Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate AO353_07810 AO353_07810 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07810 Length = 567 Score = 339 bits (870), Expect = 2e-97 Identities = 214/548 (39%), Positives = 299/548 (54%), Gaps = 27/548 (4%) Query: 33 THAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNY--HWIHIPVGYLYCINNPR 90 +H +DYI++GAG+AG LA RL+ D VLL+EAGG D +P + + R Sbjct: 2 SHEYDYIIIGAGSAGNTLATRLTEDAGVTVLLLEAGGPDYRLDFRTQMPAALAFPLQGRR 61 Query: 91 TDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWD 150 +W + T+P+P ++GR + RGK LGG S INGM Y+RG A DYDGWA+ G + W + Sbjct: 62 YNWAYETDPEPHMDGRRMECGRGKGLGGSSLINGMCYIRGNAMDYDGWAKNPGLEDWTYL 121 Query: 151 NCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKW---QVLADFATAAVEA 207 +CLP ++R E D P+ Y HGGE + K + A V+A Sbjct: 122 DCLP-------YFRKAETRDIGPNDY----HGGEGPVSVTTPKAGNNPLFHAMVEAGVQA 170 Query: 208 GVPRTRDFNRGDNEGVDAFEVNQR-SGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFA 266 G PRT D N EG + G R + ++ +L ++R L + K+ F Sbjct: 171 GYPRTEDLNGYQQEGFGPMDRTVTPKGRRSSTARGYLDIAKKRSTLNIVTHALTDKILF- 229 Query: 267 SGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPV 326 EG V A + V AR EV+L +GAI SPQ+LQ SG+GP LL IPV Sbjct: 230 --EGKRAIGVRYLVGSAEEPVEARARKEVLLCSGAIASPQILQRSGVGPAKLLKSLDIPV 287 Query: 327 VADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLI--GKAKIGLEYILKRSGPMSMAP 384 V DLPGVGENLQDHL++ Y +L SL+ + IG E++ +G + Sbjct: 288 VHDLPGVGENLQDHLELYLQYACTQPVSLYP---SLLWYNQPAIGAEWLFNGTGIGASNQ 344 Query: 385 SQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSG 444 + F R+ ++E PN++YH P+++ G A + ++ SRG +++KS Sbjct: 345 FEAGGFIRTRPDFEWPNIQYHFLPVAINYNGSNGVKEHGFQAHMGSMRSPSRGRIQVKSK 404 Query: 445 NPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLAR 504 +PRQ P+I NY++TE+D Q D +R+TR I QPA + E PG++ Q+DE L + Sbjct: 405 DPRQHPSILFNYMATEQDWQEFRDGIRLTREIMQQPALDAFRGRELSPGIEVQTDEQLDK 464 Query: 505 LAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPT 564 + T FHP + KMG D+ MAVVD RV G+ GLRVVDASIMP IT+GN N+PT Sbjct: 465 FIREHAETAFHPSCSCKMGTDE--MAVVDGQGRVHGMQGLRVVDASIMPLITTGNLNAPT 522 Query: 565 LMIAEKAA 572 +MIAEK A Sbjct: 523 IMIAEKIA 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: 1019 Number of extensions: 51 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