GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Dehalococcoides mccartyi 195

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_010936560.1 DET_RS04340 acetolactate synthase small subunit

Query= BRENDA::P9WKJ3
         (168 letters)



>NCBI__GCF_000011905.1:WP_010936560.1
          Length = 178

 Score =  165 bits (417), Expect = 4e-46
 Identities = 81/167 (48%), Positives = 125/167 (74%), Gaps = 2/167 (1%)

Query: 1   MSPKTHTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPL 60
           MSP  HT+  LVED+PGVL R+A+LF RRGFNI+S+AVG +E    SRMTIVV   +T +
Sbjct: 1   MSPTKHTIVALVEDRPGVLNRMASLFRRRGFNIDSIAVGRSETPGFSRMTIVVDGANTMV 60

Query: 61  EQITKQLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSP 120
           EQ+ KQL+K+++V+K+ +   +  + RELALIKV++   +RS++++ V++FRA ++DV+ 
Sbjct: 61  EQVRKQLDKVVDVVKVSDITGQDIICRELALIKVKSTPANRSEIMQIVDIFRAKIVDVAS 120

Query: 121 ESLTVEATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGIGTA 167
           +SLTVE TG+  K+ +L  +L  FGI+EI ++G ++++RG  G+ TA
Sbjct: 121 DSLTVEVTGDEEKVNSLYNLLRAFGIKEITRTGRIAMTRG--GLATA 165


Lambda     K      H
   0.315    0.131    0.347 

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: 103
Number of extensions: 4
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: 168
Length of database: 178
Length adjustment: 18
Effective length of query: 150
Effective length of database: 160
Effective search space:    24000
Effective search space used:    24000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 44 (21.6 bits)

Align candidate WP_010936560.1 DET_RS04340 (acetolactate synthase small subunit)
to HMM TIGR00119 (ilvN: acetolactate synthase, small subunit (EC 2.2.1.6))

# 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/TIGR00119.hmm
# target sequence database:        /tmp/gapView.2134753.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00119  [M=158]
Accession:   TIGR00119
Description: acolac_sm: acetolactate synthase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.1e-65  204.1   4.6    6.9e-65  203.9   4.6    1.0  1  NCBI__GCF_000011905.1:WP_010936560.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000011905.1:WP_010936560.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.9   4.6   6.9e-65   6.9e-65       2     157 ..       5     160 ..       4     161 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.9 bits;  conditional E-value: 6.9e-65
                             TIGR00119   2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvl 74 
                                           kh++ +lve++pGvL+r++ lf+rrgfni+s++vg++e+++ srmtivv+g + +veq++kql+k+vdv+kv+
  NCBI__GCF_000011905.1:WP_010936560.1   5 KHTIVALVEDRPGVLNRMASLFRRRGFNIDSIAVGRSETPGFSRMTIVVDGANTMVEQVRKQLDKVVDVVKVS 77 
                                           8************************************************************************ PP

                             TIGR00119  75 dlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikeva 147
                                           d+t ++i+ rel+l+kv++++ +r+ei+++++ifr+++vDv+ dsl+ve++g+e+k++++ +ll+ fgike++
  NCBI__GCF_000011905.1:WP_010936560.1  78 DITGQDIICRELALIKVKSTPANRSEIMQIVDIFRAKIVDVASDSLTVEVTGDEEKVNSLYNLLRAFGIKEIT 150
                                           ************************************************************************* PP

                             TIGR00119 148 rsGlvalsrg 157
                                           r+G +a++rg
  NCBI__GCF_000011905.1:WP_010936560.1 151 RTGRIAMTRG 160
                                           ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (178 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: 9.32
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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