Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Pf1N1B4_2416 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2416 Length = 567 Score = 333 bits (854), Expect = 1e-95 Identities = 208/543 (38%), Positives = 297/543 (54%), Gaps = 23/543 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNY--HWIHIPVGYLYCINNPRTDW 93 FDYI++GAG+AG LA RL+ D VLL+EAGG D +P + + R +W Sbjct: 5 FDYIIIGAGSAGNTLATRLTEDEGVTVLLLEAGGPDYRLDFRTQMPAALAFPLQGRRYNW 64 Query: 94 RFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCL 153 + T+P+P ++GR + RGK LGG S INGM Y+RG A DYD W++L G + W + +CL Sbjct: 65 AYETDPEPHMDGRRMECGRGKGLGGSSLINGMCYIRGNAMDYDNWSKLPGLEDWTYLDCL 124 Query: 154 PDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKW---QVLADFATAAVEAGVP 210 P ++R E D P+ Y HGG+ + K + A V+AG P Sbjct: 125 P-------YFRKAETRDIGPNDY----HGGDGPVSVTTPKAGNNPLFHAMVEAGVQAGYP 173 Query: 211 RTRDFNRGDNEGVDAFE-VNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGE 269 RT D N EG + +G R + ++ +L ++R LT+ K+ F E Sbjct: 174 RTEDLNGYQQEGFGPMDRTVTPNGRRASTARGYLDVAKKRSTLTIVTHALTDKILF---E 230 Query: 270 GSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVAD 329 G + A ++V AR EV+L +GAI SPQ+LQ SG+GP LL + IPVV D Sbjct: 231 GKRAVGVRYLIGAAEERVEVRARKEVLLCSGAIASPQILQRSGVGPAELLKKLDIPVVHD 290 Query: 330 LPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCI 389 LPGVGENLQDHL++ Y +L + L + IG E++ +G + + Sbjct: 291 LPGVGENLQDHLELYLQYACTQPVSLYP-SLLLHNQPAIGAEWLFNGTGIGASNQFEAGG 349 Query: 390 FTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQA 449 F R+ E++ PN++YH P+++ G A + ++ SRG ++ KS +PR+ Sbjct: 350 FIRTRPEFDWPNIQYHFLPVAINYNGSNGVKEHGFQAHMGSMRSPSRGRIQAKSKDPREY 409 Query: 450 PAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDI 509 P+I NY++TE+D Q D +R+TR I QPA + E PG+ Q+DE L + + Sbjct: 410 PSILFNYMATEQDWQEFRDGIRLTREIMQQPALDAFRGREISPGIDVQTDEQLDKFIREH 469 Query: 510 GTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAE 569 T FHP + KMG D+ MAVVD RV G+ LRVVDASIMP IT+GN N+PT+M+AE Sbjct: 470 AETAFHPSCSCKMGTDE--MAVVDGEGRVHGMQALRVVDASIMPIITTGNLNAPTIMMAE 527 Query: 570 KAA 572 K A Sbjct: 528 KIA 530 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: 974 Number of extensions: 53 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: 567 Length adjustment: 36 Effective length of query: 543 Effective length of database: 531 Effective search space: 288333 Effective search space used: 288333 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