Alignments for a candidate for PAH in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for PAH in Shewanella oneidensis MR-1

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate 200831 SO1666 phenylalanine-4-hydroxylase (NCBI ptt file)

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



>FitnessBrowser__MR1:200831
          Length = 271

 Score =  556 bits (1434), Expect = e-163
 Identities = 271/271 (100%), Positives = 271/271 (100%)

Query: 1   MTIDTVHTAPYVARSADDSGYIHYPQEEHDIWRQLYARQAVNLPGRACKEYLQGLDALAM 60
           MTIDTVHTAPYVARSADDSGYIHYPQEEHDIWRQLYARQAVNLPGRACKEYLQGLDALAM
Sbjct: 1   MTIDTVHTAPYVARSADDSGYIHYPQEEHDIWRQLYARQAVNLPGRACKEYLQGLDALAM 60

Query: 61  PKDRIPQLAEIDKVLMATTGWKTADVPALISFGRFFELLANKEFPVATFIRRKEEFDYLQ 120
           PKDRIPQLAEIDKVLMATTGWKTADVPALISFGRFFELLANKEFPVATFIRRKEEFDYLQ
Sbjct: 61  PKDRIPQLAEIDKVLMATTGWKTADVPALISFGRFFELLANKEFPVATFIRRKEEFDYLQ 120

Query: 121 EPDIFHEIFGHCPLLTNPSFAHFSHMYGQLGLNASKEDRVFLARLYWFTVEFGLLKPQEG 180
           EPDIFHEIFGHCPLLTNPSFAHFSHMYGQLGLNASKEDRVFLARLYWFTVEFGLLKPQEG
Sbjct: 121 EPDIFHEIFGHCPLLTNPSFAHFSHMYGQLGLNASKEDRVFLARLYWFTVEFGLLKPQEG 180

Query: 181 ELCIYGGGILSSPGETLYAMESQVPERKPFDLLDVLRTPYRIDIMQPIYYVIEHIDVLDE 240
           ELCIYGGGILSSPGETLYAMESQVPERKPFDLLDVLRTPYRIDIMQPIYYVIEHIDVLDE
Sbjct: 181 ELCIYGGGILSSPGETLYAMESQVPERKPFDLLDVLRTPYRIDIMQPIYYVIEHIDVLDE 240

Query: 241 IAKMDIMAYVAKARQLGLFAPKYPPKAKKAS 271
           IAKMDIMAYVAKARQLGLFAPKYPPKAKKAS
Sbjct: 241 IAKMDIMAYVAKARQLGLFAPKYPPKAKKAS 271


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: 403
Number of extensions: 9
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: 271
Length of database: 271
Length adjustment: 25
Effective length of query: 246
Effective length of database: 246
Effective search space:    60516
Effective search space used:    60516
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 200831 SO1666 (phenylalanine-4-hydroxylase (NCBI ptt file))
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.30343.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.6e-106  338.5   0.0   1.1e-105  338.4   0.0    1.0  1  lcl|FitnessBrowser__MR1:200831  SO1666 phenylalanine-4-hydroxyla


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200831  SO1666 phenylalanine-4-hydroxylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.4   0.0  1.1e-105  1.1e-105       3     247 ..      16     261 ..      14     262 .. 0.98

  Alignments for each domain:
  == domain 1  score: 338.4 bits;  conditional E-value: 1.1e-105
                       TIGR01267   3 tvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwkivavpglipadv 81 
                                     +++ ++++y++eeh +w+ l+ rq+  l+grac+eyl+G++ l +++drip+l e++++l+a+tGwk + vp+li +  
  lcl|FitnessBrowser__MR1:200831  16 ADDSGYIHYPQEEHDIWRQLYARQAVNLPGRACKEYLQGLDALAMPKDRIPQLAEIDKVLMATTGWKTADVPALISFGR 94 
                                     67899************************************************************************** PP

                       TIGR01267  82 ffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvkakalgaallarlywytvefG 160
                                     ffe+lan++fpv+tf+r +ee+dylqepd+fh++fGh+pll+np fa+f ++yG++g++a+++++++larlyw+tvefG
  lcl|FitnessBrowser__MR1:200831  95 FFELLANKEFPVATFIRRKEEFDYLQEPDIFHEIFGHCPLLTNPSFAHFSHMYGQLGLNASKEDRVFLARLYWFTVEFG 173
                                     ******************************************************************************* PP

                       TIGR01267 161 lvetaag.lriyGaGilsskkelvyaleskeplrvafdllevmrtryridklqkayfvlpslkrlfdaaqedfealvae 238
                                     l++ ++g l iyG+Gilss+ e++ya+es+ p+r++fdll+v+rt+yrid++q++y+v++ ++ l ++a+ d++a va+
  lcl|FitnessBrowser__MR1:200831 174 LLKPQEGeLCIYGGGILSSPGETLYAMESQVPERKPFDLLDVLRTPYRIDIMQPIYYVIEHIDVLDEIAKMDIMAYVAK 252
                                     ***988879********************************************************************** PP

                       TIGR01267 239 akdlkaldp 247
                                     a++l++++p
  lcl|FitnessBrowser__MR1:200831 253 ARQLGLFAP 261
                                     **9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (271 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: 8.16
//
[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