Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 363 bits (932), Expect = e-105 Identities = 207/479 (43%), Positives = 289/479 (60%), Gaps = 15/479 (3%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI +FV + F +SP + T+V + DI+ A++AA AF +WS + R Sbjct: 25 FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAF-PAWSRTSATER 83 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142 +L K+AD I+ + LA +E +DNGK + + D+AL +FR AG +GS+ Sbjct: 84 SNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGSIA 143 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E + +EPIG+ GQIIPWNFP+LMA+WK+ P L GC T++K AE TP S + L Sbjct: 144 ELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMIL 203 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 +I + P GV+NVV+GFGP AG P++ P++ KVAFTG T TGR IM+ A+E NL Sbjct: 204 MEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYASE-NLNP 261 Query: 263 VTLELGGKSPNIVFD---DADVKSTIQHLVTGIFY--NTGEVCCAGSRIYVQEGIYDKIV 317 VT+ELGGKSPN+ F DAD + + L + + N GEVC SRI V E IYD + Sbjct: 262 VTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCTCPSRILVHEKIYDAFM 321 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG---- 373 + AE++++G P + T MGAQ S+ Q +KIL YIDIGK+EGA V+TGGE Sbjct: 322 EKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLNSG 381 Query: 374 -NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432 GY++KPT+ + ++ ++EIFGPV ++ FK VEE I+++ND+ YGL AGV T Sbjct: 382 LENGYYVKPTLLKGHNK-MRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVWTR 440 Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 + A V I +G +WVN Y+ + PFGGY +SG GRE L++Y Q K + I Sbjct: 441 DAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNKNMLI 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: 626 Number of extensions: 26 Number of successful extensions: 7 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: 509 Length adjustment: 34 Effective length of query: 461 Effective length of database: 475 Effective search space: 218975 Effective search space used: 218975 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