GapMind for Amino acid biosynthesis

 

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

Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate 5208501 Shew_1012 glutamate-1-semialdehyde-2,1-aminomutase (RefSeq)

Query= SwissProt::H8WR05
         (434 letters)



>FitnessBrowser__PV4:5208501
          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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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