Align Mannitol dehydrogenase DSF1; Deletion suppressor of MPT5 mutation protein 1; EC 1.1.1.67 (characterized)
to candidate 15664 b1542 predicted mannonate dehydrogenase (NCBI)
Query= SwissProt::P0CX08 (502 letters) >FitnessBrowser__Keio:15664 Length = 486 Score = 347 bits (891), Expect = e-100 Identities = 196/483 (40%), Positives = 277/483 (57%), Gaps = 11/483 (2%) Query: 17 LKSFESTLPIPTYPREGVKQGIVHLGVGAFHRSHLAVFMHRLMQEHHLKDWSICGVGLMK 76 L S ++TLP+ Y + IVHLG GAFHR+H V+ L EH DW V L+ Sbjct: 5 LLSAKATLPV--YDLNNLAPRIVHLGFGAFHRAHQGVYADILATEH-FSDWGYYEVNLIG 61 Query: 77 ADALMRDAMKAQDCLYTLVERGIKDTNAYIVGSITAYMYAP-DDPRAVIEKMANPDTHIV 135 + + D ++ QD LYT+ E A +VG + ++ D V+ M P IV Sbjct: 62 GEQQIAD-LQQQDNLYTVAEMSADVWTARVVGVVKKALHVQIDGLETVLAAMCEPQIAIV 120 Query: 136 SLTVTENGYYHSEATNSLMTDAPEIINDLNHPEKPDTLYGYLYEALLLRYKRGLTPFTIM 195 SLT+TE GY+HS AT LM D P + D+ +P +P T G + EAL R GL FT+M Sbjct: 121 SLTITEKGYFHSPATGQLMLDHPMVAADVQNPHQPKTATGVIVEALARRKAAGLPAFTVM 180 Query: 196 SCDNMPQNGVTVKTMLVAFAKLKKDEKFAAWIEDKVTSPNSMVDRVTPRCTDKERKYVAD 255 SCDNMP+NG ++ ++ ++A+ D K A WIED VT P++MVDR+ P T+ + Sbjct: 181 SCDNMPENGHVMRDVVTSYAQAV-DVKLAQWIEDNVTFPSTMVDRIVPAVTEDTLAKIEQ 239 Query: 256 TWGIKDQCPVVAEPFIQWVLEDNFSDGRPPWELVGVQVVKDVDSYELMKLRLLNGGHSAM 315 G++D V EPF QWV+EDNF GRP WE G ++V DV YE MKLR+LNG HS + Sbjct: 240 LTGVRDPAGVACEPFRQWVIEDNFVAGRPEWEKAGAELVSDVLPYEEMKLRMLNGSHSFL 299 Query: 316 GYLGYLAGYTYIHEVVNDPTINKYIRVLMREEVIPLLPKVPGVDFEEYTASVLERFSNPA 375 YLGYLAGY +I++ + D LM +E P L KV GVD ++Y ++ R+SNPA Sbjct: 300 AYLGYLAGYQHINDCMEDEHYRYAAYGLMLQEQAPTL-KVQGVDLQDYANRLIARYSNPA 358 Query: 376 IQDTVARICLMGSGKMPKYVLPSIYEQLRKPDGKYKLLAVCVAGWFRYLTGVDMNGKPFE 435 ++ +I + GS K+P+ +L S+ L D K+ LLA+ VAGW RY+ GVD G P E Sbjct: 359 LRHRTWQIAMDGSQKLPQRMLDSVRWHLAH-DSKFDLLALGVAGWMRYVGGVDEQGNPIE 417 Query: 436 IEDPMAPTLKAA---AVKGGKDPHELLNIEVLFSPEIRDNKEFVAQLTHSLETVYDKGPI 492 I DP+ P ++ A + +G LL I+ +F ++ DN F A++T + ++ G Sbjct: 418 ISDPLLPVIQKAVQSSAEGKARVQSLLAIKAIFGDDLPDNSLFTARVTETYLSLLAHGAK 477 Query: 493 AAI 495 A + Sbjct: 478 ATV 480 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: 643 Number of extensions: 30 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