Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate 354038 BT4512 putative zinc-type alcohol dehydrogenase (NCBI ptt file)
Query= SwissProt::Q0KDL6 (366 letters) >FitnessBrowser__Btheta:354038 Length = 350 Score = 184 bits (466), Expect = 4e-51 Identities = 121/371 (32%), Positives = 185/371 (49%), Gaps = 41/371 (11%) Query: 5 MKAAVFVEPGRIELADKPIPDI-GPNDALVRITTTTICGTDVHILKGEYPVA-KGLTVGH 62 M A ++E G+ EL +KP P I DA+VR+T +IC +D+HI G P A G+TVGH Sbjct: 1 MLAYTYIEHGKFELREKPEPKITDARDAIVRVTLGSICTSDLHIKHGSVPRAVPGITVGH 60 Query: 63 EPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGC--HG 120 E VG++E++G+ VT R G RV N ++ G+C HG Sbjct: 61 EMVGVVEEVGAEVTSVRPGDRVTV-----NVETFC----------------GECFFCHHG 99 Query: 121 Y-----KATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKG 175 Y GW G IDG QAEYV VP A L IPD ++DEQ L D+++TGF Sbjct: 100 YVNNCTDPNGGWALGCRIDGGQAEYVRVPYADQGLNRIPDTVSDEQALFVGDVLATGFWA 159 Query: 176 AENANIRIGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNF 235 + I DT+ + GP G+C + L II + + R++ R+ DV++ Sbjct: 160 TRISEITEKDTILLIGAGPTGICTLLCSMLKNPKRIIVCEKSPERIQFVREHYPDVLITT 219 Query: 236 -RNCDVVDEVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLS 294 NC + V++ + G D +E GT+ +F + +P ++ + +Y L PL Sbjct: 220 PENCK--EFVLQNSDHSGADVVLEVAGTEDSFRMAWDCARPNAIVTIVALYDKPLLFPLP 277 Query: 295 AFAAGLGDHKINTALCPGGKE--RMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFA 352 + N GG + ++++IE G++D L+TH+ L++I AY +F Sbjct: 278 EM------YGKNLTFKTGGVDGCDCAEILSLIEEGKIDTTPLITHRCSLNEIEEAYRIFE 331 Query: 353 NQRDGVLKIAI 363 N+ DGV+K+AI Sbjct: 332 NKLDGVIKVAI 342 Lambda K H 0.320 0.138 0.408 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: 342 Number of extensions: 18 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: 366 Length of database: 350 Length adjustment: 29 Effective length of query: 337 Effective length of database: 321 Effective search space: 108177 Effective search space used: 108177 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