Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043531345.1 JH15_RS13880 FAD-binding protein
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000759345.1:WP_043531345.1 Length = 554 Score = 382 bits (981), Expect = e-110 Identities = 225/543 (41%), Positives = 311/543 (57%), Gaps = 20/543 (3%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 EFDY++VGAG+AGC+LANRLSADP+ V L+EAG D IH P+G + +W Sbjct: 8 EFDYIVVGAGTAGCLLANRLSADPNNRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWL 67 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDW-QALGNEGWGFDDVLP 120 F+T P GL GR PRGK LGG SSINGMIY+RG D++ W + G++ W +++ L Sbjct: 68 FRTEPDAGLNGRSLLYPRGKTLGGCSSINGMIYMRGQARDYDHWAEVTGDDAWRWENCLA 127 Query: 121 YFRKSEMHH----GGSSE-----YHGGDGELYVSPA-NRHAASEAFVESALRAGHSYNPD 170 F + E H+ GG+++ +HG GE V +R + F ++A +AG D Sbjct: 128 DFTRHEDHYRLDAGGNADAQHRDFHGHGGEWRVEKQRHRWQILDDFADAAEQAGIPKTDD 187 Query: 171 FNGATQEGAGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHV------ESIVLLGK 224 FN EG GY++V R G RW+TA AFL+P R + L H+ + E+ Sbjct: 188 FNRGNNEGVGYFEVNQRAGWRWNTAKAFLRPACERRDNFTLWHSTLAHKLEFETGAHGTP 247 Query: 225 QATGVQALIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGV 284 + TGVQ +G+ +RAR+EVIL +GA GSP LL LSGIG AA L GI H+LPGV Sbjct: 248 RCTGVQVERQGTVSRVRARREVILCSGAIGSPQLLQLSGIGPAALLHKHGIPVVHDLPGV 307 Query: 285 GQNLQDHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKT 344 G+NLQDH + Y+ L S G +Y R+GP++ ++ GAF ++ Sbjct: 308 GENLQDHLQIRSVYRVTGGKTLNTLASTLWGKGLIGLEYLLTRSGPMSMAPSQLGAFTRS 367 Query: 345 DPGLERPDIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRID 404 P P+IQ H +++ + LH + VC L P S G V + S DPR+AP I Sbjct: 368 SPEHAEPNIQYHVQPLSLEAFGQPLHDYPAITASVCNLSPTSRGHVRIKSRDPREAPCIS 427 Query: 405 PNFLAHDDDVATLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTI 463 PN+L+ ++D R+TR I+AQ A + ++ +DE+L L TI Sbjct: 428 PNYLSTEEDRKVAADSLRVTRRIVAQPAFARYRPEEVKPGMQYQSDEELTRLAGDIATTI 487 Query: 464 YHPIGTCKMGQ--DEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521 +HP GT +MG+ D +AVVDS LRV G++GLRVVDA +MPT+ GNTN+ +MIAE+AA Sbjct: 488 FHPAGTTRMGRADDPLAVVDSHLRVRGVDGLRVVDAGVMPTITRGNTNSPTLMIAEKAAG 547 Query: 522 WIA 524 WIA Sbjct: 548 WIA 550 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: 857 Number of extensions: 40 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: 526 Length of database: 554 Length adjustment: 35 Effective length of query: 491 Effective length of database: 519 Effective search space: 254829 Effective search space used: 254829 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