Alignments for a candidate for PAH in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for PAH in Herbaspirillum seropedicae SmR1

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate HSERO_RS21390 HSERO_RS21390 phenylalanine 4-monooxygenase

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



>FitnessBrowser__HerbieS:HSERO_RS21390
          Length = 295

 Score =  323 bits (828), Expect = 3e-93
 Identities = 153/249 (61%), Positives = 187/249 (75%)

Query: 27  RGDYSRANADYTCPQDYAAYTDADHDTYRRLYERQRALLPGLASQAFIDALPSLGASDQI 86
           RGDYS+A+A+Y   Q++  YT A H  +RRLYERQ  L+PG A   FI++L +L  S  I
Sbjct: 24  RGDYSQADANYVVAQNWEGYTPAQHALWRRLYERQARLIPGRACDVFIESLKALDVSQGI 83

Query: 87  PRFEEVNERLYKATGWELVGVPGLIPEVPFFTLLANRQFPVTDWIRKPEEFEYIVEPDIF 146
           PRF+   + LYKATGW+LV VPGL+P+  FF  LANR+FPVT W+R+  EF+YIVEPD+F
Sbjct: 84  PRFDRTTDALYKATGWQLVAVPGLVPDQTFFEHLANRRFPVTVWLREEHEFDYIVEPDLF 143

Query: 147 HDLFGHVPLLFNPVFADYVQRYGQGGLKAQGLGSCEMLSRLYWYTIEFGLIREAGELRAY 206
           HD FGHVPLLFNPVFA+++Q YG+GGLKA  L     L+RLYWYTIEFGLI+    LR Y
Sbjct: 144 HDFFGHVPLLFNPVFANHLQEYGKGGLKALKLDGLAYLARLYWYTIEFGLIQSEAGLRIY 203

Query: 207 GAGILSSSGELAYSVQSPEPQRIPLALERTMRTRYKIDTYQQTYFVIDSFEQLFEMTAAD 266
           GAGILSS GE+ Y + S +P+R+P  +ER MRT YKIDTYQ+TYFVI  FEQLF  TA D
Sbjct: 204 GAGILSSGGEVEYCLSSDKPRRVPFQVERIMRTLYKIDTYQETYFVIRDFEQLFNDTAPD 263

Query: 267 FAPIYERLR 275
           F P YERL+
Sbjct: 264 FTPFYERLK 272


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: 319
Number of extensions: 11
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: 295
Length adjustment: 26
Effective length of query: 264
Effective length of database: 269
Effective search space:    71016
Effective search space used:    71016
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 HSERO_RS21390 HSERO_RS21390 (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.21248.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.7e-107  342.1   0.1   9.4e-107  341.8   0.1    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS21390  HSERO_RS21390 phenylalanine 4-mo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS21390  HSERO_RS21390 phenylalanine 4-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.8   0.1  9.4e-107  9.4e-107       2     245 ..      34     277 ..      33     280 .. 0.98

  Alignments for each domain:
  == domain 1  score: 341.8 bits;  conditional E-value: 9.4e-107
                                  TIGR01267   2 ftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwk 69 
                                                + vaq+++ y+  +ha w+ l++rq++l++gracd +++ ++ l++  + ip ++  ++ l ++tGw+
  lcl|FitnessBrowser__HerbieS:HSERO_RS21390  34 YVVAQNWEGYTPAQHALWRRLYERQARLIPGRACDVFIESLKALDV-SQGIPRFDRTTDALYKATGWQ 100
                                                56899*****************************************.899****************** PP

                                  TIGR01267  70 ivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkk 137
                                                +vavpgl+p+++ffehlanrrfpvt +lr+ +e+dy++epd+fhd+fGhvpll npvfa++l+ yGk+
  lcl|FitnessBrowser__HerbieS:HSERO_RS21390 101 LVAVPGLVPDQTFFEHLANRRFPVTVWLREEHEFDYIVEPDLFHDFFGHVPLLFNPVFANHLQEYGKG 168
                                                ******************************************************************** PP

                                  TIGR01267 138 gvkakalgaa.llarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrt 204
                                                g+ka +l++   larlywyt+efGl++ +aglriyGaGilss  e+ y+l s++p+rv+f+++++mrt
  lcl|FitnessBrowser__HerbieS:HSERO_RS21390 169 GLKALKLDGLaYLARLYWYTIEFGLIQSEAGLRIYGAGILSSGGEVEYCLSSDKPRRVPFQVERIMRT 236
                                                ******998769******************************************************** PP

                                  TIGR01267 205 ryridklqkayfvlpslkrlfdaaqedfealvaeakdlkal 245
                                                 y+id++q++yfv+ ++++lf+ +++df++++ ++k++++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS21390 237 LYKIDTYQETYFVIRDFEQLFNDTAPDFTPFYERLKQQEPL 277
                                                ************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (295 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.02
//
[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