GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Shewanella oneidensis MR-1

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate 201428 SO2278 acetolactate synthase III, small subunit (NCBI ptt file)

Query= BRENDA::P00894
         (163 letters)



>FitnessBrowser__MR1:201428
          Length = 164

 Score =  231 bits (588), Expect = 6e-66
 Identities = 115/163 (70%), Positives = 142/163 (87%)

Query: 1   MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQI 60
           MRRI+SVLLEN+SGALSRV+GLFSQRGYNIESLTVAPTDD TLSR+ I  V DEKVLEQI
Sbjct: 1   MRRIISVLLENQSGALSRVVGLFSQRGYNIESLTVAPTDDNTLSRLNISLVADEKVLEQI 60

Query: 61  EKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLY 120
           EKQLHKLVDVL+VS + + A++ERE+ LVK++A G  R+E+KR  +IFRGQI+DVT +LY
Sbjct: 61  EKQLHKLVDVLKVSNVTESAYIERELALVKVRAQGELREEIKRTADIFRGQIVDVTANLY 120

Query: 121 TVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGDKIMR 163
           T+QL GT+ KLDAF+ S+ +V K+VEV+RSGVVGL+RG+K M+
Sbjct: 121 TIQLVGTTEKLDAFIHSMGEVTKVVEVSRSGVVGLARGEKAMK 163


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: 130
Number of extensions: 1
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: 163
Length of database: 164
Length adjustment: 18
Effective length of query: 145
Effective length of database: 146
Effective search space:    21170
Effective search space used:    21170
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 201428 SO2278 (acetolactate synthase III, small subunit (NCBI ptt file))
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.473962.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    4.5e-66  207.8   5.8    5.1e-66  207.6   5.8    1.0  1  lcl|FitnessBrowser__MR1:201428  SO2278 acetolactate synthase III


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201428  SO2278 acetolactate synthase III, small subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.6   5.8   5.1e-66   5.1e-66       1     158 []       1     159 [.       1     159 [. 0.99

  Alignments for each domain:
  == domain 1  score: 207.6 bits;  conditional E-value: 5.1e-66
                       TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldltes 79 
                                     +++++svl+en++G+Lsrv+Glf++rg+niesltv+ t++++lsr+ i + +d+kv+eqiekql+klvdvlkv+++tes
  lcl|FitnessBrowser__MR1:201428   1 MRRIISVLLENQSGALSRVVGLFSQRGYNIESLTVAPTDDNTLSRLNISLVADEKVLEQIEKQLHKLVDVLKVSNVTES 79 
                                     69***************************************************************************** PP

                       TIGR00119  80 eivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefg.ikevarsGlvalsrg 157
                                     + ++rel+lvkv+a+ge r+eik++++ifrg++vDv+ + ++++l+g+ +k++af++++ e++ ++ev+rsG+v+l+rg
  lcl|FitnessBrowser__MR1:201428  80 AYIERELALVKVRAQGELREEIKRTADIFRGQIVDVTANLYTIQLVGTTEKLDAFIHSMGEVTkVVEVSRSGVVGLARG 158
                                     *************************************************************999**************8 PP

                       TIGR00119 158 e 158
                                     e
  lcl|FitnessBrowser__MR1:201428 159 E 159
                                     5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (164 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: 12.13
//
[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