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.10127.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 9.62
//
[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:

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:

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:

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:

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