Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate AO356_28535 AO356_28535 mannitol dehydrogenase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28535 Length = 485 Score = 310 bits (795), Expect = 6e-89 Identities = 182/483 (37%), Positives = 260/483 (53%), Gaps = 11/483 (2%) Query: 13 PEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKA 72 P VK T + GI H+G+G FHRAHQA Y +N DW +C LRS +R Sbjct: 2 PVVKRVPCTGTAAQIGIVHLGLGAFHRAHQAVYLQRHLNRHGESDWGVCSANLRS-NRTL 60 Query: 73 RDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSA---QALIDKLASPEIRIVSL 129 + L QD + + E D + +R IG + L + + L+ ++A+P+ RIV+L Sbjct: 61 VEQLREQDGRYHVAEYRDCEQVTLREIGVLRQALYVGEGGPDLEQLLMRMAAPQTRIVTL 120 Query: 130 TITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSC 189 T+TE GYC+ S+G+ + P I HDLAHP +P++ G + AL +RRAAG+PAFTV+ C Sbjct: 121 TVTEKGYCLSPSSGQLRSEDPAIAHDLAHPQAPRSAPGIVLEALRRRRAAGVPAFTVLCC 180 Query: 190 DNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMT--STAHRLQLHDE 247 DN+P NG TR+A+ A AAL + L W++ V+FP+ MVDRI P + RL+ D Sbjct: 181 DNMPDNGQRTRQAVSALAALQDEALAQWVEQQVAFPSCMVDRIVPAMDGESFRRLEQLDC 240 Query: 248 HGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALT 307 H D VVCE F QWV+ED F GRP WE GVQ DDV P+E MK+ +LNGSH L Sbjct: 241 H---DPAAVVCESFSQWVIEDHFPLGRPDWEVEGVQMVDDVGPFETMKLRMLNGSHSLLA 297 Query: 308 YLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAI 367 Y+G L G+ V E ++D + + YM + P L GIDL+ Y L RF+N ++ Sbjct: 298 YVGLLVGHDTVFEAVSDANLLHLIGRYMADEAAPTLDMPAGIDLSVYAHDLKARFANDSL 357 Query: 368 ADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIP 427 +L ++ DGS K P+ + +L+ GR + AL +AAW Y ++ + Sbjct: 358 QHRLRQIAMDGSQKLPQRWLLGAQQLLDQGRGIDCTALGIAAWIHYCTQPLPGRPAHVVD 417 Query: 428 DPRAEFCQGLVS--DDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTL 485 DP + L + A +L + E+F + F A Y +L +GV + L Sbjct: 418 DPLSATFADLAGRFEGASRVDAVLDLHEVFPPRLSARAVFRDAVHHAYSALTRDGVDSLL 477 Query: 486 KHL 488 L Sbjct: 478 HTL 480 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: 639 Number of extensions: 25 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: 493 Length of database: 485 Length adjustment: 34 Effective length of query: 459 Effective length of database: 451 Effective search space: 207009 Effective search space used: 207009 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