Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate AO353_26740 AO353_26740 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26740 Length = 550 Score = 617 bits (1592), Expect = 0.0 Identities = 319/542 (58%), Positives = 384/542 (70%), Gaps = 17/542 (3%) Query: 35 AFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWR 94 A+DYIVVGAG AGCLLANRLSA+P +RVLL+EAGGRDNY WIHIPVGYLYCI NPRTDW Sbjct: 7 AYDYIVVGAGPAGCLLANRLSANPQHRVLLLEAGGRDNYPWIHIPVGYLYCIGNPRTDWC 66 Query: 95 FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154 F+TE GL GRSL YPRGK LGG SSINGM+Y+RGQA DYD WA G+ W W++ LP Sbjct: 67 FKTEAQTGLQGRSLSYPRGKVLGGSSSINGMIYMRGQAGDYDRWAA-EGNPGWSWNDVLP 125 Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214 F + E+H+ D FHG GEWR+E+QRL W +L F +AA ++G+ D Sbjct: 126 LFKQSENHFAGDSA---------FHGAAGEWRVERQRLSWPILDAFRSAAEQSGIASVDD 176 Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274 FN+GDNEG F+VNQ++G RWNA+KAFL+ V R NLTV S V ++ +G S Sbjct: 177 FNQGDNEGCGYFQVNQKAGVRWNAAKAFLKPVRHRPNLTVLTSVDVDRVLLENGRASR-- 234 Query: 275 CCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVG 334 V+ G+ + AR E++LSAG++GSP +LQ SGIGP LL I V +L GVG Sbjct: 235 ---VSARWQGQVNIFAARREIILSAGSVGSPSILQRSGIGPGDLLKRLGIGVAHELNGVG 291 Query: 335 ENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSS 394 NLQDHLQ+R IYK++ A+TLN +A SL GK +GL Y+ RSGP+SMAPSQL F RS Sbjct: 292 RNLQDHLQLRLIYKLENARTLNQIAGSLWGKIGMGLRYLYDRSGPLSMAPSQLGAFARSG 351 Query: 395 KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISP 454 E NLEYHVQPLSLE FG+PLH FPA TASVC+L P SRG V I+S +P+Q P I P Sbjct: 352 PEQTSANLEYHVQPLSLERFGEPLHAFPAFTASVCDLRPQSRGRVEIRSADPQQPPLIQP 411 Query: 455 NYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIF 514 NYLS ED +VAA+++R+TR I + PA ++P E+ PG QS+E L A IGTTIF Sbjct: 412 NYLSHPEDLRVAAEAIRLTRRIVAAPALQPFNPVEYLPGAALQSEEQLHEAAARIGTTIF 471 Query: 515 HPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGW 574 HPVGT +MG D D AVVD+ LRV G+ GLR+ DASIMP ITSGNT SPTLMIAEKAA Sbjct: 472 HPVGTCRMGNDAD--AVVDAQLRVHGIPGLRIADASIMPHITSGNTCSPTLMIAEKAAQL 529 Query: 575 IL 576 IL Sbjct: 530 IL 531 Lambda K H 0.318 0.135 0.418 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: 941 Number of extensions: 39 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: 579 Length of database: 550 Length adjustment: 36 Effective length of query: 543 Effective length of database: 514 Effective search space: 279102 Effective search space used: 279102 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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