Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_011841614.1 RSPH17029_RS11915 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_000015985.1:WP_011841614.1 Length = 277 Score = 135 bits (340), Expect = 1e-36 Identities = 95/278 (34%), Positives = 142/278 (51%), Gaps = 8/278 (2%) Query: 103 SARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTS 162 + RIAF G G+YSH A RQ AR + I C F D+ V G+AD A++P+EN++ Sbjct: 2 TGRIAFQGEPGAYSHQACRQ--ARPEMEAIP--CRTFEDVIELVRAGEADLAMLPVENST 57 Query: 163 SGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNR 222 G + D++ LL + L IV E + + LL T + + SH QC FL Sbjct: 58 YGRVADIHTLLPGSGLRIVDESFVRVHINLLTLRGTPIEQVERAMSHTVLLGQCRTFLRG 117 Query: 223 YPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVV 282 + + + T+ + VA+ P +AAL SE G +YGL V+ R +Q N TRF+V Sbjct: 118 HDIRPVTGAD-TAGSARLVAEQGDPALAALASELAGEIYGLDVVARHIEDQSNNTTRFLV 176 Query: 283 LARKAINVSDQVPAK--TTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEE 340 +AR+A + + + P K TT AL +AL + + MT+LES + G+ Sbjct: 177 MAREA-DWTRRGPGKMVTTFTFRVRNIPAALYKALGGFATNGINMTKLESYMVGGSFTAT 235 Query: 341 MFYLDIQANLESAEMQKALKELGEITRSMKVLGCYPSE 378 FY DI+ + E + AL EL T ++LG YP++ Sbjct: 236 EFYADIEGHPEDGNVALALDELRFFTSQSEILGVYPAD 273 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: 10 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: 277 Length adjustment: 28 Effective length of query: 358 Effective length of database: 249 Effective search space: 89142 Effective search space used: 89142 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: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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