Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 5209190 Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__PV4:5209190 Length = 501 Score = 206 bits (524), Expect = 2e-57 Identities = 142/474 (29%), Positives = 231/474 (48%), Gaps = 12/474 (2%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 +I+ +F+ ++ +P+ E I + A E+++ A+ +A AF ++W R Sbjct: 8 YIDGQFILGSGQQQISVTNPANNEVIATINAATVEEVETAIASAKQAF-ATWKEVPVSER 66 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIE 143 +V+++ L+ H D +A I A + GK+ +KGDV I G +E Sbjct: 67 ARVMFRYQHLLKLHHDEIATILAQETGKTFEDAKGDVWRGIEVAEHACNIASLIMGETVE 126 Query: 144 TGDTHFN-YTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 + Y+ +P+GVC I P+NFP ++ W + G T VLK +E PL+ L Sbjct: 127 NVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAIACGNTFVLKPSEQDPLTPQRL 186 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 L +EAGAP GV+ +V G TA + SH IK ++F GS G++I K + NLK+ Sbjct: 187 VELFEEAGAPKGVLQLVHG-DKTAVDVLLSHQDIKAISFVGSVGVGQYIYKTGTD-NLKR 244 Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322 V G K+ ++ DA+ + I +LV G+ C A S + V G K + E ++ Sbjct: 245 VQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMALS-VAVFVGEAKKWIPELRD 303 Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGY----F 378 A ++ G +D G S ++LK I GK+EGA + G F +GY + Sbjct: 304 AIAKVRPGVWDDKDAAYGPVISPAAKARVLKLIAQGKEEGAECLLDGSDFTVEGYENGNW 363 Query: 379 IKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAI 438 + PT+F +V D I ++EIFGPV+ + +++EE I L N+S YG + T + A Sbjct: 364 VGPTMFTNVTTDMSIYKEEIFGPVLCCMEVESLEEAIELVNNSPYGNGTSIFTACGAAAR 423 Query: 439 SVSNKINSGTIWVNTYNDFH-PMVPFGGYSQSGIGRE--MGEEALDNYTQVKAV 489 + I G + +N P F G+ S G + G++A+ YT+ K + Sbjct: 424 KYQHNIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYTETKTI 477 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: 549 Number of extensions: 27 Number of successful extensions: 6 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: 501 Length adjustment: 34 Effective length of query: 461 Effective length of database: 467 Effective search space: 215287 Effective search space used: 215287 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