Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_010961010.1 MCA_RS08650 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000008325.1:WP_010961010.1 Length = 491 Score = 232 bits (591), Expect = 3e-65 Identities = 144/449 (32%), Positives = 225/449 (50%), Gaps = 3/449 (0%) Query: 11 INGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRAR 70 I+G+WV++ + V +PAT L VP + A A A+ W RA Sbjct: 19 IDGQWVDADHSKTFSVTDPATGRALADVPAMGAAETMRAIAAAEHAWTGWRGKTAKERAA 78 Query: 71 ILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLASI 130 +L + +L+ H E+LA ++T E GK EA E+G VE+ A G+++ S Sbjct: 79 VLRRWYELILSHTEDLARILTAEQGKPLTEARNEIGYAAGFVEWFAEEAGRAYGETIPSP 138 Query: 131 ATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLVE 190 D R PIGV I P+NFP + A+A G T ++KP+E+TPL L + Sbjct: 139 VPDKRLLVIRQPIGVCAAITPWNFPAAMITRKIAPALAAGCTVVVKPAEQTPLTALALAD 198 Query: 191 LFEKAGLPKGVFNVVYGAHDVVNG-ILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQS 249 L +AG P GV NVV G + + G + +P I+ +SF GS VG + + + +K++ Sbjct: 199 LAVQAGFPPGVINVVTGDPEAIGGELTSNPLIRKLSFTGSTEVGRLLMAQCAATVKKISL 258 Query: 250 LTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKVA 309 G IV DA+L+ V + + + + G+ C+ +++ I D F +L KV Sbjct: 259 ELGGNAPFIVFEDADLDAAVEGALLSKYRNTGQTCVCTNRFLIQDSIYDAFAERLAAKVR 318 Query: 310 DIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTIF 369 +++GNGLD+GV GP+I E + +I L+ GAR++ G + G F PT+ Sbjct: 319 RLEVGNGLDEGVVQGPLIDEQALAKVERHIADALDRGARVLAGGGRHPL-GGRFFQPTVL 377 Query: 370 DNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRENI 429 +VT EM ++E F PV ++R + +EA+ IAN +E+ A +T + E + Sbjct: 378 VDVTPEMLCTREETFGPVAPLLRFGSEEEALAIANATEYGLAAYFYTRDLARAFRVGEAL 437 Query: 430 DAGMLGINLGVPAPMAFFPFSGWKSSFFG 458 + GM+GIN G+ PF G K S G Sbjct: 438 EYGMVGINTGM-LSYDVAPFGGVKQSGIG 465 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: 509 Number of extensions: 24 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: 491 Length adjustment: 34 Effective length of query: 453 Effective length of database: 457 Effective search space: 207021 Effective search space used: 207021 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 24 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