GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__ANA3:7025922
          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 (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