Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_009562902.1 RSPH17029_RS04350 betaine-aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000015985.1:WP_009562902.1 Length = 483 Score = 258 bits (660), Expect = 2e-73 Identities = 163/470 (34%), Positives = 254/470 (54%), Gaps = 7/470 (1%) Query: 9 NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68 ++++G +E +T V+ PAT E + ++ +T I+ A + A A W+ + R Sbjct: 9 HFVDGRPLEDETGAPIPVIYPATGEEIARLHEATPAVIEAALASGARAQAAWAAMRPVER 68 Query: 69 ARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMGDSL 127 ARIL L+ EEL+ L T++ GK +E L + G + +EF AG + G+++ Sbjct: 69 ARILRRASDLIRARNEELSLLETLDTGKPLQETLVADWASGADALEFFAGLAPAVTGETV 128 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 + D R P+G+ GI +N+P + CW A+ALGN + KPSE TPL K Sbjct: 129 P-LGQDF-VYTIREPLGLCVGIGAWNYPSQIACWKAAPALALGNAMVFKPSEVTPLGALK 186 Query: 188 LVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRV 247 L E+ +AGLP G+FNVV G V ++ + +S GS P G VY +E ++ V Sbjct: 187 LAEILIEAGLPPGLFNVVQGRGAVGAALVTDSRVAKVSLTGSVPTGRRVYAAAAEGVRHV 246 Query: 248 QSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEK 307 G K+ IV +DA+LE + + F SAG+ C V V++GI + F+A+L E+ Sbjct: 247 TMELGGKSPLIVFDDADLESAIGAAMLGNFYSAGQICSNGTRVFVQKGIKEAFLARLAER 306 Query: 308 VADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPT 367 I++G+ LD V +GP++ + ++ L+YIEK EG RLVC G +VS G +V PT Sbjct: 307 ADAIRMGDPLDPEVQMGPLVSQAQLEKVLAYIEKARAEGGRLVCGGEASVS-PGCYVQPT 365 Query: 368 IFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRE 427 +F +VT MT+ ++E+F PV++V+ + +EAI AN ++F A +FT++ Sbjct: 366 VFADVTDAMTLAREEVFGPVMAVLDFETEEEAIARANATDFGLAAGVFTADLTRAHRVVA 425 Query: 428 NIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477 + AG IN P+ PF G K S G NG+ +V+ YT+ K V Sbjct: 426 QLQAGTCWINAYNLTPVE-APFGGVKLS--GVGRENGRAAVEHYTQVKSV 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: 536 Number of extensions: 33 Number of successful extensions: 3 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: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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 Apr 10 2024. 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