GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Trichormus variabilis ATCC 29413

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_011320658.1 AVA_RS20105 3-isopropylmalate dehydratase small subunit

Query= curated2:Q8YX03
         (202 letters)



>NCBI__GCF_000204075.1:WP_011320658.1
          Length = 202

 Score =  390 bits (1002), Expect = e-114
 Identities = 194/201 (96%), Positives = 197/201 (98%)

Query: 1   MVSEVREVTGRAIPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRTALKGAHPFDQP 60
           MVSEV+EVTGR IPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRTALKG HPFDQP
Sbjct: 1   MVSEVKEVTGRGIPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRTALKGEHPFDQP 60

Query: 61  QYQDANILIVNRNFGCGSSREHAPQALSKWGIQAVIGESFAEIFFGNCVAIGVPCVTADE 120
           QYQ ANILIVNRNFGCGSSREHAPQALSKWGIQ+VIGESFAEIFFGNCVAIGVPCVTADE
Sbjct: 61  QYQGANILIVNRNFGCGSSREHAPQALSKWGIQSVIGESFAEIFFGNCVAIGVPCVTADE 120

Query: 121 AIVKQLQELVAANPQANVSINLETLQVQVGDFIAPISIGEGTRSTFITGAWDACGQLVAN 180
           AIVKQLQELVAANPQANVSINLETLQVQVGDF APISIGEGTRSTFITGAWDACGQLVAN
Sbjct: 121 AIVKQLQELVAANPQANVSINLETLQVQVGDFTAPISIGEGTRSTFITGAWDACGQLVAN 180

Query: 181 TEQVRVTAAKLPYVSWGKLAA 201
           TEQVRVT+AKLPYVSWGKLAA
Sbjct: 181 TEQVRVTSAKLPYVSWGKLAA 201


Lambda     K      H
   0.320    0.136    0.403 

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: 254
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: 202
Length of database: 202
Length adjustment: 21
Effective length of query: 181
Effective length of database: 181
Effective search space:    32761
Effective search space used:    32761
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)

Align candidate WP_011320658.1 AVA_RS20105 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

# 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/TIGR00171.hmm
# target sequence database:        /tmp/gapView.1081205.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00171  [M=188]
Accession:   TIGR00171
Description: leuD: 3-isopropylmalate dehydratase, 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.2e-40  124.5   0.0    2.7e-40  124.3   0.0    1.0  1  NCBI__GCF_000204075.1:WP_011320658.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011320658.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.3   0.0   2.7e-40   2.7e-40       3     175 ..       4     170 ..       2     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 2.7e-40
                             TIGR00171   3 efkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasilla 75 
                                           e+k+ tG  +pl   ++dtd iip ++lk+i+  G+++ +f + r    kG     e  +++pqyqga+il++
  NCBI__GCF_000204075.1:WP_011320658.1   4 EVKEVTGRGIPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRT-ALKG-----EHPFDQPQYQGANILIV 70 
                                           67899**************************************998.6677.....56679************ PP

                             TIGR00171  76 renfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdle 147
                                           + nfGcGssrehap al+ +G++++i  sfa+if++n++  g+  +  +e++v++l +lv+ n+  +++++le
  NCBI__GCF_000204075.1:WP_011320658.1  71 NRNFGCGSSREHAPQALSKWGIQSVIGESFAEIFFGNCVAIGVPCVTADEAIVKQLQELVAaNPQANVSINLE 143
                                           ***********************************************************999*********** PP

                             TIGR00171 148 aqkvkdsegkvysfeidefrkhcllnGl 175
                                           + +v++++  +    i e  +  ++ G 
  NCBI__GCF_000204075.1:WP_011320658.1 144 TLQVQVGD-FTAPISIGEGTRSTFITGA 170
                                           ********.7888888888888777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (202 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.83
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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