Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)
Query= reanno::Smeli:SMc00781 (498 letters) >FitnessBrowser__SB2B:6939342 Length = 506 Score = 186 bits (472), Expect = 2e-51 Identities = 145/473 (30%), Positives = 234/473 (49%), Gaps = 35/473 (7%) Query: 6 HFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQRR 65 +FI GK V G + +P G+V A + D+ A+++A AA+ W T+ R Sbjct: 21 NFIGGKWVPPVGGEYFDNVSPVDGKVFCQAARSDYRDIELALDAAHAAKDSWGKTSVTER 80 Query: 66 ARVFMKFVQLLNDNMNELAEMLSREHGKTIDDA-KGDIVRGLEVCEFVIGIPHLQKSEFT 124 + + +K + ++ LA + + E+GK + + D+ ++ + G Q Sbjct: 81 SNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQ----- 135 Query: 125 EGAGPGIDM----YSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180 EG+ +D Y + +P+G+ I P+NFP ++ W APA+A GN +LKP+E+ P+ Sbjct: 136 EGSAADLDANTVSYHLPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPA 195 Query: 181 VPIRLAELMIEAGLPAGILNVVNG---DKGAVDAILTHPDIAAVSFVGSTPIARYVYGTA 237 + L E IE LP G+LNVVNG + GA A+ T IA ++F GST + ++ A Sbjct: 196 SIMVLLE-TIEDLLPPGVLNVVNGFGAEAGA--ALATSKRIAKLAFTGSTEVGNHILKCA 252 Query: 238 AMN---------GKRAQC-FGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVA 287 A N GK F NH D LD+A ++ A + + GE C S Sbjct: 253 AENLIPSTVELGGKSPNIYFADVMNH----EDNYLDKAIEGMLLA-FFNQGEVCTCPS-R 306 Query: 288 VPVGEETANRLIDKLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKL 347 V V E + I+K++ +++R G D +G ++E +I +D G +GAK+ Sbjct: 307 VLVQESIYDAFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGRAEGAKV 366 Query: 348 VVDGRDFKLQ-GYENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMK 406 ++ G +FKLQ G E G + M +++ EIFGPV+SV ++ EAL++ Sbjct: 367 LMGG-EFKLQDGPEKGGYYIQPTILKGHNKMRVFQEEIFGPVVSVTTFKDEAEALAIAND 425 Query: 407 HEYGNGVAIYTRDGDAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFG 459 +YG G ++TRD + A+ I G V +N P A+ +FGG+K S G Sbjct: 426 TQYGLGAGVWTRDMNLAQRMGRGIQAGRVWINCYHAYP-AHAAFGGYKKSGIG 477 Lambda K H 0.319 0.137 0.409 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: 585 Number of extensions: 38 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: 498 Length of database: 506 Length adjustment: 34 Effective length of query: 464 Effective length of database: 472 Effective search space: 219008 Effective search space used: 219008 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 09 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