Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate WP_086511126.1 BZY95_RS17225 mannitol dehydrogenase family protein
Query= BRENDA::O08355 (493 letters) >NCBI__GCF_002151265.1:WP_086511126.1 Length = 491 Score = 457 bits (1177), Expect = e-133 Identities = 231/487 (47%), Positives = 306/487 (62%), Gaps = 1/487 (0%) Query: 3 LNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICG 62 L+ L+ L V +P Y + GI HIGVGGFHRAHQA Y DALMN GE LDW I G Sbjct: 4 LSNATLSHLDSRVAVPRYDRREVTPGIVHIGVGGFHRAHQAMYLDALMNRGEALDWGIVG 63 Query: 63 VGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASP 122 VG+ DR+ ++ LA QD+L+TL + E RVIG++ D L A D +A+++++A P Sbjct: 64 VGVMPGDRRMQEVLAAQDHLYTLVVKHPNGEREPRVIGAMLDYLYAPDDPEAVVERMADP 123 Query: 123 EIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIP 182 IRIVSLT+TEGGY GEF P ++HDL P++P+T FG + AL +RRA G+ Sbjct: 124 AIRIVSLTVTEGGYNFHPVTGEFDLANPDVRHDLDSPAAPRTTFGLVVEALARRRARGLA 183 Query: 183 AFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRL 242 FT+MSCDN+ NG V R+ +AFA + L +WI+A V FPNAMVDRITP+T Sbjct: 184 PFTLMSCDNIQGNGEVARRMFVAFARARDPALAEWIEAEVPFPNAMVDRITPVTQAVDIE 243 Query: 243 QLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGS 302 +L E G++DAWPVVCEPF QWVLED F+ GRPA+E+VGVQ +DV PYE MK+ LLN S Sbjct: 244 ELAGEFGVEDAWPVVCEPFTQWVLEDHFICGRPAFERVGVQVVEDVEPYELMKLRLLNAS 303 Query: 303 HLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRF 362 H AL Y G L GYR+ HE DPLFV ++ YM + +P LAPVPG+DL Y+ TL++RF Sbjct: 304 HQALCYFGTLAGYRYAHEVCRDPLFVDFLLGYMRHEGSPTLAPVPGVDLEQYRLTLIERF 363 Query: 363 SNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGV 422 +N I D L R+C++ S + PK+ VP I +A G E R+A VVA+WA Y +G+DE G Sbjct: 364 ANPEIKDTLARLCAESSDRIPKWLVPVIREQLAKGGEIHRSAAVVASWARYAEGLDEQGE 423 Query: 423 SYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVT 482 T+ D L +++ + E+FG + F A+ SL + G Sbjct: 424 PITVVDRLKHELAALAAENRTRPGAFIENRELFGD-LAEHERFRQAYLMALTSLHERGAR 482 Query: 483 TTLKHLL 489 TL+ L+ Sbjct: 483 ATLETLV 489 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: 687 Number of extensions: 24 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: 491 Length adjustment: 34 Effective length of query: 459 Effective length of database: 457 Effective search space: 209763 Effective search space used: 209763 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 24 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