Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 233 bits (593), Expect = 1e-65 Identities = 164/485 (33%), Positives = 254/485 (52%), Gaps = 19/485 (3%) Query: 9 NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68 NYI G++V Y D ++P +V + STKED++ A A EAFKTWSK + R Sbjct: 16 NYIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSSTER 75 Query: 69 ARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMGDSL 127 + IL Q + + E LA + TI+NGK +E L ++ G+++ + AG G SL Sbjct: 76 SIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEG-SL 134 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 + + + + PIGVV I P+NFP+++ W A+A GN +LKP+E TP+ Sbjct: 135 SELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMV 194 Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246 L+EL LP GV NVV G ++ ++ +P++ +F GS P G V + +EN+ Sbjct: 195 LMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATENIIP 253 Query: 247 VQSLTGAKNHTIVL------NDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300 V G K+ I +DA L+ V V A + GE C + + ++E I ++F Sbjct: 254 VTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL-NQGEICTCPSRLLIQEDIYEKF 312 Query: 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGREN---- 356 +AK+ E+ IKIG+ LD V +G + ++ +YI+ G EEGA ++ G N Sbjct: 313 IAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELPG 372 Query: 357 VSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFT 416 GY++ PTIF +M I+++EIF PVL+V K ++EAIEIAN + + GA ++T Sbjct: 373 ELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVWT 431 Query: 417 SNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKV 476 +++ + I AG + +N P A PF G+K S G N K + Y + K Sbjct: 432 RDAHELYQVPRAIQAGRVWVNQYHAYP-AGAPFGGYKQS--GVGRENHKMMLGHYRQTKN 488 Query: 477 VTARY 481 + Y Sbjct: 489 MLISY 493 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: 586 Number of extensions: 24 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: 487 Length of database: 501 Length adjustment: 34 Effective length of query: 453 Effective length of database: 467 Effective search space: 211551 Effective search space used: 211551 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