Align prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_014449221.1 LFE_RS05290 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000284315.1:WP_014449221.1 Length = 361 Score = 181 bits (460), Expect = 4e-50 Identities = 117/357 (32%), Positives = 186/357 (52%), Gaps = 16/357 (4%) Query: 264 ESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEV--MSK 321 E + LR I ID+ I+ L+ R A ++ K R P + E E L + + Sbjct: 3 EDLGNLRNSIDEIDTRIVGLLRDRAAIAARVGDYKKARALPFHVVSREREILDRITELES 62 Query: 322 TTLNPVKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYC 381 ++ IF I+S E V I+ +GP +++ + ALK G + Sbjct: 63 APFPKESIRTIFREILSACLSLEEPVV-----ISYMGPPATYTHQAALKHFGHSLKHVPA 117 Query: 382 STTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKR 441 +T E+ + VESGE YG+VPIENS G V +D L+ D+ + GE L ++HCL+ R Sbjct: 118 ATVREVFRAVESGEALYGVVPIENSTEGMVNNTLDTLVESDLRICGEIILPIHHCLLT-R 176 Query: 442 KIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSENA 499 KEI+T+Y+HPQA+AQC +++N LP + TTS + A M D +SAAI E A Sbjct: 177 ATSAKEIRTVYAHPQALAQCRIYLSNALPDASTGETTSNTKAVEMALEDPHSAAIAGEMA 236 Query: 500 ARFYRLHVLRKGIQDLKGRNITRFYLIRR-RSGRSEGKITSLFFGVEDKPGALKDVLEVF 558 A Y + + + I+D N TRF +I G++ TS+ + D+ GAL ++L + Sbjct: 237 AEVYNIPIFSRHIEDFPD-NQTRFLVIGTIDPGKTRKDQTSIMVSILDRVGALSEILSLI 295 Query: 559 HKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTFYKVVGVF 611 +G NL +LESRP+ DY+FF+++E +E+ L L+ + + +++G + Sbjct: 296 ATEGINLTRLESRPSRKKAWDYIFFMDIEGHQADENIRQLLTKLQTLCPYVRILGSY 352 Lambda K H 0.320 0.137 0.380 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: 405 Number of extensions: 16 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: 620 Length of database: 361 Length adjustment: 33 Effective length of query: 587 Effective length of database: 328 Effective search space: 192536 Effective search space used: 192536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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