Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_02464 H281DRAFT_02464 betaine aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Burk376:H281DRAFT_02464 Length = 489 Score = 256 bits (653), Expect = 2e-72 Identities = 164/482 (34%), Positives = 249/482 (51%), Gaps = 9/482 (1%) Query: 1 MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60 MA + YI G +V++ + D V+PA E L V ++ D+D A Q+A E + W Sbjct: 1 MAVFATQRLYIGGTYVDATGGETFDTVDPANGETLATVQQASSADVDRAVQSAREGQREW 60 Query: 61 SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALG-EVGRGIENVEFAAGAP 119 + + +R+RIL +L + +ELA L T + GK E ++ G + +E+ AG Sbjct: 61 AALTGMQRSRILRRAVDILRERNDELAALETRDTGKPIAETQAVDIVTGADVIEYYAGLA 120 Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179 + + G + T R P+GV GI +N+P+ + CW A+A GN I KPSE Sbjct: 121 TAIEGQQIPLRPTSFVYTR-REPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSE 179 Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYK- 238 TPL KL E++ +AG+P GVFNVV G V + HP+I+ ISF G G+ V Sbjct: 180 VTPLSALKLAEIYTEAGVPPGVFNVVQGDGRVGAMLAAHPDIEKISFTGGVETGKKVMSM 239 Query: 239 KGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIAD 298 G+ +LK V G K+ +V +DANLE + A F S+G+ C V V+ + + Sbjct: 240 AGASSLKEVTMELGGKSPLLVFDDANLERAADIAMSANFFSSGQVCTNGTRVFVQRSVLE 299 Query: 299 EFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGR---E 355 F A + E+V I++G D GP++ ++ L YI+ G++EGARL+ G+ E Sbjct: 300 RFEALVLERVKRIRVGAPGDASTNFGPLVSAAQLQKVLGYIDSGVQEGARLIAGGKRLSE 359 Query: 356 NVSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLF 415 G +V PT+F +M I ++EIF PV+S++ N EAIE AN++ + A + Sbjct: 360 GHFGQGQYVEPTVFTGCHDDMRIVREEIFGPVMSILIFDNEDEAIERANRTAYGLAAGVV 419 Query: 416 TSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475 T N ++AG+ IN +P A P G+K S G NG +++ YTR K Sbjct: 420 TENLARAHRVIHRLEAGICWINTWGESP-AEMPVGGYKQS--GVGRENGITTLEHYTRIK 476 Query: 476 VV 477 V Sbjct: 477 SV 478 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: 534 Number of extensions: 25 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: 489 Length adjustment: 34 Effective length of query: 453 Effective length of database: 455 Effective search space: 206115 Effective search space used: 206115 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