Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate PP_0056 PP_0056 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Putida:PP_0056 Length = 550 Score = 615 bits (1587), Expect = e-180 Identities = 323/544 (59%), Positives = 380/544 (69%), Gaps = 21/544 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FDY+VVGAG AGCLLANRLSADP+ RVLL+EAGGRDNY WIHIPVGYLYCI NPRTDW F Sbjct: 10 FDYVVVGAGPAGCLLANRLSADPSCRVLLLEAGGRDNYPWIHIPVGYLYCIGNPRTDWCF 69 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 +TE PGL GR+L YPRGK LGGCSSINGM+Y+RGQA DYD WA G+D W W + LP Sbjct: 70 KTEAQPGLGGRALGYPRGKVLGGCSSINGMIYMRGQAADYDHWAA-QGNDGWAWKDVLPL 128 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F E+H+ +H HG GEWR+E+QR W +L F AA ++G+ + DF Sbjct: 129 FKASENHFA------GASEH---HGAEGEWRVERQRYSWPILDAFRDAAEQSGIGKVDDF 179 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQV--LKLDFASGEGSEP 273 N GDN+G F+VNQRSG RWNASKAFLR ++ R NLTV QV + LD + Sbjct: 180 NTGDNQGCGYFQVNQRSGVRWNASKAFLRPIKDRANLTVLTGVQVDQVLLDNTRARAVKA 239 Query: 274 RCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGV 333 G E A AR E++L AGA+GSP +LQ SGIGP LL I V D+PGV Sbjct: 240 LWQGAWHEFA-------ARREIILCAGAVGSPGILQRSGIGPRQLLESLGIGVRHDMPGV 292 Query: 334 GENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRS 393 G NLQDHLQ+R IY+++ +TLN MANSL GK +GL Y+ RSGP++MAPSQL F RS Sbjct: 293 GGNLQDHLQLRLIYQIRNTRTLNQMANSLWGKMGMGLRYLYDRSGPLAMAPSQLGAFVRS 352 Query: 394 SKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAIS 453 S E NL+YHVQPLSLE FG+PLH FPA TASVCNL P SRG + I S + P I Sbjct: 353 SPEQATANLQYHVQPLSLERFGEPLHQFPAFTASVCNLRPASRGRIDICSTDMNSTPRID 412 Query: 454 PNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTI 513 PNYLS +D +VAAD++R+TR I PA A ++P+E+ PG QS+EDL AG IGTTI Sbjct: 413 PNYLSAPQDLRVAADAIRLTRRIVQAPALAAFEPKEYLPGPALQSEEDLFEAAGKIGTTI 472 Query: 514 FHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAG 573 FHPVGT +MG + M VVD+ LRV G+ GLRV DASIMP ITSGNT SPTLMIAEKAA Sbjct: 473 FHPVGTCRMG--NGAMDVVDNQLRVHGIPGLRVADASIMPQITSGNTCSPTLMIAEKAAQ 530 Query: 574 WILK 577 ILK Sbjct: 531 LILK 534 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: 949 Number of extensions: 32 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: 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