Alignments for a candidate for PAH in Polaromonas naphthalenivorans CJ2

GapMind for catabolism of small carbon sources

Alignments for a candidate for PAH in Polaromonas naphthalenivorans CJ2

Align phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate WP_011800527.1 PNAP_RS05595 phenylalanine 4-monooxygenase

Query= BRENDA::P30967
         (297 letters)



>NCBI__GCF_000015505.1:WP_011800527.1
          Length = 299

 Score =  332 bits (851), Expect = 6e-96
 Identities = 153/261 (58%), Positives = 198/261 (75%)

Query: 26  DFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGLERLEVDADRVPDFNKLNQ 85
           D+T+ Q  DRY+A++HATW TL++RQ +LL GRACDEF+ G+  L + AD++PDF +L+ 
Sbjct: 25  DWTIEQGWDRYTAQEHATWKTLFERQSRLLLGRACDEFVSGMADLPIGADQIPDFRRLSD 84

Query: 86  KLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGHVP 145
            LM  TGW++VAVPGL+PD+VFFEHLANRRFP   ++R+P QLDYL+EPDVFHD+FGHVP
Sbjct: 85  ILMQRTGWQVVAVPGLVPDEVFFEHLANRRFPAGQFIRKPDQLDYLEEPDVFHDVFGHVP 144

Query: 146 LLINPVFADYLEAYGKGGVKAKALGALPMLARLYWYTVEFGLINTPAGMRIYGAGILSSK 205
           +L+NP  ADY++AYG GG++A+ LG L  LAR+YWYTVEFGL+    G+RIYGAGI SS 
Sbjct: 145 MLMNPAIADYIQAYGAGGLRAQQLGVLDKLARVYWYTVEFGLVKQKDGLRIYGAGIASSA 204

Query: 206 SESIYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDATAPDFAPLYLQL 265
           SES++ LD ASPNR+ FDL R+M T YRID FQ+TYFVID+  +L      DFAPLY ++
Sbjct: 205 SESVFALDDASPNRIRFDLERVMRTNYRIDDFQETYFVIDNLDELLALARIDFAPLYERV 264

Query: 266 ADAQPWGAGDVAPDDLVLNAG 286
                +  G V   D V+  G
Sbjct: 265 QGQPDYEPGSVLACDQVITQG 285


Lambda     K      H
   0.323    0.140    0.445 

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: 348
Number of extensions: 12
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: 297
Length of database: 299
Length adjustment: 27
Effective length of query: 270
Effective length of database: 272
Effective search space:    73440
Effective search space used:    73440
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_011800527.1 PNAP_RS05595 (phenylalanine 4-monooxygenase)
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.6457.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-107  344.7   0.1   1.4e-107  344.5   0.1    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011800527.1  PNAP_RS05595 phenylalanine 4-mon


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011800527.1  PNAP_RS05595 phenylalanine 4-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.5   0.1  1.4e-107  1.4e-107       1     245 [.      25     270 ..      25     273 .. 0.98

  Alignments for each domain:
  == domain 1  score: 344.5 bits;  conditional E-value: 1.4e-107
                                 TIGR01267   1 dftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwk 69 
                                               d+t++q++dry+++eha+w+tl++rq +ll gracde++ G+  l + ad+ipd+  +++ l++ tGw+
  lcl|NCBI__GCF_000015505.1:WP_011800527.1  25 DWTIEQGWDRYTAQEHATWKTLFERQSRLLLGRACDEFVSGMADLPIGADQIPDFRRLSDILMQRTGWQ 93 
                                               6799***************************************************************** PP

                                 TIGR01267  70 ivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkg 138
                                               +vavpgl+p++vffehlanrrfp  +f+r+p++ldyl epdvfhd+fGhvp+l+np  ad+++ayG +g
  lcl|NCBI__GCF_000015505.1:WP_011800527.1  94 VVAVPGLVPDEVFFEHLANRRFPAGQFIRKPDQLDYLEEPDVFHDVFGHVPMLMNPAIADYIQAYGAGG 162
                                               ********************************************************************* PP

                                 TIGR01267 139 vkakalgaa.llarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtry 206
                                               ++a++lg    lar+ywytvefGlv++++glriyGaGi ss +e+v+al+ ++p+r+ fdl++vmrt+y
  lcl|NCBI__GCF_000015505.1:WP_011800527.1 163 LRAQQLGVLdKLARVYWYTVEFGLVKQKDGLRIYGAGIASSASESVFALDDASPNRIRFDLERVMRTNY 231
                                               *******9769********************************************************** PP

                                 TIGR01267 207 ridklqkayfvlpslkrlfdaaqedfealvaeakdlkal 245
                                               rid +q++yfv+++l++l  +a+ df++l+ + + +  +
  lcl|NCBI__GCF_000015505.1:WP_011800527.1 232 RIDDFQETYFVIDNLDELLALARIDFAPLYERVQGQPDY 270
                                               ******************************998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (299 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.84
//
[ok]

This GapMind analysis is from Sep 24 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