Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate RR42_RS25010 RR42_RS25010 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS25010 Length = 485 Score = 438 bits (1127), Expect = e-127 Identities = 224/473 (47%), Positives = 305/473 (64%), Gaps = 2/473 (0%) Query: 20 PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAF-HSSWSTS 78 P L I +V++ S KTF ++PSTEE + V EA S DID AV AA AF +SSW Sbjct: 12 PKRLLIGGRWVEAASGKTFEVINPSTEELLCHVAEANSADIDAAVAAARHAFDNSSWVGM 71 Query: 79 DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIK 138 P R + L ++AD ID HAD LA IE LDNG L S A FR GW KI Sbjct: 72 SPHARTRALLRIADQIDRHADELAAIETLDNGMPLWFSTAVATTAADIFRYYGGWCTKIL 131 Query: 139 GSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLS 198 GS I + + F YT REP+GVCGQIIPWN P+LMAS KL LC G T +LK AE L+ Sbjct: 132 GSTIPSDASGFVYTLREPLGVCGQIIPWNVPILMASIKLANALCCGNTLILKPAELACLT 191 Query: 199 ALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAES 258 +L LA LI+E PPGV+N++ GFG TAGA ++ HP + K+AFTGSTA G+ I++A+ S Sbjct: 192 SLRLAELIQETDLPPGVINMLPGFGATAGAALALHPDVDKIAFTGSTAIGKQIVQAST-S 250 Query: 259 NLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVS 318 NLKKVTLELGGKSPN++F DAD+ +Q V N+G+VC AG+R++V E ++D++ Sbjct: 251 NLKKVTLELGGKSPNVIFADADLDKAVQAAVKTFCGNSGQVCSAGTRLFVHESVHDEVSE 310 Query: 319 EFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYF 378 A + +GDP DT +G S Q D++L YI+ G+ GA++ GG ++ +GYF Sbjct: 311 RVTRLAATYTVGDPLAPDTKLGPLISAKQRDRVLSYIEAGQAGGASLQLGGSQWSGRGYF 370 Query: 379 IKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAI 438 + P +F V +I ++EIFGPV++I F+ ++ + ND+ YGL+A V T +++ A Sbjct: 371 VAPAVFDGVTNGMRIAQEEIFGPVLSIIPFRDEDDAVFKGNDTTYGLSAAVWTRDVARAH 430 Query: 439 SVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 V+ + +G +W+NTY + P +PFGGY QSG GRE G+E++D YTQVKAV + Sbjct: 431 KVARALKAGRVWINTYGEADPAMPFGGYKQSGWGREFGQESIDAYTQVKAVML 483 Lambda K H 0.316 0.133 0.389 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: 618 Number of extensions: 23 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: 495 Length of database: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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 (21.6 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