GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Shewanella loihica PV-4

Align tyrosine transaminase (EC 2.6.1.5) (characterized)
to candidate 5208501 Shew_1012 glutamate-1-semialdehyde-2,1-aminomutase (RefSeq)

Query= BRENDA::H8WR05
         (434 letters)



>lcl|FitnessBrowser__PV4:5208501 Shew_1012
           glutamate-1-semialdehyde-2,1-aminomutase (RefSeq)
          Length = 428

 Score =  224 bits (571), Expect = 4e-63
 Identities = 139/417 (33%), Positives = 215/417 (51%), Gaps = 24/417 (5%)

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

Query: 81  YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140
            GH+ P+IR AV++A++ G++      LE R+A  + E  P +EQ+R  +SGTEA + A+
Sbjct: 64  LGHNHPKIRQAVLDAVENGLSFGAPTELEVRMAEKVIEMVPSMEQVRMVSSGTEATMSAI 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
           + ++ +   E++  EIA +++EP+ G   CIP  P FL+ LR    Q GALL+ DEVMT 
Sbjct: 183 ELESVKTLFEQYPEEIACIILEPVAGNMNCIPPIPGFLEGLRALCDQYGALLIIDEVMTG 242

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

Query: 305 VMTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQ 364
            + M+AG A + +L        LA + + +     A     G+ +    +G +    F +
Sbjct: 302 PIAMSAGLAQMEELCAEGLYEELAAKTKRIAEGFKAAANKHGIPLSINYVGGMFGFFFTE 361

Query: 365 -GDVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGFVV--LSLPLTDADIDRYVAA 418
              V   + +   D    +  +  +L+E +Y +P  +    LS+   + +++  +AA
Sbjct: 362 LEQVTRFDQVTQCDAEAFRTFYHGMLDEGVYLAPSAYEAGFLSMAHGEKELEETLAA 418


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: 438
Number of extensions: 19
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: 428
Length adjustment: 32
Effective length of query: 402
Effective length of database: 396
Effective search space:   159192
Effective search space used:   159192
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.

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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