GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Desulfovibrio vulgaris Hildenborough

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate 206819 DVU1377 acetolactate synthase, small subunit

Query= BRENDA::P9WKJ3
         (168 letters)



>MicrobesOnline__882:206819
          Length = 162

 Score =  151 bits (381), Expect = 6e-42
 Identities = 78/154 (50%), Positives = 111/154 (72%)

Query: 6   HTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQITK 65
           H LSVLVE++PGVL+RVA LFS RGFNIESL V  T  +  S MTI    ++   EQI K
Sbjct: 3   HVLSVLVENEPGVLSRVAGLFSGRGFNIESLNVAPTLDRGVSLMTISTRGDEQVKEQIVK 62

Query: 66  QLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTV 125
           QL KL+ VIK+V+ +   +V RE+ ++KVQA+   R++V+   ++FR  V+DVS   LT+
Sbjct: 63  QLRKLVTVIKVVDFEGLATVEREMVIVKVQAEDTRRAEVLRIADIFRCKVVDVSLNDLTL 122

Query: 126 EATGNRGKLEALLRVLEPFGIREIAQSGMVSLSR 159
           EATG+ GK+EA++ +L+ FGI+E+A++G V+L R
Sbjct: 123 EATGDHGKIEAIISLLQKFGIKEVARTGTVALRR 156


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: 97
Number of extensions: 3
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: 162
Length adjustment: 18
Effective length of query: 150
Effective length of database: 144
Effective search space:    21600
Effective search space used:    21600
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: 43 (21.2 bits)

Align candidate 206819 DVU1377 (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.16147.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    7.6e-63  197.3   6.2    8.6e-63  197.1   6.2    1.0  1  lcl|MicrobesOnline__882:206819  DVU1377 acetolactate synthase, s


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206819  DVU1377 acetolactate synthase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.1   6.2   8.6e-63   8.6e-63       1     157 [.       1     157 [.       1     158 [. 0.99

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 8.6e-63
                       TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldltes 79 
                                     ++hvlsvlvenepGvLsrv+Glf+ rgfniesl v+ t ++++s mti ++gd++v eqi kql+klv v+kv+d++  
  lcl|MicrobesOnline__882:206819   1 MRHVLSVLVENEPGVLSRVAGLFSGRGFNIESLNVAPTLDRGVSLMTISTRGDEQVKEQIVKQLRKLVTVIKVVDFEGL 79 
                                     69***************************************************************************** PP

                       TIGR00119  80 eivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlvalsrg 157
                                     ++v+re+v+vkv+a  ++r+e+ ++++ifr +vvDvs + l++e +g+++ki+a+++ll++fgikevar+G+val r+
  lcl|MicrobesOnline__882:206819  80 ATVEREMVIVKVQAEDTRRAEVLRIADIFRCKVVDVSLNDLTLEATGDHGKIEAIISLLQKFGIKEVARTGTVALRRS 157
                                     ***************************************************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (162 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.49
//
[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