Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= reanno::Caulo:CCNA_01360 (500 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 215 bits (547), Expect = 5e-60 Identities = 151/472 (31%), Positives = 230/472 (48%), Gaps = 32/472 (6%) Query: 8 FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67 FIGG A G+ +P G A+V + ++ A+ A+ AQ AWA Q A Sbjct: 36 FIGG--TFQAPGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRAQPAWARLGGQGWA 93 Query: 68 RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKG-DIQRGLEVIEFACGVPHLLKGEYTQ 126 RV++ RLL+ H A L + ++GK I +S+ DI + G+ L++ E Sbjct: 94 RVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDELPD 153 Query: 127 GAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRL 186 R P+GV I P+NFP ++ W PA+A GN +LKP+E P + Sbjct: 154 -----------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALLF 202 Query: 187 AELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAAGKRVQ 246 AE+ EAG+PPGV+N+V GD A++ HP + ++F GS+D+ + + + GK + Sbjct: 203 AEICGEAGVPPGVVNIVTGDGATGAALVSHPGVDKIAFTGSTDVGREIRRATAGTGKALT 262 Query: 247 AMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALREKLVAA 306 G K+ +V DADLD AV ++ A + + G+ C A ++ V E A A KL A Sbjct: 263 LELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLL-VQEGIAEAFYAKLRAR 321 Query: 307 IGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQG---HEEG 363 + LR+G D G +V AH A++ AE+V G Q EG Sbjct: 322 MATLRIGDPLDKCIDVGAMVDPAHCAKV-----------AEMVAGSNGEVHQPGTVPAEG 370 Query: 364 FFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDA 423 F PTL ++P DEIFGPVL + E + +A+ +YG +++ N + Sbjct: 371 AFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINR 430 Query: 424 AREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTR 475 A + A ++ G+V +N A FGG + SGFG + G +G+R YT+ Sbjct: 431 ALDIAPKLAAGVVWVNATNLFDAA-AGFGGVRESGFG--REGGWEGLRAYTK 479 Score = 70.9 bits (172), Expect = 2e-16 Identities = 56/249 (22%), Positives = 108/249 (43%), Gaps = 9/249 (3%) Query: 8 FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67 +IGG++ SG V+ P G + S ++ A+ A A+W T RA Sbjct: 511 YIGGKQARPDSGYSRPVWSPK-GVLLGHAPEGSRKDIRNAV-EAATGAASWGRTTGHLRA 568 Query: 68 RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLKGEYTQG 127 ++++ L +E A ++ G + ++ ++ ++ + G Sbjct: 569 QILYYVAENLSARTEEFATRIAEMTGSRVPRAEAEVSAAIDRLFTYAAWADKYDGAVKPV 628 Query: 128 AGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRLA 187 G+ + +M +P+GV+ P + P + + + G A+A GN +L PSE P L Sbjct: 629 PIRGVAL-AMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLY 687 Query: 188 ELMIEAGLPPGVLNVVHGDKDCV-EAILDHPDIKAVSFVGSSDIAQSVFQRAGAAGKRVQ 246 +++ + +P GV+N+V G + + + + H + AV +DI+ ++ A KR Sbjct: 688 QVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGADISTTIEAEAAGNLKRTW 747 Query: 247 AMGGAKNHG 255 NHG Sbjct: 748 V-----NHG 751 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: 975 Number of extensions: 55 Number of successful extensions: 5 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: 500 Length of database: 780 Length adjustment: 37 Effective length of query: 463 Effective length of database: 743 Effective search space: 344009 Effective search space used: 344009 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: 54 (25.4 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