Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::Caulo:CCNA_01360 (500 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 210 bits (534), Expect = 1e-58 Identities = 150/469 (31%), Positives = 233/469 (49%), Gaps = 19/469 (4%) Query: 8 FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67 ++ G V GR +V DP TG + A V A E AI A+ A W + RA Sbjct: 28 YVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWNPWRQRTAKDRA 87 Query: 68 RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLKGEYTQG 127 VM + L+ H D LA LLS+E GK +A++ G+I G I + G+ Sbjct: 88 AVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAEEGKRAYGDLIPT 147 Query: 128 AGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRLA 187 + M+QP+GVVA +TP+NFP + PA+A G ++KP+E P + LA Sbjct: 148 TASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 207 Query: 188 ELMIEAGLPPGVLNVVHGDKDCVEA--ILDHPDIKAVSFVGSSDIAQSVFQRAGAAGKRV 245 EL AGLP G+ N+V + + + ++ +SF GS+ + + + + K+V Sbjct: 208 ELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQCAETVKKV 267 Query: 246 QAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMA---LPVVVPVGEKTATALREK 302 G +V D DLD AVA + + Y ++G+ C+ V + E A L EK Sbjct: 268 SLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYEDFAVKLAEK 327 Query: 303 LVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEE 362 A + VG + GP+++AA A++ +++ V +GA ++ GR +L G Sbjct: 328 AAA----MAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGRPHALGG--- 380 Query: 363 GFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGD 422 GF+ PT+ V P + +E FGPV ++R E+ E IALA+ ++G ++R D Sbjct: 381 GFW-QPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYSR--D 437 Query: 423 AAREF--ADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFG-DLNQYGMD 468 AR F A+ +E GMVG+N + + FGG K SG G + ++YG+D Sbjct: 438 VARVFRVAEALECGMVGVNESL-ISNEVAPFGGIKESGLGREGSKYGLD 485 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: 603 Number of extensions: 28 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: 500 Length of database: 499 Length adjustment: 34 Effective length of query: 466 Effective length of database: 465 Effective search space: 216690 Effective search space used: 216690 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