Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate CCNA_00994 CCNA_00994 oxidoreductase, GMC family
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Caulo:CCNA_00994 Length = 555 Score = 419 bits (1076), Expect = e-121 Identities = 241/557 (43%), Positives = 334/557 (59%), Gaps = 35/557 (6%) Query: 37 DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRD----------NYHWIHIPVGYLYCI 86 DY++VGAG+AGC+LA RLS + +V+L+EAGG D + IHIPVGY + Sbjct: 8 DYVIVGAGSAGCVLAARLSENGRYKVVLLEAGGDDRPTKNLSQFASNMMIHIPVGYSSTL 67 Query: 87 NNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDA 146 +P+ +W F TEPDPG GRS ++PRGK LGG SSIN MLY+RGQA DYDGW +L G + Sbjct: 68 KDPKVNWLFTTEPDPGTGGRSHVWPRGKVLGGSSSINAMLYVRGQAADYDGWRQL-GCEG 126 Query: 147 WRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVE 206 W WD+ LP F + ++ E G D H GG + R + A + Sbjct: 127 WAWDDVLPYFRKAQN----QERGACD-----LHATGGPLNVADMRDAHPISEALIEACDQ 177 Query: 207 AGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFA 266 AG+PR D N D EG ++V Q++G R +++ A+L +R NL V + ++ F Sbjct: 178 AGIPRYPDLNGADQEGATWYQVTQKNGARCSSAVAYLHPAMKRPNLRVETNALAGRVLF- 236 Query: 267 SGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPV 326 EG R GV + G++ AR EV+L+ GAI SPQLLQLSG+G LL EH I V Sbjct: 237 --EGK--RAVGVEFMQNGERRAAMARGEVILAGGAINSPQLLQLSGVGAGGLLREHGIEV 292 Query: 327 VADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGK-AKIGLEYILKRSGPMSMAPS 385 VADLPGVGENLQDH + + Y++K T++ S G+ A ++Y+L R G ++++ + Sbjct: 293 VADLPGVGENLQDHYIVAARYRLKSG-TVSVNEQSKGGRLAAEAMKYLLFRKGLLTLSAA 351 Query: 386 QLCIFTRSSKEYEHPNLEYHVQPLSLE---AFGQ---PLHDFPAITASVCNLNPTSRGTV 439 + F +S + P++++H+ P +++ F + L P +T + C L P SRG + Sbjct: 352 HVAAFCKSRPDLAGPDIQFHILPATMDLDKLFNEQKMELEGAPGMTIAPCQLRPESRGYI 411 Query: 440 RIKSGNPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSD 499 RIKS +P PAI NYL+ D++V L+ R I QPA A+Y E PG++ Q+D Sbjct: 412 RIKSADPSVYPAIFANYLADPLDQEVIVAGLKWARKIGQQPAIAQYVESEMNPGLEVQTD 471 Query: 500 EDLARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGN 559 E L A G+T++HPVG+ +MG PMAVVD+ LRVRGV GLRVVDASIMP + SGN Sbjct: 472 EQLLDFARQTGSTLYHPVGSCQMG--TGPMAVVDAQLRVRGVEGLRVVDASIMPRLISGN 529 Query: 560 TNSPTLMIAEKAAGWIL 576 TN+P++MI EK A IL Sbjct: 530 TNAPSIMIGEKGADMIL 546 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: 921 Number of extensions: 39 Number of successful extensions: 8 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: 555 Length adjustment: 36 Effective length of query: 543 Effective length of database: 519 Effective search space: 281817 Effective search space used: 281817 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