GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Phyllobacterium endophyticum PEPV15

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_106715300.1 CU100_RS04475 prephenate dehydratase

Query= CharProtDB::CH_024084
         (386 letters)



>NCBI__GCF_003010935.1:WP_106715300.1
          Length = 288

 Score =  147 bits (370), Expect = 5e-40
 Identities = 99/277 (35%), Positives = 139/277 (50%), Gaps = 9/277 (3%)

Query: 105 RIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSG 164
           RI+F G  G+ S  A R      F       C  F D FN VE+G AD A++PIENT +G
Sbjct: 7   RISFQGEPGANSDTACRDM----FPNMEPMPCPTFEDAFNAVESGTADLAMIPIENTIAG 62

Query: 165 AINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYP 224
            + D++ LL  + L IVGE  L I   L+V   T  S I +V+SH     QC K++ R  
Sbjct: 63  RVADIHHLLPESRLHIVGEYFLPIHFQLMVLPGTTRSEITSVHSHIHALGQCRKYI-RQN 121

Query: 225 HWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLA 284
            WK      T+ A   VA+ K   +AAL      +LYGL +LE    +   N TRFVVL 
Sbjct: 122 GWKPVIAGDTAGAARLVAEVKDKTMAALAPRLASSLYGLDILEEDVEDTENNVTRFVVLT 181

Query: 285 RK---AINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEM 341
           +    A   SD++   TT +        AL +A+     + + MT+LES  I G      
Sbjct: 182 KTKEWAPRTSDKL-MMTTFVFRVRNVPAALYKAMGGFATNMVNMTKLESYQIDGKFTATQ 240

Query: 342 FYLDIQANLESAEMQKALKELGEITRSMKVLGCYPSE 378
           FY DI+ + +   +  AL EL   +R +++LG YP++
Sbjct: 241 FYADIEGHPDDKNVAHALDELEFFSREVRILGVYPAD 277


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: 190
Number of extensions: 8
Number of successful extensions: 3
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: 288
Length adjustment: 28
Effective length of query: 358
Effective length of database: 260
Effective search space:    93080
Effective search space used:    93080
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