Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate SMc04390 SMc04390 L-sorbose dehydrogenase, FAD dependent protein
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Smeli:SMc04390 Length = 551 Score = 333 bits (854), Expect = 1e-95 Identities = 210/537 (39%), Positives = 285/537 (53%), Gaps = 18/537 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYI+ GAG AGC+LANRLS DP RVLL+EAGG D H+P G+ + W + Sbjct: 3 YDYIITGAGPAGCVLANRLSEDPDVRVLLLEAGGGDWNPLFHMPAGFAKMTKGVAS-WGW 61 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 T P + GR L Y + K +GG SSIN LY RG A DYD WA G W + + LP Sbjct: 62 HTVPQKHMKGRVLRYTQAKVIGGGSSINAQLYTRGNAADYDLWASEEGCAGWDYRSVLPY 121 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F R ED+ R + +H +GG + + + A E G+P DF Sbjct: 122 FKRAEDNQRFADD---------YHSYGGPLGVSMPVSALPICDAYIRAGQELGIPYNHDF 172 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N GV +++ QR+ R +AS A+L ++ R NLTV +V ++ EG R Sbjct: 173 NGRQQAGVGFYQLTQRNRRRSSASLAYLSPIKDRPNLTVRTGARVARIML---EGR--RA 227 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV V + A EV++S+GAIGSP+LL SGIGP L + V DLPGVG Sbjct: 228 VGVEVVTGRGSEIIRADREVLVSSGAIGSPKLLLQSGIGPADHLRSVGVEVRHDLPGVGG 287 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395 NLQDHL + I + G T + +A L GL+Y+L RSGP++ + + F + Sbjct: 288 NLQDHLDLFVISECTGDHTYDGVAR-LHRTLWAGLQYVLFRSGPVASSLFETGGFWYADP 346 Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455 P++++H+ S G +T + L+P SRGTVR+ S +P AP I PN Sbjct: 347 NARSPDIQFHLGLGSGIEAGVARLKNAGVTLNSAYLHPRSRGTVRLSSADPAAAPLIDPN 406 Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFH 515 Y DRQ++ + L++ R I QPA + +E PG ++DE L T H Sbjct: 407 YWEDPHDRQMSLEGLKIAREIMQQPALKPFVLDERLPGNGIRTDEQLFDYGCANAKTDHH 466 Query: 516 PVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572 PVGT KMG D AVVD L+VRG+ GLRV D+S+MP + S NTN PT+M+ EK A Sbjct: 467 PVGTCKMG--TDAAAVVDLELKVRGIEGLRVCDSSVMPRVPSCNTNGPTIMMGEKGA 521 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: 907 Number of extensions: 52 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: 551 Length adjustment: 36 Effective length of query: 543 Effective length of database: 515 Effective search space: 279645 Effective search space used: 279645 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