GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Lacinutrix algicola AKS293

Align Aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_055435681.1 ASC41_RS05720 pyridoxal phosphate-dependent aminotransferase

Query= curated2:O58489
         (391 letters)



>NCBI__GCF_001418085.1:WP_055435681.1
          Length = 396

 Score =  191 bits (484), Expect = 4e-53
 Identities = 132/396 (33%), Positives = 222/396 (56%), Gaps = 23/396 (5%)

Query: 9   IAERVLLIKRSKIRELF---ERASKM-EDVISLGIGEPDFDTPKNIKEAAKRALDEGWTH 64
           I+++ L +  S IR+L    E A+K  + +  L IG+PD  TP+   +A K    E    
Sbjct: 4   ISKKGLSMPESPIRKLVPFAEIATKQGKSIYHLNIGQPDIKTPQIALDAVKNNSLEILA- 62

Query: 65  YTPNAGIPELREAVVEYYKKFYGIDIEVENVIITAGAYEGTYLAFESLLERGDEVIIPDP 124
           YT + G    R+ + +YY K   I+++ +++I+T G  E    AF S+++  DEVIIP+P
Sbjct: 63  YTRSEGSETYRQKIADYYAK-NDINVKHDDIIVTTGGSEALLFAFGSIMDVDDEVIIPEP 121

Query: 125 AFVSYAEDAKVAEAKPVRIPLREENNFLPDPNELLEK-ISKNTRMIVINYPNNPTGATLD 183
            + +Y   +  +  K V +  + E+NF   P E  EK I+  T+ I+I  P NPTG    
Sbjct: 122 FYANYNGFSTASGVKVVPVISKIEDNFALPPIEEFEKLITPKTKAILICNPGNPTGYLYS 181

Query: 184 KELAKTIADIAEDYNIYILSDEPYEHFIYEDAKHYPMI--KFAPENTILANSFSKTFAMT 241
           KE  K +ADI + +++++++DE Y  F Y+ AKHY ++  +   +  I+ +S SK ++M 
Sbjct: 182 KEEIKKLADIVKKHDLFLIADEVYREFAYDGAKHYSILQEEGLDDYAIVIDSVSKRYSMC 241

Query: 242 GWRLGFVVAPS-QVIKEMTKLHAYVIGNVASFVQIAGIEALRSEESWKAVEEMKKEYNER 300
           G R+G +V+ + QVIK   K  A    +  +  QIA   AL + +S+   +++ +EY ER
Sbjct: 242 GARIGCLVSKNKQVIKTALKF-AQARLSPPTLAQIASEAALETPQSY--FDDVIEEYVER 298

Query: 301 RKIVVKRLKNMPGIKVKEPKGAFYVFPNISGTGMSSEKFSEWLLEK-----ARVVVIPGT 355
           R  ++  L  + G+KV  PKGAFY    +     +S+KF++WLLE+       ++V P  
Sbjct: 299 RNTLITELNKIEGVKVGNPKGAFYCIAEL--PIKNSDKFAQWLLEEFDVDGETIMVAPAA 356

Query: 356 AF---GRMGEGYVRISYATSKEKLIEAMNRIEKALE 388
            F     +G   +RI+Y  +KE LI+++N +++AL+
Sbjct: 357 GFYSTPGVGLNQIRIAYVLNKESLIKSVNILKEALK 392


Lambda     K      H
   0.316    0.135    0.382 

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: 389
Number of extensions: 24
Number of successful extensions: 7
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: 391
Length of database: 396
Length adjustment: 31
Effective length of query: 360
Effective length of database: 365
Effective search space:   131400
Effective search space used:   131400
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 (21.6 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