Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate WP_011841461.1 RSPH17029_RS10740 mannitol dehydrogenase family protein
Query= BRENDA::Q4WQY4 (502 letters) >NCBI__GCF_000015985.1:WP_011841461.1 Length = 464 Score = 338 bits (867), Expect = 2e-97 Identities = 190/439 (43%), Positives = 266/439 (60%), Gaps = 18/439 (4%) Query: 36 GIVHIGVGGFHRAHLAVYIDQLMQKHGVNDYAICGVGLQPFDSAMRDALASQDHLYTLIE 95 GIVH+G+G F RAH AVY+ + M+ G D+ I GV LQ MRDALA Q Y +E Sbjct: 11 GIVHLGLGAFFRAHGAVYVARAMESSG-GDWGILGVSLQ--SPTMRDALAPQGFAYHAVE 67 Query: 96 RSAKGSFAHVIGSINSYLFAPDNREAVIAKMAHPDTKIVSLTITESGYYYNENTHELQSE 155 + +G I + L A ++ EAV+A MA P KIVSLT+TE GY +N T L + Sbjct: 68 QGPEGETVRPIDVVRQVLVAREDPEAVLAAMADPGVKIVSLTVTEKGYCHNPATGALNPD 127 Query: 156 HPDIQFDLDPANEKAPRTTFGFLYAGLTRRYQQGLKPFTVMSCDNMQKNGSITRHMLESF 215 HPDI D+ E PR+ G++ L RR GL+PFTV+ CDN+ +NG + R ++ Sbjct: 128 HPDIAHDMA---EALPRSAPGYIVRALERRRAAGLRPFTVLCCDNLPENGRVVRGVVLDL 184 Query: 216 ARLRNPEVAEWIAEEGAFPNAMVDRITPQTSETDKTALAEKFGIVDSWPVVTEPFTQWVI 275 AR +P +A+WIAEEG FP+ MVDRI P T D L + GI D+ PV+ EPF+QWV+ Sbjct: 185 ARRLDPALADWIAEEGRFPSTMVDRIVPATKPEDIARLRAQ-GIEDNLPVMHEPFSQWVV 243 Query: 276 EDQFSDG-RPPFEKVGVQVVKDVHAVEQFEKHKLRLLNGSHSALGYPGQLAGFQYVHEVM 334 ED F DG RP VGVQ+V DV FE KLR+LNG+HS+L Y G LAG + + E + Sbjct: 244 EDDFVDGARPDLGVVGVQLVGDV---TPFEHMKLRMLNGTHSSLAYLGYLAGHETISETV 300 Query: 335 ANPLFRKFVWQMMQEEVKPLLPEIPGVDIDEYCNTLIERFTNPTIMDQLPRICLNASGKI 394 A+P+F FV + +EE+ P L PGVD+ Y + L+ R+ NP I + +I ++ S K+ Sbjct: 301 ADPVFAAFVQHLWREEIVPALAPPPGVDLASYADELLARYRNPAIRHRTWQIAMDGSQKL 360 Query: 395 PQFIMPSIAE--AIWETGPFRRLCFVAAAWFHYIKGVDDRGKPFEVVDPMREELQAKARA 452 PQ I+ ++AE A+ P L A W Y+ G D++G+P EV DP+ ++L+A+A Sbjct: 361 PQRILGTLAENAAVGRASP--GLMLAVAGWMRYVSGTDEKGQPIEVKDPLADDLRARAAE 418 Query: 453 GGNDPSELLSIKSLFGDDL 471 G LL+++++F + L Sbjct: 419 G---VEALLALRAVFPEAL 434 Lambda K H 0.320 0.137 0.412 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: 669 Number of extensions: 29 Number of successful extensions: 7 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: 464 Length adjustment: 34 Effective length of query: 468 Effective length of database: 430 Effective search space: 201240 Effective search space used: 201240 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 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