GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Shewanella sp. ANA-3

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 7023122 Shewana3_0360 alanine-glyoxylate aminotransferase (RefSeq)

Query= BRENDA::P74281
         (384 letters)



>FitnessBrowser__ANA3:7023122
          Length = 377

 Score =  186 bits (471), Expect = 1e-51
 Identities = 120/366 (32%), Positives = 195/366 (53%), Gaps = 12/366 (3%)

Query: 4   KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTS- 62
           +++LM PGP+ V  +VL A A+  +GH    F  ++ EL + +++  QT+N++ M  ++ 
Sbjct: 14  RRILMGPGPSDVYPEVLAAQARPTVGHLDPLFVGMMDELKSLIQYAFQTKNEMTMAVSAP 73

Query: 63  GTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKT 122
           G+  ME   +N + PG++V+V  NG FG+R  +  +  G     +  EWG  +D    + 
Sbjct: 74  GSAGMETCFVNLVEPGEKVIVCRNGVFGERMRQNVERVGAIAVLVDNEWGTPVDAAAVEA 133

Query: 123 LLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAIDD 182
            L+A+ D   K L   H+ETSTG L+D   + A AK +G  L IVDAVTSLG   + +D+
Sbjct: 134 ALKANPDA--KFLAFVHAETSTGALSDAKTLCALAKQYG-CLSIVDAVTSLGGVELRVDE 190

Query: 183 LGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIP--RFYLD----LKKYKKSTDE 236
            G+D + SGSQK     PGL  VS S  A +  +    P   ++LD    +  +  +  +
Sbjct: 191 WGIDAIYSGSQKCLSCVPGLSPVSFSPNAVEKLKNRKTPVQSWFLDQSLVMAYWTSAGGK 250

Query: 237 DSSPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAAS 296
            S   T P+N +Y L  SL+++  EGL+  + RHQ      R  ++ L L     + +  
Sbjct: 251 RSYHHTAPVNALYALHESLRLLAEEGLENAWKRHQDMHLVLRAGLEKLGLKFVVAEASRL 310

Query: 297 NAITAV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRD-ILSCIG 354
             + A+  P GV+   +R+ + K +++ +  G   L GK +RIG +GF   R+ +  C+ 
Sbjct: 311 PQLNAIYIPEGVDDAAVRARLLKDYNLEIGAGLGALAGKAWRIGLMGFGARRENVALCLR 370

Query: 355 ALEATL 360
           ALE  L
Sbjct: 371 ALEEVL 376


Lambda     K      H
   0.317    0.134    0.386 

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: 316
Number of extensions: 13
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: 384
Length of database: 377
Length adjustment: 30
Effective length of query: 354
Effective length of database: 347
Effective search space:   122838
Effective search space used:   122838
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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