Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_086510929.1 BZY95_RS16195 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_002151265.1:WP_086510929.1 Length = 549 Score = 392 bits (1008), Expect = e-113 Identities = 229/541 (42%), Positives = 311/541 (57%), Gaps = 19/541 (3%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 EFDY++VGAG+AGC+LANRLSADP+ V L+EAG D +H P+G + +W Sbjct: 5 EFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWVHIPVGYLYCINNPRTDWC 64 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQAL-GNEGWGFDDVLP 120 FKT P GL GR PRGK LGG SSINGM+Y+RG D++ W L G++ W +++ LP Sbjct: 65 FKTEPDKGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELVGDDDWRWENCLP 124 Query: 121 YFRKSEMHH----GGSSE-----YHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPD 170 F K E H+ GG ++ YHG GE + + + F E+A++AG D Sbjct: 125 DFMKHEDHYRLDEGGDADAAHRDYHGHGGEWRIEKQRLKWEVLDDFAEAAVQAGVPRTRD 184 Query: 171 FNGATQEGAGYYDVTIRDGRRWSTATAFLKPV-RHRSNLTVLTHTHVESIVL---LGK-Q 225 FN EG Y++V RDG RW+ A AFL+PV R N T+ T V ++ GK + Sbjct: 185 FNRGDNEGVDYFEVNQRDGWRWNAAKAFLRPVCEKRDNFTLWHSTQVHRLLFDTAEGKPR 244 Query: 226 ATGVQALIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVG 285 A+GV+ G+ + A++EVIL+AGA GSP LL LSGIG AA L GI HELPGVG Sbjct: 245 ASGVELERNGTVSRVSAKREVILAAGAIGSPQLLQLSGIGPAALLAEHGIPLVHELPGVG 304 Query: 286 QNLQDHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTD 345 +NLQDH + YK L + + K +Y R GP++ ++ F ++ Sbjct: 305 ENLQDHLQIRSVYKVTGAKTLNTLAASWLGKAKIGMEYLLRRTGPMSMAPSQLCIFTRSS 364 Query: 346 PGLERPDIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDP 405 E P+I+ H +++ + LH + VC L P S GSV + S DPR+AP I P Sbjct: 365 DEYEHPNIEYHVQPLSLEAFGQPLHDYPAITASVCNLNPTSRGSVRIKSRDPRQAPAIAP 424 Query: 406 NFLAHDDDVATLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIY 464 N+L+ ++D R+TR I Q A + ++ +DE L L TI+ Sbjct: 425 NYLSTEEDRRVAADSLRVTRRIAEQPAFAKYRPEEVKPGVQYQSDEDLARLAGDIGTTIF 484 Query: 465 HPIGTCKMGQ--DEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEW 522 HP+GT KMG+ D MAVVDS+LRV G+EGLRVVDAS+MPT+ GNTN+ +MIAE+AA W Sbjct: 485 HPVGTAKMGRGDDPMAVVDSRLRVRGVEGLRVVDASVMPTITSGNTNSPTLMIAEKAAAW 544 Query: 523 I 523 I Sbjct: 545 I 545 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: 795 Number of extensions: 41 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: 549 Length adjustment: 35 Effective length of query: 491 Effective length of database: 514 Effective search space: 252374 Effective search space used: 252374 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