Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate GFF2489 PS417_12695 mannitol dehydrogenase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__WCS417:GFF2489 Length = 493 Score = 948 bits (2451), Expect = 0.0 Identities = 466/492 (94%), Positives = 476/492 (96%) Query: 1 MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSI 60 MKLNKQNL QLA +VKLP Y +A T QGIAHIGVGGFHRAHQAYYTDALMNTG GLDWSI Sbjct: 1 MKLNKQNLAQLALQVKLPTYEIASTTQGIAHIGVGGFHRAHQAYYTDALMNTGVGLDWSI 60 Query: 61 CGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLA 120 CGVGLR+EDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAED AQALIDKLA Sbjct: 61 CGVGLRAEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDGAQALIDKLA 120 Query: 121 SPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAG 180 P IRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPS+PKTVFGFICAALT+RRAAG Sbjct: 121 DPAIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSAPKTVFGFICAALTKRRAAG 180 Query: 181 IPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAH 240 PAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKA+VSFPNAMVDRITPMTSTAH Sbjct: 181 TPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKANVSFPNAMVDRITPMTSTAH 240 Query: 241 RLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLN 300 RLQLHD+HGIDDAWPVVCEPFVQWVLEDKFVNGRPAWE VGVQFTDDVTPYEEMKIGLLN Sbjct: 241 RLQLHDDHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWETVGVQFTDDVTPYEEMKIGLLN 300 Query: 301 GSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVD 360 GSHLALTYLGFLKGYRFVHETMNDP+FVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVD Sbjct: 301 GSHLALTYLGFLKGYRFVHETMNDPVFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVD 360 Query: 361 RFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDEN 420 RFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDEN Sbjct: 361 RFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDEN 420 Query: 421 GVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNG 480 GVSY IPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSP FVAAFERC+ SLRDNG Sbjct: 421 GVSYKIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPGFVAAFERCFVSLRDNG 480 Query: 481 VTTTLKHLLKKP 492 VT TL+HLLKKP Sbjct: 481 VTATLQHLLKKP 492 Lambda K H 0.321 0.137 0.414 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: 1023 Number of extensions: 33 Number of successful extensions: 1 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: 493 Length of database: 493 Length adjustment: 34 Effective length of query: 459 Effective length of database: 459 Effective search space: 210681 Effective search space used: 210681 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 (21.8 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