GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpA in Thioalkalivibrio paradoxus ARh 1

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_006748160.1 THITH_RS10410 tryptophan synthase subunit alpha

Query= uniprot:H0BV16
         (269 letters)



>NCBI__GCF_000227685.2:WP_006748160.1
          Length = 277

 Score =  269 bits (688), Expect = 4e-77
 Identities = 140/245 (57%), Positives = 180/245 (73%), Gaps = 4/245 (1%)

Query: 1   MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60
           MSRIA  F+ ++A GR AL+PY+TAG P   +T  LMH +V AGA+++ELGVPFSDPMAD
Sbjct: 1   MSRIAERFAEIRAAGRAALVPYITAGDPAPGVTVPLMHDLVAAGAEMLELGVPFSDPMAD 60

Query: 61  GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120
           GPVIQ+A E+AL+ G  +  VL+ VREFR++++ TPV+LMGY NPVER     G  AF  
Sbjct: 61  GPVIQQACERALAHGTSLRDVLEMVREFRQQDSRTPVILMGYLNPVERM----GAEAFAA 116

Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180
           ++AAAGVDGVL+VD PPEE     A L   G+D IFLLAPT++ ER+  VA  A G++YY
Sbjct: 117 EAAAAGVDGVLVVDLPPEESGDLTAVLEPAGIDPIFLLAPTTSGERVQHVAAAARGFIYY 176

Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240
           VSLKGVTGS ALD  A+   L  IR    +P+GVGFGIRDA TA  + +VADAVV+GS +
Sbjct: 177 VSLKGVTGSQALDADALGARLDSIRGLTALPLGVGFGIRDADTAAKVARVADAVVVGSAL 236

Query: 241 IQLIE 245
           ++L++
Sbjct: 237 VRLVD 241


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: 281
Number of extensions: 13
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: 277
Length adjustment: 25
Effective length of query: 244
Effective length of database: 252
Effective search space:    61488
Effective search space used:    61488
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_006748160.1 THITH_RS10410 (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.2581524.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.9e-78  248.9   0.0    2.2e-78  248.7   0.0    1.0  1  NCBI__GCF_000227685.2:WP_006748160.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000227685.2:WP_006748160.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.7   0.0   2.2e-78   2.2e-78       1     255 [.       8     261 ..       8     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 248.7 bits;  conditional E-value: 2.2e-78
                             TIGR00262   1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvek 73 
                                           f+++++++  a+vp++tagdP   +++ +++ lv aGa++lElGvpfsDP+aDGp+iq+a  RAl++g+++++
  NCBI__GCF_000227685.2:WP_006748160.1   8 FAEIRAAGRAALVPYITAGDPAPGVTVPLMHDLVAAGAEMLELGVPFSDPMADGPVIQQACERALAHGTSLRD 80 
                                           678899999**************************************************************** PP

                             TIGR00262  74 alellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqifl 146
                                           +le+++++r++ s  P++l+ y n++ ++g e+F a+a++agvdgvlv+DlP ee++dl+ + +  g+++ifl
  NCBI__GCF_000227685.2:WP_006748160.1  81 VLEMVREFRQQDSRTPVILMGYLNPVERMGAEAFAAEAAAAGVDGVLVVDLPPEESGDLTAVLEPAGIDPIFL 153
                                           ************************************************************************* PP

                             TIGR00262 147 vaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkel 219
                                            aPt++ er++++a  ++Gf+Y vs  Gvtg +   ++++ + +  ++ l++ P  vGFGi  ++ + ++  +
  NCBI__GCF_000227685.2:WP_006748160.1 154 LAPTTSGERVQHVAAAARGFIYYVSLKGVTGSQALDADALGARLDSIRGLTALPLGVGFGIRDADTAAKVARV 226
                                           ************************************************************************9 PP

                             TIGR00262 220 gadgvivGsAlvkiieeklddeekaleeleefvkel 255
                                            ad+v+vGsAlv+++++  +d++ +  + ++ v+e+
  NCBI__GCF_000227685.2:WP_006748160.1 227 -ADAVVVGSALVRLVDQYPGDPDGFRSAAAATVREM 261
                                           .899************99988887777777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (277 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: 13.71
//
[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