Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate SM_b20496 SM_b20496 GMC oxidoreductase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Smeli:SM_b20496 Length = 536 Score = 615 bits (1587), Expect = e-180 Identities = 307/542 (56%), Positives = 385/542 (71%), Gaps = 17/542 (3%) Query: 35 AFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWR 94 ++D+IV+GAG+AGC+LANRLSADP NRVLL+EAGG D YHW+H+P+GYLYC+ NPRTDW Sbjct: 10 SYDFIVIGAGSAGCVLANRLSADPKNRVLLLEAGGSDRYHWVHVPIGYLYCMGNPRTDWM 69 Query: 95 FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154 RT +PGLNGRSL YPRGK LGGCSSINGM+Y+RGQA DYDGW + G+ W WD+ LP Sbjct: 70 MRTAAEPGLNGRSLPYPRGKLLGGCSSINGMIYMRGQAADYDGWRQ-AGNTGWGWDDVLP 128 Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214 F++ ED++R HG GGEWR+E+QRL W +L F AA E G+P+ D Sbjct: 129 YFLKSEDNFR---------GKSPMHGAGGEWRVERQRLSWPILDAFRDAAEELGIPKAED 179 Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274 FN GDNEG FEVNQR G RWN SKAFLR +R NL V + +L F R Sbjct: 180 FNTGDNEGSGYFEVNQRGGVRWNTSKAFLRPAMKRPNLRVLTGAETERLIFDGR-----R 234 Query: 275 CCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVG 334 GV G+ V A EV+LSAGAI SP++L+LSG+G +++ VV DLPGVG Sbjct: 235 TKGVRFRLNGRIQVARATREVILSAGAINSPKILELSGVGRPDVVSAAGAEVVHDLPGVG 294 Query: 335 ENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSS 394 ENLQDHLQIR++++++GAKTLN + +S+ + +G EY+L+RSGP+SMAP QL IF +SS Sbjct: 295 ENLQDHLQIRTVFRIEGAKTLNQLYHSIFSRIGMGAEYMLRRSGPLSMAPRQLGIFAKSS 354 Query: 395 KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISP 454 +LEYHVQPLS + G+PLH +PA+T SVCNL P SRG+V + + AP I P Sbjct: 355 PSVATADLEYHVQPLSTDRLGEPLHRYPAVTVSVCNLRPESRGSVHVTTAESSAAPDIRP 414 Query: 455 NYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIF 514 NYLST DR +AA ++R R++ + A A++ P E PG ++QS+++L R AGDI TTIF Sbjct: 415 NYLSTPGDRLLAAHAIRHARNLMATKAIARFRPAEMLPGSEFQSEDELIRRAGDIATTIF 474 Query: 515 HPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGW 574 HPVGT KMG DPMAVVD L+V G+ GLRVVDASIMP+I SGNTNSP +MIAEKAA Sbjct: 475 HPVGTCKMG--TDPMAVVDPSLKVHGLDGLRVVDASIMPSIVSGNTNSPVIMIAEKAAEA 532 Query: 575 IL 576 IL Sbjct: 533 IL 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: 947 Number of extensions: 45 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: 536 Length adjustment: 36 Effective length of query: 543 Effective length of database: 500 Effective search space: 271500 Effective search space used: 271500 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