Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF3501 PGA1_c35540 alcohol dehydrogenase AlkJ
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Phaeo:GFF3501 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:
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