GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Pseudomonas fluorescens FW300-N2E2

Align periplasmic dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate Pf6N2E2_5062 3-dehydroquinate dehydratase II (EC 4.2.1.10)

Query= metacyc::MONOMER-15328
         (160 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062
          Length = 147

 Score =  181 bits (460), Expect = 3e-51
 Identities = 82/143 (57%), Positives = 108/143 (75%)

Query: 15  PLITVLNGPNLNMLGLRQPGIYGHATLDDVEQVCIQAAERLDVAIDFRQTNGEGELVSWV 74
           P++ VLNGPNLN+LG R+P  YGH TL D+  +C +AAE   +A++FRQTN EGEL+ W+
Sbjct: 3   PIVLVLNGPNLNLLGTREPATYGHETLADISALCGRAAEEFGLAVEFRQTNQEGELLDWI 62

Query: 75  QECRGRADGIVINPAAYGHTSIALLDALLAVELPVIEVHISNIHRREPFRHHTYVSQAAI 134
              RGR  GIVINPAA+ HTS+A+ DAL+A E+PVIEVH+SN+H RE FRHH++VS  AI
Sbjct: 63  HGARGRCAGIVINPAAWTHTSVAIRDALVASEVPVIEVHLSNVHARETFRHHSFVSSVAI 122

Query: 135 GVICGLGVRGYAHALQAITDMIE 157
           GV+CG G  GY  AL+  +  ++
Sbjct: 123 GVMCGFGSHGYRLALEHFSQRLK 145


Lambda     K      H
   0.322    0.139    0.414 

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: 120
Number of extensions: 3
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: 160
Length of database: 147
Length adjustment: 17
Effective length of query: 143
Effective length of database: 130
Effective search space:    18590
Effective search space used:    18590
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: 43 (21.2 bits)

Align candidate Pf6N2E2_5062 (3-dehydroquinate dehydratase II (EC 4.2.1.10))
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (EC 4.2.1.10))

# 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/TIGR01088.hmm
# target sequence database:        /tmp/gapView.30550.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01088  [M=141]
Accession:   TIGR01088
Description: aroQ: 3-dehydroquinate dehydratase, type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    4.2e-63  197.3   0.0    4.7e-63  197.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062  3-dehydroquinate dehydratase II 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062  3-dehydroquinate dehydratase II (EC 4.2.1.10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2   0.0   4.7e-63   4.7e-63       2     139 ..       5     142 ..       4     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 4.7e-63
                                      TIGR01088   2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq 65 
                                                    +lvlnGPnlnlLG+rep+ yG+ tl +i++l+ +aa+e ++ ve++q+n+egel+d+ih a ++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062   5 VLVLNGPNLNLLGTREPATYGHETLADISALCGRAAEEFGLAVEFRQTNQEGELLDWIHGARGR 68 
                                                    89************************************************************** PP

                                      TIGR01088  66 vdgivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakg 129
                                                      givinpaa+thtsva+rDal+a ++Pv+evhlsnvhare fr++s+++ va Gv++G+G +g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062  69 CAGIVINPAAWTHTSVAIRDALVASEVPVIEVHLSNVHARETFRHHSFVSSVAIGVMCGFGSHG 132
                                                    **************************************************************** PP

                                      TIGR01088 130 yklalealve 139
                                                    y+lale   +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5062 133 YRLALEHFSQ 142
                                                    *****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (141 nodes)
Target sequences:                          1  (147 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: 6.22
//
[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