GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Dechlorosoma suillum PS

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate Dsui_3339 Dsui_3339 branched-chain amino acid aminotransferase, group I

Query= BRENDA::P0AB80
         (309 letters)



>FitnessBrowser__PS:Dsui_3339
          Length = 306

 Score =  291 bits (745), Expect = 1e-83
 Identities = 146/297 (49%), Positives = 199/297 (67%), Gaps = 2/297 (0%)

Query: 8   YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKI 67
           +IW +G++V W +A  H ++H+LHYG +VFEG+R Y + KG  +FR ++H QRL  SA I
Sbjct: 9   FIWQDGKLVPWREATTHALTHSLHYGMAVFEGVRAYQTDKGTAIFRLQDHTQRLARSAHI 68

Query: 68  YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPW 127
           ++  +  S +EL EA ++VIR NNL S YIRPL F G   MGV+ P G    VIIAA+PW
Sbjct: 69  FQMALPYSQEELNEAQKEVIRANNLESGYIRPLAFYGSEKMGVS-PKGAKVHVIIAAWPW 127

Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187
           GAYLG E +++GI    SS+ R   N     AKA GNY++S+L  +EA   GY E + LD
Sbjct: 128 GAYLGEEGMQRGIRIKTSSFTRHHVNITMVRAKASGNYMNSILANNEALTDGYDEAMLLD 187

Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESL 247
             GY+ EGAGEN+F VK+G L+TP  T S L GITR  +I+LA E+GIEV E+ ++R+ +
Sbjct: 188 PEGYVCEGAGENIFIVKNGKLYTPDLT-SCLEGITRATVIQLAGEMGIEVVEKRITRDEV 246

Query: 248 YLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWL 304
           Y ADE F +GTAAE+TP+R +D  Q+G G  GPVTK +Q+ +F +  G +     WL
Sbjct: 247 YCADEAFFTGTAAEVTPIRELDNRQIGVGHRGPVTKALQEKYFDVVNGRSAAHADWL 303


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: 293
Number of extensions: 12
Number of successful extensions: 3
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: 306
Length adjustment: 27
Effective length of query: 282
Effective length of database: 279
Effective search space:    78678
Effective search space used:    78678
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