Align Mannitol 2-dehydrogenase; Short=M2DH; Short=MDH; EC 1.1.1.67 (characterized, see rationale)
to candidate GFF1300 PGA1_c13160 mannitol 2-dehydrogenase MtlK
Query= uniprot:P33216 (477 letters) >FitnessBrowser__Phaeo:GFF1300 Length = 488 Score = 486 bits (1252), Expect = e-142 Identities = 249/476 (52%), Positives = 308/476 (64%), Gaps = 1/476 (0%) Query: 1 MTRSVTRPSYDRKALTPGIVHIGVGNFHRAHQAVYLDDLFALGEGHDWAILGAGVRPTDA 60 + +++ RPSYDR ++PGIVHIG+GNFHRAHQA YL L G DW I+GAGVR DA Sbjct: 11 LPQTIGRPSYDRAEISPGIVHIGLGNFHRAHQAWYLHALMQSGLAMDWGIIGAGVRAADA 70 Query: 61 RMREALAAQDNLSTVIELDPAGHRARQVGAMVGFLPVEADNAALIEAMSDPRIRIVSLTV 120 MR+ L AQD L+T+IELDP G A +G ++ FLPVEADNA+LI M+ IRIVSLTV Sbjct: 71 GMRDRLLAQDCLTTLIELDPTGRSAEVIGPLIDFLPVEADNASLIRCMAGSPIRIVSLTV 130 Query: 121 TEGGYYVDASG-AFDPTHPDIVADAAHPARPATAFGAILAALRARRDAGVTPFTVMSCDN 179 TEGGYY DA D H DI D A P RP T FGAI+ ALR RR G+ FTV SCDN Sbjct: 131 TEGGYYQDAQHKGLDLNHEDIRHDIARPDRPRTVFGAIVEALRLRRGRGLPAFTVQSCDN 190 Query: 180 LPGNGHVTRNAVVGLAELYDAELAGWVKAQVAFPNGMVDRITPATGPHERELAQGFGLAD 239 L GNG +TR AVV LA+ D ELA W+ AFPN MVD I PATGP E LA+G+G+ D Sbjct: 191 LQGNGQITRTAVVTLAQQTDPELAAWIDQTGAFPNSMVDCIVPATGPAEIALARGYGIED 250 Query: 240 PVPVTCEPFRQWVIEDHFPAGRPALEKVGVTFTPHVHAYEAMKIRILNGGHAVIAYPSAL 299 PVT E +R WVIED F AGRP + G FT VH YE+MKIR+LN GH V+A L Sbjct: 251 TAPVTHENYRHWVIEDEFCAGRPPWDLAGAIFTDDVHGYESMKIRVLNAGHQVLANAGEL 310 Query: 300 MDIQLVHAAMAHPLIAAFLHKVEVEEILPHVPPVPDTSIPDYLTLIESRFSNPEIADTTR 359 + I + M PL+AAF V+ EILPHV VP+ + DYLTLIE+RFSNPEI DTTR Sbjct: 311 LSIATIADCMKDPLLAAFFRTVQTAEILPHVIAVPEMAPKDYLTLIEARFSNPEIRDTTR 370 Query: 360 RLCLDGSNRQPKFIVPSLRDNLAAGTVPKGLVLLSALWCRYCFGTTDSGVVVEPNDPNWT 419 R+ DGS+R P F++P LRD + + GL L+ ALW + C G + + PNDP+W Sbjct: 371 RVAYDGSSRHPGFVMPILRDAVRSKGAIDGLCLVEALWAQMCTGLREDASEIAPNDPDWE 430 Query: 420 ALQDRARRAKETPAEWLAMTEVYGDLAQNDLLAAEFAAALEAVWRDGAEAVLRRFL 475 + A RA++ P WL +++YGDL++ + F+ L + G A L +L Sbjct: 431 TRKSAAERAQKNPEVWLQQSQIYGDLSEQPGVVERFSYWLSMIRSQGCRAALSEYL 486 Lambda K H 0.321 0.136 0.418 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: 641 Number of extensions: 20 Number of successful extensions: 3 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: 477 Length of database: 488 Length adjustment: 34 Effective length of query: 443 Effective length of database: 454 Effective search space: 201122 Effective search space used: 201122 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 (21.9 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