Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Ac3H11_4659 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4659 Length = 529 Score = 355 bits (910), Expect = e-102 Identities = 217/537 (40%), Positives = 292/537 (54%), Gaps = 18/537 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 FDYIVVG G+AG +LA RL+ DP+ RV L+EAG DN IH P G W F Sbjct: 2 FDYIVVGGGSAGSVLAGRLTEDPSVRVCLLEAGPADNSVLIHCPAGLAVMAKFELNGWGF 61 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 T P LN R PRGK LGG SSIN M+Y+RGQ DYD WA G+ W W++ P Sbjct: 62 NTTPQAALNNRRGYQPRGKVLGGSSSINAMVYIRGQHADYDHWA-AQGNPGWGWEDVKPY 120 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F+R E + R G DA +HG GG + + R + F A V+AG P DF Sbjct: 121 FLRAEHNER---GADA------WHGQGGPFNVADLRSTNRFSHHFTEAGVQAGYPHNTDF 171 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N EGV ++V ++G R +A+K +L R NL V ++ F +G+ R Sbjct: 172 NGATQEGVGLYQVTHKNGERHSAAKGYLTPHLARSNLQVITDAHATRILF---DGT--RA 226 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 GV + G A EV+LSAGA+ SPQLL LSG+GP A L +H IPV+ DLPGVG+ Sbjct: 227 VGVEYRQGGALKQVRAGREVLLSAGALLSPQLLMLSGVGPAAHLQQHGIPVLHDLPGVGQ 286 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGL-EYILKRSGPMSMAPSQLCIFTRSS 394 +L DH + + K L ++ S + + G+ E+ R+G ++ ++ F +S Sbjct: 287 HLHDHPDVVQVLDAPELKDLFGLSLSGMAQTLRGIVEWRKHRTGMLTTNFAEAGGFIKSD 346 Query: 395 KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISP 454 P+L+ H L G+ +A VC L P SRG+V + S +P P + P Sbjct: 347 PSEAAPDLQLHFVIGKLVDHGRKTVFGHGYSAHVCLLQPKSRGSVTLASRDPMALPLVDP 406 Query: 455 NYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIF 514 N+L+ +D + TR I SQPA AK+ +E +SD ++ + TI+ Sbjct: 407 NFLADPDDMLRMVRGFQRTREILSQPALAKFGAKELAASASARSDAEIGQFIRQYADTIY 466 Query: 515 HPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571 HPVGT +MG P+ VVD+ LRV G+ GLRVVDASIMP I SGNTN+PT+MIAEKA Sbjct: 467 HPVGTCRMG--PGPLDVVDAELRVHGLAGLRVVDASIMPRIVSGNTNAPTVMIAEKA 521 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: 899 Number of extensions: 47 Number of successful extensions: 6 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: 529 Length adjustment: 36 Effective length of query: 543 Effective length of database: 493 Effective search space: 267699 Effective search space used: 267699 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