Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate 3608021 Dshi_1428 glucose-methanol-choline oxidoreductase (RefSeq)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Dino:3608021 Length = 544 Score = 230 bits (587), Expect = 1e-64 Identities = 173/547 (31%), Positives = 264/547 (48%), Gaps = 53/547 (9%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +D+IV+G G+AG +L+ A R+L++EAG D+ +H + + T W F Sbjct: 46 YDFIVIGTGSAGAACVYQLAQTGA-RILVLEAGRNDDLEEVHDSRLWAASLGTDATKW-F 103 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 T P +GR+ ++PRG LGG S++N M+Y RG D+D W E G W +++ LP Sbjct: 104 ETLPSSHTDGRNHMWPRGNVLGGTSALNAMVYARGHRTDFDVW-ETMGATGWSYEDVLPH 162 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQR--LKWQVLADFATAAVEAGVPRTR 213 FM E + + GG+ G G + + + + + F AA G T Sbjct: 163 FMAMESY---EPGGEN-------RGTSGPIFVSQPQDPHRHEGAVAFMDAAAGLGYKETP 212 Query: 214 DFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEP 273 FN G + N + R +++ AFLR + GN+T+ V KL EG+ Sbjct: 213 SFNSDRMSGQAWIDFNIKDQRRQSSAVAFLRPAIENGNITLLTDAPVQKLTL---EGT-- 267 Query: 274 RCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGV 333 +C GVT G V A EV+LSAGAI SP+LL LSGIG + L + I V DLP V Sbjct: 268 KCTGVTYLHNGAPVSVRAANEVILSAGAIDSPRLLMLSGIGIASDLRQVGIDAVVDLP-V 326 Query: 334 GENLQDHLQIRSI-YKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392 G LQDH+ + Y+ KG ++ +S + Y+ +RS P +P + ++ Sbjct: 327 GVGLQDHILGAGVNYEAKGPVPVSHYNHSEV--------YMWERSDPGLRSPDMIALYVS 378 Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452 L+Y H + ++ P SRG V++ S + AP I Sbjct: 379 VPFASTGHKLDYE-------------HGYCILSGVA---TPQSRGYVKLASDDIADAPII 422 Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQ-SDEDLARLAGDIGT 511 NYL+ E+D + + + R + + A+A++ E P + +D + Sbjct: 423 ETNYLAEEQDWKSYRAATELCRELGASDAYAEFRKRESLPQKDGELTDAEWRDFLSASVN 482 Query: 512 TIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571 T FHP T ++G+ VV+ LRV+G+ GLRV DAS+MP IT+ NTN+PT+MI +A Sbjct: 483 TYFHPTSTCQIGK------VVEPDLRVKGIEGLRVADASVMPQITTSNTNAPTMMIGWRA 536 Query: 572 AGWILKS 578 I K+ Sbjct: 537 GDMISKA 543 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: 848 Number of extensions: 52 Number of successful extensions: 9 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: 544 Length adjustment: 36 Effective length of query: 543 Effective length of database: 508 Effective search space: 275844 Effective search space used: 275844 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