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 3609562 Dshi_2946 histidinol-phosphate aminotransferase (RefSeq)

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



>FitnessBrowser__Dino:3609562
          Length = 361

 Score =  234 bits (597), Expect = 3e-66
 Identities = 141/342 (41%), Positives = 200/342 (58%), Gaps = 7/342 (2%)

Query: 30  GLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWV 89
           GLD  T++KL+SNENPLG   +A  A   AA EL RYP  +   L+ A++E YG+  + +
Sbjct: 25  GLD--TVIKLSSNENPLGPSPAAIAAYKAAAGELHRYPSTDHAGLRGAIAEVYGLDPERI 82

Query: 90  TLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLDAM 149
             G GS++I+     A+V  G  +++ ++ FA+Y ++T   G   + VP  +   D+DA+
Sbjct: 83  ICGAGSDEIIAFLCQAYVGPGDEVIHTEHGFAMYRISTLAAGGTPVEVPERERVTDVDAI 142

Query: 150 LAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDS 209
           LA V+D TRL+F+ANPNNPTGT I G  L    D +P   ++VLD AY EY+P    YD+
Sbjct: 143 LAGVTDRTRLVFIANPNNPTGTMIGGNALARLADGLPEGCLLVLDGAYAEYVPD---YDA 199

Query: 210 -IAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIA 268
             A V    N++++RTFSK +GL  LRVG+      + D+LNRVR PFN++T A AAA A
Sbjct: 200 GKALVESRENVVMTRTFSKIYGLGALRVGWGYGPRHVIDVLNRVRGPFNLSTGALAAAEA 259

Query: 269 ALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELL 328
           A+ D+A+ E   A NA+    L      LG+    S  NFVL R  + + AG   +  L 
Sbjct: 260 AVRDRAYTETCRAENAKWRGWLASELAALGIPSDTSSANFVLARFASPEEAGACDDF-LK 318

Query: 329 KQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTLAAA 370
            +G+IVR V  Y LP  LR+T+G  E   A + A+    A A
Sbjct: 319 ARGIIVRRVSGYKLPAALRMTVGDAEGCRALVDAVAAFKAQA 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: 349
Number of extensions: 9
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: 361
Length adjustment: 30
Effective length of query: 340
Effective length of database: 331
Effective search space:   112540
Effective search space used:   112540
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