Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate RR42_RS26255 RR42_RS26255 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS26255 Length = 499 Score = 384 bits (987), Expect = e-111 Identities = 208/476 (43%), Positives = 288/476 (60%), Gaps = 5/476 (1%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQV 82 +I+ + + TF T++P+T + + +V ++D+D AV AA AF S WS + Sbjct: 24 YIDGRWADAADGATFETINPATGKALARVAACGAQDVDRAVAAARKAFQSGVWSDTPRSA 83 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSV 141 R L +L+ LI+ H + LA +E LD GK + + + D+ + A DKI + Sbjct: 84 RKATLLRLSHLIETHREELALLETLDMGKPIAETLQYDIPEAGRTYAWYAEAIDKIYDEI 143 Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201 TG REP+GV ++PWN+PLLMASWK+ P L G + VLK AE +PL+AL Sbjct: 144 APTGPGVLATITREPLGVVAAVVPWNYPLLMASWKVAPALAAGNSVVLKPAEQSPLTALR 203 Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261 LA L +EAG P GV NVV G G AG + HP + +AFTGSTATG+ M+ + +SNLK Sbjct: 204 LAELAEEAGIPAGVFNVVPGLGAAAGQALGRHPDVDCIAFTGSTATGKRFMEYSGQSNLK 263 Query: 262 KVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320 +V LE GGKSP+IVFDD D+ Q GIF N GE+C AGSR+YVQ GIYD + + Sbjct: 264 RVWLECGGKSPHIVFDDCPDLDRAAQAAAIGIFSNQGEICIAGSRLYVQSGIYDAFMEKL 323 Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGER--FGNKGYF 378 + A ++ GDP T MGA QL +++ Y+ G+ EGA + GG+R + G++ Sbjct: 324 EAHAARMQPGDPLDPATAMGAIVDGAQLQRVMSYVKSGEDEGARLRAGGKRAHTDSGGFY 383 Query: 379 IKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAI 438 ++PTIF + IVR+EIFGPV+ +T+F++ EE I +ANDS YGL +G+ T+NLS A Sbjct: 384 MQPTIFECPTQSLTIVREEIFGPVLAVTRFESEEEAIRMANDSPYGLGSGLWTSNLSRAH 443 Query: 439 SVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLS 494 VS K+ +G +WVN Y D VPFGG QSG GR+ ALD YT +K I L+ Sbjct: 444 RVSRKLQAGLVWVNCYMDSDVTVPFGGVKQSGSGRDKSLHALDKYTDLKTTWISLA 499 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: 575 Number of extensions: 23 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: 495 Length of database: 499 Length adjustment: 34 Effective length of query: 461 Effective length of database: 465 Effective search space: 214365 Effective search space used: 214365 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