GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Shewanella sp. ANA-3

Align tyrosine transaminase (EC 2.6.1.5) (characterized)
to candidate 7025922 Shewana3_3071 glutamate-1-semialdehyde aminotransferase (RefSeq)

Query= BRENDA::H8WR05
         (434 letters)



>lcl|FitnessBrowser__ANA3:7025922 Shewana3_3071
           glutamate-1-semialdehyde aminotransferase (RefSeq)
          Length = 430

 Score =  220 bits (561), Expect = 6e-62
 Identities = 136/397 (34%), Positives = 204/397 (51%), Gaps = 22/397 (5%)

Query: 24  SQRQFEAQARYMPGANSRSVLFY---APFPLTIARGEGAALWDADGHRYADFIAEYTAGV 80
           S+  FE   + +PG  +  V  +      PL I + +GA ++DADG  Y D++  +   +
Sbjct: 4   SEALFEQAKKTIPGGVNSPVRAFNGVGGSPLFIEKADGAYIYDADGKAYIDYVGSWGPMI 63

Query: 81  YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140
            GH+ P+IR+AV+ A+  G++      LE ++A  +    P IEQ+R  +SGTEA + A+
Sbjct: 64  LGHNHPKIREAVLAAVHNGLSFGAPTELEVQMAEKVIAMVPSIEQVRMVSSGTEATMSAI 123

Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPFDF----LVLPYN 185
             A  FT R KI+ F G YHG           G L  G +PS   +P DF    L   YN
Sbjct: 124 RLARGFTNRDKILKFEGCYHGHADCLLVKAGSGALTLG-QPSSPGIPEDFAKHTLTAVYN 182

Query: 186 DAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS 245
           D  + R+  E++  EI+ +++EP+ G   CIP  P FL+ LR    + GALL+ DEVMT 
Sbjct: 183 DLDSVRSLFEQYPTEISCIIIEPVAGNMNCIPPIPGFLEGLRAMCDEFGALLIIDEVMTG 242

Query: 246 -RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNN 304
            R++  G     G+  DLTTLGK IGGGM  GAFGGR +VM    P TGP+  +GT + N
Sbjct: 243 FRVSRSGAQGHYGVTPDLTTLGKVIGGGMPVGAFGGRKEVMQFIAP-TGPVYQAGTLSGN 301

Query: 305 VMTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQ 364
            + M+AG A +  L       AL+ + + +     A     G+ M    +G +    F +
Sbjct: 302 PIAMSAGLAQMEALCEEGLYEALSAKTKRIAEGFKAAADKHGIPMAINYVGGMFGFFFTE 361

Query: 365 GDVRSSEDLAAVDGRLRQLLFFH-LLNEDIYSSPRGF 400
            +  +  D            F+H +L+E +Y +P  +
Sbjct: 362 QEQITRFDQVTKCNIEHFRTFYHGMLDEGVYLAPSAY 398


Lambda     K      H
   0.322    0.138    0.408 

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: 452
Number of extensions: 22
Number of successful extensions: 4
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: 434
Length of database: 430
Length adjustment: 32
Effective length of query: 402
Effective length of database: 398
Effective search space:   159996
Effective search space used:   159996
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 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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