Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF3501 PGA1_c35540 alcohol dehydrogenase AlkJ
Query= metacyc::MONOMER-15202 (579 letters) >lcl|FitnessBrowser__Phaeo:GFF3501 PGA1_c35540 alcohol dehydrogenase AlkJ Length = 538 Score = 332 bits (850), Expect = 3e-95 Identities = 207/546 (37%), Positives = 288/546 (52%), Gaps = 31/546 (5%) Query: 37 DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCI-NNPR-TDWR 94 DY++VG G+AG LA+RLS DP V L+EAGGR + + P + + P+ +W Sbjct: 4 DYVIVGGGSAGSTLASRLSEDPDVTVCLLEAGGRGDGLLVRAPAAVVAMLPGRPKINNWA 63 Query: 95 FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154 + T P PGLNGR PRGK LGG S+IN MLY+RG ++DYD WA L G + W W + LP Sbjct: 64 YETVPQPGLNGRRGYQPRGKGLGGSSAINAMLYIRGHSKDYDEWAAL-GCEGWDWQSVLP 122 Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214 F + E++ R D+ HG G ++ Q+ + F A + D Sbjct: 123 YFRKSENNERGDDA---------LHGAAGPLQVSNQKSPRPITDAFVKAGRSLQIRHRED 173 Query: 215 FNRGDNEGVDAFEVNQ-----RSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGE 269 FN GDNEG+ ++V Q R+G R +A+ A+L V R NLTV Q + F E Sbjct: 174 FNSGDNEGIGHYQVTQFHRDDRNGERCSAAAAYLHPVMDRPNLTVITRAQASSVAF---E 230 Query: 270 GSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329 G R GV + G+ + AR EV+LS GA SPQLLQLSG+G + H I +V + Sbjct: 231 GK--RAVGVRYSQGGRAHMVRARREVILSGGAFNSPQLLQLSGVGRPDDICPHGIDMVHE 288 Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCI 389 LPGVG+NLQDHL YK + + + + G ++ ++ Sbjct: 289 LPGVGQNLQDHLDFTLAYKSRDRDNFGISLPGSVSLLRHIWNWRKTGRGMIATPFAEGAA 348 Query: 390 FTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQA 449 F ++ + +++ H ++ + LH + +C L P SRG+V + S +P+ A Sbjct: 349 FLKTDPNKKRADVQLHFVISIVDDHARKLHMGHGFSCHICVLRPKSRGSVGLNSADPKAA 408 Query: 450 PAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDI 509 P I P +L+ ED V +R TR I + A Y E + + D A L I Sbjct: 409 PRIDPQFLADPEDLAVLIKGVRKTRQIMAAEPLAGYVHRE----LFINGEPDDAALEQHI 464 Query: 510 ---GTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLM 566 TI+HPVGT KMG DP++VVD LRV G+ GLRVVDAS+MP + GNTN+PT+M Sbjct: 465 RARADTIYHPVGTCKMG--TDPLSVVDPSLRVHGLQGLRVVDASVMPRLIGGNTNAPTIM 522 Query: 567 IAEKAA 572 IAEKAA Sbjct: 523 IAEKAA 528 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: 957 Number of extensions: 51 Number of successful extensions: 9 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: 538 Length adjustment: 36 Effective length of query: 543 Effective length of database: 502 Effective search space: 272586 Effective search space used: 272586 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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