Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate H281DRAFT_05794 H281DRAFT_05794 Choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Burk376:H281DRAFT_05794 Length = 550 Score = 335 bits (858), Expect = 4e-96 Identities = 208/549 (37%), Positives = 292/549 (53%), Gaps = 26/549 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSAD-PANRVLLIEAGGRDNYHW-IHIPVGYLYCINNP-RTD 92 +DYI+VGAG+ GC LA+RL+ D P + L+EAG N + +++PVG + N +T+ Sbjct: 3 YDYIIVGAGSGGCALASRLADDCPDATIALVEAGPHTNRNLLVNMPVGVAAVVPNKLKTN 62 Query: 93 WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152 + + T P PGL GR PRG+ GG S+IN M+Y RG DYD WAE +G D W W + Sbjct: 63 YGYLTTPQPGLAGRQGYQPRGRGFGGSSAINAMIYTRGHPLDYDEWAE-SGCDGWSWHDV 121 Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212 LP F R E + R G DA +HG G + R + F AA+EAG Sbjct: 122 LPYFRRAEGNER---GADA------WHGDSGPLTVSDLRYRNPFSRRFVQAAIEAGYKPN 172 Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSE 272 DFN D EG+ ++V QR G R + ++A++ E R NL VL++ F + Sbjct: 173 DDFNGPDQEGIGFYQVTQRDGRRCSVARAYVYDRE-RANLHTIADATVLRVVF-----EQ 226 Query: 273 PRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332 R CGV + R G++ + AR EVV++AGA SPQLL SG+GP A L H I V+ D P Sbjct: 227 KRACGVEIVRGGRREMLKARAEVVVAAGAFNSPQLLMCSGVGPAAHLQAHGIEVLHDAPE 286 Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392 VG+NL DH+ +V + + +I G +S ++ F + Sbjct: 287 VGQNLIDHVDFTINKRVSSIEPTGFSVRGIGRMVPQFATFIRHGRGMLSSNVAEAGGFLK 346 Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452 S E P+L+ H ++ + +H + VC L P SRGTV + S + R AP I Sbjct: 347 SKPTLERPDLQLHFCAALVDDHNRHMHWGHGYSLHVCVLRPFSRGTVTLASADARAAPVI 406 Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEF--KPGVQYQSDEDLARLAGDIG 510 P + S D + + +++ R I P+ A + E +PG Q+D L Sbjct: 407 DPRFFSDSRDLDLLVEGVQMARRILDAPSLALHGGRELYTRPG---QTDAQLREAIARHA 463 Query: 511 TTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEK 570 TI+HPV T +MG D +VVD LRVRGVTGLR+VDAS+MPT+ GNTN+PT+MI E+ Sbjct: 464 DTIYHPVATCRMG--GDAASVVDPQLRVRGVTGLRIVDASVMPTLIGGNTNAPTVMIGER 521 Query: 571 AAGWILKSQ 579 AA I S+ Sbjct: 522 AAELIAASR 530 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: 925 Number of extensions: 55 Number of successful extensions: 8 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: 550 Length adjustment: 36 Effective length of query: 543 Effective length of database: 514 Effective search space: 279102 Effective search space used: 279102 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