Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Pf1N1B4_4450 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4450 Length = 549 Score = 622 bits (1604), Expect = 0.0 Identities = 319/541 (58%), Positives = 388/541 (71%), Gaps = 17/541 (3%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYIVVGAG AGCLLANRLSA+P +RVLL+EAGGRDNY WIHIPVGYL+CI NPRTDW F Sbjct: 8 YDYIVVGAGPAGCLLANRLSANPQHRVLLLEAGGRDNYPWIHIPVGYLFCIGNPRTDWCF 67 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 +TE PGL GR+L YPRGK LGGCSSINGM+Y+RGQA DYDGWA G+ W W + LP Sbjct: 68 KTETQPGLQGRALSYPRGKVLGGCSSINGMIYMRGQAGDYDGWAA-EGNAGWGWQDVLPL 126 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F + E+H+ GD++ FHG G+WR+E+QRL W +L F TAA ++G+ DF Sbjct: 127 FKQSENHF----AGDSE-----FHGAAGQWRVERQRLSWPILDAFRTAAEQSGIASIDDF 177 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N+GDNEG F+VNQ++G RWNA+KAFL+ + QR NLTV +V ++ +G S Sbjct: 178 NQGDNEGCGYFQVNQKAGIRWNAAKAFLKPIRQRANLTVLTDVEVDRVLLENGRAS---- 233 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 V+ + AR E+VL AGA+GSP +LQ SGIGP LL + I V +LPGVG Sbjct: 234 -AVSARWQDQAKTFKARKEIVLCAGAVGSPGILQRSGIGPRPLLQKLGIGVTHELPGVGG 292 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395 NLQDHLQ+R IYK++ A+TLN +A +L GK +GL Y+ RSGP+SMAPSQL F RS Sbjct: 293 NLQDHLQLRLIYKLENARTLNQIAGTLWGKMGMGLRYLYDRSGPLSMAPSQLGAFARSGP 352 Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISPN 455 E NLEYHVQPLSLE FG+PLH FPA TASVC+L P SRG + I+S +PR+AP I PN Sbjct: 353 EQTSANLEYHVQPLSLERFGEPLHAFPAFTASVCDLRPQSRGRIDIRSADPREAPLIQPN 412 Query: 456 YLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIFH 515 YLS ED +VAAD++R+TR I S PA + P E+ PG QS+E L A IGTTIFH Sbjct: 413 YLSHPEDLRVAADAIRLTRRIVSAPALQAFKPVEYLPGDSLQSEEQLHEAAARIGTTIFH 472 Query: 516 PVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGWI 575 PVGT +MG +D AVVD+ LRV G+ GLR+ DASIMP ITSGNT SPTLMIAEKAA + Sbjct: 473 PVGTCRMG--NDAHAVVDAELRVHGIPGLRIADASIMPRITSGNTCSPTLMIAEKAAQLM 530 Query: 576 L 576 L Sbjct: 531 L 531 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: 950 Number of extensions: 36 Number of successful extensions: 5 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: 549 Length adjustment: 36 Effective length of query: 543 Effective length of database: 513 Effective search space: 278559 Effective search space used: 278559 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