GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Ruegeria conchae TW15

Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_010439643.1 G7G_RS0106265 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9UWT5
         (433 letters)



>NCBI__GCF_000192475.1:WP_010439643.1
          Length = 435

 Score =  254 bits (648), Expect = 5e-72
 Identities = 140/390 (35%), Positives = 212/390 (54%), Gaps = 6/390 (1%)

Query: 24  QTLNLIASENVMSPLAESVYMSDFMSRYAEGKPYKRYYQGTKYTDEIETLTMELMNEITN 83
           +  NL  + NVM+P AE++  S   SR + G P  +Y  G +  ++IE +  EL  E+ +
Sbjct: 50  ECFNLNPATNVMNPKAEALLSSGIGSRPSLGYPGDKYEMGMEAIEQIEVIAAELCAEVFD 109

Query: 84  SKDCDLRPTSGTIANAAVFRVLAEPGDKALIAPVQAGAHVSHTKFGTLGALGIQHIEMPF 143
           ++  ++R  SG IAN   F    + GD  +  P   G HV+H   G  G  G++ IE P 
Sbjct: 110 ARFAEVRVPSGAIANLYGFMATCKAGDTIIAPPGSIGGHVTHHAAGCAGLFGLRTIEAPV 169

Query: 144 DEENINVDVDKAIKMIEEVKPKFVVLGGSLYLFPHPTKELAQHVHAVGAKLVYDAAHVYG 203
           + +   VDVD+   + +  +P+ + +GGSL LF HP  E+      +GAK+++DAAH  G
Sbjct: 170 NADGYTVDVDQLRALAKTERPRLITIGGSLNLFEHPVAEVRAIADEIGAKVMFDAAHQCG 229

Query: 204 LIEGKVWSNPLKDGADIMTVSTHKTFPGPQGGAIFSDGSEVFKQVSKTIFPWFVSNHHLH 263
           +I G+ WSNPLK+GA  MT+ST+K+  GP GG I +D  E+ K +    FP   +N    
Sbjct: 230 IIAGRAWSNPLKEGAHFMTMSTYKSLGGPAGGLIVTDDEEIAKALDAIAFPGMTANFDAA 289

Query: 264 RLPATAVTAIEMKYFGESYANQILRNSKALAEALAERGFKVIGENLGYTKSHQVAVDVRQ 323
           +  A AVT ++ K FG +YAN+++  +KAL+ AL  +G  V     G+T SHQ AV    
Sbjct: 290 KTAALAVTMLDWKAFGSAYANEMIAMAKALSNALDTKGVPVFSGTRGFTNSHQFAVLAAP 349

Query: 324 FGGGNKIAKLLEDANIIVNKNLLPYDKPEDVSDPSGLRIGVQEMTRYGMKEGEMEEIAEL 383
           +GGG   +K L     +     LP +  E   D +GLRIG  E+ R+GM  G+ E +A L
Sbjct: 350 YGGGQAASKQLRKCGFLACGIGLPVELVE--GDMNGLRIGTPELVRWGMTSGDAERLANL 407

Query: 384 FKKVIIDKKDVNEVKKEVIEMRRNFLEVKY 413
             + +       +++ EV   RR F  + Y
Sbjct: 408 IMRGL----GGEQIQSEVSAWRREFDTLHY 433


Lambda     K      H
   0.316    0.134    0.379 

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: 410
Number of extensions: 12
Number of successful extensions: 2
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: 433
Length of database: 435
Length adjustment: 32
Effective length of query: 401
Effective length of database: 403
Effective search space:   161603
Effective search space used:   161603
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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