Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate RR42_RS29710 RR42_RS29710 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Cup4G11:RR42_RS29710 Length = 531 Score = 470 bits (1210), Expect = e-137 Identities = 255/543 (46%), Positives = 341/543 (62%), Gaps = 16/543 (2%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FDY++VGAG+AG +LANRLS V L+EAG +D Y WIHIP+GY + +P+ +WRF Sbjct: 4 FDYVIVGAGSAGSVLANRLSESGKYTVCLLEAGPKDRYPWIHIPIGYAKTMQHPKYNWRF 63 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 TEP+P L R + PRG+TLGG SSING++Y+RGQ RDYD W +L G+ W WD+ LP Sbjct: 64 YTEPEPELANRKIYQPRGRTLGGSSSINGLIYIRGQKRDYDEWRDL-GNPGWGWDDVLPY 122 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F + E + D G A G G + +++ F A+ GVPRT DF Sbjct: 123 FRKLETN---DLGASAT------RGDSGPMHATSVPPEHELVDAFIGASERLGVPRTNDF 173 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N G EGV F+V+ ++G+R + + +L+ + R NL + Q K+ F EG R Sbjct: 174 NDGRQEGVGYFQVSTKNGFRCSTAVGYLKPAKSRANLHIETLAQATKVLF---EGK--RA 228 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV R G+ + A EV+L AGAI SPQLLQLSG+GP ALL+E I V PGVGE Sbjct: 229 TGVRYVRDGRTLEVKATREVLLCAGAIQSPQLLQLSGVGPAALLSEFGIKPVHVSPGVGE 288 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRS-S 394 NLQDHLQ+R +Y+V T N SL G+AK+GL+++L+RSGP+++ + +F R+ Sbjct: 289 NLQDHLQVRLMYEVTKPITTNDAVRSLTGRAKMGLQWLLRRSGPLAVGINHGGMFCRALP 348 Query: 395 KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISP 454 E P++++H LS ++ +HDFP T S+C L P SRG VRI+S + P I Sbjct: 349 DENATPDIQFHFAALSADSTAGEVHDFPGCTYSICQLRPESRGFVRIRSLEALEPPRIQC 408 Query: 455 NYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIF 514 NYLSTE DR+ ++ R +A+ A Y E++PG ++D+++ + + GTTIF Sbjct: 409 NYLSTETDRRTTVAGVKFARKVAATEPMAAYMKREYRPGPNVRTDDEILQFCREYGTTIF 468 Query: 515 HPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGW 574 HP GTAKMG DDPMAVVD LRVRGV GLRV+D SIMPT+ SGNTN PT+MIAEKAA Sbjct: 469 HPSGTAKMGSADDPMAVVDGELRVRGVEGLRVIDCSIMPTLISGNTNIPTVMIAEKAADM 528 Query: 575 ILK 577 ILK Sbjct: 529 ILK 531 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: 827 Number of extensions: 39 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: 531 Length adjustment: 36 Effective length of query: 543 Effective length of database: 495 Effective search space: 268785 Effective search space used: 268785 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