GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Rhodomicrobium vannielii ATCC 17100

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_013420621.1 RVAN_RS15315 histidinol-phosphate transaminase

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



>NCBI__GCF_000166055.1:WP_013420621.1
          Length = 366

 Score =  243 bits (621), Expect = 5e-69
 Identities = 142/357 (39%), Positives = 203/357 (56%), Gaps = 8/357 (2%)

Query: 8   SYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYP 67
           S V AI PY+ G+  S++A      E  ++KL+SNE PLG    A  A   AAS L RYP
Sbjct: 11  SGVLAIDPYVPGR--SKLA-----GEGPVIKLSSNETPLGPSPHAVEAYRAAASHLDRYP 63

Query: 68  DANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALAT 127
           D     L+ A+   YG+    +  GNGS+++  I A A++  G   +Y ++ F VY +A 
Sbjct: 64  DGACTALREAIGAAYGLNPAHIICGNGSDELFHILAQAYLGPGDEAIYTEHGFLVYRIAI 123

Query: 128 QGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPR 187
              GA  +V P       +D++L  V+  T+ +F+ANPNNPTGT++   ++      +P 
Sbjct: 124 LAAGAEPVVAPEKNLTASVDSILECVTPRTKAVFIANPNNPTGTYLPHQEVRRLRAALPD 183

Query: 188 HVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTD 247
           +V++VLD AY EY+ +      I  V   PN +++RTFSK FGLA  RVG+A A   + D
Sbjct: 184 NVLLVLDGAYAEYVNRNDYEAGIEMVATTPNTIMTRTFSKIFGLAAARVGWAYAPAAIAD 243

Query: 248 LLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGN 307
            LNR+R PFN+   +  AAIAAL DKA +E + A N      +T  F K+G +   S GN
Sbjct: 244 ALNRIRSPFNLAQPSMDAAIAALADKAHIEAAKAHNNTWRDIVTLEFRKMGFDVRSSAGN 303

Query: 308 FVLVRVGNDDA-AGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAAL 363
           FVL+  G++        +  L ++ +I+R V  YGLP  LR+TIGL EEN A +AAL
Sbjct: 304 FVLIPFGSEQGRTAQDADAFLNERRIILRQVSAYGLPHALRMTIGLEEENRAVLAAL 360


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: 384
Number of extensions: 21
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: 366
Length adjustment: 30
Effective length of query: 340
Effective length of database: 336
Effective search space:   114240
Effective search space used:   114240
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 Apr 10 2024. The underlying query database was built on Apr 09 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