GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Desulfacinum hydrothermale DSM 13146

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_212636831.1 B9A12_RS05520 aspartate aminotransferase family protein

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_900176285.1:WP_212636831.1
          Length = 449

 Score =  191 bits (484), Expect = 5e-53
 Identities = 131/432 (30%), Positives = 225/432 (52%), Gaps = 32/432 (7%)

Query: 39  VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYEN 98
           V++RGEGI ++D DGN + D + G  V+++GH  P ++EA+K+QA + +    + F  E 
Sbjct: 21  VVDRGEGIHIWDKDGNRYIDGSGGACVVSLGHGVPEILEAMKEQAARISFAHGSHFTSEA 80

Query: 99  AIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY---GTGRK---QFLAFYHAFH 152
           A   A++L+ LAP     +V + + G+EA E A+K+V+      GR    + ++ + +FH
Sbjct: 81  ARECADRLVRLAPDPSLSRVYFLSGGSEAVETAVKVVRQYWREVGRPDKYKVISRWVSFH 140

Query: 153 GRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIE 212
           G T   ++L      ++  + P      HI     YR  +G     EP   +    + +E
Sbjct: 141 GNTMGAVAL-GGHTARRRHYHPHFLHTPHIEPAYCYRCPFG----REPQTCSLECAEQLE 195

Query: 213 EYVFRHVPPHEIGAIFFEPIQG-EGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGR 271
             + ++  P  + A   EP+ G   G +VP  G+++ +++  D Y + L  DEV  G+GR
Sbjct: 196 RTI-KYEGPDAVAAFIAEPVVGATAGALVPRDGYWQRIREICDTYEVKLIADEVMTGVGR 254

Query: 272 TGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGV-----IHRADITFDKPGRHATTFGGNP 325
           TG+ + ++H+ V PD+I   K +  G  PL  V     IH A  +      H  T+  NP
Sbjct: 255 TGRNFCLDHWSVVPDVIVSAKGLSSGYTPLGAVIVKEEIHDAIRSGSGAFVHGHTYSQNP 314

Query: 326 VAIAAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKS 383
           +++A G  V+  +  K+L+     +G+   + L    E+  ++GD RGLGL   VE+V++
Sbjct: 315 LSVAVGAAVLRYLEEKDLIARCATMGEVFLEKLRGLLER-PMVGDVRGLGLFAGVELVQN 373

Query: 384 KETKEKYP---ELRDRIVKESAKRGLVLL-------GCGDNSIRFIPPLIVTKEEIDVAM 433
           KETK  +    ++  R+ +E+ +RGL+         G   + I   PP I+T+EE+D  +
Sbjct: 374 KETKAPFAPSGKISARVAQEAFRRGLITYPGSGGADGINGDHILLAPPFIITEEELDEIV 433

Query: 434 EIFEEALKAALK 445
            I  EA++A  K
Sbjct: 434 RILGEAIQAVEK 445


Lambda     K      H
   0.320    0.141    0.418 

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: 555
Number of extensions: 32
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: 445
Length of database: 449
Length adjustment: 33
Effective length of query: 412
Effective length of database: 416
Effective search space:   171392
Effective search space used:   171392
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 (21.7 bits)
S2: 51 (24.3 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