GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Allochromatium vinosum DSM 180

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_043795594.1 ALVIN_RS09555 aspartate aminotransferase family protein

Query= curated2:Q5JFW3
         (362 letters)



>NCBI__GCF_000025485.1:WP_043795594.1
          Length = 392

 Score =  264 bits (675), Expect = 3e-75
 Identities = 152/373 (40%), Positives = 219/373 (58%), Gaps = 23/373 (6%)

Query: 12  RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEM 71
           RGEGV++WD  G+RYLD ++GI V  LGHAHP     +  Q  +++    ++   E+E +
Sbjct: 18  RGEGVWLWDTNGKRYLDALSGIAVCGLGHAHPAVRDALCEQAGRLIHTSNIYGVAEQERL 77

Query: 72  LEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGR-----SEIVAMTNAFHGRTLGSLS 126
              L+     + V+  NSG EA EAAIK ARL   R       I+   ++FHGRTL +LS
Sbjct: 78  GALLTEQAGMDRVFFANSGAEANEAAIKLARLHAHRRGIENPAILVAEHSFHGRTLATLS 137

Query: 127 ATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITK--ETAAVIFEPIQGEGGIVPADEEF 184
           AT  +K + GF PLV GF  +P+++++A + A T      A++ EPIQGEGGI    +++
Sbjct: 138 ATGNRKVQAGFEPLVQGFVRVPYDDLDAIETAATNRPNIVAILIEPIQGEGGIRLPSDDY 197

Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL- 242
           +  LR++ +  G LL+ DE+Q+G+ RTG+  A +H G++PD+VT+ KG+GNG P+   L 
Sbjct: 198 LVRLREICDRSGWLLMLDEIQTGMGRTGRLFAFQHAGIQPDVVTLAKGLGNGMPIGACLA 257

Query: 243 ----TDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAG-------EKFMEFSG 291
                ++  P G HGSTFGGNPLACR     L  L  + L E A        +      G
Sbjct: 258 RGAAAEVFSP-GSHGSTFGGNPLACRVGRAVLETLIDENLTENAAAQGAYLLDSLRAALG 316

Query: 292 ER--VVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEE 349
           E   +V+ RGRGLM+GI L RP G  V    + G+L+N    RVIRLLPPLII+   ++E
Sbjct: 317 ETHGLVEIRGRGLMVGIELDRPCGELVGRALDAGLLINVTAERVIRLLPPLIIDRAQIDE 376

Query: 350 ARKEIEGVLNDIL 362
               + G+++  L
Sbjct: 377 LVATLTGLIHGFL 389


Lambda     K      H
   0.320    0.140    0.410 

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: 378
Number of extensions: 19
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: 362
Length of database: 392
Length adjustment: 30
Effective length of query: 332
Effective length of database: 362
Effective search space:   120184
Effective search space used:   120184
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 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