GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Marinobacter adhaerens HP15

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate GFF448 HP15_436 branched-chain-amino-acid aminotransferase

Query= BRENDA::P0AB80
         (309 letters)



>FitnessBrowser__Marino:GFF448
          Length = 308

 Score =  273 bits (697), Expect = 5e-78
 Identities = 135/299 (45%), Positives = 191/299 (63%), Gaps = 2/299 (0%)

Query: 9   IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68
           IW +GEMV W DAK HV++H LHYG   FEG+R Y++  GP +FR +EH  RL  SA I 
Sbjct: 10  IWMDGEMVPWRDAKTHVLTHTLHYGLGCFEGVRAYNTANGPAIFRLKEHTDRLFRSAHIL 69

Query: 69  RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128
              +  S DE+ EA R  +R+NNL  AY+RP+ F+G  GMG+         V++AA+ W 
Sbjct: 70  NMKMPFSKDEINEAQRAAVRENNLDEAYLRPMAFLGSEGMGLRAD-NLKVHVMVAAWSWP 128

Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188
           +Y+  EA E GI    SS+ R   N     AKA GNY++S+L  +EA   G +E + LD 
Sbjct: 129 SYMSPEAKEMGIKVRTSSYTRHHVNITMCKAKANGNYINSMLALNEAISGGAEEALLLDN 188

Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248
            GY++EG+GEN+F ++DGVL TP  T S L GITR  I+  A+EL I ++E+ ++R+ +Y
Sbjct: 189 EGYVAEGSGENIFIMRDGVLHTPELT-SCLEGITRATIMDFARELNIPIKERRITRDEVY 247

Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307
           +ADE F +GTAAE+ P+R +DG  +G G+ GPVT+++Q  +F    G+  +  GWL  V
Sbjct: 248 IADEAFFTGTAAEVLPIRELDGRVIGAGKRGPVTEKLQAMYFDAVKGKLAEHSGWLTHV 306


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: 292
Number of extensions: 14
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: 308
Length adjustment: 27
Effective length of query: 282
Effective length of database: 281
Effective search space:    79242
Effective search space used:    79242
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