Align mannitol 2-dehydrogenase (NADP+) (EC 1.1.1.138) (characterized)
to candidate N515DRAFT_2489 N515DRAFT_2489 alcohol dehydrogenase, propanol-preferring
Query= BRENDA::Q1ACW3 (345 letters) >FitnessBrowser__Dyella79:N515DRAFT_2489 Length = 343 Score = 115 bits (288), Expect = 2e-30 Identities = 103/335 (30%), Positives = 157/335 (46%), Gaps = 21/335 (6%) Query: 19 AVVEVPLPTLRDNDVLIKVKACGVCGTDLHIHEGEFIA--KFPLIPGHETVGVVAAIGKD 76 ++ EVP+PT +VL+K++ACGVC TDLH +G++ K P IPGHE VG V AIG Sbjct: 18 SIDEVPVPTPGLGEVLVKIEACGVCHTDLHAVDGDWPVKPKPPFIPGHEGVGYVVAIGPG 77 Query: 77 VKGFTVGERVCAD-NSELCNECFYCRRGQLLLCEKFEAHGVTMDGGFAEYCAYPAGKVFK 135 V G+RV C C +C G LCE + G +++GGFAEY A V Sbjct: 78 VTHLKEGDRVGIPWLYSACGHCEHCLGGWETLCESQQNTGYSVNGGFAEYALAAADYVG- 136 Query: 136 IHNLSDVDATLLEPASCAA----HGLEKIAPKIGSSVLMFGAGPTGLCLAQLPHNGASHV 191 H + + P CA GL+ + G+ V++ G G G Q +V Sbjct: 137 -HLPDGIGFVEIAPVLCAGVTVYKGLKVTDTRPGNWVVISGIGGLGHMAVQYAAAMGLNV 195 Query: 192 VIAAPEGLKMDLAKKLDCADIYVPLSRSNPQAQFDQIKSDNPYGFDIVVEATGSPKILED 251 + K+DLA++L A + + ++P A +K + +V A SPK Sbjct: 196 AAVDIDDAKLDLARRLG-AQLIINARHADPVA---VVKKEIGGAHGALVTAV-SPKAFGQ 250 Query: 252 AINYVRRGGKLVVYGVYSDAARVSWPPSKIFGDEITIIGSFSETYM-FPATIGYLDTGKV 310 A+N VRRGG + + G+ + +S + G +T+ GS T + ++ + GKV Sbjct: 251 AMNMVRRGGTVSLNGLPPGSFDLSIFDMVLNG--VTVRGSIVGTRLDLQESLDFAKAGKV 308 Query: 311 KVEGIVNKTYKLEQWGECLEAMRNKSAIKAAIVFE 345 K T +LE E M ++ I+ +V + Sbjct: 309 KA---TVTTDRLENINEVFRRM-HQGQIEGRVVLD 339 Lambda K H 0.320 0.138 0.420 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: 308 Number of extensions: 19 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: 345 Length of database: 343 Length adjustment: 29 Effective length of query: 316 Effective length of database: 314 Effective search space: 99224 Effective search space used: 99224 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: 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