Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate N515DRAFT_4337 N515DRAFT_4337 Choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Dyella79:N515DRAFT_4337 Length = 533 Score = 357 bits (915), Expect = e-103 Identities = 222/554 (40%), Positives = 304/554 (54%), Gaps = 39/554 (7%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPR----- 90 +DY++VG G+AGC+LANRLSA P RVLL+EAG RD IH+P G + + R Sbjct: 3 YDYVIVGGGSAGCVLANRLSAQPGKRVLLLEAGPRDLNPLIHMPAGIAKLVGDHRGLARL 62 Query: 91 -----TDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDD 145 +W +RTEP L R L +PRGKTLGG SSIN M Y+RG A DY+ WA+ TGD+ Sbjct: 63 YGSGRINWGYRTEPQAQLMNRRLWWPRGKTLGGSSSINAMCYIRGAAGDYEAWAQATGDE 122 Query: 146 AWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAV 205 WRWD L F+R ED+ R A P +HG GG + R ++ F A Sbjct: 123 RWRWDAVLSWFLRGEDNAR-----GAGP----WHGAGGPLSVADLRFHSELSDAFVAAGA 173 Query: 206 EAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDF 265 AG R DFN +G ++V QR G R +A+ A+LR QR NL V V ++ Sbjct: 174 AAGFARNDDFNGARQDGFGLYQVTQRDGARCSAAVAYLRPALQRANLEVRTGALVQRVLI 233 Query: 266 ASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIP 325 G R GV V G+++ EV+L+AGA+ +PQLL LSGIGP L EH +P Sbjct: 234 EQG-----RAVGVQV--GGRRIEAG---EVILAAGAVNTPQLLMLSGIGPADHLREHGVP 283 Query: 326 VVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPS 385 V+ D P VG +LQDHL I S+ T + + N L + Y R G + + Sbjct: 284 VLLDQPHVGAHLQDHLDICSVVGTHSRATFDHL-NDL----AVAWRYARHRDGIGTSNAA 338 Query: 386 QLCIFTRS-SKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSG 444 + F RS E ++++H P L+ G T C L+P SRG +R++S Sbjct: 339 EAGGFVRSRHAPDERCDIQFHFIPAQLDDHGAHALPGRGYTVHACYLHPRSRGRLRLRSA 398 Query: 445 NPRQAPAISPNYLSTEE--DRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDL 502 +P AI NYL + D ++ ++ R++R I +Q F + +P + ++D + Sbjct: 399 DPAVPIAIHANYLGDAQGHDLKLMIEAARLSREILAQAPFDAFRGAPVQPAGELRTDTEY 458 Query: 503 ARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNS 562 A TI+HPVGT +MGR+ + AVVDS LRV G+ GLRV DAS+MPT+ +GNTN+ Sbjct: 459 ADFIRRRAETIYHPVGTCRMGREHE--AVVDSELRVWGLPGLRVADASVMPTLVTGNTNA 516 Query: 563 PTLMIAEKAAGWIL 576 PTLMIAE+AA +L Sbjct: 517 PTLMIAERAAALML 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: 967 Number of extensions: 49 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: 533 Length adjustment: 36 Effective length of query: 543 Effective length of database: 497 Effective search space: 269871 Effective search space used: 269871 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