GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Bacteroides thetaiotaomicron VPI-5482

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate 351604 BT2076 acetohydroxyacid synthase small subunit (NCBI ptt file)

Query= BRENDA::P9WKJ3
         (168 letters)



>FitnessBrowser__Btheta:351604
          Length = 187

 Score = 69.7 bits (169), Expect = 3e-17
 Identities = 48/161 (29%), Positives = 85/161 (52%), Gaps = 3/161 (1%)

Query: 1   MSPKT-HTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTP 59
           MS KT +T+ V  E+  G+L +V A+F+RR  NIESL V A+  K   + TI    +   
Sbjct: 1   MSDKTLYTIIVHSENIAGLLNQVTAVFTRRQINIESLNVSASSIKGVHKYTITAWTDKDT 60

Query: 60  LEQITKQLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRS-QVIEAVNLFRANVIDV 118
           +E++ KQ+ K I+VI+     ++     E+AL KV   A   + +  + +  + A +++V
Sbjct: 61  IEKVVKQIEKKIDVIQAHYFTEDEIYFHEIALYKVSTPAFQETPEASKVIRRYNARIVEV 120

Query: 119 SPESLTVEATGNRGKLEALLRVLEPFG-IREIAQSGMVSLS 158
           +P    VE  G   ++ +L   L     + +  +SG V+++
Sbjct: 121 NPVFSIVEKNGMSEEITSLYEELRALKCVLQFVRSGRVAIT 161


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: 61
Number of extensions: 4
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: 187
Length adjustment: 19
Effective length of query: 149
Effective length of database: 168
Effective search space:    25032
Effective search space used:    25032
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: 44 (21.6 bits)

Align candidate 351604 BT2076 (acetohydroxyacid synthase 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.615188.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    9.2e-30   89.8   2.1    1.2e-29   89.4   2.1    1.0  1  lcl|FitnessBrowser__Btheta:351604  BT2076 acetohydroxyacid synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351604  BT2076 acetohydroxyacid synthase small subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   2.1   1.2e-29   1.2e-29       5     155 ..       9     161 ..       4     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.2e-29
                          TIGR00119   5 lsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldltese 80 
                                        + v  en +G L++v+ +f+rr+ niesl v+ +  k++ + ti++ +d++++e++ kq+ek +dv++ + +te+e
  lcl|FitnessBrowser__Btheta:351604   9 IIVHSENIAGLLNQVTAVFTRRQINIESLNVSASSIKGVHKYTITAWTDKDTIEKVVKQIEKKIDVIQAHYFTEDE 84 
                                        445568899******************************************************************* PP

                          TIGR00119  81 ivkrelvlvkvsalge.erneikelteifrgrvvDvsedslivelsgkedkisaflkllkefg.ikevarsGlval 154
                                        i   e++l kvs+++  e  e  +++  + +r+v+v +   ive  g ++ i ++ + l+ +  ++  +rsG va+
  lcl|FitnessBrowser__Btheta:351604  85 IYFHEIALYKVSTPAFqETPEASKVIRRYNARIVEVNPVFSIVEKNGMSEEITSLYEELRALKcVLQFVRSGRVAI 160
                                        *************98615679***************************************9987**********98 PP

                          TIGR00119 155 s 155
                                        +
  lcl|FitnessBrowser__Btheta:351604 161 T 161
                                        6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (187 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: 16.14
//
[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