAA
Sbjct: 241 YKIDTYQQTYFVIDSFEQLFEMTAADFAPIYERLRGLPEFAADEREAVAA 290


Lambda     K      H
   0.321    0.139    0.417 

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: 492
Number of extensions: 13
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: 290
Length of database: 290
Length adjustment: 26
Effective length of query: 264
Effective length of database: 264
Effective search space:    69696
Effective search space used:    69696
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: 48 (23.1 bits)

Align candidate Ac3H11_1847 (Phenylalanine-4-hydroxylase (EC 1.14.16.1))
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.25610.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
     2e-104  334.2   0.0   2.5e-104  333.9   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1847  Phenylalanine-4-hydroxylase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1847  Phenylalanine-4-hydroxylase (EC 1.14.16.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.9   0.0  2.5e-104  2.5e-104       1     241 [.      36     276 ..      36     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 333.9 bits;  conditional E-value: 2.5e-104
                                        TIGR01267   1 dftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevnekl 62 
                                                      d+t +qd+  y++ +h +++ l++rq  ll+g+a + ++d +  lg   d+ip +eevne+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1847  36 DYTCPQDYAAYTDADHDTYRRLYERQRALLPGLASQAFIDALPSLGA-SDQIPRFEEVNERL 96 
                                                      6899******************************************9.9************* PP

                                        TIGR01267  63 raltGwkivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsn 124
                                                       ++tGw++v vpglip+ +ff +lanr+fpvt ++r+pee++y++epd+fhdlfGhvpll n
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1847  97 YKATGWELVGVPGLIPEVPFFTLLANRQFPVTDWIRKPEEFEYIVEPDIFHDLFGHVPLLFN 158
                                                      ************************************************************** PP

                                        TIGR01267 125 pvfadfleayGkkgvkakalgaa.llarlywytvefGlvetaaglriyGaGilsskkelvya 185
                                                      pvfad+++ yG++g+ka+ lg+  +l+rlywyt+efGl+++a++lr+yGaGilss  el y+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1847 159 PVFADYVQRYGQGGLKAQGLGSCeMLSRLYWYTIEFGLIREAGELRAYGAGILSSSGELAYS 220
                                                      *********************988************************************** PP

                                        TIGR01267 186 leskeplrvafdllevmrtryridklqkayfvlpslkrlfdaaqedfealvaeakd 241
                                                      ++s ep+r+++ l++ mrtry+id++q++yfv++s+++lf++++ df++++ +++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1847 221 VQSPEPQRIPLALERTMRTRYKIDTYQQTYFVIDSFEQLFEMTAADFAPIYERLRG 276
                                                      ***************************************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (290 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: 00:00:00.00
# Mc/sec: 8.30
//
[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