Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate RR42_RS01280 RR42_RS01280 GMC family oxidoreductase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Cup4G11:RR42_RS01280 Length = 559 Score = 345 bits (886), Expect = 2e-99 Identities = 219/550 (39%), Positives = 293/550 (53%), Gaps = 29/550 (5%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRT---D 92 FDY+VVG G+AGC LA RL+ ++ V ++E GG D++ + P G + PR + Sbjct: 5 FDYLVVGGGSAGCALAGRLADSGSDSVAVLETGGHDHHVLVSTPAGCAAML--PRAGSHN 62 Query: 93 WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152 + +RT P PGLNGR PRG+ LGG SS+N M+Y RG DYD WA G D W WD+ Sbjct: 63 YGYRTVPQPGLNGRRGYQPRGRGLGGSSSLNAMIYTRGTPADYDRWAS-AGCDGWAWDDV 121 Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212 LP F R E + R+ G D DP +HG G + R F AA +AG R Sbjct: 122 LPYFRRAECNERV-AGRDDDP----WHGGSGPLHVSDLRTPNPFGQRFIEAAQQAGYRRN 176 Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQ--------RGNLTVWHSTQVLKLD 264 DFN D EG ++V Q G RWNA++A+L + R NL V TQVL++ Sbjct: 177 DDFNGVDQEGAGWYQVTQHGGERWNAARAYLHRGDAADHASNGGRENLAVMTGTQVLRIA 236 Query: 265 FASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAI 324 F EG GV V G++ + AR EV++SAGA GSPQLL +SG+GP + L E I Sbjct: 237 F---EGRH--AVGVVVRLDGRETLLRARREVIVSAGAFGSPQLLMVSGVGPASHLRELGI 291 Query: 325 PVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAP 384 PVV DLPGVG NLQDHL I +V ++ L Y +R+G ++ Sbjct: 292 PVVHDLPGVGANLQDHLDIIVHKRVAASELFGVSVGGAFRLLAEILRYRRERTGMLTSNF 351 Query: 385 SQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSG 444 ++ F +S + P+L+ H + + + + VC L P SRG VR+ S Sbjct: 352 AEAGAFLKSHAGLDEPDLQLHFVVGMADDHMRRIRLGHGYSCHVCVLRPKSRGEVRLASP 411 Query: 445 NPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPG---VQYQSDED 501 + R+AP I P +LS D +R+ R I +QP A + +E D Sbjct: 412 DIREAPMIDPCFLSDPRDLDGLVAGVRIVRRILAQPQLAAFGGKELYSAHLPADGGDDSA 471 Query: 502 LARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTN 561 + + TI+HPVGT +MG D+ AVVD LRVRGV GLRVVDASIMPT+ GNTN Sbjct: 472 IRAMIRAHADTIYHPVGTCRMGMDE--YAVVDPQLRVRGVEGLRVVDASIMPTLIGGNTN 529 Query: 562 SPTLMIAEKA 571 +P +MI E+A Sbjct: 530 APAIMIGERA 539 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: 927 Number of extensions: 48 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: 559 Length adjustment: 36 Effective length of query: 543 Effective length of database: 523 Effective search space: 283989 Effective search space used: 283989 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