GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Dinoroseobacter shibae DFL-12

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate 3608695 Dshi_2088 aminotransferase class I and II (RefSeq)

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



>FitnessBrowser__Dino:3608695
          Length = 372

 Score =  152 bits (383), Expect = 2e-41
 Identities = 114/372 (30%), Positives = 173/372 (46%), Gaps = 5/372 (1%)

Query: 1   MTASFGPSYVRAIAPYIAGKP-ISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQA 59
           MT + GP +        A  P +    +E         +L +NE+  G    A  AMA+A
Sbjct: 1   MTHTPGPRFTPLAQSLPATVPFVGPETQERARGRPFAARLGANESAFGPSPRAVAAMAEA 60

Query: 60  ASELGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYS 119
           A+    Y D  + +L+AAL+  + V  + V +G G + +L       V  G ++V +  +
Sbjct: 61  ATGAWMYGDPESHDLRAALAAHHRVGMENVIVGEGIDGLLGYLVRLLVAPGDTVVTSAGA 120

Query: 120 FAVYALATQGLGARAIVVPAVKYGHDLDAML-AAVSDDTRLIFVANPNNPTGTFIEGPKL 178
           +  +     G G     VP      D  A+L  A + D + I++ANP+NP G++     +
Sbjct: 121 YPTFNYHVAGFGGTLHAVPYRDDHEDPQALLDMARAVDAKAIYLANPDNPMGSWHAAGVI 180

Query: 179 EAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGF 238
              +D +P   +++LDEAY E  P     +        P ++  RTFSKA GLAG RVG+
Sbjct: 181 TDMIDALPPGCLLLLDEAYIELAPDGTAPEIAP---DDPRVIRLRTFSKARGLAGARVGY 237

Query: 239 AIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLG 298
            IA P L     +VR  F ++ ++QAAA+AAL D   L K  A  A    R+ E     G
Sbjct: 238 GIAAPGLISAFGKVRNHFGMSRVSQAAALAALQDSDHLAKVVAKTAAARTRIAEIGAAHG 297

Query: 299 LEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEA 358
           L  +PS  NFV +  G D A    +   L+ + + VR        + +RI+ G PE  + 
Sbjct: 298 LRALPSATNFVTLDCGGDGARAKAILEALIARDIFVRMPFVAPQDRCIRISCGTPEMLDL 357

Query: 359 FIAALERTLAAA 370
               L   LAAA
Sbjct: 358 LAERLPDALAAA 369


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: 358
Number of extensions: 12
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: 372
Length adjustment: 30
Effective length of query: 340
Effective length of database: 342
Effective search space:   116280
Effective search space used:   116280
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