Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate SMc01501 SMc01501 mannitol 2-dehydrogenase
Query= curated2:P39160 (486 letters) >FitnessBrowser__Smeli:SMc01501 Length = 494 Score = 291 bits (746), Expect = 3e-83 Identities = 182/469 (38%), Positives = 242/469 (51%), Gaps = 9/469 (1%) Query: 14 PSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLE-STDSDWGICEVNLMPGNDRVLIENL 72 P++ L + IVH G G FHRAHQA+Y L D DW I ++P +D+V+ + L Sbjct: 20 PNYGRHDLRAGIVHFGVGNFHRAHQAVYLDDLFNLGRDRDWAIIGAGVLP-SDKVMRDKL 78 Query: 73 KKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGY 132 + Q L TV E+ T + G+M L P I+ +A P IVSLT+TE GY Sbjct: 79 EAQDFLTTVVEQDNNRTGAHVTGAMIAYLEP--GDTPAIVAQLASPLIRIVSLTITEGGY 136 Query: 133 CADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENG 192 D ASG D +P I D +P APK+ G I+ L RR KG+ FT+MSCDN+ NG Sbjct: 137 FIDPASGVFDPAHPAIVEDARDPAAPKTVFGLILAGLAERRAKGIPPFTIMSCDNIPGNG 196 Query: 193 HVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAI 252 V AV GLA+ DP A WI+ NV FP MVDRI PA + +A Q G+ D + Sbjct: 197 EVTHAAVSGLARLSDPGFADWIDANVAFPNGMVDRITPATGAREIGIVASQYGIDDAWPV 256 Query: 253 ACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYE 312 CE F+QWV+ED F GRP ++VG QFV DV P+E MK+R+LNG H+ +AY L Sbjct: 257 FCEEFKQWVLEDRFPQGRPALEEVGVQFVPDVAPYEHMKIRILNGGHAAIAYPAALLDIH 316 Query: 313 TIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAM 372 + + + P R L E P + TDL Y L+ RFSNP + ++A Sbjct: 317 FVHEAMEEPLIRAFLSKLEHDEIIPVIPPVPDTDLKDYYKLIETRFSNPKIGDTVARLAQ 376 Query: 373 DGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQK 432 DGS + P+ +L L+ G L+L A W RY G + G I D A + Sbjct: 377 DGSNRQPKFILPSTADRLRRGEDVVGLSLVSALWCRYFAGKSDSGKEIVFND---ANADR 433 Query: 433 INAQYQGA-DRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGAR 480 ++A A D A L LS IF D+ Q+ F A + L E+G R Sbjct: 434 LHAAAVAAKDDPMAFLALSDIFG-DVAQSDLFRRRFAHALKVLWEKGTR 481 Lambda K H 0.320 0.135 0.408 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: 597 Number of extensions: 24 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: 486 Length of database: 494 Length adjustment: 34 Effective length of query: 452 Effective length of database: 460 Effective search space: 207920 Effective search space used: 207920 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 (21.8 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