Align Mannitol dehydrogenase DSF1; Deletion suppressor of MPT5 mutation protein 1; EC 1.1.1.67 (characterized)
to candidate WP_011842437.1 RSPH17029_RS17930 mannitol dehydrogenase family protein
Query= SwissProt::P0CX08 (502 letters) >NCBI__GCF_000015985.1:WP_011842437.1 Length = 466 Score = 222 bits (565), Expect = 3e-62 Identities = 154/455 (33%), Positives = 230/455 (50%), Gaps = 22/455 (4%) Query: 38 IVHLGVGAFHRSHLAVFMHRLMQEHHLKDWSICGVGLMKADALMRDAMKAQDCLYTLVER 97 I+HL GAFHR+H AV+ L++ H + I V L L+ A AQ Y ++ Sbjct: 6 ILHLSPGAFHRAHQAVYAEALIRAGH-PEAGIRDVCLFPP--LIGAAHAAQGGTYHVL-- 60 Query: 98 GIKDTNAYIVGSITAYMYAPDDPRAVIEKMANPDTHIVSLTVTENGYYHSEATNSLMTDA 157 ++D + ITA D P + + +P +V++T+TE GY H T L D Sbjct: 61 -LRDQTREDLRRITAIREVLDRPHP--DMLCDPALRLVTMTLTEKGYCHVPGTERL--DP 115 Query: 158 PEIINDLNHPEKPDTLYGYLYEALLLRYKRGLTPFTIMSCDNMPQNGVTVKTMLVAFAKL 217 + DL P+ P T G+L AL+ R GL T+ SCDN+P NG ++ +L A+ Sbjct: 116 AAVAQDLADPQHPRTALGWLALALVRRRAAGLPGITLASCDNIPVNGRLLEAVLTAYVA- 174 Query: 218 KKDEKFAAWIEDKVTSPNSMVDRVTPRCTDKERKYVADTWGIKDQCPVVAEPFIQWVLED 277 + W+ VT P SMVDR+ PR + +A G D VVAEPF QWV+ED Sbjct: 175 EAFPDLLDWMAANVTFPVSMVDRIVPRVDAAAAESLAALAGAPDALGVVAEPFGQWVIED 234 Query: 278 NFSDGRPPWELVGVQVVKDVDSYELMKLRLLNGGHSAMGYLGYLAGYTYIHEVVNDPTIN 337 F+ PP + VGVQ+V DV +E MK R+LNG +A+ +LG L+G+ + +DP + Sbjct: 235 RFALPIPPLDKVGVQIVADVAPFERMKHRILNGAQTAIAHLGALSGFATSFDAASDPVMG 294 Query: 338 KYIRVLMREEVIPLLPKVPGVDFEEYTASVLERFSNPAIQDTVARICLMGSGKMPKYVLP 397 ++ + L PG D Y + +ER NP I+ + +I S K+ + ++ Sbjct: 295 VWLERFCAAQA-RTLACPPGEDLAAYCRATMERLRNPHIRHPLTQIGTDSSFKLGQRIVE 353 Query: 398 SIYEQLRKPDGKYKLLAVCVAGWFRYLTGVDMNGKPFEIEDPMAPTLKAAAVKGGKDPHE 457 + L P+ +L A+ +A W RY TG D G+P +EDP+AP + + G DP Sbjct: 354 AAEHHLDGPEA--RLYALTIAAWMRYNTGRDAAGRPIPVEDPLAPVFRDIDLAAGGDPSA 411 Query: 458 L----LNIEVLFSPEIRDNKEF---VAQLTHSLET 485 L L ++ LF +R N+ F + L +LET Sbjct: 412 LVAGYLQLD-LFEGPLRQNEPFRRRLVALCTALET 445 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: 589 Number of extensions: 36 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: 466 Length adjustment: 34 Effective length of query: 468 Effective length of database: 432 Effective search space: 202176 Effective search space used: 202176 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 Apr 10 2024. 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