GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Flavobacterium glycines Gm-149

Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_066326600.1 BLR17_RS06720 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::H8WR05
         (434 letters)



>NCBI__GCF_900100165.1:WP_066326600.1
          Length = 428

 Score =  203 bits (516), Expect = 1e-56
 Identities = 140/417 (33%), Positives = 208/417 (49%), Gaps = 21/417 (5%)

Query: 23  ASQRQFEAQARYMPGANS--RSVLFYAPFPLTIARGEGAALWDADGHRYADFIAEYTAGV 80
           +SQ   EA+     G NS  R+       P+ + + +GA L+D DG+R  D+I  +   +
Sbjct: 6   SSQLFAEAEKVIPGGVNSPVRAFKSVGGTPIFVKQAKGAYLYDEDGNRLIDYINSWGPMI 65

Query: 81  YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140
            GH+   +  AV E  + G +      LE ++A L     P I+++RF NSGTEA + A+
Sbjct: 66  LGHAFEPVVQAVTEKAKLGTSFGMPTELETQIAALAVSMVPNIDKIRFVNSGTEACMSAV 125

Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSP---TTVPFDFLVLPYND 186
             A  FT R KI+ F+G YHG           G + FG   SP        D L+  YND
Sbjct: 126 RLARGFTKRDKIIKFAGCYHGHSDSFLIQAGSGAMTFGTPNSPGVTAGTAKDTLLAKYND 185

Query: 187 AQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS- 245
            +  R+ IE +  EIA ++VEP+ G  GC+P    FL+ +R+  ++ G LL+FDEVMT  
Sbjct: 186 LENVRSLIEANPNEIAAIIVEPVAGNMGCVPPIKGFLEGVRQLCSENGILLIFDEVMTGF 245

Query: 246 RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNV 305
           RLA  G    L I +D+   GK IGGG+  GAF  R ++M    P  GP+  +GT + N 
Sbjct: 246 RLAKGGAQELLNINADIVCFGKVIGGGLPVGAFAAREEIMNYLAP-LGPVYQAGTLSGNP 304

Query: 306 MTMAAGYAGLTKLFTPEAA-GALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQ 364
           + MAAG A L  L T  A    L E+   L A ++ +     +      +GS+++ HF  
Sbjct: 305 LAMAAGKAMLESLNTDAAIFQRLEEKTAYLEAGIHRVLKANNIIYTINRVGSMISVHFDA 364

Query: 365 GDVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGFVV--LSLPLTDADIDRYVAAI 419
             V   +  A  D    +  F  LL E +Y +P  +    ++  L+  D+D  + AI
Sbjct: 365 SPVVDFQTAAKGDNETFKKFFHGLLQEGVYIAPSAYETWFITDALSYEDLDFTINAI 421


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: 389
Number of extensions: 18
Number of successful extensions: 5
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 Jul 26 2024. The underlying query database was built on Jul 25 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