Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012592831.1 MSIL_RS19705 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000021745.1:WP_012592831.1 Length = 507 Score = 437 bits (1125), Expect = e-127 Identities = 234/484 (48%), Positives = 311/484 (64%), Gaps = 12/484 (2%) Query: 20 PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTS 78 P + I+ ++V+S S KTF P+T E+I V E + D+D AV AA AF S WS Sbjct: 25 PRPMLIDGKWVKSVSGKTFDVFDPATGEKIASVAEGDAADVDLAVAAARRAFESGPWSRM 84 Query: 79 DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKI 137 P R ++++++ DLI +HAD LA IE+LDNGK +K DV L+A F +GW K+ Sbjct: 85 TPSERGRIIHRIGDLILDHADELAAIESLDNGKPKAVAKAADVTLSADMFHYMSGWATKL 144 Query: 138 KGSVIET------GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKT 191 +G I G + TR EPIGV GQIIPWNFPLLMA+WKL P L TGC VLK Sbjct: 145 EGKHIPISALTAPGMEFVSMTRLEPIGVVGQIIPWNFPLLMAAWKLAPALTTGCAVVLKI 204 Query: 192 AESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHI 251 AE TPLSAL L L+ EAG P GVVN+V GFG TAGA ++ HP + KVAFTGST GR I Sbjct: 205 AEETPLSALRLGELLIEAGVPDGVVNIVPGFGETAGAALAGHPGVDKVAFTGSTEVGRLI 264 Query: 252 MKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEG 311 ++AA+ +LKKV+LELGGKSPNIV DAD + I IF+N G+ C AGSR++VQ Sbjct: 265 VQAASR-DLKKVSLELGGKSPNIVLGDADPEMAIAGATAAIFFNHGQCCNAGSRLFVQRN 323 Query: 312 IYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGER 371 ++DK+V AE +K+G +T MG S++Q D++ + G++EGA + GGE Sbjct: 324 LFDKVVEGIAAQAEKIKLGHGLNAETEMGPLVSRVQYDRVTGLLASGRQEGARAVCGGEG 383 Query: 372 FGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEE-VIALANDSEYGLAAGVH 430 G GYF+ PT+ D ++VR+EIFGPV+ T F ++ +IA AN++ YGLAAGV Sbjct: 384 LGGAGYFVPPTVLVDTNPGMRVVREEIFGPVLVATPFDEPDDALIAEANNTIYGLAAGVW 443 Query: 431 TTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV- 489 + N A ++N++ +GT+W+N Y+ F +PFGGY QSG GREMG+ L NY + KA+ Sbjct: 444 SGNTGRAHQIANRLRAGTVWINCYHVFDAALPFGGYKQSGWGREMGQAVLSNYLEAKAIT 503 Query: 490 -RIG 492 RIG Sbjct: 504 TRIG 507 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: 647 Number of extensions: 27 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: 507 Length adjustment: 34 Effective length of query: 461 Effective length of database: 473 Effective search space: 218053 Effective search space used: 218053 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 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