Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 207896 DVU2405 alcohol dehydrogenase, iron-containing
Query= BRENDA::A4IP64 (395 letters) >MicrobesOnline__882:207896 Length = 393 Score = 223 bits (567), Expect = 1e-62 Identities = 140/385 (36%), Positives = 215/385 (55%), Gaps = 14/385 (3%) Query: 9 PPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68 P ++ +G GA + ++K LG L++TD +VK G++ Q+T L + VY + Sbjct: 13 PRVTLIGIGASKAIPEKIKALGGSKPLIVTDMGIVKAGILKQITDLLDAAKMAYSVYDET 72 Query: 69 VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRT 128 +P P + K V + K D +I +GGGS+ D K ++ + G + D+ G Sbjct: 73 IPNPTDDNVHKGVDVYKKNKCDSLITLGGGSSHDCGKGIGLVVANGGKIHDF---EGVDK 129 Query: 129 LEKKGLPKILIPTTSGTGSEVTNISVLSLETTKDV---VTHDYLLADVAIVDPQLTVSVP 185 ++ P + + TT+GT SE+T +++ +T++ V + + ++A+ DP L + +P Sbjct: 130 STQRMPPYLAVNTTAGTASEMTRFCIIT-DTSRKVKMAIVDWRVTPNIALDDPLLMLGMP 188 Query: 186 PRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMA 245 P +TAATG+DALTHAVEAYVS A+P +D A AI LI+ LR+AVANG D +AR M Sbjct: 189 PALTAATGMDALTHAVEAYVSTIATPMTDACAEQAITLIATFLRRAVANGQDLEARERMC 248 Query: 246 NGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIF 305 YLAG+AF NA + VHA+A+ LGG + + HGE NA+LLP+V + + R A I Sbjct: 249 FAQYLAGMAFNNASLGHVHAMAHQLGGFYDLPHGECNAILLPHVSKFNLIAKLDRYARIA 308 Query: 306 NALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFG------IPESALESLTKDAV 359 +G N + LS EA+ R + ++ DVGIP L G + + + +TK+A Sbjct: 309 QLMGENIAGLSTREAAERAISAIKCLSTDVGIPAGLVALGKRYGKDVKAADIAIMTKNAQ 368 Query: 360 QQKRLLARSPLPLLEADIRAIYEAA 384 + L P +AD+ AIYEAA Sbjct: 369 KDACGLTNPRCP-TDADVAAIYEAA 392 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: 412 Number of extensions: 17 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: 393 Length adjustment: 31 Effective length of query: 364 Effective length of database: 362 Effective search space: 131768 Effective search space used: 131768 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