Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF3193 HP15_3135 iron-containing alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Marino:GFF3193 Length = 387 Score = 200 bits (509), Expect = 5e-56 Identities = 121/385 (31%), Positives = 204/385 (52%), Gaps = 7/385 (1%) Query: 2 SVARIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYS 61 S+ + V P + G G+ + GA+H+ +++DP + G VD++ + L G Sbjct: 7 SLRKFVSPEIVF-GAGSRKSVANFASNFGARHVFLVSDPGVAAAGWVDEIVTLLTDAGIR 65 Query: 62 VHVYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYL 121 VYT V P P ++ + + D+++ +GGGS +D AK ++A H S+ ++ Sbjct: 66 STVYTGVSPNPKVDEVMTGAELYKSNECDVIVAIGGGSPMDCAKGIGIVATHGRSILEF- 124 Query: 122 NLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQ 179 G T+ P ILIPTT+GT ++V+ +++S K + ++ DV+++DP+ Sbjct: 125 --EGVDTITNPSPPLILIPTTAGTSADVSQFAIISDPNRRFKFSIISKAVVPDVSLIDPE 182 Query: 180 LTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQ 239 +T ++ +TA TG+DAL HA+EAYVS + P +D A+ AIRLI+R+L V N +D Sbjct: 183 VTETMDAYLTACTGVDALVHAIEAYVSTGSGPLTDTHALEAIRLINRNLEPLVDNTADPY 242 Query: 240 ARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTK 299 R + S AGLAF NA + VHA+++ LGG + HG NA+LL +V+ Y QS Sbjct: 243 LREQIMLASMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNALLLEHVVAYNFQSAED 302 Query: 300 RMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAV 359 R + A+ ++ +++ E R + + VG+ L G+ S + L+ A+ Sbjct: 303 RFRRVAEAMDIDTRGMAKPEIKKRLMNRIVELKRRVGLEARLAQLGVSVSDIPHLSGFAL 362 Query: 360 QQKRLLARSPLPLLEADIRAIYEAA 384 Q +L +P D++ +YE A Sbjct: 363 QDPCILT-NPRKSSLRDVQVVYEEA 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: 398 Number of extensions: 21 Number of successful extensions: 3 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: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 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