Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate RR42_RS24385 RR42_RS24385 hypothetical protein
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Cup4G11:RR42_RS24385 Length = 541 Score = 371 bits (952), Expect = e-107 Identities = 234/558 (41%), Positives = 306/558 (54%), Gaps = 27/558 (4%) Query: 26 MADQTNNTHAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYC 85 M T++T FDYIVVGAG+AGC+LANRLSA P VLL+EAG W+ P G Sbjct: 1 MNSSTHDTE-FDYIVVGAGSAGCVLANRLSASPNVSVLLLEAGKDAEPFWVRTPAGVGNL 59 Query: 86 INNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDD 145 N R +W+F TEP+ L R + +PRGK LGG SSINGM+Y+RG A DYD W + G+ Sbjct: 60 FFNERLNWKFFTEPEANLGDRQVYWPRGKILGGSSSINGMVYVRGFASDYDRW-QAQGNP 118 Query: 146 AWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAV 205 W W + LP F R E + D G + G GG + + F A Sbjct: 119 GWAWSDVLPYFKRAEHN---DYGAS------ESRGVGGPLHVSFPHRQHPTTEAFVRAGA 169 Query: 206 EAGVPRTRD-FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLD 264 G+ R D GD EGV + G RW+++ A++R V QR NL + V +L Sbjct: 170 AVGLTRHDDVVAGGDAEGVGYLQHTIGEGRRWSSAHAYVRPVRQRTNLAIESEAVVTRLH 229 Query: 265 FASGEGSEPRC-CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHA 323 + RC GV R G+ AR EV+LSAGAIGSP LL LSGIGP L E Sbjct: 230 L------DGRCVVGVEYIRRGQSRTIRARREVILSAGAIGSPHLLMLSGIGPPDHLQEMG 283 Query: 324 IPVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMA 383 + V LPGVG NLQDHL I + Y+V+ +LN A S K G++Y+L R GP+++ Sbjct: 284 VRVRHALPGVGCNLQDHLAINACYEVRKDASLNA-ALSGWHKYLNGVDYLLHRRGPLAIG 342 Query: 384 PSQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQP----LHDFPAITASVCNLNPTSRGTV 439 S F SS + P+++ +PLS AF +H F + + L P SRG + Sbjct: 343 ASHAVAFVCSSTSIKVPDIQLSFRPLSF-AFDSKNKLRMHTFAGVQFASAMLRPRSRGQI 401 Query: 440 RIKSGNPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSD 499 ++S NP AP I NYL+ +D +V +L TR +A+ A E+ PG +S Sbjct: 402 LLRSPNPFDAPVIHANYLTDPDDMRVMVATLEWTRRLAATAPLADMVVREYLPGENVRSA 461 Query: 500 EDLARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGN 559 ++ T+FHP GT KMG D +AVVD LRVRG+ LRVVDAS+MPTI SGN Sbjct: 462 SEVVEFIRRSSQTLFHPAGTCKMG--SDSLAVVDERLRVRGIENLRVVDASVMPTIVSGN 519 Query: 560 TNSPTLMIAEKAAGWILK 577 TN+PT+MIAEKA+ IL+ Sbjct: 520 TNAPTIMIAEKASDMILE 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: 828 Number of extensions: 35 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: 541 Length adjustment: 36 Effective length of query: 543 Effective length of database: 505 Effective search space: 274215 Effective search space used: 274215 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