Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF2678 PGA1_c27200 alcohol dehydrogenase, iron containing
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Phaeo:GFF2678 Length = 381 Score = 179 bits (454), Expect = 1e-49 Identities = 121/381 (31%), Positives = 191/381 (50%), Gaps = 13/381 (3%) Query: 8 FPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTD 67 +P G G + +L G K L++TD L + + L G ++ + Sbjct: 9 YPTAIKFGAGRIRELAEACATAGMKKPLLVTDKGLADLPVTQSTLDILEAAGLGRAMFCE 68 Query: 68 VVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTG-- 125 V P P + E VA + G D VI GGGS LDL K+ A + + V D+ ++ Sbjct: 69 VDPNPNEKNLEAGVAAYKAGDHDGVIAFGGGSGLDLGKMVAFMCGQNRPVWDFEDIGDWW 128 Query: 126 TRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLTVS 183 TR P I +PTT+GTGSEV SV++ T K ++ H +L V I DP+LTV Sbjct: 129 TRADADAIAPIIAVPTTAGTGSEVGRASVITDSVTHQKKIIFHPKVLPTVVICDPELTVG 188 Query: 184 VPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARID 243 +P +TA TG+DA H VEA+ S + P S G+A+ +RL+ L +A A+G+D +AR Sbjct: 189 MPKFITAGTGLDAFAHCVEAFSSPHYHPMSQGIALEGMRLVKEYLPRAYADGTDIEARAQ 248 Query: 244 MANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMAD 303 M + + + G F G+ +HA+++P+G F+ HG +NAV + V+ + R Sbjct: 249 MMSAAAM-GATAFQKGLGAIHAMSHPIGALFNTHHGTTNAVCMLAVLAFNAPEIADRFKT 307 Query: 304 IFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKR 363 + LG + F E V+EL +GIP+ L G+ E+A+ L K A+ Sbjct: 308 AADYLGIDGGF----EGVCAYVQELN---DSLGIPRGLSELGVTEAAIPELVKGALIDPS 360 Query: 364 LLARSPLPLLEADIRAIYEAA 384 +P+ L +A++ +++ A Sbjct: 361 -CGGNPVVLDQANLTQLFKDA 380 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: 384 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: 381 Length adjustment: 30 Effective length of query: 365 Effective length of database: 351 Effective search space: 128115 Effective search space used: 128115 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