Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_054339706.1 Nant_RS00625 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_001305295.1:WP_054339706.1 Length = 533 Score = 430 bits (1105), Expect = e-125 Identities = 232/522 (44%), Positives = 308/522 (59%), Gaps = 2/522 (0%) Query: 4 DYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAFK 63 DY+IVGAGSAGCVLANRLSADP+ V LLEAG ED P IH P+G + +W FK Sbjct: 9 DYIIVGAGSAGCVLANRLSADPNNRVLLLEAGGEDTYPWIHIPIGYIYTMNNPKTDWCFK 68 Query: 64 TTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYFR 123 T GL GR PRGKVLGGSSSINGMIY+RG + D++ W +LGN+GW +D+VLPYF+ Sbjct: 69 TQADAGLNGRALNYPRGKVLGGSSSINGMIYMRGQKQDYDHWASLGNKGWSWDEVLPYFK 128 Query: 124 KSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAGYY 182 KSE H+ G+S+ HG GE V + F ++A G DFN EG Y+ Sbjct: 129 KSEDHYSGASDMHGSGGEWRVEEQRLSWEVLDGFRQAAAETGIPSIDDFNTGDNEGFSYF 188 Query: 183 DVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLRA 242 V + GRRWS+A FL P++HR NLT++T HV+ + ++ K G+ I G + Sbjct: 189 QVNQKKGRRWSSARGFLDPIKHRPNLTIITKAHVDRLHIVNKTVIGIAFDINGMPSYAGV 248 Query: 243 RKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSND 302 KE++L AG+ SP +L SGIG+ L+ I H+LPGVG+NLQDH V +K + Sbjct: 249 NKEILLCAGSVISPVILQRSGIGNTDLLKQHKIDVVHDLPGVGENLQDHLQVRAVFKVKN 308 Query: 303 TSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIGTV 362 T L + K +FDYA R GP + ++ G F K+ E +++ H + Sbjct: 309 TLTLNEQANSLFGKMKMVFDYAFFRRGPFSMAPSQLGGFAKSSAEYETANLEYHIQPLSC 368 Query: 363 DDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKGYR 422 + LH + VC LRPKS G + L S DP AP I PN+L+H +D + Sbjct: 369 EKLGDPLHTFPAITASVCNLRPKSRGHIRLRSKDPYAAPIITPNYLSHKEDKQVAADALK 428 Query: 423 ITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAVVD 481 +TR I + + +++DE LI+ TI+HP+GTCKMG D+M+VVD Sbjct: 429 LTRRICQANAFKKYQPEEFKPGLAINSDEDLIKAAGDIATTIFHPVGTCKMGSDQMSVVD 488 Query: 482 SQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 QL+V+GIE LRVVDASIMPT+ GNTN+ IMIAE+AAE I Sbjct: 489 YQLKVYGIERLRVVDASIMPTITSGNTNSPTIMIAEKAAEMI 530 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: 719 Number of extensions: 30 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: 526 Length of database: 533 Length adjustment: 35 Effective length of query: 491 Effective length of database: 498 Effective search space: 244518 Effective search space used: 244518 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