GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvI in Sphingomonas koreensis DSMZ 15582

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate Ga0059261_0067 Ga0059261_0067 acetolactate synthase, small subunit (EC 2.2.1.6)

Query= BRENDA::P00894
         (163 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_0067 Ga0059261_0067
           acetolactate synthase, small subunit (EC 2.2.1.6)
          Length = 171

 Score =  133 bits (334), Expect = 2e-36
 Identities = 72/159 (45%), Positives = 109/159 (68%), Gaps = 3/159 (1%)

Query: 2   RRILSVLLENESGALSRVIGLFSQRGYNIESLTVAP-TDDPTLSRMTIQTVGDEKVLEQI 60
           R  L+V+++NE G L+R+ GLF+ RGYNIESLTV+  T+D  +SR+TI T      LEQI
Sbjct: 10  RHTLAVIVDNEPGILARIAGLFTARGYNIESLTVSEITEDKAVSRITIVTSASPATLEQI 69

Query: 61  EKQLHKLVDVLRVSEL-GQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSL 119
             QL +LV V +V +L  +G HVERE+ LVK+  +G  R E  R +E++R +++D T S 
Sbjct: 70  VAQLDRLVPVHKVHDLTAEGEHVERELALVKVAGTGDHRIEALRLSEVYRARVVDATISS 129

Query: 120 YTVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRG 158
           +  ++ GT+ K+D F+  + +V  ++EVAR+G+V +SRG
Sbjct: 130 FVFEVTGTTEKIDKFIELMGEVG-LIEVARTGIVAISRG 167


Lambda     K      H
   0.318    0.136    0.360 

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: 87
Number of extensions: 4
Number of successful extensions: 4
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: 163
Length of database: 171
Length adjustment: 18
Effective length of query: 145
Effective length of database: 153
Effective search space:    22185
Effective search space used:    22185
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 (21.7 bits)
S2: 43 (21.2 bits)

Align candidate Ga0059261_0067 Ga0059261_0067 (acetolactate synthase, small subunit (EC 2.2.1.6))
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.4550.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.8e-57  178.4   3.2    5.5e-57  178.3   3.2    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0067  Ga0059261_0067 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0067  Ga0059261_0067 acetolactate synthase, small subunit (EC 2.2.1.6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3   3.2   5.5e-57   5.5e-57       2     157 ..      10     167 ..       9     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 5.5e-57
                                 TIGR00119   2 khvlsvlvenepGvLsrvsGlfarrgfniesltvge.teekdlsrmtivvegddkvveqiekqleklvd 69 
                                               +h+l+v+v+nepG+L+r++Glf++rg+niesltv+e te+k +sr+tiv+++   ++eqi  ql++lv+
  lcl|FitnessBrowser__Korea:Ga0059261_0067  10 RHTLAVIVDNEPGILARIAGLFTARGYNIESLTVSEiTEDKAVSRITIVTSASPATLEQIVAQLDRLVP 78 
                                               8*********************************9669******************************* PP

                                 TIGR00119  70 vlkvldlt.eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkl 137
                                               v kv+dlt e e+v+rel+lvkv  +g +r e  +l e++r+rvvD + +s++ e++g+ +ki+ f++l
  lcl|FitnessBrowser__Korea:Ga0059261_0067  79 VHKVHDLTaEGEHVERELALVKVAGTGDHRIEALRLSEVYRARVVDATISSFVFEVTGTTEKIDKFIEL 147
                                               *******84679********************************************************* PP

                                 TIGR00119 138 lkefgikevarsGlvalsrg 157
                                               + e+g+ evar+G+va+srg
  lcl|FitnessBrowser__Korea:Ga0059261_0067 148 MGEVGLIEVARTGIVAISRG 167
                                               *******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (171 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: 4.38
//
[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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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