Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= reanno::Caulo:CCNA_01360 (500 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 221 bits (563), Expect = 5e-62 Identities = 139/464 (29%), Positives = 238/464 (51%), Gaps = 9/464 (1%) Query: 8 FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67 F+ G+ +D SG+ EV +P G V V + A E AI A+ A AW A + RA Sbjct: 25 FVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWPAWRALTAKERA 84 Query: 68 RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLKGEYTQG 127 + + + L+ + +++A ++++E GK +A+++G++ IE+ + G+ Sbjct: 85 KTLRTWFDLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAEEGKRVYGDTIPQ 144 Query: 128 AGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRLA 187 PG + ++P+GV A ITP+NFPA + GPA+A G ++KP+ P + +A Sbjct: 145 HLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPATATPLTALAMA 204 Query: 188 ELMIEAGLPPGVLNVVHGDKDCVEA-ILDHPDIKAVSFVGSSDIAQSVFQRAGAAGKRVQ 246 L AG+P G+L+VV G + + +P ++ ++F GS++I + + + K+V Sbjct: 205 VLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELMAQCAGTVKKVS 264 Query: 247 AMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALREKLVAA 306 G LV DADLD+AV I + Y + G+ C+ ++ V A KL A Sbjct: 265 LELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLL-VQSGVYDAFAAKLAEA 323 Query: 307 IGGLRVGVS-TDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEEGFF 365 + L+VG T A GP++ A ++E +I+ ++GA +V+ G+ L G F Sbjct: 324 VKALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKRHELGGS----F 379 Query: 366 VGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDAAR 425 PT+ V P + +E FGPV + R E+ EE + +A+ ++G ++R+ Sbjct: 380 FEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYSRDIGRVW 439 Query: 426 EFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFG-DLNQYGMD 468 A+ +E G+VGIN I + FGG K SG G + ++YG++ Sbjct: 440 RVAEALEYGIVGINEGI-ISTEVAPFGGMKESGIGREGSKYGIE 482 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: 27 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: 497 Length adjustment: 34 Effective length of query: 466 Effective length of database: 463 Effective search space: 215758 Effective search space used: 215758 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