Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate SMa1414 SMa1414 Dehydrogenase, FAD-dependent
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Smeli:SMa1414 Length = 531 Score = 328 bits (840), Expect = 4e-94 Identities = 193/542 (35%), Positives = 284/542 (52%), Gaps = 21/542 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FDY++VG G++GC+LA RLS +P+ RV LIEAGGRD + IH+PVG+ P T W Sbjct: 5 FDYVIVGGGSSGCVLAARLSENPSVRVCLIEAGGRDRHPLIHMPVGFAKMTAGPMT-WGL 63 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 T P N R + Y + + LGG SSIN +Y RG RDYD W E G D W + P Sbjct: 64 TTAPQKHANNREIPYAQARVLGGGSSINAEVYTRGHPRDYDRWVE-EGADGWSFQEVKPY 122 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F+R E + L ++HG G + + F + E G+P DF Sbjct: 123 FLRSEGNTILSG---------EWHGTDGPLGVSNLPDPQPMTRAFVQSCQELGIPYNPDF 173 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N EG ++ R+ R +A+ +LR R NL + VL++ F R Sbjct: 174 NGPVQEGAGVYQTTIRNSRRCSAAVGYLRPALARKNLMLITGALVLRIVFQGR-----RA 228 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV G + A EV++++GAIG+P+L+ LSG+GP A L H I VV D+ GVG+ Sbjct: 229 VGVEYSTGGAAKIARAESEVLVTSGAIGTPKLMMLSGVGPAASLRSHGIDVVQDMAGVGQ 288 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395 NL DH + + ++KG +L+ N G+EY L +SGP++ + F + Sbjct: 289 NLHDHFGVDIVAELKGHDSLDKY-NKFHWMLLAGIEYALFKSGPVASNVVEGGAFWYGDR 347 Query: 396 EYEHPNLEYHVQPLSLEAFGQPL--HDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAIS 453 +P+L++H + G P +T + + P SRG+V ++S +PR P + Sbjct: 348 ASPYPDLQFHFLAGAGAEAGVPSVPKGSSGVTLNSYTVRPKSRGSVTLRSADPRALPIVD 407 Query: 454 PNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTI 513 PN+L +D +++ + +R++R I QP+ KY P ++ D A G T Sbjct: 408 PNFLDDPDDLRISVEGIRISREIFGQPSLQKYIKTIRFPDESVRTQADFEAYARQYGRTS 467 Query: 514 FHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAG 573 +HP T KMGRDD M+VVD LRV G+ G+R+ D+S+MP++ NTN+ T+MI EKAA Sbjct: 468 YHPTCTCKMGRDD--MSVVDPQLRVHGLDGIRICDSSVMPSLVGSNTNAATIMIGEKAAD 525 Query: 574 WI 575 I Sbjct: 526 LI 527 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: 879 Number of extensions: 50 Number of successful extensions: 7 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: 531 Length adjustment: 36 Effective length of query: 543 Effective length of database: 495 Effective search space: 268785 Effective search space used: 268785 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