GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Desulfovibrio vulgaris Hildenborough

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 208718 DVU3197 branched-chain amino acid aminotransferase

Query= BRENDA::P0AB80
         (309 letters)



>MicrobesOnline__882:208718
          Length = 309

 Score =  289 bits (740), Expect = 5e-83
 Identities = 150/302 (49%), Positives = 200/302 (66%), Gaps = 3/302 (0%)

Query: 4   KKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGP-VVFRHREHMQRLH 62
           +K++ IWF+G+ V W++A VHV++HALHYG  VFEGIR Y    G   VFR REH+QRL 
Sbjct: 5   QKSETIWFDGKQVPWDEANVHVLTHALHYGVGVFEGIRAYRCADGSSAVFRLREHVQRLF 64

Query: 63  DSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVII 122
            SAKI R  +  + D + +A  + +++N L   YIRPL FVG   MGV P        II
Sbjct: 65  SSAKILRMEIPFTEDAIFDAIVETLQRNRLAEGYIRPLSFVGAGAMGVYP-GDNPVQTII 123

Query: 123 AAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQE 182
           A +PWGAYLGAEALE+GI    SS+ R   N + T AKA GNY++S+L   EA+  GY E
Sbjct: 124 AVWPWGAYLGAEALEKGIRVKTSSFARHHVNAMMTKAKASGNYVNSVLAKMEAKADGYDE 183

Query: 183 GIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVL 242
            + LDV+G++SE  GEN+F V++GV+ T P T S L GITR++++ LA++LG EV EQ  
Sbjct: 184 ALMLDVSGFVSEATGENIFMVRNGVIKTTPLT-SILDGITRNSLMTLARDLGYEVVEQQF 242

Query: 243 SRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWG 302
           +R+ LY+ADE F  GTAAE+TP+R VD   +G+G  GPVTK +QQ +F    G+      
Sbjct: 243 TRDELYVADEAFFCGTAAEVTPIREVDRRVIGKGSAGPVTKHLQQEYFKAVKGDNPSYDH 302

Query: 303 WL 304
           WL
Sbjct: 303 WL 304


Lambda     K      H
   0.319    0.136    0.413 

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: 304
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: 309
Length of database: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
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: 48 (23.1 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