GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Streptacidiphilus oryzae TH49

Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_037572571.1 BS73_RS14690 branched-chain amino acid aminotransferase

Query= CharProtDB::CH_024500
         (309 letters)



>NCBI__GCF_000744815.1:WP_037572571.1
          Length = 359

 Score =  134 bits (338), Expect = 2e-36
 Identities = 105/320 (32%), Positives = 149/320 (46%), Gaps = 36/320 (11%)

Query: 10  WFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPV-VFRHREHMQRLHDSAKIY 68
           W + ++V +   ++   +  LHY   +FEG++ Y    G V +FR   +  R   SA+  
Sbjct: 45  WHDAQLVPYGPLEMDPANMTLHYAQEIFEGLKAYRQPDGGVALFRPERNALRFQHSARTL 104

Query: 69  RFPVSQSIDELMEACRDVIRKN--------NLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120
             P    ++  +EAC  ++ ++           S Y+RP +   +VG+GV P   Y    
Sbjct: 105 AMP-ELPVETFIEACDALVAQDVEWVPPHGGEASLYLRPFMIASEVGLGVKPANEYL--F 161

Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWN-----RAAPNTIPTAAKAGGNYLSSLLVGSEA 175
           ++ A P G Y        G    VS W      RA P  +  A K GGNY +SLL  +EA
Sbjct: 162 LVIASPAGPYF------PGGVKPVSIWISQDRVRAVPGGMGDA-KTGGNYAASLLAQAEA 214

Query: 176 RRHGYQEGIALDV--NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKEL 233
              G  +   LD     ++ E  G NL+ V    + TP  T S L G+TRD+++ LA++L
Sbjct: 215 AEQGCAQVAYLDAVERRWVEELGGMNLYFVYGDRIVTPALTGSLLEGVTRDSLLTLARDL 274

Query: 234 GIEVREQVLS----RESLYLAD--EVFMSGTAAEITPVRSVD----GIQVGEGRCGPVTK 283
           G E  E  +S    RE        EVF  GTAA ITPV  V         G G  GPVT 
Sbjct: 275 GYESEEARISVDQWREDTANGSLTEVFACGTAAVITPVGEVKTKGAAWTQGSGEPGPVTL 334

Query: 284 RIQQAFFGLFTGETEDKWGW 303
           R+++A   L TG  ED  GW
Sbjct: 335 RLREALLSLQTGNAEDPHGW 354


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: 317
Number of extensions: 22
Number of successful extensions: 6
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: 359
Length adjustment: 28
Effective length of query: 281
Effective length of database: 331
Effective search space:    93011
Effective search space used:    93011
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: 49 (23.5 bits)

This GapMind analysis is from Jul 26 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