Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 209 bits (532), Expect = 2e-58 Identities = 142/462 (30%), Positives = 233/462 (50%), Gaps = 17/462 (3%) Query: 9 NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68 N+I G++V +Y DV++P +V +V DI+ A A +AF WS+ + R Sbjct: 24 NFIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPAWSRTSATER 83 Query: 69 ARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMGDSL 127 + IL + E LA + TI+NGK +E + ++ +++ + AG G S+ Sbjct: 84 SNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEG-SI 142 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 A + + N + PIG+VG I P+NFPM++ W A+A G I+KP+E+TP Sbjct: 143 AELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMI 202 Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246 L+E+ LP GV NVV G + + + P + ++F G G + + SENL Sbjct: 203 LMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYASENLNP 261 Query: 247 VQSLTGAKNHTIVL------NDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300 V G K+ + +D L+ + V A + GE C + + V E I D F Sbjct: 262 VTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFAL-NQGEVCTCPSRILVHEKIYDAF 320 Query: 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGR----EN 356 M K+ + I++G+ LD +G +D ++ LSYI+ G +EGA ++ G + Sbjct: 321 MEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLNS 380 Query: 357 VSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFT 416 ++GY+V PT+ +M ++++EIF PV SV K+++EAI I+N + + GA ++T Sbjct: 381 GLENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVWT 439 Query: 417 SNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458 +++ I AG + +N P A PF G+K S FG Sbjct: 440 RDAHEAYQVPRAIKAGRVWVNCYHAYP-AHAPFGGYKKSGFG 480 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: 598 Number of extensions: 26 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: 509 Length adjustment: 34 Effective length of query: 453 Effective length of database: 475 Effective search space: 215175 Effective search space used: 215175 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