GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Sphingomonas koreensis DSMZ 15582

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Ga0059261_3754 Ga0059261_3754 Threonine dehydratase

Query= BRENDA::Q74FW6
         (402 letters)



>FitnessBrowser__Korea:Ga0059261_3754
          Length = 322

 Score =  168 bits (426), Expect = 2e-46
 Identities = 112/285 (39%), Positives = 152/285 (53%), Gaps = 12/285 (4%)

Query: 30  SEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAKGVITASAGNHAQGVAFSADL 89
           +E  GIP+ FK E LQ  GAFKIRGA + +T+   E   KGV+  S+GNHAQGVA++A  
Sbjct: 31  AEIRGIPVMFKAECLQPIGAFKIRGAWHRLTAIDPEQREKGVVAFSSGNHAQGVAWAAKR 90

Query: 90  LGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYAAAVQAQEERGALFVHPFDDP 149
           LG+P+ + MP   P  K  +T   GAEVV   R  ++    A      RGA  V PFDDP
Sbjct: 91  LGIPAVIVMPADAPAAKRDSTLALGAEVVAYDRMKEDRVKIAAHLAHARGATLVPPFDDP 150

Query: 150 LVMAGQGTIGLEVLQE-----LPDVANILVPIGGGGLIAGIATAIRETHPHVRIIGVETA 204
            ++ GQG++ +EVL +     LPD   I+VP GGGGL +G+  A+ E    +    VE  
Sbjct: 151 WIIEGQGSMAIEVLTQAAEMRLPDPGRIVVPCGGGGLASGVTLALPEAQTTI----VEPE 206

Query: 205 AAPSAHYSLQKGKIVQVPVT--VTLADGIAVKKPGVNTFPIIRDLVDEVVLVEEEEIALA 262
                  SL  G I  +  +   T  D +   +P   TF ++       V V E E+  A
Sbjct: 207 GWDDMCRSLANGWIESIGESPPPTACDALQTFQPAQLTFDVLSRRGATGVAVSEAEVRAA 266

Query: 263 IVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGNID 307
                 + +L+VE  GAV LAALL  +V D +  T+ +LSGGN D
Sbjct: 267 QRWAARKLRLVVEPGGAVALAALLAGKV-DPTPDTLVILSGGNAD 310


Lambda     K      H
   0.319    0.137    0.383 

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: 264
Number of extensions: 12
Number of successful extensions: 4
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: 402
Length of database: 322
Length adjustment: 29
Effective length of query: 373
Effective length of database: 293
Effective search space:   109289
Effective search space used:   109289
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: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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