Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate CA265_RS24860 CA265_RS24860 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Pedo557:CA265_RS24860 Length = 382 Score = 174 bits (441), Expect = 4e-48 Identities = 120/380 (31%), Positives = 185/380 (48%), Gaps = 12/380 (3%) Query: 8 FPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTD 67 FP G GA+ +L + K L++TDP + ++ ++ L+ +G +V V++D Sbjct: 11 FPTTIRFGAGAVKELPAYLSEHNLKAPLIVTDPTIAQLPFFKRIAEDLKAKGIAVEVFSD 70 Query: 68 VVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTR 127 + P K D +IG+GGG+ALD+A+ + H + Y +L G Sbjct: 71 IHKNPVKSDVYKGTEVWDATNRDSIIGIGGGAALDVARAIVLRVNHREDLFKYDDLIGGD 130 Query: 128 TLEKKGLPK-ILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLTVSV 184 +P I IPTTSGTGSEV ++++ + T K ++ L+A + DP+LT+ + Sbjct: 131 IYVTNDVPHFITIPTTSGTGSEVGRSAIIADDETHQKKILFSPKLMAQIVFADPELTMDL 190 Query: 185 PPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDM 244 PP +TAATG+DALTH +EAY++ N P DG+A+ I LI +L +A N D ++R M Sbjct: 191 PPFITAATGMDALTHNMEAYLAKNFHPMCDGIALEGISLIKDALERA-TNNPDLESRSKM 249 Query: 245 ANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADI 304 S + +A F G+ VH+LA+PL HG +NAV +PY M + R I Sbjct: 250 LMASMMGAIA-FQKGLGVVHSLAHPLSSLLDTHHGLANAVNIPYGMQFNIAGFEDRFKKI 308 Query: 305 FNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRL 364 L + E V+ L V IP L G+ +E+L D Sbjct: 309 ARTLD------LKDENGEAVVKYLFDLNTKVNIPHKLSDIGVKNEHIETLA-DLAFADFA 361 Query: 365 LARSPLPLLEADIRAIYEAA 384 +P P+ AD + +Y A Sbjct: 362 HPNNPKPVSRADFKQLYLTA 381 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: 359 Number of extensions: 17 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: 395 Length of database: 382 Length adjustment: 30 Effective length of query: 365 Effective length of database: 352 Effective search space: 128480 Effective search space used: 128480 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