Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate HSERO_RS05395 HSERO_RS05395 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__HerbieS:HSERO_RS05395 Length = 484 Score = 235 bits (599), Expect = 3e-66 Identities = 137/450 (30%), Positives = 234/450 (52%), Gaps = 3/450 (0%) Query: 10 YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRA 69 ++NG+W ++ + V NPA E+L VP+ + A + A A+ W K R+ Sbjct: 15 FVNGQWCDADQGERLAVHNPANGELLGHVPLMGAAETRRAIEAANAAWPAWKKKTAKERS 74 Query: 70 RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129 IL + +L+ + ++LA ++T E GK EA GE+G +E+ A GD++ S Sbjct: 75 AILRRWYELMLANTDDLALIMTAEQGKPLAEARGEIGYAASFIEWFAEEGKRTYGDTIPS 134 Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189 + + IGV I P+NFP + A+A G +LKP+E TP L Sbjct: 135 PSPSNRIVVIKEAIGVCAAITPWNFPAAMITRKAGPALAAGCPMVLKPAEATPFSALALA 194 Query: 190 ELFEKAGLPKGVFNVVYGAHDVVNG-ILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQ 248 L E+AG+P GVF+VV G + G + +P ++ ISF GS VG+ + ++ + ++K++ Sbjct: 195 VLAERAGIPAGVFSVVTGTPKGIGGEMTSNPIVRKISFTGSTGVGKLLMQQSASSIKKLS 254 Query: 249 SLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKV 308 G IV +DA+L+ V + + + +AG+ C+ + V++G+ D F AKL E V Sbjct: 255 LELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRIYVQDGVYDAFAAKLVEAV 314 Query: 309 ADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTI 368 K+G G ++GV GP+I E ++ ++ + +GAR++ G+ + +F PT+ Sbjct: 315 KKFKVGQGTEEGVTQGPLINEQAVQKVEQHVADAVAKGARVLLGGKRHALGHSFF-EPTV 373 Query: 369 FDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFREN 428 +VT M + ++E F P+ + R K +E + +AN +EF + ++ + I E Sbjct: 374 LADVTPAMQVAREETFGPMAPLFRFKTDEEVLALANDTEFGLASYFYSRDIGRIWRVAEG 433 Query: 429 IDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458 +++GM+GIN G+ PF G K S G Sbjct: 434 LESGMVGINTGL-ISNEVAPFGGVKQSGLG 462 Lambda K H 0.318 0.136 0.396 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: 554 Number of extensions: 21 Number of successful extensions: 3 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: 487 Length of database: 484 Length adjustment: 34 Effective length of query: 453 Effective length of database: 450 Effective search space: 203850 Effective search space used: 203850 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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