Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_008630494.1 C943_RS17395 hypothetical protein
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000330725.2:WP_008630494.1 Length = 532 Score = 435 bits (1119), Expect = e-126 Identities = 243/532 (45%), Positives = 332/532 (62%), Gaps = 12/532 (2%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60 M FDY+I+GAGSAGCVLANRLS + +V LLEAG D IH P G L +W Sbjct: 1 MTFDYIIIGAGSAGCVLANRLSENSKNSVLLLEAGNPDTKKDIHIP-GAYTNLHRSDTDW 59 Query: 61 AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120 AF T PQ + GR + PRGK LGGSSS N M Y+RG+ DF++W+ALGN+GW + DVLP Sbjct: 60 AFWTEPQEHVDGRRIFIPRGKTLGGSSSTNAMAYVRGNPADFDEWEALGNKGWSYKDVLP 119 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQEGA 179 +F+KSE + ++Y G +G L+V + + H + F+++ +G NPD+NG Q GA Sbjct: 120 FFQKSEHNENLDAKYCGKNGPLHVGYSKQPHFLGQKFLDACSASGIPQNPDYNGPDQIGA 179 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIK-GSRV 238 TI++ R STATAFLKP+ +R NLTV T + V IVL G +A V+ L K G +V Sbjct: 180 AMLQFTIKNNVRQSTATAFLKPILNRPNLTVKTGSRVSRIVLEGNKAVAVEVLTKDGKKV 239 Query: 239 HLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298 KE+ILSAGA SP +L+LSGIG L GI P++ LPGVGQNLQDH + Sbjct: 240 TYTCEKEIILSAGAIQSPQILLLSGIGDRDYLGHFGIEPKNHLPGVGQNLQDHIWSGVIA 299 Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLH-S 357 +SN + ++MGKA+F Y + GP+ + A AFL +D R DIQ H + Sbjct: 300 RSNVPT--NNHTLKPLEMGKALFRYLLFKKGPLGESPLTANAFLSSDGRSSRQDIQFHFA 357 Query: 358 VIGTVDDHNRKLH------WGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHD 411 V G +D++ ++ GFS V +LRP+S G +GL S DP P I PN L+ + Sbjct: 358 VTGIAEDYSTDIYDLSTFPKESGFSIMVILLRPESRGFIGLKSADPLAEPIIQPNLLSQE 417 Query: 412 DDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCK 471 +D+ LL G + ++++ Q+P+ + ++Y + L LRK +T+YHP+GTCK Sbjct: 418 EDIKKLLWGLKKAKEVMDQSPLKQYHQGNVYLPWDFRKDALEWHLRKSLETLYHPVGTCK 477 Query: 472 MGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 MGQD+ +VVD +LRVHGI+GLR+ DASIMPT++ GNTNAA IMI E+AA+ + Sbjct: 478 MGQDDASVVDEKLRVHGIKGLRIADASIMPTIISGNTNAACIMIGEKAADMV 529 Lambda K H 0.319 0.137 0.419 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: 731 Number of extensions: 37 Number of successful extensions: 6 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: 526 Length of database: 532 Length adjustment: 35 Effective length of query: 491 Effective length of database: 497 Effective search space: 244027 Effective search space used: 244027 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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