Align Mannitol dehydrogenase DSF1; Deletion suppressor of MPT5 mutation protein 1; EC 1.1.1.67 (characterized)
to candidate 18347 b4323 D-mannonate oxidoreductase, NAD-binding (NCBI)
Query= SwissProt::P0CX08 (502 letters) >FitnessBrowser__Keio:18347 Length = 486 Score = 350 bits (897), Expect = e-101 Identities = 188/476 (39%), Positives = 277/476 (58%), Gaps = 9/476 (1%) Query: 21 ESTLPI--PTYPREGVKQGIVHLGVGAFHRSHLAVFMHRLMQEHHLKDWSICGVGLMKA- 77 +S LP+ P++ ++ IVHLG GAFHR+H A++ H L++ DW IC V LM Sbjct: 6 DSNLPVARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTD-SDWGICEVNLMPGN 64 Query: 78 DALMRDAMKAQDCLYTLVERGIKDTNAYIVGSITAYMYAP-DDPRAVIEKMANPDTHIVS 136 D ++ + +K Q LYT+ E+G + T I+GS+ ++ D ++ MA P T IVS Sbjct: 65 DRVLIENLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVS 124 Query: 137 LTVTENGYYHSEATNSLMTDAPEIINDLNHPEKPDTLYGYLYEALLLRYKRGLTPFTIMS 196 LTVTE GY A+ L + P I +DL +P P + GY+ EAL LR ++GL FT+MS Sbjct: 125 LTVTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMS 184 Query: 197 CDNMPQNGVTVKTMLVAFAKLKKDEKFAAWIEDKVTSPNSMVDRVTPRCTDKERKYVADT 256 CDN+ +NG K ++ A+ + D + AAWIE+ VT P +MVDR+ P T + + +AD Sbjct: 185 CDNVRENGHVAKVAVLGLAQAR-DPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQ 243 Query: 257 WGIKDQCPVVAEPFIQWVLEDNFSDGRPPWELVGVQVVKDVDSYELMKLRLLNGGHSAMG 316 G+ D C + EPF QWV+EDNF +GRP W+ VG Q V DV +E+MKLR+LNG HS + Sbjct: 244 LGVYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLA 303 Query: 317 YLGYLAGYTYIHEVVNDPTINKYIRVLMREEVIPLLPKVPGVDFEEYTASVLERFSNPAI 376 YLGYL GY I + V +P K LM +E P L G D Y ++ERFSNP++ Sbjct: 304 YLGYLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSL 363 Query: 377 QDTVARICLMGSGKMPKYVLPSIYEQLRKPDGKYKLLAVCVAGWFRYLTGVDMNGKPFEI 436 + +I + GS K+P+ +L + L+ G ++ LA+ VAGW RY GVD G ++ Sbjct: 364 RHRTWQIAMDGSQKLPQRLLDPVRLHLQN-GGSWRHLALGVAGWMRYTQGVDEQGNAIDV 422 Query: 437 EDPMAPTLKA--AAVKGGKDPHELLNIEVLFSPEIRDNKEFVAQLTHSLETVYDKG 490 DPM + A +G LL + +F+ ++ N +FV +T + + + ++G Sbjct: 423 VDPMLAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERG 478 Lambda K H 0.319 0.136 0.409 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: 662 Number of extensions: 33 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: 502 Length of database: 486 Length adjustment: 34 Effective length of query: 468 Effective length of database: 452 Effective search space: 211536 Effective search space used: 211536 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 (21.7 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