Align Kynurenine 3-monooxygenase; PfKMO; Kynurenine 3-hydroxylase; EC 1.14.13.9 (characterized)
to candidate N515DRAFT_2874 N515DRAFT_2874 kynurenine 3-monooxygenase
Query= SwissProt::Q84HF5 (461 letters) >FitnessBrowser__Dyella79:N515DRAFT_2874 Length = 470 Score = 436 bits (1122), Expect = e-127 Identities = 242/471 (51%), Positives = 294/471 (62%), Gaps = 18/471 (3%) Query: 3 ATDNARQVTIIGAGLAGTLVARLLARNGWQVNLFERRPDPRIETGARGRSINLALAERGA 62 A+ +T+IG GL G L+A+ LAR G+ V ++E+R DPR GRSINLALAERG Sbjct: 2 ASTQQPSITLIGGGLVGALLAQQLARRGFPVEVYEKRADPRRAGFTGGRSINLALAERGL 61 Query: 63 HALRLAGLEREVLAEAVMMRGRMVHVPGTPPNLQPYGRDDSEVIWSINRDRLNRILLDGA 122 ALR AGL +VL AVMMRGRMVH LQ YG DDSEVIWS++R LN +LLD A Sbjct: 62 QALRTAGLADDVLTRAVMMRGRMVHTRDGRSGLQRYGVDDSEVIWSVSRGALNMLLLDAA 121 Query: 123 EAAGASIHFNLGLDSVDFARQRLTLSNVSGERLEKRFHLLIGADGCNSAVRQAMASVVDL 182 EAAG HF L + DF +R+ L++ G +LIGADG SA+R AM + L Sbjct: 122 EAAGVRFHFGQSLVAADFDARRVRLADEQGVERSIDAGVLIGADGAGSALRAAMHAYRPL 181 Query: 183 GEHLETQPHGYKELQITPEASA------------QFNLEPNALHIWPHGDYMCIALPNLD 230 GE +E H YKEL+I P QF +EP+ALHIWP G YMCIALPN + Sbjct: 182 GERIEPLGHAYKELEIPPAGQLPAGLLGDSGGHDQFAIEPHALHIWPRGGYMCIALPNTE 241 Query: 231 RSFTVTLFLHHQSPAAQPASPCFAQLVDGHAARRFFQRQFPDLSPMLDSLEQDFEHHPTG 290 SFTVTLFL AQ A P FA L D AA FF+ FPDL P++ D+ HP G Sbjct: 242 GSFTVTLFL-----PAQGAHPSFATLPDAAAAETFFRDDFPDLLPLIPDFADDYGSHPVG 296 Query: 291 KLATLRLTTWHVGGQAVLLGDAAHPMVPFHGQGMNCALEDAVALAEHLQSA-ADNASALA 349 L+TL L WH+ G+A+L+GDAAH +VPFHGQGMNC ED VALA L A D A A A Sbjct: 297 TLSTLYLERWHIDGRALLIGDAAHAIVPFHGQGMNCGFEDTVALAALLAEAPQDVADAFA 356 Query: 350 AFTAQRQPDALAIQAMALENYVEMSSKVASPTYLLERELGQIMAQRQPTRFIPRYSMVTF 409 F RQP+A AI AMALENY+EM VA P YL +RELG ++A+R P F+ RY MVTF Sbjct: 357 EFQRVRQPNANAIAAMALENYIEMRDSVADPHYLAKRELGVLLAERAPQHFMARYRMVTF 416 Query: 410 SRLPYAQAMARGQIQEQLLKFAVANHSDLTSINLDAVEHEVTRCLPPLSHL 460 + LPYA A RG+ Q+QLL+ + +D S++LDA + LPPL L Sbjct: 417 THLPYAYAYDRGRAQDQLLQQLLRGSTDPRSVDLDAATTALQATLPPLPSL 467 Lambda K H 0.321 0.134 0.399 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: 622 Number of extensions: 21 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: 461 Length of database: 470 Length adjustment: 33 Effective length of query: 428 Effective length of database: 437 Effective search space: 187036 Effective search space used: 187036 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: 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