Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate BPHYT_RS31860 BPHYT_RS31860 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__BFirm:BPHYT_RS31860 Length = 393 Score = 197 bits (501), Expect = 4e-55 Identities = 138/393 (35%), Positives = 203/393 (51%), Gaps = 16/393 (4%) Query: 4 ARIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVH 63 A + P L +G GA+ + +R G H L++TDP ++K L+ +T L Sbjct: 5 ALLYSPRLLDIGGGAVRRTAALCRRFGISHPLIVTDPYMIKSKLICVLTDTLSAASIEFA 64 Query: 64 VYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLA-----VHDGSVA 118 +++D V +P E + V G FD VI GGGS +D AK +LA + Sbjct: 65 IFSDTVADPTDEVVDVGVELLNSGNFDAVIAFGGGSPIDTAKAINILAHARRTEPSACMR 124 Query: 119 DYLNLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLS---LETTKDVVTHDYLLADVAI 175 DY + LP I IPTT+GTGSEVT +V++ L+ K +++ L AI Sbjct: 125 DYKM---PELADHAALPLIAIPTTAGTGSEVTRFTVITDIGLDE-KMLISGLGALPIAAI 180 Query: 176 VDPQLTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANG 235 VD QLT+ +PPR+TA TGID+ THA+EA+VS +A+ SD A +A+ LI L+ A Sbjct: 181 VDYQLTLDMPPRLTADTGIDSFTHALEAFVSRHANANSDLFARSALSLIGTHLKTAYTEP 240 Query: 236 SDKQARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQ 295 + AR M G+ AG+A A VA VH +A P+G FH+ HG SNA++LP V Y + Sbjct: 241 HNHAAREAMMLGATHAGIACSIAPVALVHGMARPIGAHFHVPHGLSNAMMLPAVTAYSLR 300 Query: 296 SCTKRMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGI-PES--ALE 352 S R A++ G ++ ++ EA + VE L D+ +P +GI P+ A + Sbjct: 301 SALPRYAEVARLAGFATASDNDEEAGLKLVEGLREMNRDLTVPSP-RAYGINPDGWHAKK 359 Query: 353 SLTKDAVQQKRLLARSPLPLLEADIRAIYEAAF 385 +L + A +P +ADI +YE F Sbjct: 360 TLMAEQALASGSPANNPKVPTKADIETLYEQVF 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: 390 Number of extensions: 17 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: 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