Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_104914315.1 C3B54_RS06570 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_002950575.1:WP_104914315.1 Length = 497 Score = 272 bits (696), Expect = 2e-77 Identities = 155/480 (32%), Positives = 258/480 (53%), Gaps = 10/480 (2%) Query: 20 PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS--WST 77 PTGLFI+ E++++ + ++PS + EIT+V + A+EA AA S+ W Sbjct: 18 PTGLFIDGEWLRTGQE--IPVINPSDKSEITKVADGSG---GHALEALAAADRSAQQWRH 72 Query: 78 SDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKI 137 P+ R + + L+ E AD A + +++GK + G+ L+A +F A + Sbjct: 73 WAPRARADLFHLAHGLLIERADAFADVMTMESGKPRAEALGEFNLSAGFFLWYAEQVAHL 132 Query: 138 KGSVIETGDTHFNYTR-REPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTP 196 G E + +P+G + PWNFP+LM++ K G L GCT V+K+A TP Sbjct: 133 HGRYQEGSPGGYRVIETHQPVGPSFLVTPWNFPMLMSARKAGAALAAGCTVVIKSARETP 192 Query: 197 LSALYLASLIKEAGAPPGVVNVV-SGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAA 255 L+A ++EAG P GVVN++ + I + ++KKV+FTGS+A G ++K A Sbjct: 193 LTAALFIDTLQEAGFPAGVVNLIHTSNSAEVSEQIMADSRLKKVSFTGSSAVGTVLLKQA 252 Query: 256 AESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDK 315 + + ++ELGG P IV DDADV ++ V F N G+ C A +RI + E I ++ Sbjct: 253 SNLIINS-SMELGGDGPFIVLDDADVDLAVREAVICKFRNAGQACVAANRIILHESIAEE 311 Query: 316 IVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK 375 +F A +LK+GD F + +G ++ QL+++ ++ + G T++ GG + Sbjct: 312 FTEKFLAATAALKVGDGFDPEVSVGPIITERQLNRVSGLVESFQSAGGTLLAGGNVIDGE 371 Query: 376 GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLS 435 G+F +PT+F DH DE+F P+ + TV+E + AND+ YGL+A V + +LS Sbjct: 372 GFFFEPTVFRFDSYDHDFCNDELFAPIAALYTVTTVDEALRFANDTHYGLSAYVFSKDLS 431 Query: 436 TAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLSQ 495 ++V+ +++ G + VN P PFGG +SG+GRE G E + + + K + + + + Sbjct: 432 RVVTVAERLDFGMVGVNRGIMSDPKAPFGGIKESGLGREAGHEGIYEFLEPKYIALTIDE 491 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: 557 Number of extensions: 22 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: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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 24 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