Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF3617 PGA1_262p00210 alcohol dehydrogenase AlkJ
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Phaeo:GFF3617 Length = 552 Score = 324 bits (830), Expect = 7e-93 Identities = 201/552 (36%), Positives = 294/552 (53%), Gaps = 29/552 (5%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FDYI++GAG+AGC+LA+RLS ++VL++EAGGR WI +P+GY +P +W++ Sbjct: 20 FDYIIIGAGSAGCVLADRLSRSGRHKVLILEAGGRGRSPWIALPLGYGKTFFDPAVNWKY 79 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 + + L GR+ +PRGK +GG +IN ++Y RG +D+D W E G W W + Sbjct: 80 ESVREEALAGRAGYWPRGKGVGGSGAINALVYARGLPQDFDDW-EAAGAIGWGWTSVRQG 138 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQV---LADFATAAVEAGVPRT 212 + E PD + G + Q + Q+ F AA E G+PRT Sbjct: 139 YEAMET--------QVAPDGQR----RGSGPLHVQDVSDQIHPANRHFFAAAAELGLPRT 186 Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSE 272 D N EG A+ +N G R ++++AFL +R N+T+ V ++ F EG Sbjct: 187 DDINDPGGEGATAYRINTSGGRRMHSARAFLTPALKRKNVTLMTDALVERITF---EGR- 242 Query: 273 PRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332 R V V R GK + A E+VLSAGA+ SP LLQ SGIGP LL H I +V D P Sbjct: 243 -RAVSVQVRRRGKSMSIAAGREIVLSAGAVASPGLLQKSGIGPAELLRRHGIAIVDDQPQ 301 Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392 VG NLQDHL I ++ TLN + + L GK + L Y L R GP++++ +Q + R Sbjct: 302 VGGNLQDHLGINYYFRAT-EPTLNNVLSPLTGKIRAALHYALWRRGPLALSVNQCGGYFR 360 Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHD------FPAITASVCNLNPTSRGTVRIKSGNP 446 S++ P+ + + P++ + + F PTSRG + I S + Sbjct: 361 SAQSLTRPDQQLYFNPVTYTTTPEGTREVIRPDPFAGFILGFQPSRPTSRGRIDICSADV 420 Query: 447 RQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLA 506 AP I PN L+TEEDR R+ + +A+ PA ++ +D D+ Sbjct: 421 SAAPLIRPNSLATEEDRSQVIAGGRLCQRLATTPALDGLIEVAMGTDLRQMADADILSDF 480 Query: 507 GDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLM 566 + T+FHPVGT +MG D +VV L++ G+ G+RVVDAS+ P ITSGNTN+PT+M Sbjct: 481 RERCGTVFHPVGTCRMGTDAS-TSVVCPKLKLHGLDGVRVVDASVFPNITSGNTNAPTMM 539 Query: 567 IAEKAAGWILKS 578 +A +AA IL++ Sbjct: 540 LAHRAADLILEA 551 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: 860 Number of extensions: 50 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: 552 Length adjustment: 36 Effective length of query: 543 Effective length of database: 516 Effective search space: 280188 Effective search space used: 280188 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