GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Acidovorax sp. GW101-3H11

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate Ac3H11_526 Acetolactate synthase small subunit (EC 2.2.1.6)

Query= BRENDA::P00894
         (163 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_526
          Length = 163

 Score =  188 bits (477), Expect = 4e-53
 Identities = 94/163 (57%), Positives = 128/163 (78%), Gaps = 1/163 (0%)

Query: 1   MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQI 60
           M+ I++VLLENE GALSRV+GLFS RGYNIESLTVAPT+D +LSRMTIQT G + V+EQI
Sbjct: 1   MKHIIAVLLENEPGALSRVVGLFSARGYNIESLTVAPTEDASLSRMTIQTTGSDDVIEQI 60

Query: 61  EKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLY 120
            K L++L++V++V +L +GA+ ERE+M+VK++A G  R+E+KR  +IFRG+IIDVT   Y
Sbjct: 61  TKHLNRLIEVVKVVDLTEGAYTERELMMVKVRAVGKEREEMKRMADIFRGRIIDVTEKSY 120

Query: 121 TVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGDKIMR 163
           T++L G   K DAFL +I D   I+E  R+G  G+ RG++I+R
Sbjct: 121 TIELTGDQSKNDAFLQAI-DRTAILETVRTGASGIGRGERILR 162


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: 115
Number of extensions: 5
Number of successful extensions: 2
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: 163
Length adjustment: 18
Effective length of query: 145
Effective length of database: 145
Effective search space:    21025
Effective search space used:    21025
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 Ac3H11_526 (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.12952.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
    8.5e-67  210.1   2.4    9.5e-67  210.0   2.4    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_526  Acetolactate synthase small subu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_526  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 !  210.0   2.4   9.5e-67   9.5e-67       1     157 [.       1     157 [.       1     158 [. 0.99

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 9.5e-67
                                       TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekq 63 
                                                     +kh+++vl+enepG+Lsrv+Glf++rg+niesltv+ te++ lsrmti+++g d+v+eqi+k 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_526   1 MKHIIAVLLENEPGALSRVVGLFSARGYNIESLTVAPTEDASLSRMTIQTTGSDDVIEQITKH 63 
                                                     79************************************************************* PP

                                       TIGR00119  64 leklvdvlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsg 126
                                                     l++l++v+kv+dlte +  +rel++vkv+a+g+er+e+k++++ifrgr++Dv+e+s+++el+g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_526  64 LNRLIEVVKVVDLTEGAYTERELMMVKVRAVGKEREEMKRMADIFRGRIIDVTEKSYTIELTG 126
                                                     *************************************************************** PP

                                       TIGR00119 127 kedkisaflkllkefgikevarsGlvalsrg 157
                                                     ++ k +afl+++   +i+e +r+G  ++ rg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_526 127 DQSKNDAFLQAIDRTAILETVRTGASGIGRG 157
                                                     **************************99998 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: 6.65
//
[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