Align Mannitol dehydrogenase DSF1; Deletion suppressor of MPT5 mutation protein 1; EC 1.1.1.67 (characterized)
to candidate H281DRAFT_04152 H281DRAFT_04152 D-arabinitol 4-dehydrogenase
Query= SwissProt::P0CX08 (502 letters) >FitnessBrowser__Burk376:H281DRAFT_04152 Length = 470 Score = 249 bits (636), Expect = 1e-70 Identities = 162/453 (35%), Positives = 234/453 (51%), Gaps = 10/453 (2%) Query: 38 IVHLGVGAFHRSHLAVFMHRLMQEHHLKD--WSICGVGLMKADA-LMRDAMKAQDCLYTL 94 I+H+G G+FHR+H A ++HRL + + + WS+ VG +++D + +A+ AQD +YTL Sbjct: 14 ILHIGAGSFHRAHQAWYLHRLNEANLPGEPHWSLT-VGNIRSDMNAVLEALAAQDGVYTL 72 Query: 95 VERGIKDTNAY-IVGSITAYMYAPDDPRAVIEKMANPDTHIVSLTVTENGYYHSEATNSL 153 + AY + SI + + A+IE A+P I+S TVTE GYY E + L Sbjct: 73 ETVTPQGERAYETIRSIERVVPWTESLDALIEAGADPACKIISFTVTEGGYYLDEH-DQL 131 Query: 154 MTDAPEIINDLNHPEKPDTLYGYLYEALLLRYKRGLTPFTIMSCDNMPQNGVTVKTMLVA 213 T P++ DL T+YG L L R K G P T+ +CDN+ +NG + A Sbjct: 132 DTANPDLSTDLKGGHT--TIYGALAAILEARMKNGAGPVTLQTCDNLRRNGERFHAGMSA 189 Query: 214 FAKLKKDEKFAAWIEDKVTSPNSMVDRVTPRCTDKERKYVADTWGIKDQCPVVAEPFIQW 273 F +L+ + A W +D P+SMVDR+TPR T R+ V G+ D CPV+ E FIQW Sbjct: 190 FLELRGAGELAQWFDDNTACPSSMVDRITPRPTPDVRERVKAATGVDDACPVMGEAFIQW 249 Query: 274 VLEDNFSDGRPPWELVGVQVVKDVDSYELMKLRLLNGGHSAMGYLGYLAGYTYIHEVVND 333 V+E+ F GRP WE VG ++V V YE K+R+LN HS + + G L G YIHE D Sbjct: 250 VIEERFIAGRPAWEKVGAELVDSVLPYEEAKIRILNATHSCIAWAGTLVGLNYIHEGTQD 309 Query: 334 PTINKYIRVLMREEVIPLLPKVPGVDFEEYTASVLERFSNPAIQDTVARICLMGSGKMPK 393 I K+ + E+VIP L P +D E Y VLERF NP IQDT R+ G K+P Sbjct: 310 ADIRKFAFDYVTEDVIPCLSPSP-LDLERYRDVVLERFGNPYIQDTNQRVAADGFSKLPG 368 Query: 394 YVLPSIYEQLRKPDGKYKLLAVCVAGWFRYLTGVDMNGKPFEIEDPMAPTLKAAAVKGGK 453 ++ P++ E + A+ A +FR+L P+ +D + A Sbjct: 369 FIAPTLAECFER-GVTPAATAMLPALFFRFLERWQAGTLPYTYQDGVMDERVARRFFAAP 427 Query: 454 DPHELLNIEVLFSPEIRDNKEFVAQLTHSLETV 486 DP + + L + E + L +L V Sbjct: 428 DPLQAFAADRLLWGSMAQTPELESALAGALARV 460 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: 588 Number of extensions: 32 Number of successful extensions: 4 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: 470 Length adjustment: 34 Effective length of query: 468 Effective length of database: 436 Effective search space: 204048 Effective search space used: 204048 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