Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_054342102.1 Nant_RS13025 alcohol dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_001305295.1:WP_054342102.1 Length = 544 Score = 420 bits (1079), Expect = e-122 Identities = 235/535 (43%), Positives = 329/535 (61%), Gaps = 15/535 (2%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 +DY+IVGAGSAGCV+ANRLSADP+V+VCL+EAG +SPL+ P G+ + + ++ F Sbjct: 4 YDYIIVGAGSAGCVVANRLSADPAVSVCLIEAGGGGKSPLVSIPAGIFGLYGNKKYDYTF 63 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 + PQ L R RGK LGGSS+IN M+YIRG+++D++ W LG +GW + DVLP F Sbjct: 64 EGVPQRHLNNRTMMVNRGKALGGSSAINSMVYIRGNKNDYDGWAKLGCQGWSYADVLPLF 123 Query: 123 RKSEMHHGG-SSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPDFNGATQEGAG 180 ++ E + G S++YHG +GEL V+ P + + + FV++ AG N DFN ATQ G G Sbjct: 124 KQMEANQNGQSADYHGFNGELSVTKPQDPNPVDQVFVKAGKAAGLPENTDFNAATQFGLG 183 Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240 YDV G R S+ TAF+KPV R NLT++T+T V S+ + G TG++ + G+ Sbjct: 184 IYDVKQHRGERVSSYTAFVKPVLSRPNLTLMTYTEVVSLQIQGDTVTGLEVEVNGNAQQW 243 Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300 R KEVIL AG SP LL+ SGIG L GI + +PGVG+NLQDH D ++ +S Sbjct: 244 RCNKEVILCAGTILSPRLLLASGIGDQTALSALGIECKQHVPGVGENLQDHVDSMVTVRS 303 Query: 301 NDTSLLGFSLSGGV-KMGKAMFDYARHRNGPVASNCAEAGAFLKT------DPGL--ERP 351 + + +G SL + + A F Y R G +N EAG F KT +PG P Sbjct: 304 STSDSIGISLGTILPHIIPAPFKYWLARKGWWTTNYVEAGGFAKTKLAEAAEPGSADADP 363 Query: 352 DIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHD 411 D+Q H +K GHG+S CVLRP+S G+V L++ R+ ID NF A + Sbjct: 364 DVQFHLTPLYRSPRGKKFELGHGYSVFTCVLRPRSAGTVKLSNDGTRRNVLIDHNFFADE 423 Query: 412 DDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLH--NDEQLIELLRKRTDTIYHPIGT 469 D L++G + R+I+A +M + G H DEQ+++ L T T+YHP+GT Sbjct: 424 RDQKVLIEGLKKAREILAAPEFDPLRGEEM-APGKHIQTDEQILDYLINTTTTVYHPVGT 482 Query: 470 CKMGQDEMAVVD-SQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 CKMG DEMAVVD + L+V G++ LRV+DAS+MPTL+ GNT+A ++MIAE+ ++ I Sbjct: 483 CKMGIDEMAVVDPATLKVKGMQNLRVMDASVMPTLISGNTSAPSMMIAEKGSQMI 537 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: 815 Number of extensions: 41 Number of successful extensions: 7 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: 544 Length adjustment: 35 Effective length of query: 491 Effective length of database: 509 Effective search space: 249919 Effective search space used: 249919 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