Align Kynurenine 3-monooxygenase; Kynurenine 3-hydroxylase; EC 1.14.13.9 (characterized)
to candidate Echvi_1450 Echvi_1450 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
Query= SwissProt::Q11PP7 (449 letters) >FitnessBrowser__Cola:Echvi_1450 Length = 451 Score = 362 bits (929), Expect = e-104 Identities = 191/434 (44%), Positives = 269/434 (61%), Gaps = 6/434 (1%) Query: 2 KEQITICGAGLVGSLLAVYLIERGFSVRVFEKRKDPR-KNEADAGRSINLAISHRGIHAL 60 K ++I GAGL+GSLL +YL +RG V ++EKR D R K A AGRSIN+A+S RG AL Sbjct: 3 KNDVSIIGAGLIGSLLGIYLQKRGLDVSIYEKRPDLRDKKYAPAGRSINMALSDRGWKAL 62 Query: 61 KDAQTGLEKEALKLAVPMYGRAIHDLHGHVSFQAYGEASQHINSIGRGALNKLLITTAEN 120 + GL + +PMYGR +HD HG SF YG+ +Q I SI RG N +L+ AE Sbjct: 63 D--KIGLREMVAPYVIPMYGRRVHDEHGETSFLPYGKENQAIYSISRGKFNHMLVDEAER 120 Query: 121 LGVHFLFEHTCTDYHAAGEQWLFSDITGNTVATQSKEIVIGADGAFSIVRSFLSKQQQPQ 180 G F H+C + A + + + T + +++IGADGA+S +R + +Q + Sbjct: 121 YGAKMNFNHSCEEISIA-DTAIKVVLPDGTQEYRETDVIIGADGAYSSLRDAMQRQTRLN 179 Query: 181 PQIETLEYGYKELEIA-SAHTETITNNQALHIWPRERFMLIALPNEDGSYTATLFLPLKG 239 + E + +GYKEL I +A E + ALHIWPR +FMLIALPN D S+T TLFLP +G Sbjct: 180 YKQEYISHGYKELTIPPTAEGEFAMDPNALHIWPRGQFMLIALPNPDKSFTCTLFLPFEG 239 Query: 240 -EISFEALQSDQDIQLFFKKYFPDTENLFPDLTEQFYRHPTSKLFTIHSSNWFNAHTLLI 298 ++ F+ + ++D++ FK YF D L PDL ++++ +PTS L + W ++LI Sbjct: 240 GKVCFDKINDEEDLESVFKTYFADAFALMPDLNKEYFGNPTSSLINVECFPWLANKSMLI 299 Query: 299 GDAAHALVPFYGQGMNAGFEDCRILAEIIDGKSKTNWSEIFAEFYNQRKENADAISDLAL 358 GDA HA+VPF+GQGMN GFEDC IL +I+ T+W +F +F RK + DAIS++A Sbjct: 300 GDACHAMVPFFGQGMNCGFEDCFILDGLIEKYGTTSWELVFEKFQKVRKPDTDAISEMAR 359 Query: 359 QNFIEMRDHVADASFLLRKKIEKHLHQELEDAFIPQYTMVSFTDISYKEAMETGLLHQKI 418 NF EMRD VA+ FL+RKKIE LH+ +IP YTMV+F+D+ Y +A G L ++ Sbjct: 360 NNFTEMRDSVANPRFLVRKKIEAKLHELYPTEWIPLYTMVTFSDMKYADAYAQGKLQDEV 419 Query: 419 LDEIMAIPDIEAAW 432 +D++M P I W Sbjct: 420 MDKVMEDPMIMQNW 433 Lambda K H 0.320 0.135 0.395 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: 540 Number of extensions: 21 Number of successful extensions: 6 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: 449 Length of database: 451 Length adjustment: 33 Effective length of query: 416 Effective length of database: 418 Effective search space: 173888 Effective search space used: 173888 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 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