Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Ga0059261_2901 Ga0059261_2901 Choline dehydrogenase and related flavoproteins
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Korea:Ga0059261_2901 Length = 562 Score = 152 bits (385), Expect = 3e-41 Identities = 178/600 (29%), Positives = 248/600 (41%), Gaps = 110/600 (18%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAG-----GRDNYHWIHIPVGYLYCINNPR 90 + +I++G G+AG +LA+RLS AN+VLLIEAG G + + G Y + R Sbjct: 3 YSHIIIGGGSAGSVLASRLSERGANQVLLIEAGPDTPPGDEPAAILDSYPGSAYL--DAR 60 Query: 91 TDW---RFRTEPDPGLNGRSLIYPR----GKTLGGCSSINGMLYLRGQARDYDGWAELTG 143 W R P L +++ PR + LGG S+ING L RG D++ W G Sbjct: 61 FVWSNRRVTVAPTGNLQPGTMLPPRKYEQARVLGGGSAINGQLANRGLPWDFEDWVA-RG 119 Query: 144 DDAWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEK-QRLKWQVLAD-FA 201 W WD+ LP F + E+ D HG+ G I + W A F+ Sbjct: 120 AMGWGWDDVLPFFRKLENDLDFDG---------PLHGNTGPLPIRRIPEAFWPGQAKAFS 170 Query: 202 TAAVEAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLR-GVEQRGNLTVWHSTQV 260 A EAG+P D N +G ++ R A+ A+L V R NL + +T V Sbjct: 171 AALTEAGLPFLADQNGEFGDGHYPLPISNIDNHRVTAAMAWLTLQVRSRSNLQIRTNTTV 230 Query: 261 LKLDFASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLA 320 L F R GV RAG +V+ ++LSAGA+ +P+LL SGIGP LA Sbjct: 231 EALLFDG-----LRAIGV---RAGGEVLLGKT--IILSAGALMTPELLLRSGIGPADDLA 280 Query: 321 EHAIPVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPM 380 + V + PGVG L DH I + A L ++ + + +G M Sbjct: 281 RVGVEVRLNAPGVGRGLTDHPSIAIASYLPSAARLRRQRRHILLGVRFSTDTNRFPAGDM 340 Query: 381 SMAPSQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVR 440 S I T+++ +H A G+ L A N + G + Sbjct: 341 SG-----LISTKAA---------WH-------AVGERL----GTLAFWINRPLSEDGRIH 375 Query: 441 IKSGNPRQAPAISPNYLSTEED--------RQVAADSLRVTRHIASQPAF-AKYDPEEFK 491 + S +PRQA + N LS D R++AA L A+ AF A Y + + Sbjct: 376 LTSADPRQAAQVDFNLLSDSRDVERLMRGFRRMAALHLSPLLGNAALDAFPASYSEKVRQ 435 Query: 492 PGVQYQSDEDLARLAG------------------------------DIGTTIF------- 514 G + L RLA D +F Sbjct: 436 IGTINLKNRILTRLAALFLDGPAPIRRAFIENLVMEGESIADLLSDDAKLEVFVRSAVAG 495 Query: 515 --HPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572 H + +MG DDPMAV+ RV+G+ GLRV DAS P I S NTN LM+AEK A Sbjct: 496 VWHASCSCRMGAADDPMAVLTPDGRVKGIEGLRVSDASAFPAIPSANTNLAVLMLAEKLA 555 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: 805 Number of extensions: 40 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 579 Length of database: 562 Length adjustment: 36 Effective length of query: 543 Effective length of database: 526 Effective search space: 285618 Effective search space used: 285618 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