Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate WP_086511126.1 BZY95_RS17225 mannitol dehydrogenase family protein
Query= curated2:P39160 (486 letters) >NCBI__GCF_002151265.1:WP_086511126.1 Length = 491 Score = 357 bits (915), Expect = e-103 Identities = 201/478 (42%), Positives = 274/478 (57%), Gaps = 7/478 (1%) Query: 11 VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDS-DWGICEVNLMPGNDRVLI 69 VA P +D + IVH+G G FHRAHQA+Y L+ ++ DWGI V +MPG DR + Sbjct: 16 VAVPRYDRREVTPGIVHIGVGGFHRAHQAMYLDALMNRGEALDWGIVGVGVMPG-DRRMQ 74 Query: 70 ENLKKQQLLYTVAEKGAEST-ELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVT 128 E L Q LYT+ K E ++IG+M + L+ D E ++ MA P IVSLTVT Sbjct: 75 EVLAAQDHLYTLVVKHPNGEREPRVIGAMLDYLYAP-DDPEAVVERMADPAIRIVSLTVT 133 Query: 129 EKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNV 188 E GY +G+ DL NP ++HDL++P AP++ G +VEAL RR +GL FT+MSCDN+ Sbjct: 134 EGGYNFHPVTGEFDLANPDVRHDLDSPAAPRTTFGLVVEALARRRARGLAPFTLMSCDNI 193 Query: 189 RENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYD 248 + NG VA+ + A+ARDP LA WIE V FP MVDRI P ++E+A + GV D Sbjct: 194 QGNGEVARRMFVAFARARDPALAEWIEAEVPFPNAMVDRITPVTQAVDIEELAGEFGVED 253 Query: 249 PCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYL 308 + CEPF QWV+ED+F+ GRP +++VG Q V DV P+E+MKLR+LN SH L Y G L Sbjct: 254 AWPVVCEPFTQWVLEDHFICGRPAFERVGVQVVEDVEPYELMKLRLLNASHQALCYFGTL 313 Query: 309 GGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTW 368 GY + +P + M E +PTL+ G DL Y LIERF+NP ++ Sbjct: 314 AGYRYAHEVCRDPLFVDFLLGYMRHEGSPTLAPVPGVDLEQYRLTLIERFANPEIKDTLA 373 Query: 369 QIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLA 428 ++ + S ++P+ L+ +R L GG A VA W RY +G+DEQG I VVD + Sbjct: 374 RLCAESSDRIPKWLVPVIREQLAKGGEIHRSAAVVASWARYAEGLDEQGEPITVVDRLKH 433 Query: 429 EFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAAL 486 E + A + R A + +F DL ++ F A A L ERGAR + L Sbjct: 434 ELAALAA--ENRTRPGAFIENRELFG-DLAEHERFRQAYLMALTSLHERGARATLETL 488 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: 667 Number of extensions: 30 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: 491 Length adjustment: 34 Effective length of query: 452 Effective length of database: 457 Effective search space: 206564 Effective search space used: 206564 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 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