Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate PfGW456L13_2692 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2692 Length = 567 Score = 362 bits (930), Expect = e-104 Identities = 221/551 (40%), Positives = 308/551 (55%), Gaps = 25/551 (4%) Query: 26 MADQTNNTHAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYC 85 M Q T +DYI++GAG+AGC+LANRLS DPA VL++E GG D I +P + Sbjct: 1 MTTQKMATQKYDYIIIGAGSAGCVLANRLSEDPATSVLVLEFGGSDKSVVIQMPSAFSIP 60 Query: 86 INNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDD 145 +N + +WR+ TEP+ LNGR + PRGK LGG SSING++Y+RG A D+D W L G + Sbjct: 61 MNTKKYNWRYETEPETHLNGRRIHCPRGKVLGGSSSINGLVYIRGHALDFDEWESL-GAE 119 Query: 146 AWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEK-QRLKWQVLADFATAA 204 W + NCLP F R E + + GGD+ + G G +K + + A Sbjct: 120 GWGYRNCLPYFKRAESY---ESGGDS------YRGQTGPLHTTNGNHMKNPLYGAWVEAG 170 Query: 205 VEAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLD 264 EAG +T D N EG A + ++G R + + A+LR R NLTV ++ Sbjct: 171 AEAGYIKTEDCNGYMQEGFGAMHMTVKNGVRCSTANAYLRPAMGRPNLTVITHAMTRQVI 230 Query: 265 FASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAI 324 EG R GV + G+ EV++S+G IGSP LLQ SGIGP +L + I Sbjct: 231 L---EGK--RAVGVMYDHGGQTHQVYCNREVLISSGPIGSPHLLQRSGIGPADVLRKAGI 285 Query: 325 PVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAP 384 V DLPGVGENLQDH ++ + K TLN+ + L K IGL ++L + G + Sbjct: 286 GVRHDLPGVGENLQDHAEVYIQFGCKEPVTLNSKMDPL-SKLMIGLRWLLFKDGLGATNH 344 Query: 385 SQLCIFTRSSKEYEHPNLEYHVQPLSLEAFG-QPL--HDFPAITASVCNLNPTSRGTVRI 441 + F RS K P++++H P ++ G +P+ H F +T P SRG VR+ Sbjct: 345 FEAGGFIRSEKGLRWPDIQFHFLPAAMRYDGNKPIKGHGFMVLTGP---NKPKSRGYVRV 401 Query: 442 KSGNPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDED 501 +S +P + P I NYL EEDR+ +R+TR I Q A ++ E PG Q SDED Sbjct: 402 RSADPYEHPEIRFNYLEREEDREGFRRCIRLTREIIGQKAMDRFRDGEIAPGAQVTSDED 461 Query: 502 LARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTN 561 L D + +HP G+ +MG D+ MAVVDS LRVRG+ GLRV+D+S+ PT +GN N Sbjct: 462 LDAFVRDNLESTYHPCGSCRMGEDE--MAVVDSELRVRGIAGLRVIDSSVFPTEPNGNLN 519 Query: 562 SPTLMIAEKAA 572 +PT+M+AE+A+ Sbjct: 520 APTIMLAERAS 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: 928 Number of extensions: 42 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