Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate CCNA_00865 CCNA_00865 alpha-ketoglutaric semialdehyde dehydrogenase xylA
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Caulo:CCNA_00865 Length = 478 Score = 283 bits (725), Expect = 7e-81 Identities = 162/471 (34%), Positives = 255/471 (54%), Gaps = 5/471 (1%) Query: 7 LKNYINGEWVESKTDQYEDVVNPA-TKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65 L++YI GE V + D + +NP+ T +V+ +VP+ + ++D A A +AF W+ + Sbjct: 5 LRHYIGGERVAA--DAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASP 62 Query: 66 PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGD 125 R+ +L + ++ L+ E GK E +GE R ++ AG G Sbjct: 63 EVRSDLLDKVGSTIIARSADIGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQ 122 Query: 126 SLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLT 185 +L S VE YR +GV G I P+NFP+ +P W A+A GNT ++KP+ TP Sbjct: 123 NLESTRPGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATA 182 Query: 186 EKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLK 245 L ++ + G P GVFN+++G + + +++H ++ +SF GS+ VG V Sbjct: 183 NVLADIMAECGAPAGVFNMLFGRGSMGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQA 242 Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQ 305 RVQ G KN IVL+DA+LE V + +F + G+RC A + + V++GI D+F+A L Sbjct: 243 RVQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLA 302 Query: 306 EKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYFV 364 EKVA +++G+ LD +GP + ED + + YI+ EG R+V G R + + G++V Sbjct: 303 EKVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGWYV 362 Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424 PT+ + M I +E+F PV S IRVK+ +EA+EIAN EF A + T++ R+ Sbjct: 363 RPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHARH 422 Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475 F+ AGM +NL PF G KSS +G G +V+F+T+ K Sbjct: 423 FQRYARAGMTMVNLATAGVDYHVPFGGTKSSSYGA-REQGFAAVEFFTQTK 472 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: 532 Number of extensions: 20 Number of successful extensions: 2 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: 478 Length adjustment: 34 Effective length of query: 453 Effective length of database: 444 Effective search space: 201132 Effective search space used: 201132 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