Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate BPHYT_RS30565 BPHYT_RS30565 dihydropteridine reductase
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__BFirm:BPHYT_RS30565 Length = 393 Score = 268 bits (684), Expect = 3e-76 Identities = 160/401 (39%), Positives = 219/401 (54%), Gaps = 14/401 (3%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 ML A+ A VKAT+PLL G LT HFYD + + +PE++ +FN++NQ +G Q+ AL N Sbjct: 1 MLSAEHRAIVKATVPLLESGGEALTTHFYDMLISEHPEVRPMFNLANQASGAQQRALANG 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFS---PGQEVL 117 + YA +I+ L L V +I KH + I PE Y IVG+ LL ++ E+ V+ Sbjct: 61 VLMYARHIDQLEQLGGLVSQIINKHVALNILPEHYPIVGQCLLRSIREVLGAEIATDAVI 120 Query: 118 DAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDG 177 +AW AY LA++ E ++Y E + GGW GTR FR+ K S ITSF L P D Sbjct: 121 EAWAAAYQQLADLLSGLEEKMYAEREAAPGGWRGTRLFRVARKVRESDEITSFYLRPADN 180 Query: 178 GAVAEYRPGQYLGVWLKPEGFPHQEIRQ-YSLTRKPDGKGYRIAVKREEGGQVSNWLHNH 236 G + + PGQY+GV L +G +E+R+ YSL+ +G+ YRI+VKRE G+VSN LH Sbjct: 181 GELLAFHPGQYIGVRLVIDG---EEVRRNYSLSAMSNGEEYRISVKREANGKVSNHLHAR 237 Query: 237 ANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHAA 296 N D V+L APAGDF + D P+ LIS GVG TP LAML K V++ H+A Sbjct: 238 VNENDTVELFAPAGDFKLE-DSDKPLVLISGGVGITPTLAMLQAALKTDR--PVHFIHSA 294 Query: 297 ENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAF-SDP 355 +G VHAF D + +L P+ Y Q D G +D +L+ Sbjct: 295 RHGGVHAFRDVIDQLAARHPKLKRFYCYEQRRAED---ADAHGIGYLDEKRLDAWLPRTR 351 Query: 356 TMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396 + Y GP+ FM+ K L +GV + YE FGP L Sbjct: 352 DVDVYFLGPIAFMKAIKKHLKAIGVPESQSRYEFFGPASAL 392 Lambda K H 0.318 0.135 0.404 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: 373 Number of extensions: 24 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: 396 Length of database: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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