GapMind for Amino acid biosynthesis

 

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

Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate 3606714 Dshi_0145 Aspartate transaminase (RefSeq)

Query= BRENDA::P95468
         (394 letters)



>lcl|FitnessBrowser__Dino:3606714 Dshi_0145 Aspartate transaminase
           (RefSeq)
          Length = 392

 Score =  334 bits (857), Expect = 2e-96
 Identities = 176/392 (44%), Positives = 242/392 (61%), Gaps = 3/392 (0%)

Query: 1   MLGNLKPQAPDKILALMGEFRADPRQGKIDLGVGVYKDATGHTPIMRAVHAAEQRMLETE 60
           M  +L+PQA D IL LM  F+ADPR GK+DLG+GV++DA G TP+  AV  AE+R+  T+
Sbjct: 1   MFAHLRPQADDPILVLMRAFQADPRPGKVDLGIGVWRDAEGRTPVFGAVKTAEERLWRTQ 60

Query: 61  TTKTYAGLSGEPEFQKAMGELILGDGLKSETTATLATVGGTGALRQALELARMANPDLRV 120
            TK+Y   +G+P F  A+G+L+LG   +    A  AT GGT A++  L L+++A P  +V
Sbjct: 61  DTKSYVSFAGDPAFHAAVGDLLLGSVTRPR--AVTATTGGTSAVQTLLALSQVARPAAQV 118

Query: 121 FVSDPTWPNHVSIMNFMGLPVQTYRYFDAETRGVDFEGMKADLAAAKKGDMVLLHGCCHN 180
           ++   TWPNH  +   +GL  + + Y   E  G+D E +  DLA A+ GD+V+LH CCHN
Sbjct: 119 WIPAETWPNHRVLAEHLGLATRAFTYLAPEGTGIDREVLLRDLAQAQAGDVVILHACCHN 178

Query: 181 PTGANLTLDQWAEIASILEKTGALPLIDLAYQGFGDGLEEDAAGTRLIASRIPEVLIAAS 240
           PTG +   +  AEI   L +TGA+PL+D AY GFG   E DAA  R +AS +PE ++A S
Sbjct: 179 PTGIDPDPELQAEIVDSLARTGAVPLVDCAYLGFGAVPEADAAFLRRLAS-LPEAMLAFS 237

Query: 241 CSKNFGIYRERTGCLLALCADAATRELAQGAMAFLNRQTYSFPPFHGAKIVSTVLTTPEL 300
            SK+FG+YRER G  L L       E  Q  +  LNR  YSFPP HGA++V+ +L  P L
Sbjct: 238 GSKSFGLYRERVGLALVLLEQPGVVEAVQSQLTRLNRVNYSFPPDHGARVVTEILADPAL 297

Query: 301 RADWMAELEAVRSGMLRLREQLAGELRDLSGSDRFGFVAEHRGMFSRLGATPEQVKRIKE 360
           R  W AEL A+R+ +   R+ LA  LR    SDRF  +A   GMF+ L    E+V R++E
Sbjct: 298 RTAWEAELAAIRTALSANRQALAKALRARLQSDRFDGLAAQSGMFAMLPLGKERVMRMRE 357

Query: 361 EFGIYMVGDSRINIAGLNDNTIPILARAIIEV 392
           +F +Y VG  R+N+AG+   T   +A AI  V
Sbjct: 358 DFAVYAVGTGRVNLAGVTPRTTDRVAEAIAAV 389


Lambda     K      H
   0.320    0.136    0.398 

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: 406
Number of extensions: 19
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: 394
Length of database: 392
Length adjustment: 31
Effective length of query: 363
Effective length of database: 361
Effective search space:   131043
Effective search space used:   131043
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