GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH 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)



>FitnessBrowser__Korea:Ga0059261_0067
          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.20561.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: 7.89
//
[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