Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF827 PS417_04200 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__WCS417:GFF827 Length = 481 Score = 274 bits (701), Expect = 4e-78 Identities = 166/475 (34%), Positives = 252/475 (53%), Gaps = 6/475 (1%) Query: 1 MAEIRKLKNYINGEWVESKTDQYEDVVNPAT-KEVLCQVPISTKEDIDYAAQTAAEAFKT 59 M++ ++ NYING+WV Y +NP+ +V+ + + ++ A A AF Sbjct: 1 MSQAQRFDNYINGQWVAGA--DYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPA 58 Query: 60 WSKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAP 119 WS + R L + +EEL L+ E GK EA+GEV R +F AG Sbjct: 59 WSTSGIQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGEC 118 Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179 + GD + S+ V R +GVVG I P+NFP+ +P W A+A GN ++KP+E Sbjct: 119 LRLSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAE 178 Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGIL-EHPEIKAISFVGSKPVGEYVYK 238 P L E+ +AG P GVFN+V G+ VV +L P++ ISF GS VG + Sbjct: 179 LVPGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAV 238 Query: 239 KGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIAD 298 +VQ G KN I+L+DA+L+ V V +AF S G+RC A + + V GI D Sbjct: 239 SCVSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHD 298 Query: 299 EFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS 358 +F+A + E++ IK+G+ L G +GPV+ + + L YI+ G EGARLV G Sbjct: 299 QFVAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTC 358 Query: 359 D-DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417 D +GY++ PT+F + M I ++EIF PV +V+RV + + A+ +AN +EF A + T+ Sbjct: 359 DTEGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATT 418 Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYT 472 + +F+ + AGM+ +NL PF G K S +G+ G+ + +FYT Sbjct: 419 SLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYT 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: 553 Number of extensions: 31 Number of successful extensions: 4 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: 481 Length adjustment: 34 Effective length of query: 453 Effective length of database: 447 Effective search space: 202491 Effective search space used: 202491 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