Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Ac3H11_3320 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3320 Length = 562 Score = 778 bits (2008), Expect = 0.0 Identities = 387/555 (69%), Positives = 439/555 (79%), Gaps = 11/555 (1%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FD I++G GTAG LLANRLSAD +RVLLIEAG +D+YHWIHIPVGYLYCI NPRTDW + Sbjct: 6 FDTIIIGGGTAGALLANRLSADGRHRVLLIEAGRKDDYHWIHIPVGYLYCIGNPRTDWLY 65 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 TEPD GLNGR+L YPRGKTLGGCSSINGM+Y+RGQARDYD WAELTGD WRWDN LP Sbjct: 66 NTEPDTGLNGRTLRYPRGKTLGGCSSINGMIYMRGQARDYDQWAELTGDAGWRWDNALPY 125 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHG-----GEWRIEKQRLKWQVLADFATAAVEAGVP 210 F RHEDH+RLD+ G A+ + + HG+ GEWR+EKQRL+W VL FA AA +AG+P Sbjct: 126 FRRHEDHWRLDQPGSANENFKRLHGNKATGSTGEWRVEKQRLRWDVLDAFAHAAQQAGIP 185 Query: 211 RTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGV-EQRGNLTVWHSTQVLKLDFASGE 269 T DFN G NEGV FEVNQ+SGWRWN +KAFLR R N +W S Q KL + Sbjct: 186 ATDDFNGGSNEGVGYFEVNQKSGWRWNTAKAFLRPTCYGRPNFEMWTSAQAAKLVVETQP 245 Query: 270 GSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329 RC GV V + V A EV+LSAGA+ SPQLLQLSGIGP ALL +H I V D Sbjct: 246 DGSKRCTGVMVWDGQEMVTAQATGEVILSAGAVNSPQLLQLSGIGPAALLRQHGIDVAVD 305 Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCI 389 LPGVG NLQDHLQIR+++KV+G +TLNTMANSL+GKAKIGLEY LKRSGPMSMAPSQL Sbjct: 306 LPGVGANLQDHLQIRAVFKVQGVQTLNTMANSLVGKAKIGLEYALKRSGPMSMAPSQLGA 365 Query: 390 FTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQA 449 FTRSS + +PN+EYHVQPLSL+AFG+PLH FPA TASVCNLNPTSRGTV IKS + + A Sbjct: 366 FTRSSADQPYPNIEYHVQPLSLDAFGEPLHSFPAFTASVCNLNPTSRGTVNIKSADFKTA 425 Query: 450 PAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDI 509 PAI+PNYLST EDRQVAADSLRVTR I +QPA AKY PEE+KPGVQ++SDEDLARLAGDI Sbjct: 426 PAIAPNYLSTPEDRQVAADSLRVTRRIVAQPALAKYRPEEWKPGVQFESDEDLARLAGDI 485 Query: 510 GTTIFHPVGTAKMGRDDDPMAVVDSHLRVRG-----VTGLRVVDASIMPTITSGNTNSPT 564 TTIFHPVGT KMG D DPMAV+D+ +RVR V GLRVVDA MPTITSGNTNSPT Sbjct: 486 ATTIFHPVGTTKMGLDGDPMAVLDAQMRVRDGRGGVVAGLRVVDAGAMPTITSGNTNSPT 545 Query: 565 LMIAEKAAGWILKSQ 579 LM+AEKAA WI+ ++ Sbjct: 546 LMMAEKAAEWIIAAR 560 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: 1052 Number of extensions: 27 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: 579 Length of database: 562 Length adjustment: 36 Effective length of query: 543 Effective length of database: 526 Effective search space: 285618 Effective search space used: 285618 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