GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate Echvi_2511 Echvi_2511 tryptophan synthase, alpha subunit

Query= uniprot:A0A3N7DTH5
         (255 letters)



>FitnessBrowser__Cola:Echvi_2511
          Length = 258

 Score =  302 bits (774), Expect = 4e-87
 Identities = 145/242 (59%), Positives = 189/242 (78%), Gaps = 1/242 (0%)

Query: 1   MNRINKLFQEKK-NILSIYYTAGYPNLGDTVAIAEELERSGADLLEIGFPYSDPVADGPV 59
           MNRI++LFQEKK NILSIY+TAG+P L DT+AI E +E +GAD++E+G PYSDPVADGP 
Sbjct: 1   MNRIDQLFQEKKGNILSIYFTAGFPKLDDTLAIMEAIEGAGADIIEVGMPYSDPVADGPT 60

Query: 60  IQASSKTALDGGMTLKLLFEQLKDLRKTVNIPVLLMGYVNPMLQYGVENFCKSCAEVGVD 119
           IQ S+K AL+ GM +K +F+QL+ +R+TV IPV+LMGY+NP+LQYG+E FCK C EVGVD
Sbjct: 61  IQESNKAALENGMNMKKMFQQLEKMRETVTIPVVLMGYLNPILQYGIEAFCKKCNEVGVD 120

Query: 120 GCIVPDLPMVEYEELYSGVFEANGLTNIFLVTPQTSTERIRKIDGLSNGFIYLLSSSATT 179
           G IVPDLP+ +Y++ Y  +F+   L N FL++PQTS ERIR+ID  S+GFIY++SS + T
Sbjct: 121 GLIVPDLPIQQYQDDYKALFDEYDLRNTFLISPQTSEERIREIDQQSDGFIYMVSSHSIT 180

Query: 180 GQNLQVSENTEAYFSRIAEMKLNNPTMIGFGISSKETFDKACQYANGAIIGSAFVKSLKS 239
           G    +S+  EAYF R+  M+L NP +IGFGIS   TF KA  Y++GAIIGSAF+K L +
Sbjct: 181 GAKSGISDEQEAYFERVKSMELENPRLIGFGISDHATFSKASSYSHGAIIGSAFIKVLSN 240

Query: 240 GK 241
            K
Sbjct: 241 AK 242


Lambda     K      H
   0.317    0.135    0.382 

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: 230
Number of extensions: 6
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: 255
Length of database: 258
Length adjustment: 24
Effective length of query: 231
Effective length of database: 234
Effective search space:    54054
Effective search space used:    54054
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: 47 (22.7 bits)

Align candidate Echvi_2511 Echvi_2511 (tryptophan synthase, alpha subunit)
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.17632.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    2.9e-76  241.7   0.1    3.4e-76  241.5   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2511  Echvi_2511 tryptophan synthase, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2511  Echvi_2511 tryptophan synthase, alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.5   0.1   3.4e-76   3.4e-76       4     242 ..       8     246 ..       5     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 241.5 bits;  conditional E-value: 3.4e-76
                            TIGR00262   4 lkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalel 77 
                                          +++k+ + +  ++tag P+l+ +l i++ +  aGad++E+G+p+sDP+aDGptiq++++ Al++g++++k+++ 
  lcl|FitnessBrowser__Cola:Echvi_2511   8 FQEKKGNILSIYFTAGFPKLDDTLAIMEAIEGAGADIIEVGMPYSDPVADGPTIQESNKAALENGMNMKKMFQQ 81 
                                          567788888899************************************************************** PP

                            TIGR00262  78 lkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPlee.addlleaakkhgvkqiflvaPt 150
                                          l+k+re+ ++iP+vl+ y n+i+++g+e+F +k++e+gvdg++v+DlP+++ +dd+     ++++++ fl++P+
  lcl|FitnessBrowser__Cola:Echvi_2511  82 LEKMRET-VTIPVVLMGYLNPILQYGIEAFCKKCNEVGVDGLIVPDLPIQQyQDDYKALFDEYDLRNTFLISPQ 154
                                          ******9.*****************************************982456677789************* PP

                            TIGR00262 151 aeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkals.kkPvlvGFGiskkeqvkelkelgadg 223
                                          ++eer+++i+++s+Gf+Y+vs+  +tga++ +++e ++  ++vk++  + P l+GFGis +    ++ +  + g
  lcl|FitnessBrowser__Cola:Echvi_2511 155 TSEERIREIDQQSDGFIYMVSSHSITGAKSGISDEQEAYFERVKSMElENPRLIGFGISDHATFSKASSY-SHG 227
                                          ********************************************986489******************99.889 PP

                            TIGR00262 224 vivGsAlvkiieeklddee 242
                                          +i+GsA++k++++ +d + 
  lcl|FitnessBrowser__Cola:Echvi_2511 228 AIIGSAFIKVLSNAKDLKA 246
                                          ***********99987433 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (258 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.28
//
[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