GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Magnetospirillum magneticum AMB-1

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_043743277.1 AMB_RS02850 branched-chain amino acid aminotransferase

Query= BRENDA::P0AB80
         (309 letters)



>NCBI__GCF_000009985.1:WP_043743277.1
          Length = 290

 Score =  200 bits (508), Expect = 4e-56
 Identities = 108/263 (41%), Positives = 156/263 (59%), Gaps = 10/263 (3%)

Query: 8   YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKI 67
           ++WF+G++V W DAK+HV++H LHYG+ VFEG R Y    G  VF+ REH QRL DS +I
Sbjct: 12  FLWFDGKLVPWRDAKIHVLTHGLHYGSCVFEGERVY----GGKVFKLREHSQRLIDSGRI 67

Query: 68  YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV--IIAAF 125
             F V  +++E+ EA    ++ NN+   Y+RP+ + G   MGV   A  +T +   +A +
Sbjct: 68  LGFEVPWTVEEIDEATMATVKANNIVDGYVRPVAWRGSEMMGV---AAQTTKIRFAVATW 124

Query: 126 PWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIA 185
            W +Y   EA  +GI   +S+W R  P T PTA+KA G Y+   +   +A   GY++ + 
Sbjct: 125 SWPSYWSPEARMKGIRLNISTWKRPHPETAPTASKAAGLYMICTMSKHKAEGDGYEDSLM 184

Query: 186 LDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRE 245
           LD  G ++E  G N+F V    L TP      L GITR  +I LAK+ GI V E+ +  E
Sbjct: 185 LDWRGQVAEATGANIFFVFGNELHTPT-PDCFLNGITRQTVIALAKKRGITVVERAIFPE 243

Query: 246 SLYLADEVFMSGTAAEITPVRSV 268
            +  A E F++GTAAE+TPVR +
Sbjct: 244 EMTKASECFLTGTAAEVTPVREI 266


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: 233
Number of extensions: 11
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: 290
Length adjustment: 27
Effective length of query: 282
Effective length of database: 263
Effective search space:    74166
Effective search space used:    74166
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