GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Phaeobacter inhibens BS107

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate GFF2362 PGA1_c23930 putative histidinol-phosphate aminotransferase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>FitnessBrowser__Phaeo:GFF2362
          Length = 369

 Score =  159 bits (401), Expect = 1e-43
 Identities = 103/334 (30%), Positives = 170/334 (50%), Gaps = 4/334 (1%)

Query: 38  KLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSND 97
           +L +NEN  G    A  AM  +  E+ +Y DA + +L+AAL+  + V  + + +G G + 
Sbjct: 36  RLGANENIFGPSPKAIAAMQGSLGEIWKYGDAESHDLRAALAAHHSVAPENIMIGEGIDG 95

Query: 98  ILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSD-D 156
           +L       + +G ++V +  ++  +     G G     VP      D  A+ A  ++ D
Sbjct: 96  LLGYLVRLLIGEGDAVVTSLGAYPTFNYHVAGFGGVLHTVPYQDDHEDPAALFAKAAEVD 155

Query: 157 TRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRY 216
            +L+++ANP+NP G++  G  L A +D +P   +++LDEAY +  P      ++      
Sbjct: 156 AKLVYLANPDNPMGSWHSGAGLLAAMDALPEGCLLLLDEAYIDCAPDGT---ALPIDIND 212

Query: 217 PNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFL 276
           P ++ +RTFSKA+G+AG RVG+ +A+  L    N+VR  F +N  AQ  A+AAL D+A+L
Sbjct: 213 PRVIRTRTFSKAYGMAGARVGYVLAEAGLISAFNKVRNHFGMNRTAQIGALAALRDQAWL 272

Query: 277 EKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRP 336
            +     A    R+ +     GL  +PS  NFV +  G D A    V   L+ QGV VR 
Sbjct: 273 AEVLGRIATARNRIAQIARDNGLTPLPSATNFVAIDCGADGAFAKSVLEGLVDQGVFVRM 332

Query: 337 VGNYGLPQWLRITIGLPEENEAFIAALERTLAAA 370
                  + +R++ G  ++  +F  AL   L  A
Sbjct: 333 PFAAPQNRCIRVSCGPEDQLNSFARALPLALERA 366


Lambda     K      H
   0.318    0.135    0.385 

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: 337
Number of extensions: 13
Number of successful extensions: 3
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: 370
Length of database: 369
Length adjustment: 30
Effective length of query: 340
Effective length of database: 339
Effective search space:   115260
Effective search space used:   115260
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: 49 (23.5 bits)

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

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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