GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpA in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_018231055.1 THITHI_RS0100240 tryptophan synthase subunit alpha

Query= uniprot:H0BV16
         (269 letters)



>NCBI__GCF_000378965.1:WP_018231055.1
          Length = 267

 Score =  277 bits (709), Expect = 1e-79
 Identities = 147/249 (59%), Positives = 180/249 (72%), Gaps = 4/249 (1%)

Query: 1   MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60
           MSRIA  F +L+A GRKALIPYVTAG P  + T  LMH MVEAGAD+IELGVPFSDPMAD
Sbjct: 1   MSRIAGRFESLRAAGRKALIPYVTAGDPNPENTVPLMHAMVEAGADIIELGVPFSDPMAD 60

Query: 61  GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120
           GPVIQ+A E+AL   + +  VLD VR FR+R++ TPVV MGY NPVE    ++    F R
Sbjct: 61  GPVIQQACERALRHHVSLRGVLDMVRRFRERDDETPVVFMGYLNPVEIMGYEN----FAR 116

Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180
            +A AGVDG+L VD PPEE +   A+L AHG+D IFLLAPTS + R++ +   ASG+VYY
Sbjct: 117 AAAEAGVDGLLTVDLPPEEGDELVAALHAHGIDPIFLLAPTSHEARISRICAAASGFVYY 176

Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240
           VSLKGVTG+  LD  AV + L  IR H  +PVGVGFGIRDA +A  +  VADAVV+GS +
Sbjct: 177 VSLKGVTGAATLDVDAVAEKLAAIRAHTDLPVGVGFGIRDADSAARVAAVADAVVVGSAL 236

Query: 241 IQLIEDQEH 249
           +  I + E+
Sbjct: 237 VNRIAEHEN 245


Lambda     K      H
   0.321    0.137    0.389 

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: 277
Number of extensions: 14
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: 269
Length of database: 267
Length adjustment: 25
Effective length of query: 244
Effective length of database: 242
Effective search space:    59048
Effective search space used:    59048
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: 47 (22.7 bits)

Align candidate WP_018231055.1 THITHI_RS0100240 (tryptophan synthase subunit alpha)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))

# 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/TIGR00262.hmm
# target sequence database:        /tmp/gapView.675886.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00262  [M=256]
Accession:   TIGR00262
Description: trpA: tryptophan synthase, alpha 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.8e-82  261.4   0.0    3.2e-82  261.3   0.0    1.0  1  NCBI__GCF_000378965.1:WP_018231055.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_018231055.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.3   0.0   3.2e-82   3.2e-82       1     255 [.       8     261 ..       8     262 .. 0.98

  Alignments for each domain:
  == domain 1  score: 261.3 bits;  conditional E-value: 3.2e-82
                             TIGR00262   1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvek 73 
                                           fe l++++ ka++p+vtagdP+ e+++ +++ +v+aGad++ElGvpfsDP+aDGp+iq+a  RAl++ v+++ 
  NCBI__GCF_000378965.1:WP_018231055.1   8 FESLRAAGRKALIPYVTAGDPNPENTVPLMHAMVEAGADIIELGVPFSDPMADGPVIQQACERALRHHVSLRG 80 
                                           7899********************************************************************* PP

                             TIGR00262  74 alellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqifl 146
                                           +l++++++re+  + P+v++ y n++  +g e+F + a+eagvdg+l +DlP ee d+l+ a + hg+++ifl
  NCBI__GCF_000378965.1:WP_018231055.1  81 VLDMVRRFRERDDETPVVFMGYLNPVEIMGYENFARAAAEAGVDGLLTVDLPPEEGDELVAALHAHGIDPIFL 153
                                           ************************************************************************* PP

                             TIGR00262 147 vaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkel 219
                                            aPt++e r+ +i   ++GfvY vs  Gvtga +   ++v e ++ ++a+++ Pv vGFGi  ++ + ++ ++
  NCBI__GCF_000378965.1:WP_018231055.1 154 LAPTSHEARISRICAAASGFVYYVSLKGVTGAATLDVDAVAEKLAAIRAHTDLPVGVGFGIRDADSAARVAAV 226
                                           **********************************9999********************************999 PP

                             TIGR00262 220 gadgvivGsAlvkiieeklddeekaleeleefvkel 255
                                            ad+v+vGsAlv++i+e+ +d+e+  +++ e+  e+
  NCBI__GCF_000378965.1:WP_018231055.1 227 -ADAVVVGSALVNRIAEHENDPEAGRRAVSELLAEM 261
                                           .899********************999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (267 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: 14.67
//
[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