GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Xanthobacter autotrophicus Py2

Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_012114576.1 XAUT_RS12870 branched-chain amino acid aminotransferase

Query= CharProtDB::CH_024500
         (309 letters)



>NCBI__GCF_000017645.1:WP_012114576.1
          Length = 297

 Score =  194 bits (493), Expect = 2e-54
 Identities = 105/261 (40%), Positives = 152/261 (58%), Gaps = 6/261 (2%)

Query: 8   YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKI 67
           +IW++G  V W DAK+HV+SH LHYG++VFEG R Y    G  +F+  EH +RL  SA++
Sbjct: 14  WIWYDGVFVPWADAKLHVLSHGLHYGSTVFEGERAY----GGTIFKSAEHSERLRLSAEM 69

Query: 68  YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPW 127
             F +  +I E+  A +  + KNNL  AYIRP+ + G   MGV      +  + I  + W
Sbjct: 70  LDFTIPYTIGEIDAAKKATLEKNNLVDAYIRPVAWRGSEMMGVAAQKN-TIHLAIGVWEW 128

Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187
            +Y   E  ++G+   +S W R  P TIP  AKA G Y+   +    A R G+ + + LD
Sbjct: 129 PSYFDPEQRQKGLRLDLSEWRRPDPATIPCKAKAAGLYMICTISKHRAERRGFADALMLD 188

Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESL 247
             GY++E  G N+F VKDGV+ TP      L G+TR  +I +A+  G+EV E+ +  E L
Sbjct: 189 YRGYVAECTGANVFFVKDGVIHTPT-PDCFLDGLTRRTVIDIARRHGMEVVERHIKPEEL 247

Query: 248 YLADEVFMSGTAAEITPVRSV 268
               E F++GTAAE+TPV S+
Sbjct: 248 SSFTECFITGTAAEVTPVGSI 268


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: 237
Number of extensions: 16
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: 297
Length adjustment: 27
Effective length of query: 282
Effective length of database: 270
Effective search space:    76140
Effective search space used:    76140
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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