Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF2071 PS417_10560 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__WCS417:GFF2071 Length = 548 Score = 627 bits (1618), Expect = 0.0 Identities = 322/544 (59%), Positives = 392/544 (72%), Gaps = 17/544 (3%) Query: 33 THAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTD 92 T +DYIVVGAG AGCLLANRLSA+PA+RVLL+EAGGRDNY WIHIPVGYL+CI NPRTD Sbjct: 5 TAEYDYIVVGAGPAGCLLANRLSANPAHRVLLLEAGGRDNYPWIHIPVGYLFCIGNPRTD 64 Query: 93 WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152 W F+TE GL GR+L YPRGK LGGCSSINGM+Y+RGQA+DYDGWA G+ W W + Sbjct: 65 WCFKTEAQEGLQGRALSYPRGKVLGGCSSINGMIYMRGQAQDYDGWAA-EGNAGWAWKDV 123 Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212 LP F + E+H+ GG +FH GGEWR+E+QRL W +L F AA ++G+ Sbjct: 124 LPLFKQSENHFA---GGS------EFHSDGGEWRVEQQRLHWPILDAFRDAAAQSGIAPV 174 Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSE 272 DFN+GDNEG F+VNQ++G RWNA+KAFL+ V QR NLTV V ++ +G S+ Sbjct: 175 NDFNQGDNEGCGYFQVNQKAGVRWNAAKAFLKPVRQRPNLTVLTDVDVNRVLLENGRASQ 234 Query: 273 PRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332 V + G++V AR E+VL AG++GSP +LQ SGIGP+ +L I V+ +LPG Sbjct: 235 -----VIARQHGQQVSWKARKEIVLCAGSVGSPGILQRSGIGPSNVLKPLGIDVLHELPG 289 Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392 VG NLQDHLQ+R IYK++ A+TLN +A +L GK +GL Y+ RSGP+SMAPSQL F R Sbjct: 290 VGGNLQDHLQLRLIYKLENARTLNQIAGTLWGKMGMGLRYLYDRSGPLSMAPSQLGAFAR 349 Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452 S E NLEYHVQPLSLE FG+PLH FPA TASVC+L P SRG + I+S NP AP I Sbjct: 350 SGPEQTSANLEYHVQPLSLERFGEPLHAFPAFTASVCDLRPQSRGRIDIRSANPADAPLI 409 Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTT 512 PNYLS ED +VAAD++R+TR I + PA +++ P E+ PG QS+E L A IGTT Sbjct: 410 RPNYLSHPEDLRVAADAIRLTRRIVAAPALSQFKPVEYLPGDSLQSEEQLHEAAARIGTT 469 Query: 513 IFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572 IFHPVGT +MG D D AVVD+ LRV GV GLR+ DAS+MP ITSGNT SPTLMIAEKAA Sbjct: 470 IFHPVGTCRMGSDKD--AVVDAQLRVHGVPGLRIADASVMPRITSGNTCSPTLMIAEKAA 527 Query: 573 GWIL 576 IL Sbjct: 528 QLIL 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: 940 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: 548 Length adjustment: 36 Effective length of query: 543 Effective length of database: 512 Effective search space: 278016 Effective search space used: 278016 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