Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate CCNA_02725 CCNA_02725 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__Caulo:CCNA_02725 Length = 555 Score = 379 bits (974), Expect = e-109 Identities = 225/543 (41%), Positives = 304/543 (55%), Gaps = 19/543 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNP-RTDWR 94 FDYIV+GAG+AGC+LA RL+ DP +VLL+EAGG++ + +P G I + +W Sbjct: 6 FDYIVIGAGSAGCVLAARLTEDPNIKVLLLEAGGKNKSILVKMPAGVGQLIKDKGEQNWG 65 Query: 95 FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154 F TE +P L+ R L +PRGK LGG S+INGM+Y+RG ARDYD W ++ G W + LP Sbjct: 66 FWTEAEPHLDNRKLWWPRGKGLGGSSAINGMIYIRGHARDYDQWRQM-GLTGWSYSEVLP 124 Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214 F R E H+ GGDA +HG G + K + A +AG T+D Sbjct: 125 YFKRSETHHA---GGDA------YHGGSGPLHVSKGESDSPFYSTLVEAGRQAGHKTTKD 175 Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHS--TQVLKLDFASGEGSE 272 FN EG +++ R G RW+A+ A+L R NLT T + LD G E Sbjct: 176 FNGYQQEGFGPYDLTIRDGQRWSAAMAYLNQALSRPNLTCVTEACTTRIILDKRRAVGVE 235 Query: 273 PRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332 V ++ +K V A EV+LSAGA+ SPQ+LQLSGIG LA H I V + G Sbjct: 236 -----YVVGKSREKQVAYADAEVLLSAGAVQSPQILQLSGIGAAEDLAPHGIAVAHESKG 290 Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392 VG NLQDHL + + K KT + AN + K +G+ Y+ G + F + Sbjct: 291 VGANLQDHLDVCVSWTAKNLKTAYS-ANKGLNKLGVGMNYMFFGKGLGRQQFLESGAFLK 349 Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452 S + + P+L+ H ++ G+ + + T VC L P SRG V ++S +P P I Sbjct: 350 SRPDLDRPDLQIHGVLAIMQDHGKVVVEKDGFTLHVCQLRPESRGKVGLRSADPFDDPTI 409 Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTT 512 NYL+TEEDR+ + +R+ R +Q AF Y E+ PG +SD DL T Sbjct: 410 LGNYLATEEDRRAIREGVRIARETVAQAAFDPYRDAEYAPGADVKSDADLDAWIRSKAET 469 Query: 513 IFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572 I+HPVGT +MG DPMAVVD LRV+GV GLRV+DAS+MPT+ GNTN+PT+MIAE+AA Sbjct: 470 IYHPVGTCRMGVAGDPMAVVDDQLRVQGVQGLRVIDASVMPTLIGGNTNAPTIMIAERAA 529 Query: 573 GWI 575 I Sbjct: 530 DLI 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: 878 Number of extensions: 42 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: 555 Length adjustment: 36 Effective length of query: 543 Effective length of database: 519 Effective search space: 281817 Effective search space used: 281817 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