Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P51648 (485 letters) >FitnessBrowser__Cola:Echvi_1497 Length = 469 Score = 336 bits (861), Expect = 1e-96 Identities = 180/446 (40%), Positives = 271/446 (60%), Gaps = 9/446 (2%) Query: 5 VRRVRQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLCKSEFNVYSQEVITV 64 V+ +Q L + L R+++LE L+ ++ +K+I A+ ADL K V E V Sbjct: 6 VQAQKQKALKNQQSTLSSRIKKLEQLKEWIKSNQKEIEKALYADLRKPAAEVAVTETSFV 65 Query: 65 LGEIDFMLENLPEWVTAKPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLIG 124 + EI+ L+ LP+W V + + + +AY+Q +P G VLII WNYPF L++ PL+ Sbjct: 66 VMEINAALKQLPKWTAPTKVGQPIHMLGTQAYLQAEPKGAVLIISPWNYPFNLSVAPLVS 125 Query: 125 AIAAGNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFYT 184 AIAAG + +KPSE S +T+ +L +++ + + + GGV T+ELL+Q FDHIF+T Sbjct: 126 AIAAGCSACLKPSEHSPHTSALLRRMVTELFAVEDVTIFEGGVPVTSELLEQPFDHIFFT 185 Query: 185 GNTAVGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIAP 244 G+T VGKIVM+AAAK+LT VTLELGGKSP ID+ DL+ ++I GK++N GQTCIAP Sbjct: 186 GSTEVGKIVMKAAAKNLTSVTLELGGKSPAIIDQGFDLEDAAKKIAIGKFINSGQTCIAP 245 Query: 245 DYILCEASLQNQIVWKIKETVKEFY---GENIKESPDYERIINLRHFKRILSLL-----E 296 DY+ S + + +K V Y G+ +PDY RII+ H R+ ++L + Sbjct: 246 DYLFVHESQKQDFIETLKAQVNRMYNANGKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTK 305 Query: 297 GQKIAFGGETDEATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINERE 356 G + FGG+ +++ PTV+++V +M+EEIFGPILPI+ +D+ I I + Sbjct: 306 GAHVEFGGKNSLDQQFMEPTVVSNVSEAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKP 365 Query: 357 KPLALYVFSHNHKLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSF 416 KPLA+Y F+ + ++I+++ TSSG + ND + F + PFGG+G+SGMG HG F Sbjct: 366 KPLAVYAFTTDDRIIEQLSKNTSSGALVINDCAIQFLHSELPFGGIGASGMGRSHGHAGF 425 Query: 417 DTFSHQRPCLLKSLKREGANKLRYPP 442 FS+++ +LK + KL YPP Sbjct: 426 LAFSNEK-AILKQRTGKTLPKLLYPP 450 Lambda K H 0.321 0.139 0.411 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: 503 Number of extensions: 25 Number of successful extensions: 3 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: 485 Length of database: 469 Length adjustment: 33 Effective length of query: 452 Effective length of database: 436 Effective search space: 197072 Effective search space used: 197072 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 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