GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Lacinutrix algicola AKS293

Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_055434904.1 ASC41_RS01645 aspartate aminotransferase family protein

Query= reanno::Btheta:353284
         (373 letters)



>NCBI__GCF_001418085.1:WP_055434904.1
          Length = 376

 Score =  431 bits (1108), Expect = e-125
 Identities = 216/374 (57%), Positives = 275/374 (73%), Gaps = 1/374 (0%)

Query: 1   MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL 60
           M LF+VYPL+DI  VK     V+DEN T+YLDLYGGHAVISIGH+HP YV  IS+QVA L
Sbjct: 1   MSLFNVYPLFDITPVKAVDVFVYDENETKYLDLYGGHAVISIGHSHPKYVAAISDQVAKL 60

Query: 61  GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS 120
           GFYSNS+ N LQ Q+A +L ++SG +DY LFL NSGAEANENALKLASF+NG+ K+I+F 
Sbjct: 61  GFYSNSIQNPLQVQLANKLEQLSGCKDYELFLCNSGAEANENALKLASFHNGKKKIIAFK 120

Query: 121 KAFHGRTSLAVEATNNPTIIAPINNNGHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQGV 180
             FHGRTS AV AT+N  IIAPIN    V  L L D++ +++ LAK DVCAVIIE IQGV
Sbjct: 121 NGFHGRTSAAVAATDNAKIIAPINAQQEVEILELGDLKGVEKALAKNDVCAVIIECIQGV 180

Query: 181 GGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIG 240
           GG+   TTEF + L ++C +  T  I DE+QSG+GR+G FFA Q  ++ PDII++AKG+G
Sbjct: 181 GGLDESTTEFYEGLDELCEKYNTCFIADEVQSGFGRTGDFFAFQKYNVMPDIISIAKGMG 240

Query: 241 NGFPMAGVLISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLE 300
           NGFP+ G+LI P  K  +G LGTTFGGNHLAC A+  V++VI+++NL++NAK +  Y +E
Sbjct: 241 NGFPIGGILIHPNIKASFGLLGTTFGGNHLACVASSTVLEVIKEENLMQNAKDISAYFVE 300

Query: 301 ELKKFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTG-ASGTNVLRLLPPLCLSM 359
           + K    IK ++GRGLM+GLEF+ PI ELR +LI+D  +FTG A   N+LR+LPPL +  
Sbjct: 301 KAKGISAIKNIKGRGLMLGLEFDFPIAELRKKLIFDHKIFTGSAKNPNLLRILPPLTIKK 360

Query: 360 EEADEFLARFKRVL 373
           E  D F    K  L
Sbjct: 361 EHVDLFFEALKSEL 374


Lambda     K      H
   0.320    0.139    0.403 

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: 406
Number of extensions: 12
Number of successful extensions: 2
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: 373
Length of database: 376
Length adjustment: 30
Effective length of query: 343
Effective length of database: 346
Effective search space:   118678
Effective search space used:   118678
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