Align (S)-2-hydroxyglutarate oxidase (characterized)
to candidate BPHYT_RS28480 BPHYT_RS28480 hydroxyglutarate oxidase
Query= metacyc::G1G01-3089-MONOMER (416 letters) >FitnessBrowser__BFirm:BPHYT_RS28480 Length = 398 Score = 454 bits (1169), Expect = e-132 Identities = 226/392 (57%), Positives = 284/392 (72%), Gaps = 1/392 (0%) Query: 2 YDFIIIGGGIVGMSTAMHLIKVYPDAKMLLLEKESGPARHQTGHNSGVIHAGVYYTPGSL 61 YDF IIGGGIVG++TAM L++ P A +LLLEKE+ A+HQTGHNSGVIHAG+YY PGSL Sbjct: 3 YDFCIIGGGIVGLATAMELLQREPTASLLLLEKETTLAKHQTGHNSGVIHAGIYYQPGSL 62 Query: 62 KARFCLEGNKATKAFCTQHGIRFDECGKLLVATNDLEMQRMKALWERTAANGLERYWLSA 121 KA C G +ATK FCT+H I FD CGKLLVA+N LE+ RM+AL+ R+ NGL L A Sbjct: 63 KAELCKRGAEATKQFCTEHAIPFDVCGKLLVASNPLELSRMEALYARSQQNGLRVERLDA 122 Query: 122 DELREREPNIVGMGGIFVPSSGIVNYAQVTAAMAAEFQRAGGEIRYGAEVVGLQEQANEV 181 EL+ REPNIVG+GG+F+ ++GIV+Y QV AMA ++AGGEIR G +V + E + V Sbjct: 123 AELQRREPNIVGLGGLFLDATGIVDYRQVCEAMARVIEKAGGEIRLGTQVTSIAEVGDYV 182 Query: 182 IV-RTQRDELHSRFLVTCSGLMADRVVGMLGLRTEFVICPFRGEYYLLPKQHNQIVNHLI 240 V + + ++ LV C GL +DR+ + G++ + I PFRGEYY LP N +V HLI Sbjct: 183 TVGASDEQQWRAKKLVVCGGLQSDRLARLAGVKIDHQIVPFRGEYYRLPASKNDVVRHLI 242 Query: 241 YPIPDPSMPFLGVHLTRMIDGTVTVGPNAVLAMKREGYRKTDVSPSDLFQTLTTPGILKV 300 YPIPDP +PFLGVHLTRMIDG+VTVGPNAVL RE Y K V+ D+ + PG K Sbjct: 243 YPIPDPDLPFLGVHLTRMIDGSVTVGPNAVLGFGRENYPKFSVNLRDVAEYAAFPGFWKT 302 Query: 301 LAKNFRPGLIEMKNSLFKGGYLKQVQKYCPSIIKADLTPYPAGVRAQAVSRDGKLIDDFL 360 + +N G+ EMKNSLFK GYL+Q +KYCPS+ DL PY AG+RAQAV RDG L+ DFL Sbjct: 303 IWRNLGSGMGEMKNSLFKRGYLEQCRKYCPSLTVDDLLPYEAGIRAQAVMRDGTLVHDFL 362 Query: 361 FVNTARSVNVCNAPSPAATSAIPIGAYIVEKV 392 F +T R V+VCNAPSPAATSA+PIG+ I +++ Sbjct: 363 FADTPRMVHVCNAPSPAATSAMPIGSMIADRI 394 Lambda K H 0.321 0.137 0.409 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: 528 Number of extensions: 22 Number of successful extensions: 2 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: 416 Length of database: 398 Length adjustment: 31 Effective length of query: 385 Effective length of database: 367 Effective search space: 141295 Effective search space used: 141295 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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