Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 8500233 DvMF_0990 iron-containing alcohol dehydrogenase (RefSeq)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Miya:8500233 Length = 386 Score = 183 bits (464), Expect = 8e-51 Identities = 123/375 (32%), Positives = 191/375 (50%), Gaps = 9/375 (2%) Query: 15 GWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEP-P 73 G+GA + LGA LV++D + G D V LR EG + + V P Sbjct: 17 GYGAAGLAGRHARNLGASRCLVVSDQGVAAAGHTDAVARTLRDEGIACATFLGVSENPRD 76 Query: 74 LETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKG 133 E + + F +G D ++ VGGGS +D AK ++ + G + DY G + K Sbjct: 77 TEVMQGSEVFRAEG-CDAIVAVGGGSPMDCAKGIGIVVANGGHILDY---EGVDAIPKPM 132 Query: 134 LPKILIPTTSGTGSEVTNISVL--SLETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAA 191 P + +PTT+G+ ++V+ +++ + K + + DVA+VDP T++ P +TAA Sbjct: 133 PPLVCVPTTAGSSADVSQFAIIRDTPRRVKIAIVSKANVPDVALVDPLTTLTKPRELTAA 192 Query: 192 TGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLA 251 TG+DALTHAVEAY S SP +D A+ A+R I +L + + ++ AR MA GS A Sbjct: 193 TGLDALTHAVEAYASNAHSPVTDMFALEAVRGIGSALFDVLDDLGNRDARARMALGSMNA 252 Query: 252 GLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALG-G 310 GLAF NA + VHAL++ LGG + HGE NA+LLP+V+ + +R + ALG Sbjct: 253 GLAFSNAILGAVHALSHSLGGLLDLPHGECNALLLPFVVRRNYVAAPQRYRRVAEALGVA 312 Query: 311 NSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPL 370 ++ + E L G K L +G+ L L + A++ L+ +P+ Sbjct: 313 DALAAPDDEVRDALFARLGAMRRRAGFDKGLAQYGVTRDQLAELARLALEDP-CLSTNPV 371 Query: 371 PLLEADIRAIYEAAF 385 PL ++ +Y AF Sbjct: 372 PLDARELEQLYAEAF 386 Lambda K H 0.318 0.135 0.381 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: 383 Number of extensions: 19 Number of successful extensions: 4 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: 395 Length of database: 386 Length adjustment: 31 Effective length of query: 364 Effective length of database: 355 Effective search space: 129220 Effective search space used: 129220 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 (21.7 bits) S2: 50 (23.9 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