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.
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:
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