GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Novosphingobium barchaimii LL02

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_059152706.1 V474_RS17425 prephenate dehydratase

Query= CharProtDB::CH_024084
         (386 letters)



>NCBI__GCF_001046635.1:WP_059152706.1
          Length = 299

 Score =  122 bits (305), Expect = 2e-32
 Identities = 88/273 (32%), Positives = 131/273 (47%), Gaps = 10/273 (3%)

Query: 106 IAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGA 165
           +A  G  G   H AA +Y A      +   C  F D  + V+ G+A  A++PIEN+  G 
Sbjct: 27  VALQGAPGCNGHRAALEYDA----DCLPLPCFSFEDALDAVKEGRAARAIIPIENSQHGR 82

Query: 166 INDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPH 225
           + D++ LL  + LSIVGE  ++I H L+          +  YSHPQ   Q   +L     
Sbjct: 83  VADIHFLLPESGLSIVGEHFMSIHHALMALPGAK-GPFSAAYSHPQALGQSRHYLRERGI 141

Query: 226 WKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLAR 285
             + Y + T+ A   V +A  P+  A+  +    LYGL V+E    +   N TRFVVLAR
Sbjct: 142 VPMAYAD-TAGAAALVREAGDPNSCAIAPKLAAQLYGLDVIEENVEDAADNTTRFVVLAR 200

Query: 286 KAIN---VSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMF 342
           + ++   + DQ PA TT +        AL +AL     + + MT+LES     +     F
Sbjct: 201 EPLDPFELKDQ-PAMTTFIFEVKNIPAALYKALGGFATNGVNMTKLESYQAQASFAATTF 259

Query: 343 YLDIQANLESAEMQKALKELGEITRSMKVLGCY 375
           Y DI+     A +  AL+EL    + ++ LG Y
Sbjct: 260 YADIEGAPGEARVDMALQELAFHCKYVRPLGTY 292


Lambda     K      H
   0.318    0.132    0.374 

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: 231
Number of extensions: 12
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: 386
Length of database: 299
Length adjustment: 28
Effective length of query: 358
Effective length of database: 271
Effective search space:    97018
Effective search space used:    97018
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 (21.8 bits)
S2: 49 (23.5 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