Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate H281DRAFT_01519 H281DRAFT_01519 fructuronate reductase
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__Burk376:H281DRAFT_01519 Length = 498 Score = 304 bits (779), Expect = 4e-87 Identities = 174/466 (37%), Positives = 263/466 (56%), Gaps = 12/466 (2%) Query: 27 GIVHFGVGNFFRAHEAFYVEQ-ILEHAPDWAIVGVGLTGSDRSKKKAEEFKAQDCLYSLT 85 GIVH G+GNF RAH+A Y E+ +L DW I GV L G D +K+ A Q+ +YS+ Sbjct: 36 GIVHLGIGNFHRAHQALYTEEAMLAEGGDWGICGVTLQG-DVAKRNA--LMEQEGVYSVV 92 Query: 86 ETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVDPAIRIVSMTITEGGYNINETTGAFD 145 E P G + V V+ ALR+ L P D +A+ L DP++RIVS+T+TE GY N TG Sbjct: 93 ERGPEG-AKVTVVRALREVLAMPHDHDALFARLADPSVRIVSLTVTEKGYCRNAKTGDVA 151 Query: 146 LENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGKAFTVMSCDNLRHNGNVARKAFLGY 205 L+N AV DL +P P +V G +V ALR+R DA + FTV+SCDNL HNG R+ + Sbjct: 152 LDNPAVVHDLSHPHAPRSVPGILVAALRQRRDAAREPFTVLSCDNLAHNGAALRQVVCSF 211 Query: 206 AKARDPELAKWIEENATFPNGMVDRITPTVSAEIAKKLNAASGLDDDLPLVAEDFHQWVL 265 A+ DP LA WI FP+ MVDRI P + + AA G D P+ E F QWV+ Sbjct: 212 AREFDPALADWIAVEVAFPSTMVDRIAPATTDFEHATVAAALGYRDAAPVPCEPFRQWVI 271 Query: 266 EDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVMLCFPGILVGYENVDDAIEDSE 325 ED+F GRP G Q+V DVT +E K+RMLN H L + +L G+ +D+AI D Sbjct: 272 EDRFPAGRPAWHAVGAQLVDDVTPFELAKLRMLNGTHSTLAYLSMLGGFTTIDEAIADPA 331 Query: 326 LLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNKAMSDQTLRIASDGCSKVQVFW 385 + + + +++ PTL P+ + YRD++++R++N A+ + +IA DG K+ Sbjct: 332 MRNLIHAMMTEEIAPTLNMPASFDVANYRDALLARYANPALKHRCAQIAMDGSQKIPPRL 391 Query: 386 TETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKGGTYESSEPTYGDAEWKLAKADDFES 445 T+ I+ + +R+A +A ++ LRG + G Y+ S+P + + A A+ Sbjct: 392 LGTIAARIDAGQPFTRLALAVAGWMTFLRGYADDGSRYDISDPLAENLKALAASANGDPR 451 Query: 446 SLKLPAFDGWRDLDTSELDQK------VIVLRKIIREKGVKAAIPA 485 +L + G R++ T+EL + ++ +++++ G +AA+ A Sbjct: 452 AL-MDTLLGVREIFTAELAAQPAFRAALLHALQLLQDNGARAAVAA 496 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: 580 Number of extensions: 26 Number of successful extensions: 2 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: 498 Length adjustment: 34 Effective length of query: 451 Effective length of database: 464 Effective search space: 209264 Effective search space used: 209264 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