Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_011652372.1 RL_RS14710 3-keto-5-aminohexanoate cleavage protein
Query= reanno::psRCH2:GFF3449 (361 letters) >NCBI__GCF_000009265.1:WP_011652372.1 Length = 630 Score = 177 bits (448), Expect = 9e-49 Identities = 112/325 (34%), Positives = 172/325 (52%), Gaps = 6/325 (1%) Query: 17 GFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVLNGSPTGHVHA 76 G EF+EF A +AE ++L MGF +H+SK V L +Q INI+LN TG ++ Sbjct: 290 GVEFIEF-ATSAEDADELAAFLHIMGFKTYGRHKSKAVTLLRQGGINILLNTERTGFAYS 348 Query: 77 FAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEGIGGSLLYLVD 136 HG SA A+ +V +A A ++ GA+ + GEL IP + G+GG L+Y VD Sbjct: 349 SFVVHGTSAYAVCLKVDDARDAVERAKALGAEPFEQSVSPGELTIPAIRGVGGGLVYFVD 408 Query: 137 RYGDK-SIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDVWSGFYERIANFREIR 195 + S++ +DFE +E T A GL +DH+ + ++ W FY I + R+ Sbjct: 409 EKSELGSLWGIDFEPVE-ETDAGMAAGLFRVDHVGQTMKADELPSWLLFYLSIFDLRKTP 467 Query: 196 YFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQHIALSTDDIY 255 DI + S+ + + G +RI +N + + ++ FI E G IQH+A +T DI+ Sbjct: 468 MIDIVDPSGLVRSQVVESADGALRITMNGADNRRTLAGHFIAENFGSSIQHLAFATADIF 527 Query: 256 ATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAPGDDGILLQIFT 315 AT L+ANG + P YY+ V+ R + D LRE NIL D + G LQ+++ Sbjct: 528 ATAEALKANGFSPLKIPRNYYDDVEARFGLNPVMADRLREANILYD--RDEQGEYLQLYS 585 Query: 316 NTVIGPIFFEIIQRKGN-QGFGEGN 339 + FFEI++R+G +G+G N Sbjct: 586 PSFREGFFFEIVERRGGYRGYGAPN 610 Lambda K H 0.320 0.139 0.412 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: 560 Number of extensions: 30 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: 361 Length of database: 630 Length adjustment: 33 Effective length of query: 328 Effective length of database: 597 Effective search space: 195816 Effective search space used: 195816 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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