GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PAH in Shewanella amazonensis SB2B

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate 6938101 Sama_2222 phenylalanine 4-monooxygenase (RefSeq)

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



>FitnessBrowser__SB2B:6938101
          Length = 263

 Score =  416 bits (1068), Expect = e-121
 Identities = 200/258 (77%), Positives = 230/258 (89%), Gaps = 1/258 (0%)

Query: 11  YVARSADDSGYIHYPQEEHDIWRQLYARQAVNLPGRACKEYLQGLDALAMPKDRIPQLAE 70
           YVAR  D  G I YP +E++IW +LYARQAVNLPGRAC+EYL GL+ LA+PKDR+PQLAE
Sbjct: 5   YVARKPDAHGVIAYPDQENEIWAELYARQAVNLPGRACQEYLDGLERLALPKDRVPQLAE 64

Query: 71  IDKVLMATTGWKTADVPALISFGRFFELLANKEFPVATFIRRKEEFDYLQEPDIFHEIFG 130
           +D+VL+ TTGWKTA VPALISF RFFELLA+++FPVATFIR +EEFDYLQEPDIFHEIFG
Sbjct: 65  VDEVLLDTTGWKTAAVPALISFERFFELLASRQFPVATFIRSREEFDYLQEPDIFHEIFG 124

Query: 131 HCPLLTNPSFAHFSHMYGQLGLNASKEDRVFLARLYWFTVEFGLLKPQEGELCIYGGGIL 190
           HCPLLTNP+FA+FSH+YG+LGL A+KE+RV+LARLYWFTVEFGLLKP++GEL IYGGGIL
Sbjct: 125 HCPLLTNPAFANFSHIYGKLGLAATKEERVYLARLYWFTVEFGLLKPRDGELRIYGGGIL 184

Query: 191 SSPGETLYAMESQVPERKPFDLLDVLRTPYRIDIMQPIYYVIEHIDVLDEIAKMDIMAYV 250
           SSPGETLYAM  + P RKPFDLLDVLRTPYRIDIMQP+Y+ IEHID LDEIA+MDIM  V
Sbjct: 185 SSPGETLYAMGDK-PLRKPFDLLDVLRTPYRIDIMQPVYFEIEHIDFLDEIARMDIMQSV 243

Query: 251 AKARQLGLFAPKYPPKAK 268
            +ARQLGL AP + PKAK
Sbjct: 244 TRARQLGLHAPLFEPKAK 261


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: 323
Number of extensions: 7
Number of successful extensions: 2
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: 263
Length adjustment: 25
Effective length of query: 246
Effective length of database: 238
Effective search space:    58548
Effective search space used:    58548
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 6938101 Sama_2222 (phenylalanine 4-monooxygenase (RefSeq))
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.aa/TIGR01267.hmm
# target sequence database:        /tmp/gapView.1927.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-104  334.5   0.0   1.9e-104  334.3   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6938101  Sama_2222 phenylalanine 4-monoox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938101  Sama_2222 phenylalanine 4-monooxygenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.3   0.0  1.9e-104  1.9e-104       3     247 ..      10     254 ..       8     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 334.3 bits;  conditional E-value: 1.9e-104
                         TIGR01267   3 tvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwkivavpglipa 79 
                                       ++a++ + y+++e+++wa l+ rq+  l+grac+eyldG+e+l l++dr+p+l ev+e+l  +tGwk +avp+li +
  lcl|FitnessBrowser__SB2B:6938101  10 PDAHGVIAYPDQENEIWAELYARQAVNLPGRACQEYLDGLERLALPKDRVPQLAEVDEVLLDTTGWKTAAVPALISF 86 
                                       7889999********************************************************************** PP

                         TIGR01267  80 dvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvkakalgaallarlywyt 156
                                       + ffe+la+r+fpv+tf+r +ee+dylqepd+fh++fGh+pll+np fa+f ++yGk+g+ a++++++ larlyw+t
  lcl|FitnessBrowser__SB2B:6938101  87 ERFFELLASRQFPVATFIRSREEFDYLQEPDIFHEIFGHCPLLTNPAFANFSHIYGKLGLAATKEERVYLARLYWFT 163
                                       ***************************************************************************** PP

                         TIGR01267 157 vefGlvetaag.lriyGaGilsskkelvyaleskeplrvafdllevmrtryridklqkayfvlpslkrlfdaaqedf 232
                                       vefGl++  +g lriyG+Gilss+ e++ya  +++plr++fdll+v+rt+yrid++q++yf ++ ++ l ++a+ d+
  lcl|FitnessBrowser__SB2B:6938101 164 VEFGLLKPRDGeLRIYGGGILSSPGETLYA-MGDKPLRKPFDLLDVLRTPYRIDIMQPVYFEIEHIDFLDEIARMDI 239
                                       ******987766******************.89******************************************** PP

                         TIGR01267 233 ealvaeakdlkaldp 247
                                       +  v++a++l++++p
  lcl|FitnessBrowser__SB2B:6938101 240 MQSVTRARQLGLHAP 254
                                       ***********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (263 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: 00:00:00.01
# Mc/sec: 5.56
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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