Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__HerbieS:HSERO_RS09465 Length = 506 Score = 361 bits (926), Expect = e-104 Identities = 210/489 (42%), Positives = 286/489 (58%), Gaps = 15/489 (3%) Query: 17 YEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWS 76 ++Q FI +FV + F +SP +V + +ED++ A++AA AA SW Sbjct: 15 FKQRYDNFIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAA-KKSWG 73 Query: 77 TSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTD 135 + P R +L K+AD ++ + + LA E LDNGK + D+ L +FR A Sbjct: 74 KTSPTERANMLLKIADRMEANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVR 133 Query: 136 KIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAEST 195 +GS+ + + Y EP+GV GQIIPWNFP+LMA WKL P L G VLK AE T Sbjct: 134 TQEGSICPIDNDTYAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQT 193 Query: 196 PLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAA 255 P S + L LI + PPGVVN+V GFG AG P++S+ +I K+AFTG T TGR IM+ A Sbjct: 194 PASIMVLIELIADL-IPPGVVNIVQGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYA 252 Query: 256 AESNLKKVTLELGGKSPNIVFDDADVKST--IQHLVTGIFY---NTGEVCCAGSRIYVQE 310 ++ NL VTLELGGKSPNI F D K + G N GEVC SR+ VQE Sbjct: 253 SQ-NLIPVTLELGGKSPNIFFADVLDKDDDFFDKALEGFAMFALNQGEVCTCPSRVLVQE 311 Query: 311 GIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG- 369 IY++ + ++K G+P + T +GAQ SQ QL+KIL YIDIGK+EGA V+ GG Sbjct: 312 SIYERFIERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVLAGGG 371 Query: 370 -ERFGN---KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGL 425 E G GY++KPT+F +I ++EIFGPVV++T FK EE +A+AND+ YGL Sbjct: 372 REELGGDLASGYYVKPTVFQG-NNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYGL 430 Query: 426 AAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQ 485 AG+ T + + A + +I +G +W N Y+ + FGGY QSGIGRE + LD+Y Q Sbjct: 431 GAGLWTRDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQQ 490 Query: 486 VKAVRIGLS 494 K + + S Sbjct: 491 TKNLLVSYS 499 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: 605 Number of extensions: 34 Number of successful extensions: 8 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: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 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