Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_017547432.1 C792_RS0100265 L-glutamate gamma-semialdehyde dehydrogenase
Query= reanno::Caulo:CCNA_01360 (500 letters) >NCBI__GCF_000330705.1:WP_017547432.1 Length = 514 Score = 178 bits (451), Expect = 5e-49 Identities = 135/462 (29%), Positives = 217/462 (46%), Gaps = 18/462 (3%) Query: 6 PHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQR 65 P IGG+ ++ + + + V+ A+ G ++ A A A W+ +P+ Sbjct: 38 PLIIGGEHIE-TDDQITSYNPSDKEQAVGHVSKATQGHIDAAFQAAGEAFETWSEWDPKD 96 Query: 66 RARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEF-ACGVPHLLKGEY 124 RA ++ ++ E +AL+ E GK ++ GD G++ IE+ A + L G+ Sbjct: 97 RAELLIRVAAIIRRRKHEFSALMVHEAGKPWNEADGDTNEGIDFIEYYARSMMELADGKP 156 Query: 125 TQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPV 184 + Y QP+G I+P+NFP I I GN +LKP+E P + Sbjct: 157 VLDREGEHNKY-FYQPMGTGVTISPWNFPFAIMTGTTVAPIIAGNTVLLKPAEDTPLISY 215 Query: 185 RLAELMIEAGLPPGVLNVVHGDKDCV-EAILDHPDIKAVSFVGSSDIAQSVFQRAGAAG- 242 +L E+ EAGLP GV+N V GD + + ++DH ++F GS + +RA Sbjct: 216 KLMEVFEEAGLPKGVVNFVTGDPGVIGDYMVDHHKTHFITFTGSKSTGLRISERASVVQE 275 Query: 243 -----KRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTAT 297 KRV G K+ +V ADLD A I+ +A+G AG++C A V + E Sbjct: 276 GQHFLKRVITEMGGKDTIIVDKTADLDLAADSIVSSAFGFAGQKCSAGSRAV-IHEDVYD 334 Query: 298 ALREKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSL 357 + +K V L VG D + + GPV+S I+ YI +G EG L + G Sbjct: 335 EVLKKAVELTEELTVGNPVD-ETYMGPVISRKQFDMIKGYIDIGKGEGT-LKIGGE---- 388 Query: 358 QGHEEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIF 417 +G+F+ PT+F + P +R +EIFGPV+ +A+ +E + +A+ YG ++ Sbjct: 389 TDDSKGYFIQPTIFADLDPKARIMQEEIFGPVVAFAKAKDFDELLEIANNTVYGLTGSVI 448 Query: 418 TRNGDAAREFADQVEVGMVGINVPIPVPV-AYHSFGGWKRSG 458 T + + + VG + +N V YH FGG+K SG Sbjct: 449 TNTRENWIKAQKKFHVGNLYLNRGCTAAVMGYHPFGGFKLSG 490 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: 611 Number of extensions: 36 Number of successful extensions: 6 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: 514 Length adjustment: 34 Effective length of query: 466 Effective length of database: 480 Effective search space: 223680 Effective search space used: 223680 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 24 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