Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate PP_1949 PP_1949 Oxidoreductase, GMC family
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Putida:PP_1949 Length = 550 Score = 372 bits (954), Expect = e-107 Identities = 229/548 (41%), Positives = 302/548 (55%), Gaps = 25/548 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYI++GAG+AGC+LANRLSA+P + VLL+EAG R W +P G I T+W + Sbjct: 8 YDYIIIGAGSAGCVLANRLSANPEHSVLLLEAGSRPKGLWASMPAGVSRVILPGPTNWAY 67 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 ++EPDP L GR + PRGK LGG S+INGM YLRG DYD W L G W WD+ LP Sbjct: 68 QSEPDPSLAGRRIYVPRGKALGGSSAINGMAYLRGHREDYDHWVSL-GCAGWGWDDVLPF 126 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 + + E +EG +A F G GE + K F + VEAG+PR D Sbjct: 127 YKKFEHR---EEGDEA------FRGRDGELWVTDPVFKHPSSQAFIESCVEAGIPRLDDL 177 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N EG + + G R +A+ AFL+ V +R NL V V K+ + R Sbjct: 178 NAPSPEGTGFLQFTIKGGRRHSAATAFLQPVLKRPNLHVLTGALVQKIVIEA-----ERA 232 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV + + AR E++LSAGAI SP+LL LSG+GP L H IPV+ DLPGVGE Sbjct: 233 TGVEYSLGNQSIFAAAR-EIILSAGAIDSPKLLMLSGVGPAQELTRHGIPVLRDLPGVGE 291 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395 NL DH+ + S + +LN L + G+ Y+L+ G ++M SQ + Sbjct: 292 NLHDHVYVHSGIETDRVASLNKDLRGLRSVLQ-GMNYLLRGKGCLTMGASQAVALAQVLP 350 Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDF---PAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452 P+ + + +PLS Q L + A+T S C LNP SRG + +KS NP APAI Sbjct: 351 GARRPDTQINYRPLSWHFNKQGLVEIGKDNAVTISTCQLNPLSRGRLTLKSSNPIDAPAI 410 Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIG-T 511 PNY E D A ++R R I+ AK+ P SD ++A G + Sbjct: 411 YPNYFGNERDMVAAIAAVRKVREISCVGPLAKHIVNISPP--DSMSDGEIADYIRQEGAS 468 Query: 512 TIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571 ++ H VG+ KMG D MAVVD L+VRG+ GLRVVDASIMPTITSGNTN+PT+MI EK Sbjct: 469 SMMHWVGSCKMGIDS--MAVVDERLKVRGLQGLRVVDASIMPTITSGNTNAPTIMIGEKG 526 Query: 572 AGWILKSQ 579 A IL+ + Sbjct: 527 AAMILEDR 534 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: 883 Number of extensions: 45 Number of successful extensions: 7 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