Align Mannitol dehydrogenase DSF1; Deletion suppressor of MPT5 mutation protein 1; EC 1.1.1.67 (characterized)
to candidate H281DRAFT_02952 H281DRAFT_02952 fructuronate reductase
Query= SwissProt::P0CX08 (502 letters) >FitnessBrowser__Burk376:H281DRAFT_02952 Length = 497 Score = 333 bits (853), Expect = 1e-95 Identities = 189/476 (39%), Positives = 266/476 (55%), Gaps = 15/476 (3%) Query: 26 IPTYPREGVKQGIVHLGVGAFHRSHLAVFM-HRLMQEHHLKDWSICGVGLMKADALMRDA 84 +PTY R + GIVHLG+GAFHR+H AV+ H L H W I GV L +AD +A Sbjct: 21 VPTYDRASLAPGIVHLGLGAFHRAHQAVYTEHTLRAGDHR--WGIVGVSLRRADT--SEA 76 Query: 85 MKAQDCLYTLVERGIKDTNAYIVGSITAYMYAPDDPRAVIEKMANPDTHIVSLTVTENGY 144 + AQD LYT+ R + +VG++ A + AP P AV++ M +P HIVSLT+TE GY Sbjct: 77 LTAQDHLYTVDVRDGAADSFQVVGALIASLVAPQSPAAVLDAMTDPRGHIVSLTITEKGY 136 Query: 145 YHSEATNSLMTDAPEIINDLNHPEKPDTLYGYLYEALLLRYKRGLTPFTIMSCDNMPQNG 204 + A+ +L D P+I +DL P + G++ AL LR GL P T+MSCDN+P NG Sbjct: 137 CRNPASGALEFDHPDIDHDLREGSAPRSAIGFVVRALALRRAAGLRPLTVMSCDNLPSNG 196 Query: 205 VTVKTMLVAFAKLKKDEKFAAWIEDKVTSPNSMVDRVTPRCTDKERKYVADTWGIKDQCP 264 T++ + +AFA+ + D A WIE + PN+MVDR+ P TD +R VA+ G D P Sbjct: 197 DTMRALTLAFAR-EADPALADWIEREGAFPNTMVDRIVPLTTDADRTRVAEELGAYDAWP 255 Query: 265 VVAEPFIQWVLEDNFSDGRPPWELVGVQVVKDVDSYELMKLRLLNGGHSAMGYLGYLAGY 324 V+ EPF QWV+ED F+ RP WE G +V+D YE KLR+LNG HSA+ YLG L GY Sbjct: 256 VITEPFSQWVIEDRFAGPRPAWERAGATLVRDARPYEQAKLRMLNGAHSALAYLGSLIGY 315 Query: 325 TYIHEVVNDPTINKYIRVLMREEVIPLLPKVPGVDFEEYTASVLERFSNPAIQDTVARIC 384 + + + P + ++ ++R+EV P L + Y A + RF N A+ + +I Sbjct: 316 DTVDQAIGAPALLNFVESMLRDEVEPTLSRPA---LARYRADLFTRFRNTALDHRLQQIA 372 Query: 385 LMGSGKMPKYVLPSIYEQLRKPDGKYKLLAVCVAGWFRYLTGVDMNGKPFEIEDPMAPTL 444 GS K+P+ L S+ L K + LA +AGW YL G D G+ + I DP+A TL Sbjct: 373 TDGSQKLPQRWLESVRANL-KSGAPTECLAFALAGWIAYLGGQDETGRTYVIADPLAGTL 431 Query: 445 KAAA-----VKGGKDPHELLNIEVLFSPEIRDNKEFVAQLTHSLETVYDKGPIAAI 495 A L IE +F ++R + FVAQ+ L + +G + A+ Sbjct: 432 AEAVRLTLHADAIDAVQALFEIESIFGCDLRAHPRFVAQVAAHLAAIRAEGVVKAL 487 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: 616 Number of extensions: 24 Number of successful extensions: 5 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: 497 Length adjustment: 34 Effective length of query: 468 Effective length of database: 463 Effective search space: 216684 Effective search space used: 216684 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