Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_013075305.1 BTUS_RS06425 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000092905.1:WP_013075305.1 Length = 489 Score = 442 bits (1136), Expect = e-128 Identities = 232/474 (48%), Positives = 307/474 (64%), Gaps = 5/474 (1%) Query: 20 PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTS 78 PT LFI+ FV S S + F V+P++ E+I +V A +D+D AV+AA W+ Sbjct: 12 PTQLFIDGRFVDSLSGEKFAVVNPASGEQIGEVPLADEKDVDCAVQAARRVVDGGRWAAW 71 Query: 79 DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKI 137 +P R ++++++ADLI+ HADTLA +E D GK L +K D+ LT FR AGW KI Sbjct: 72 NPYERERLIHRVADLIEAHADTLALLETCDTGKPLRDAKAVDIPLTIQCFRYYAGWPSKI 131 Query: 138 KGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197 KG + YT REP+GV QIIPWNFPL MA+ K+ P L TG VLK AE TPL Sbjct: 132 KGETVPVRGQFLTYTLREPVGVVAQIIPWNFPLYMAAIKVAPALATGNAVVLKPAEETPL 191 Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257 SALYLA L+KEAG P GV NVV+G G GA + HP + K++FTGSTA G+ IM A A Sbjct: 192 SALYLARLMKEAGIPDGVFNVVTGDGEKTGAALVRHPGVDKISFTGSTAVGQQIM-AQAA 250 Query: 258 SNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 S +K+V+LELGGKSP+IVF DAD+ + ++ +V GIFYN GEVC AGSR++VQ +Y+K++ Sbjct: 251 SGIKRVSLELGGKSPHIVFADADLSAAVKGIVGGIFYNQGEVCLAGSRVFVQRPVYNKVL 310 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN--K 375 E + AA +KIG+P E T G S ++ +Y+ +G +EGA +I GG N Sbjct: 311 EEVRGAARKVKIGNPLDESTTFGPLISAEHQSRVHRYVKMGVEEGAQLIEGGSAPANLES 370 Query: 376 GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLS 435 GYF +PTI + + R+EIFGPV + F T EEV+ LAND+ YGLAAG+ T +LS Sbjct: 371 GYFYEPTILVGDHLGYTVAREEIFGPVAFVMPFDTPEEVVGLANDTRYGLAAGLWTRDLS 430 Query: 436 TAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 A + + +GT+W+N YN PFGGY SG GRE+GEEALD YT++K V Sbjct: 431 LAHRTARALKAGTVWINAYNLLDAAAPFGGYRMSGFGRELGEEALDLYTELKTV 484 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: 618 Number of extensions: 29 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: 489 Length adjustment: 34 Effective length of query: 461 Effective length of database: 455 Effective search space: 209755 Effective search space used: 209755 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