Align Kynurenine 3-monooxygenase; PfKMO; Kynurenine 3-hydroxylase; EC 1.14.13.9 (characterized)
to candidate WP_007508973.1 R2APBS1_RS11660 FAD-dependent monooxygenase
Query= SwissProt::Q84HF5 (461 letters) >NCBI__GCF_000230695.2:WP_007508973.1 Length = 467 Score = 442 bits (1138), Expect = e-129 Identities = 242/464 (52%), Positives = 298/464 (64%), Gaps = 18/464 (3%) Query: 10 VTIIGAGLAGTLVARLLARNGWQVNLFERRPDPRIETGARGRSINLALAERGAHALRLAG 69 +T+IG GL G L+A+ LA G+ V+++E+RPDPR+ GRSINLALAERG ALR AG Sbjct: 6 ITLIGGGLVGALLAQQLAGRGFTVDVYEKRPDPRLAGFIGGRSINLALAERGLQALRTAG 65 Query: 70 LEREVLAEAVMMRGRMVHVPGTPPNLQPYGRDDSEVIWSINRDRLNRILLDGAEAAGASI 129 L +VL AVMMRGRMVH LQ YG DDSEVIWS++R LN +LLD AEAAGA Sbjct: 66 LAEDVLQRAVMMRGRMVHDRDGHSGLQRYGVDDSEVIWSVSRGALNMLLLDAAEAAGARF 125 Query: 130 HFNLGLDSVDFARQRLTLSNVSGERLEKRFHLLIGADGCNSAVRQAMASVVDLGEHLETQ 189 HF L DF RQR+ L++ +G + E+ LLIGADG S VR AM + LGE +E+ Sbjct: 126 HFGQSLVGADFGRQRIRLADEAGVQHERDAGLLIGADGAGSTVRAAMNAHAPLGERIESL 185 Query: 190 PHGYKELQITPEASA------------QFNLEPNALHIWPHGDYMCIALPNLDRSFTVTL 237 HGYKEL+I P QF LEP+ALHIWP G YMCIALPN + SFTVTL Sbjct: 186 GHGYKELEIPPAGELPAAVLSHSGGRDQFALEPHALHIWPRGGYMCIALPNTEGSFTVTL 245 Query: 238 FLHHQSPAAQPASPCFAQLVDGHAARRFFQRQFPDLSPMLDSLEQDFEHHPTGKLATLRL 297 FL AQ A+P FA L D AA FF+ QFP L P++ +DF+ HP G L+TL L Sbjct: 246 FL-----PAQSAAPSFASLPDAAAAAAFFREQFPGLLPLIPRFNEDFDSHPVGTLSTLYL 300 Query: 298 TTWHVGGQAVLLGDAAHPMVPFHGQGMNCALEDAVALAEHLQSA-ADNASALAAFTAQRQ 356 WH+ G+A+LLGDAAH +VPFHGQGMNC ED V LA L A D+A A F RQ Sbjct: 301 ERWHLDGRALLLGDAAHAIVPFHGQGMNCGFEDTVVLANLLAEAPGDSADVFAEFQRVRQ 360 Query: 357 PDALAIQAMALENYVEMSSKVASPTYLLERELGQIMAQRQPTRFIPRYSMVTFSRLPYAQ 416 P+A AI AMALENYVEM VA P YL +RELG +A+R P ++ RY MVTF+ +PYA Sbjct: 361 PNADAIAAMALENYVEMRDSVADPHYLAKRELGTKLAERIPGHYMARYRMVTFTHVPYAY 420 Query: 417 AMARGQIQEQLLKFAVANHSDLTSINLDAVEHEVTRCLPPLSHL 460 A+ RG+ Q+ LL+ + + + I+++A L PL L Sbjct: 421 ALERGRAQDHLLEQLLRDTPRVADIDIEAAARLFQSTLEPLPRL 464 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: 637 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: 467 Length adjustment: 33 Effective length of query: 428 Effective length of database: 434 Effective search space: 185752 Effective search space used: 185752 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 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