Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_057687529.1 ABB28_RS16885 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >NCBI__GCF_001431535.1:WP_057687529.1 Length = 559 Score = 336 bits (862), Expect = 1e-96 Identities = 206/542 (38%), Positives = 298/542 (54%), Gaps = 21/542 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNY--HWIHIPVGYLYCINNPRTDW 93 +DYI++GAG+AG +LA RL+ D VLL+EAGG D +P + + R +W Sbjct: 7 YDYIIIGAGSAGNVLATRLTEDADVSVLLLEAGGPDYRLDFRTQMPAALAFPLQGKRYNW 66 Query: 94 RFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCL 153 ++T+P+P +N R + RGK LGG S INGM Y+RG A DYD WA + G + W + +CL Sbjct: 67 AYKTDPEPHMNNRRMDCGRGKGLGGSSLINGMCYIRGNAMDYDNWASMPGLEDWTYADCL 126 Query: 154 PDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRL-KWQVLADFATAAVEAGVPRT 212 P F + E D GG+ +HG G ++ + ++ A A V+AG PRT Sbjct: 127 PYFRKAETR---DIGGN------DYHGSDGPLQVTTPKNGNNELFAAMIEAGVQAGYPRT 177 Query: 213 RDFNRGDNEGVDAFE--VNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEG 270 D N EG + V R G R + ++ +L +R NLT+ ++ FA Sbjct: 178 DDLNGYQQEGFGPMDRTVTPR-GRRSSTARGYLDQARERPNLTIVTHALTDRILFAG--- 233 Query: 271 SEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADL 330 R GV R + AR EV+L GAI SPQ+LQ SG+GP LL I VV DL Sbjct: 234 --KRAVGVAWLRNDEPQKARARREVLLCGGAIASPQVLQRSGVGPADLLRGLGIEVVHDL 291 Query: 331 PGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIF 390 PGVG NLQDHL++ Y+ + +L A L + IG E++ +G + + F Sbjct: 292 PGVGANLQDHLEMYLQYECRKPVSL-APALKLYNQPAIGAEWLFNGTGIGASNQFEGGGF 350 Query: 391 TRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAP 450 RS++E++ PNL+YH P+++ G + V ++ SRG + ++S +PR P Sbjct: 351 IRSNEEFDWPNLQYHFLPVAINYNGSNPIKEHSFQMHVGSMRSPSRGRIHVRSTDPRVHP 410 Query: 451 AISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIG 510 +I NY+S E+D + D +R+TR I QPA + Y E PG Q ++D ++ + Sbjct: 411 SILFNYMSHEQDWREFRDGIRITREIFGQPALSPYTGREISPGSQLRTDAEIDAFVREHA 470 Query: 511 TTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEK 570 T +HP + KMG DPMAVVD H RV G+ GLR++DASIMP + +GN N+PT+M+AEK Sbjct: 471 ETAYHPSCSNKMGSAADPMAVVDGHGRVHGMEGLRIIDASIMPQVVTGNLNAPTIMMAEK 530 Query: 571 AA 572 A Sbjct: 531 LA 532 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: 978 Number of extensions: 50 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: 559 Length adjustment: 36 Effective length of query: 543 Effective length of database: 523 Effective search space: 283989 Effective search space used: 283989 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 24 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