Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate 16281 b2172 predicted dehydrogenase, NAD-dependent (NCBI)
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__Keio:16281 Length = 488 Score = 352 bits (903), Expect = e-101 Identities = 196/485 (40%), Positives = 278/485 (57%), Gaps = 11/485 (2%) Query: 11 LAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDR 70 L V P Y + I H G G FHRAHQA TD ++N +G DW IC + L S D+ Sbjct: 9 LPHHVHAPRYDRQQLQSRIVHFGFGAFHRAHQALLTDRVLNA-QGGDWGICEISLFSGDQ 67 Query: 71 KARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAE-DSAQALIDKLASPEIRIVSL 129 L Q++L+T+ E G D +V ++G++ + L A+ DS A+I+K P++ IVSL Sbjct: 68 -LMSQLRAQNHLYTVLEKG-ADGNQVIIVGAVHECLNAKLDSLAAIIEKFCEPQVAIVSL 125 Query: 130 TITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSC 189 TITE GYCID + G P+I HDL P P + G + AL +RR G+ FTV+SC Sbjct: 126 TITEKGYCIDPATGALDTSNPRIIHDLQTPEEPHSAPGILVEALKRRRERGLTPFTVLSC 185 Query: 190 DNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHG 249 DN+P NG V + A+L A + EL WIK HVSFP MVDRI P + +++ G Sbjct: 186 DNIPDNGHVVKNAVLGMAEKRSPELAGWIKEHVSFPGTMVDRIVPAATDESLVEISQHLG 245 Query: 250 IDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYL 309 ++D + CEPF+QWV+ED FV GRPAWE GVQ +DV P+EEMK+ +LNGSH L YL Sbjct: 246 VNDPCAISCEPFIQWVVEDNFVAGRPAWEVAGVQMVNDVLPWEEMKLRMLNGSHSFLAYL 305 Query: 310 GFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIAD 369 G+L G+ + + M D F R M + P L + +DLT Y L+ RF+N A+ Sbjct: 306 GYLSGFAHISDCMQDRAFRHAARTLMLDEQAPTL-QIKDVDLTQYADKLIARFANPALKH 364 Query: 370 QLERVCSDGSSKFPKFTVPTINRLIADGRETERA--ALVVAAWALYLKGVDENGVSYTIP 427 + ++ DGS K P+ + I I GRET+ + AL VA W Y+ GVD+ G + + Sbjct: 365 KTWQIAMDGSQKLPQRMLAGIR--IHQGRETDWSLLALGVAGWMRYVSGVDDAGNAIDVR 422 Query: 428 DPRAEFCQGLVSDDALISQ--RLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTL 485 DP ++ + LV+ + + LL++ E+FG +P++P FV A E+ + + G L Sbjct: 423 DPLSDKIRELVAGSSSEQRVTALLSLREVFGDDLPDNPHFVQAIEQAWQQIVQFGAHQAL 482 Query: 486 KHLLK 490 + LK Sbjct: 483 LNTLK 487 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: 635 Number of extensions: 33 Number of successful extensions: 6 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: 488 Length adjustment: 34 Effective length of query: 459 Effective length of database: 454 Effective search space: 208386 Effective search space used: 208386 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