Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate 3607129 Dshi_0551 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= BRENDA::Q8KQG6 (338 letters) >FitnessBrowser__Dino:3607129 Length = 347 Score = 122 bits (306), Expect = 1e-32 Identities = 101/326 (30%), Positives = 160/326 (49%), Gaps = 35/326 (10%) Query: 3 ALVLTGTKKLEVKDIDRPKVL-PNEVLIHTAFAGICGTDHALYA-GLPGSADAVPPIVLG 60 ALVL +KL ++DID P L P +V I G+CG+D Y G G P+VLG Sbjct: 4 ALVLEAARKLALRDIDLPDELGPEDVRIAIDTVGVCGSDVHYYTHGKIGPFVVKQPMVLG 63 Query: 61 HENSGVVAEIGSAVTNVKVGDRVTVDPNIYCGQCKYCRTARPELCENLSAVGVTRDGGFE 120 HE +G+V EIG+AVT++ +GDRV ++P I G K S +GV Sbjct: 64 HEAAGIVTEIGAAVTHLALGDRVCMEPGIPNGSSK------------ASKLGVYNVDPAV 111 Query: 121 EFFTAP-------ASVVYP------IPDNVSLKSAAVVEPISCAVHGIQLLKVTPYQKAL 167 +F+ P SVV+P +PD+VS A+VEP + + ++ P AL Sbjct: 112 QFWATPPVHGCLTPSVVHPAAFTFKLPDHVSFAEGAMVEPFAIGMQAAAKARIKPGDVAL 171 Query: 168 VIGDGFMGELFVQILQAYGIHQVDLAGIVDEKLAM-----NKEKFGVKNTYNTMKGDKIP 222 V G G +G + A G +V ++ +V++KLA+ N + + Sbjct: 172 VTGAGPIGVMVALAALAGGCAKVFVSDLVEDKLAIAAGYDNIHPILIPRDNPAEVLQEAT 231 Query: 223 EG-EYDVIIEAVGLPQTQEAAIEASARGAQVLMFGVGGPDAKFQMNTYEVFQKQLTIQGS 281 EG DV+ E G + +AA+EA+A V+ VG P ++ ++L ++ Sbjct: 232 EGWGADVVFECAGAAASIQAALEAAAPAGCVVW--VGMPVDPVPVDIVLAQSRELRMETV 289 Query: 282 FINPNAFEDSLALLSSGKLNVEALMS 307 F N ++ ++ALL+SGK++++ L+S Sbjct: 290 FRYANMYDRAIALLASGKVDLKPLIS 315 Lambda K H 0.317 0.136 0.390 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: 267 Number of extensions: 10 Number of successful extensions: 5 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: 338 Length of database: 347 Length adjustment: 29 Effective length of query: 309 Effective length of database: 318 Effective search space: 98262 Effective search space used: 98262 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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