Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate CCNA_01337 CCNA_01337 GMC family oxidoreductase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Caulo:CCNA_01337 Length = 540 Score = 577 bits (1487), Expect = e-169 Identities = 297/552 (53%), Positives = 375/552 (67%), Gaps = 15/552 (2%) Query: 26 MADQTNNTHAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYC 85 M D+ + +DYIVVGAG+AGCLLANRLSADP RVLL+EAGG DN+ W H+PVGYL+ Sbjct: 1 MGDEAIHLGDYDYIVVGAGSAGCLLANRLSADPRRRVLLLEAGGDDNWIWFHVPVGYLFA 60 Query: 86 INNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDD 145 I NPR DW T P GL+GR L YPRGK +GG S+IN M+Y+RGQARDYDGW + G Sbjct: 61 IGNPRADWMLETTPQAGLDGRVLAYPRGKVIGGSSAINAMIYMRGQARDYDGWRQ-RGLA 119 Query: 146 AWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAV 205 W W + LP F++HEDH +D G+ H GGE+R+E R++W VL A Sbjct: 120 GWGWPDVLPYFLKHEDH--IDPRGE-------HHRAGGEYRVEHPRVRWDVLDAIRRAGE 170 Query: 206 EAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDF 265 +AG+ + DFN GDN G F+VNQR+G RW+ + AFL+ V R NL + +V +L Sbjct: 171 QAGIAQVDDFNGGDNAGSSYFQVNQRAGRRWSTATAFLKPVLSRPNLRLVKGVEVERLII 230 Query: 266 ASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIP 325 +G R G+ R G V + E++L+AGAIGSP +LQ SGIG L+ + Sbjct: 231 ---DGKRVR--GLRGRRGGAAVTASVSGELILAAGAIGSPVILQRSGIGRGETLSRAGVA 285 Query: 326 VVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPS 385 +V DLPGVG NLQDHLQIR ++KV G +TLNT +L +A +GL+Y+L+RSGP++MAPS Sbjct: 286 MVHDLPGVGANLQDHLQIRPVFKVSGVRTLNTDYANLFRRAGMGLDYLLRRSGPLTMAPS 345 Query: 386 QLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGN 445 QL +F RS EYE NLE+H QPLSL+ +G+ LH F A+TASVCNL P+SRG V + Sbjct: 346 QLGMFCRSGPEYESANLEFHFQPLSLDRWGEGLHRFGAVTASVCNLRPSSRGAVSLSGPG 405 Query: 446 PRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARL 505 +P I PNYL+TEEDR+VA +SL+ R I Q A A Y PE F+PG + D L Sbjct: 406 LEHSPRIDPNYLATEEDRRVAVESLKWARRIMGQAALAAYAPEAFRPGPEVDGDAALLAA 465 Query: 506 AGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTL 565 A + TTIFHPVGTA MG D DP+AV+D+ LRVRGV GLRV+DAS MPTITSGNTN+PT+ Sbjct: 466 AKALATTIFHPVGTAAMGADGDPLAVLDARLRVRGVEGLRVIDASAMPTITSGNTNAPTV 525 Query: 566 MIAEKAAGWILK 577 MIAEK A IL+ Sbjct: 526 MIAEKGAAMILE 537 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: 984 Number of extensions: 42 Number of successful extensions: 4 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: 540 Length adjustment: 36 Effective length of query: 543 Effective length of database: 504 Effective search space: 273672 Effective search space used: 273672 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