GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Sinorhizobium meliloti 1021

Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate SMc01340 SMc01340 aminotransferase

Query= BRENDA::Q56232
         (385 letters)



>FitnessBrowser__Smeli:SMc01340
          Length = 385

 Score =  190 bits (483), Expect = 5e-53
 Identities = 130/390 (33%), Positives = 191/390 (48%), Gaps = 14/390 (3%)

Query: 1   MRGLSRRVQAMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQG 60
           M  +S+R  A++P   + V A+A   R  G  ++++  G+P    P+   +AARRAL  G
Sbjct: 1   MAQMSKR-SAVEPFHAMDVLAEATRRRDSGHPVISMAVGQPAHPAPKAALDAARRALDHG 59

Query: 61  KTKYAPPAGIPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIV 120
           +  Y    G   L+ A+A  +   +G+++ P+   VT G        F A+ DPGD V +
Sbjct: 60  RLGYTDALGTHSLKRAIAAHYHSRHGITLDPQRIAVTTGSSAGFNLAFLALFDPGDRVAI 119

Query: 121 LSPYWVSYPEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKAL---VVNSPNNPT 177
             P + +Y  ++   G  VVE+E   E GF   P+ +  A     K L   ++ SP NPT
Sbjct: 120 ARPGYPAYRNIMAALGLEVVEIEANAEAGFTLTPDSLEGAAARAGKPLKGVLLASPANPT 179

Query: 178 GAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRVAPEHTLTVNGAAKAFA 237
           G V  K  L+ALA    +H    +SDEIY  L + GE  +   VA +  + +N  +K + 
Sbjct: 180 GTVTGKAQLKALADYCRDHSIAFISDEIYHGLTFAGEETTALEVA-DDAVVINSFSKYYC 238

Query: 238 MTGWRIGYACGPKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYR 297
           MTGWRIG+   P+  ++A   ++     SP  ++Q A   AL   E    +    + AY 
Sbjct: 239 MTGWRIGWMVLPEARVRAFERIAQSLYISPPELSQIAAEAALGAHEELDGY----KRAYA 294

Query: 298 RRRDLLLEGLTALGLKAVRP-SGAFYVLMDTSPIAPDEVRAAERLL-EAGVAVVPGTDFA 355
             R LLLE L  +G     P  GAFY   D S    D +  A R+L E  VA  PG DF 
Sbjct: 295 ANRALLLERLPQIGFSIASPMDGAFYAYADVSRFTNDSMAFARRMLAEIDVAATPGFDFD 354

Query: 356 AF-GH--VRLSYATSEENLRKALERFARVL 382
              GH  +R SYA +   + +A+ R AR L
Sbjct: 355 PLEGHRTMRFSYAGAATEMEEAMNRIARWL 384


Lambda     K      H
   0.317    0.133    0.379 

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: 335
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: 385
Length of database: 385
Length adjustment: 30
Effective length of query: 355
Effective length of database: 355
Effective search space:   126025
Effective search space used:   126025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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