GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Phaeobacter inhibens BS107

Align aromatic-amino-acid transaminase [EC:2.6.1.57] (characterized)
to candidate GFF2895 PGA1_c29420 aromatic-amino-acid aminotransferase TyrB

Query= reanno::Phaeo:GFF2895
         (394 letters)



>lcl|FitnessBrowser__Phaeo:GFF2895 PGA1_c29420 aromatic-amino-acid
           aminotransferase TyrB
          Length = 394

 Score =  785 bits (2027), Expect = 0.0
 Identities = 394/394 (100%), Positives = 394/394 (100%)

Query: 1   MFETLKPQPADKILALMQMYRDDPRDSKIDLGVGVYKNAEGVTPVMRAIKAAEHKLWEEQ 60
           MFETLKPQPADKILALMQMYRDDPRDSKIDLGVGVYKNAEGVTPVMRAIKAAEHKLWEEQ
Sbjct: 1   MFETLKPQPADKILALMQMYRDDPRDSKIDLGVGVYKNAEGVTPVMRAIKAAEHKLWEEQ 60

Query: 61  TSKSYVGLAGDPAYSDAMIKLILSDSVARANVAAAATPGGTGAVRQAFELIKMANPGARV 120
           TSKSYVGLAGDPAYSDAMIKLILSDSVARANVAAAATPGGTGAVRQAFELIKMANPGARV
Sbjct: 61  TSKSYVGLAGDPAYSDAMIKLILSDSVARANVAAAATPGGTGAVRQAFELIKMANPGARV 120

Query: 121 FVSNPTWPNHISILNYLNIETVAYRYFDRETCGVDFDGMIADLKTANKGDVVLLHGCCHN 180
           FVSNPTWPNHISILNYLNIETVAYRYFDRETCGVDFDGMIADLKTANKGDVVLLHGCCHN
Sbjct: 121 FVSNPTWPNHISILNYLNIETVAYRYFDRETCGVDFDGMIADLKTANKGDVVLLHGCCHN 180

Query: 181 PTGANLNMVQWQEVVAILNERGLIPMIDIAYQGFGDGLEEDAQGVRYVAANTPECLIAAS 240
           PTGANLNMVQWQEVVAILNERGLIPMIDIAYQGFGDGLEEDAQGVRYVAANTPECLIAAS
Sbjct: 181 PTGANLNMVQWQEVVAILNERGLIPMIDIAYQGFGDGLEEDAQGVRYVAANTPECLIAAS 240

Query: 241 CSKNFGIYRERTGLLMAVSQDSGAQALNQGTLAFLNRQNYSFPPDHGARLVSMILNDDAL 300
           CSKNFGIYRERTGLLMAVSQDSGAQALNQGTLAFLNRQNYSFPPDHGARLVSMILNDDAL
Sbjct: 241 CSKNFGIYRERTGLLMAVSQDSGAQALNQGTLAFLNRQNYSFPPDHGARLVSMILNDDAL 300

Query: 301 RADWAAELEETRLGMLALRQQLADELQRLTGSDRFGFLAQHRGMFSLLGTTPEMVEKMRA 360
           RADWAAELEETRLGMLALRQQLADELQRLTGSDRFGFLAQHRGMFSLLGTTPEMVEKMRA
Sbjct: 301 RADWAAELEETRLGMLALRQQLADELQRLTGSDRFGFLAQHRGMFSLLGTTPEMVEKMRA 360

Query: 361 ESGIYMVGDSRMNIAGLNTQTVPILAQAIVDAGV 394
           ESGIYMVGDSRMNIAGLNTQTVPILAQAIVDAGV
Sbjct: 361 ESGIYMVGDSRMNIAGLNTQTVPILAQAIVDAGV 394


Lambda     K      H
   0.319    0.135    0.395 

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: 661
Number of extensions: 16
Number of successful extensions: 1
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 (21.8 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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