GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvI in Desulfovibrio vulgaris Miyazaki F

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate 8499377 DvMF_0154 acetolactate synthase 3 regulatory subunit (RefSeq)

Query= BRENDA::P9WKJ3
         (168 letters)



>lcl|FitnessBrowser__Miya:8499377 DvMF_0154 acetolactate synthase 3
           regulatory subunit (RefSeq)
          Length = 163

 Score =  157 bits (396), Expect = 1e-43
 Identities = 82/154 (53%), Positives = 112/154 (72%)

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

Query: 66  QLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTV 125
           QL KL+ VIK+V+  D  +V RE+ ++KVQAD   R++V+   ++FR  V+DVS   LT+
Sbjct: 63  QLRKLVTVIKVVDFIDVSAVEREMVMVKVQADDARRAEVLRIADIFRCKVVDVSLNDLTL 122

Query: 126 EATGNRGKLEALLRVLEPFGIREIAQSGMVSLSR 159
           EATG+ GK++A+L +L  FGI+EIA++G V++ R
Sbjct: 123 EATGDHGKIQAILSLLARFGIKEIARTGTVAMRR 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: 95
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: 163
Length adjustment: 18
Effective length of query: 150
Effective length of database: 145
Effective search space:    21750
Effective search space used:    21750
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 8499377 DvMF_0154 (acetolactate synthase 3 regulatory subunit (RefSeq))
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.23328.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    7.9e-63  197.2   6.6    8.9e-63  197.1   6.6    1.0  1  lcl|FitnessBrowser__Miya:8499377  DvMF_0154 acetolactate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499377  DvMF_0154 acetolactate synthase 3 regulatory subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.1   6.6   8.9e-63   8.9e-63       1     157 [.       1     157 [.       1     158 [. 0.99

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 8.9e-63
                         TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldlt 77 
                                       ++hvlsvlvenepGvLsrv+Glf+ rgfniesl v+ t e+++s mti+++g+++++eqi kql+klv v+kv+d+ 
  lcl|FitnessBrowser__Miya:8499377   1 MRHVLSVLVENEPGVLSRVAGLFSGRGFNIESLNVAPTLEEGVSLMTITTSGEEQIIEQIVKQLRKLVTVIKVVDFI 77 
                                       69*************************************************************************** PP

                         TIGR00119  78 eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlval 154
                                       + + v+re+v+vkv+a   +r+e+ ++++ifr +vvDvs + l++e +g+++ki+a+l+ll+ fgike+ar+G+va+
  lcl|FitnessBrowser__Miya:8499377  78 DVSAVEREMVMVKVQADDARRAEVLRIADIFRCKVVDVSLNDLTLEATGDHGKIQAILSLLARFGIKEIARTGTVAM 154
                                       ***************************************************************************** PP

                         TIGR00119 155 srg 157
                                        r+
  lcl|FitnessBrowser__Miya:8499377 155 RRS 157
                                       995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (163 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: 7.02
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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