GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Marinobacter adhaerens HP15

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate GFF1396 HP15_1363 histidinol-phosphate aminotransferase

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



>lcl|FitnessBrowser__Marino:GFF1396 HP15_1363 histidinol-phosphate
           aminotransferase
          Length = 374

 Score =  402 bits (1032), Expect = e-116
 Identities = 205/361 (56%), Positives = 264/361 (73%), Gaps = 3/361 (0%)

Query: 10  VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69
           V+A++PY  GKPI E+ARE GL+ A I+KLASNENPLG  E A  A  +A SEL  YPD 
Sbjct: 13  VQALSPYQPGKPIEELARELGLNPAEIIKLASNENPLGPSEKALSAARRALSELCLYPDG 72

Query: 70  NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129
           N F LK ALS R  V  D +TLGNGSND+LE+    F +    +V++QY+FAVY L TQ 
Sbjct: 73  NGFNLKQALSTRLNVGMDQITLGNGSNDVLEVITRCFADADSEVVFSQYAFAVYPLVTQA 132

Query: 130 LGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHV 189
           +GAR + VPA ++GHDLDAM AAV+D TRL+FVANPNNPTGT      +EAFL K+P +V
Sbjct: 133 IGARGVSVPAREWGHDLDAMAAAVTDRTRLVFVANPNNPTGTVHTAEAIEAFLKKIPENV 192

Query: 190 VVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLL 249
           +VVLDEAY EYL  ++  D +  + R+PNL+V RTFSKA+GLA LRVG++I+ P + D+L
Sbjct: 193 LVVLDEAYCEYLTGDQYPDGVELLARFPNLIVCRTFSKAWGLAALRVGYSISSPAIADIL 252

Query: 250 NRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFV 309
           NRVRQPFNV+T+A +AA A L+D+ +L++S  +N  G R+L EAFD++GL Y+PS GNFV
Sbjct: 253 NRVRQPFNVDTVALSAATAVLDDEDYLQRSRDVNTAGLRQLQEAFDRMGLGYIPSAGNFV 312

Query: 310 LVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTLAA 369
            V VG + A G  V   LL  GVIVRP+  YG+P+ LR+++GLPEENE FI AL + L A
Sbjct: 313 AVEVG-EQAMG--VYQALLAHGVIVRPIAGYGMPRHLRVSVGLPEENERFIEALAQALTA 369

Query: 370 A 370
           +
Sbjct: 370 S 370


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: 407
Number of extensions: 9
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: 370
Length of database: 374
Length adjustment: 30
Effective length of query: 340
Effective length of database: 344
Effective search space:   116960
Effective search space used:   116960
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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