Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Pf6N2E2_389 Choline dehydrogenase (EC 1.1.99.1)
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_389 Length = 521 Score = 239 bits (611), Expect = 2e-67 Identities = 191/553 (34%), Positives = 267/553 (48%), Gaps = 56/553 (10%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +D+IV GAGTAGC++A RL+ RVLLIEAG + P + + + R DW F Sbjct: 9 YDFIVCGAGTAGCVVAARLAQQDNARVLLIEAGNEYAGPEVAEPAQWPLNLGSER-DWAF 67 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 + +P LNGR L GK LGG SSIN M++ RG D+D +A +GD AW +D+ L Sbjct: 68 AGQSNPHLNGRRLSLNMGKGLGGGSSINVMVWARGHRSDWDHFAAESGDCAWGYDSVL-- 125 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEK----QRLKWQVLADFATAAVEAGVPR 211 D+YR E PD + G GG +E+ Q L W L AA G+PR Sbjct: 126 -----DYYRRIENWHGSPDAAR-RGSGGPVHVEQPASPQPLAWATLE----AASRLGIPR 175 Query: 212 TRDFNRGDNEG-----VDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFA 266 N EG + +NQ G R + +++R + NLTV V ++ Sbjct: 176 YDSPNGAMMEGPGGAAITDLRINQ--GRRESVYDSYVRPRLHQPNLTVLTGALVSRVLLR 233 Query: 267 SGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPV 326 R GV V G++ A EVVLS GA+ +P++L SGIGP + L H I Sbjct: 234 G-----TRAVGVEVIIEGQRHCFYAEAEVVLSMGAVNTPKVLMQSGIGPESELRTHGIVP 288 Query: 327 VADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQ 386 + LPGVG+NLQDH+ ++ + + G + L + +S AP Sbjct: 289 ASHLPGVGQNLQDHVAFGCTWEYLQPQAVGG------GGCETTLYW---KSDSRLDAPDL 339 Query: 387 LCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNP 446 L H LE+ V P E QP + A + P SRG +R+ P Sbjct: 340 L-----------HCQLEFAV-PSPAEVGIQPPQQGWTMFAGLA--RPVSRGRLRLSGAGP 385 Query: 447 RQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLA 506 AP I PN LS ED A S+ + R + + F E PG ++ + + Sbjct: 386 SDAPLIEPNSLSAPEDMAAAFASIDLCRALGNSETFNDLVKREVVPGP--KAHRAMEQFI 443 Query: 507 GDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLM 566 + + +HP TAKMGRD+ M+VVD LRV G+ LR+ DAS+MP IT GNT +P ++ Sbjct: 444 RNSAVSYWHPSCTAKMGRDE--MSVVDHQLRVYGIEKLRIADASVMPRITVGNTMAPCVV 501 Query: 567 IAEKAAGWILKSQ 579 I E+AA +L +Q Sbjct: 502 IGERAADLVLAAQ 514 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: 860 Number of extensions: 49 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 579 Length of database: 521 Length adjustment: 36 Effective length of query: 543 Effective length of database: 485 Effective search space: 263355 Effective search space used: 263355 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