GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Salinicoccus carnicancri Crm

Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_017549722.1 C792_RS0112120 branched-chain amino acid aminotransferase

Query= CharProtDB::CH_024500
         (309 letters)



>NCBI__GCF_000330705.1:WP_017549722.1
          Length = 355

 Score =  144 bits (364), Expect = 2e-39
 Identities = 99/316 (31%), Positives = 158/316 (50%), Gaps = 21/316 (6%)

Query: 7   DYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAK 66
           +Y W    +V +++ ++   + A+HYG SVFEG++ Y      ++FR  ++ +R+++S  
Sbjct: 40  EYGWSGASIVPYQNLQLSPSAQAIHYGQSVFEGLKAYKQGDDILLFRPDQNFKRMNESLS 99

Query: 67  IYRFP------VSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120
               P         ++ EL++  RD +      S YIRP +F  +  +GV P   Y  ++
Sbjct: 100 RLSMPEINEENALNALYELLKVERDWVPDGEGQSLYIRPFVFADEPFLGVRPSETYQFNI 159

Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180
           I++  P G Y GA  L      +   + R+    +  A K  GNY +SLL   +A   GY
Sbjct: 160 ILS--PVGGYYGATQLNPTSIYVEDDFVRSVRGGVGFA-KVSGNYAASLLAQKKANELGY 216

Query: 181 QEGIALD--VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVR 238
           ++ + LD     Y+ E    N+F V+DG L TP    S LPGITR +II+LAK  G  V+
Sbjct: 217 EQVLWLDGVEQKYVEEVGSMNIFFVRDGELITPQLNGSILPGITRKSIIELAKHKGYTVK 276

Query: 239 EQVLSRESLY------LADEVFMSGTAAEITPV--RSVDGIQ--VGEGRCGPVTKRIQQA 288
           E+ +  + L          EVF +GTAA I PV   ++ GI   V + + G V+  +   
Sbjct: 277 EEKIHIDDLVEDIHGGRVTEVFGAGTAAVIAPVGKLNIHGIDYIVNDNQVGEVSLDLFND 336

Query: 289 FFGLFTGETEDKWGWL 304
              +  G  ED +GW+
Sbjct: 337 LTDIQYGRKEDPFGWV 352


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: 11
Number of successful extensions: 5
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: 355
Length adjustment: 28
Effective length of query: 281
Effective length of database: 327
Effective search space:    91887
Effective search space used:    91887
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