Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_02464 H281DRAFT_02464 betaine aldehyde dehydrogenase
Query= reanno::Caulo:CCNA_01360 (500 letters) >FitnessBrowser__Burk376:H281DRAFT_02464 Length = 489 Score = 265 bits (677), Expect = 3e-75 Identities = 170/478 (35%), Positives = 251/478 (52%), Gaps = 15/478 (3%) Query: 8 FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67 +IGG VD G + DP G+ A V AS+ +++ A+ +A+ Q WAA +R+ Sbjct: 10 YIGGTYVDATGGETFDTVDPANGETLATVQQASSADVDRAVQSAREGQREWAALTGMQRS 69 Query: 68 RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKG-DIQRGLEVIEFACGVPHLLKGEYTQ 126 R++ +L DELAAL + + GK IA+++ DI G +VIE+ G+ ++G+ Sbjct: 70 RILRRAVDILRERNDELAALETRDTGKPIAETQAVDIVTGADVIEYYAGLATAIEGQQIP 129 Query: 127 GAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRL 186 P VY+ R+PLGV AGI +N+P I W PA+A GNA I KPSE P ++L Sbjct: 130 -LRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEVTPLSALKL 188 Query: 187 AELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAAG-KRV 245 AE+ EAG+PPGV NVV GD + HPDI+ +SF G + + V AGA+ K V Sbjct: 189 AEIYTEAGVPPGVFNVVQGDGRVGAMLAAHPDIEKISFTGGVETGKKVMSMAGASSLKEV 248 Query: 246 QAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALREKLVA 305 G K+ LV DA+L++A + A + S+G+ C V V ++ Sbjct: 249 TMELGGKSPLLVFDDANLERAADIAMSANFFSSGQVC-TNGTRVFVQRSVLERFEALVLE 307 Query: 306 AIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEEGFF 365 + +RVG D ++GP+VSAA ++ YI GV EGA L+ G+ S +G + Sbjct: 308 RVKRIRVGAPGDASTNFGPLVSAAQLQKVLGYIDSGVQEGARLIAGGKRLSEGHFGQGQY 367 Query: 366 VGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDAAR 425 V PT+F R +EIFGPV+ ++ ++ +E I A+R YG + T N A Sbjct: 368 VEPTVFTGCHDDMRIVREEIFGPVMSILIFDNEDEAIERANRTAYGLAAGVVTENLARAH 427 Query: 426 EFADQVEVGMVGINV----PIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTV 479 ++E G+ IN P +PV GG+K+SG G N G+ + YTR K+V Sbjct: 428 RVIHRLEAGICWINTWGESPAEMPV-----GGYKQSGVGREN--GITTLEHYTRIKSV 478 Lambda K H 0.320 0.137 0.409 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: 589 Number of extensions: 23 Number of successful extensions: 4 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: 500 Length of database: 489 Length adjustment: 34 Effective length of query: 466 Effective length of database: 455 Effective search space: 212030 Effective search space used: 212030 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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