GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Lentibacillus jeotgali Grbi

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_010531968.1 ON01_RS15370 pyridoxal phosphate-dependent aminotransferase

Query= curated2:B1I544
         (392 letters)



>NCBI__GCF_000224785.1:WP_010531968.1
          Length = 395

 Score =  357 bits (917), Expect = e-103
 Identities = 166/387 (42%), Positives = 243/387 (62%), Gaps = 1/387 (0%)

Query: 2   SFVEAKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIP 61
           +F ++  ++ LP   FA++     + K QG DVI+LG G+PD+PTPDHII+  ++  K P
Sbjct: 4   NFEQSDMLKRLPEQFFAKLVGRTQEFKQQGHDVINLGQGNPDLPTPDHIIQEVQEAAKNP 63

Query: 62  ANHQYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVV 121
           ANH+Y    G   ++ A A++Y R +GV LDP+ E+  L G K G+  +  C ++P D  
Sbjct: 64  ANHKYAPFRGFHYFKEAAANYYKREYGVSLDPETEIAVLFGGKAGLVEISQCLLNPNDTA 123

Query: 122 LVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTG 181
           L+PDPGYP Y  G  +A   P+ +PL   N FLPD + IP ET  +AK+MF+NYPNNPT 
Sbjct: 124 LLPDPGYPDYMSGIAMADADPYFMPLQKDNHFLPDYSTIPGETLNQAKLMFLNYPNNPTA 183

Query: 182 AVASKEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKT 241
             A+K+F+   V  A+++ I V  D AY  + FDG +P SFL+  GA+++GIE +++SKT
Sbjct: 184 VTANKDFYDETVKLAKDHHICVVQDFAYGALGFDGQKPQSFLQSEGAKDIGIEIYTLSKT 243

Query: 242 YNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRE 301
           YNM GWR  +AAGN   +EAL +++ ++   +F  +Q AA  ALN  Q  VQ L + Y E
Sbjct: 244 YNMAGWRVAFAAGNPSVIEALNKIQDHMYVSLFGAIQSAAAKALNSDQSAVQRLIDTYTE 303

Query: 302 RRDLVVDTLNDLGWRLTRPRATFYIWAPVPAGHDASSFAEMVLEKAGVVITPGTGYGTYG 361
           RRD  +  + ++GW +  P  +F+ W PVP+ + +  F+ ++LE A VV+ PG G+G YG
Sbjct: 304 RRDRFIRAIREIGWDVDTPEGSFFAWLPVPSNYTSEEFSNLLLENAHVVVAPGRGFGKYG 363

Query: 362 EGYFRISLTLPTPRLVEAMERLRGCLG 388
           +GY R+ L     RL EA  R+ G LG
Sbjct: 364 DGYVRVGLLESAERLEEAAARI-GRLG 389


Lambda     K      H
   0.321    0.139    0.430 

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: 360
Number of extensions: 12
Number of successful extensions: 1
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: 392
Length of database: 395
Length adjustment: 31
Effective length of query: 361
Effective length of database: 364
Effective search space:   131404
Effective search space used:   131404
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: 50 (23.9 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