Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 15420 b1300 gamma-Glu-gamma-aminobutyraldehyde dehydrogenase, NAD(P)H-dependent (NCBI)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Keio:15420 Length = 495 Score = 377 bits (967), Expect = e-109 Identities = 206/474 (43%), Positives = 283/474 (59%), Gaps = 5/474 (1%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFH-SSWSTSDPQ 81 LFIN E+ + +TF TV P T+ + ++ S DID A+ AA F WS S P Sbjct: 22 LFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPA 81 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGS 140 R VL KLADL++ HA+ LA +E LD GK + S + D+ A R A DK+ G Sbjct: 82 KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141 Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200 V T REP+GV I+PWNFPLL+ WKLGP L G + +LK +E +PLSA+ Sbjct: 142 VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201 Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260 LA L KEAG P GV+NVV+GFG AG +S H I +AFTGST TG+ ++K A +SN+ Sbjct: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261 Query: 261 KKVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSE 319 K+V LE GGKS NIVF D D++ GIFYN G+VC AG+R+ ++E I D+ ++ Sbjct: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321 Query: 320 FKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFI 379 K A++ + G P T MG D + +I G+ +G ++ G R I Sbjct: 322 LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG--RNAGLAAAI 379 Query: 380 KPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAIS 439 PTIF DV + + R+EIFGPV+ +T+F + E+ + LANDS+YGL A V T +LS A Sbjct: 380 GPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHR 439 Query: 440 VSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 +S ++ +G+++VN YND VPFGGY QSG GR+ AL+ +T++K + I L Sbjct: 440 MSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 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: 569 Number of extensions: 25 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: 495 Length of database: 495 Length adjustment: 34 Effective length of query: 461 Effective length of database: 461 Effective search space: 212521 Effective search space used: 212521 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