Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate BPHYT_RS23425 BPHYT_RS23425 mannitol dehydrogenase
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__BFirm:BPHYT_RS23425 Length = 496 Score = 300 bits (769), Expect = 6e-86 Identities = 181/492 (36%), Positives = 270/492 (54%), Gaps = 15/492 (3%) Query: 2 ITRETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQ-ILEHAPDWAIVGV 60 + R+ L +L ++ +P + I GIVH G+GNF RAH+A Y E+ +L DW I GV Sbjct: 10 LVRQALPTLQTHLLSPLWQEPRI--GIVHLGIGNFHRAHQALYTEEAMLAAGGDWGICGV 67 Query: 61 GLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVD 120 L G D K+ A Q LYS+ E P G + V V+ ALR+ L P D A+ L D Sbjct: 68 TLQG-DVGKRDA--LMEQQGLYSVVERGPHG-AKVTVVRALREVLAMPHDQAALFARLAD 123 Query: 121 PAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWD-AG 179 PA+RIVS+T+TE GY + TG L+N AV DL +P +P TV G +V ALR+R D A Sbjct: 124 PAVRIVSLTVTEKGYCRDPRTGEVALDNPAVAHDLASPFEPRTVPGILVAALRQRHDDAR 183 Query: 180 GKAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEI 239 G+ FTV+SCDNL HNG R+ +A+ DP LA WI + FP+ MVDRI P + Sbjct: 184 GQPFTVLSCDNLSHNGAALRQVVCSFARQLDPALADWIAAHVAFPSTMVDRIVPATTHAE 243 Query: 240 AKKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLN 299 + + A D P+ E F QWV+ED+F GRP + G Q+V DVT +E K+RMLN Sbjct: 244 SVTVAHAIVYQDAAPVPCEPFRQWVIEDRFPAGRPAWDAVGAQLVDDVTPFELAKLRMLN 303 Query: 300 AGHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVIS 359 H L + +L G+E +D AI + + + +++ PTL P+ L YRD+++ Sbjct: 304 GTHSTLAYLSMLGGFETIDAAISYPPMRNLIHAMMTEEIAPTLTMPASFDLSAYRDALLE 363 Query: 360 RFSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEK 419 R++N A+ + +IA DG K+ +T+ I+ + +R+ +A+++ LRG + Sbjct: 364 RYANPALKHRCSQIAMDGSQKIPPRLLDTIAARIDAGQSFTRLVLAVAAWMMFLRGHADD 423 Query: 420 GGTYESSEPTYGDAEWKLAKADDFESSLKLPAFDGWRDLDTSELD------QKVIVLRKI 473 G YE S+P A D +L + A R++ ++L + ++ ++ Sbjct: 424 GTRYEISDPLASRLHALAVSAHDDPQAL-MDALLSVREVFPADLTAFPEFREALLRALRL 482 Query: 474 IREKGVKAAIPA 485 +RE+G + AI A Sbjct: 483 LREEGARGAIAA 494 Lambda K H 0.317 0.135 0.398 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: 549 Number of extensions: 36 Number of successful extensions: 3 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: 485 Length of database: 496 Length adjustment: 34 Effective length of query: 451 Effective length of database: 462 Effective search space: 208362 Effective search space used: 208362 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 (21.6 bits) S2: 52 (24.6 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