Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate WP_083529425.1 AS188_RS11615 aldehyde dehydrogenase family protein
Query= BRENDA::P51648 (485 letters) >NCBI__GCF_001482365.1:WP_083529425.1 Length = 506 Score = 363 bits (933), Expect = e-105 Identities = 193/445 (43%), Positives = 273/445 (61%), Gaps = 8/445 (1%) Query: 1 MELEVRRVRQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLCKSEFNVYSQE 60 ++ V R R AF+ L RL +L+ L +V+E +++ A+AADL K + E Sbjct: 46 VDAAVARARAAFVPDLG--LEARLDRLDRLETLVREHREELEEALAADLGKPRQEAWLTE 103 Query: 61 VITVLGEIDFMLENLPEWVTAKPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQ 120 + L E+ + LP W + + + A + Q LG VL+I WNYP L + Sbjct: 104 LAFTLEEVAGLRRGLPRWTAPERTRVPLSLAPARARTERQALGTVLVIAPWNYPVQLVLG 163 Query: 121 PLIGAIAAGNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDH 180 PL GA+AAGN V++KPSE++ + A++LA+LL Q+L D V+ GGV ETT LL+ RFDH Sbjct: 164 PLAGALAAGNTVVVKPSEVTPSVARVLARLLEQHLG-DCTSVVEGGVPETTRLLEHRFDH 222 Query: 181 IFYTGNTAVGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQT 240 +FYTGN V ++V AAA+HLTPVTLELGGKSP ++D DL RRI WGKY+N GQT Sbjct: 223 VFYTGNARVARVVAAAAARHLTPVTLELGGKSPAWVDATTDLRTAARRIVWGKYLNAGQT 282 Query: 241 CIAPDYILCEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLL---EG 297 C+APD++L + ++ V++F+GE+ + S Y RI+ RH +R+ LL Sbjct: 283 CVAPDHVLGTPEALAALEPELVRAVRQFHGEDPRRSGSYGRIVTERHLERLTRLLGQVPA 342 Query: 298 QKIAFGGETDEATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREK 357 + + GG+ + A RY+APTV+ P M EEIFGP+LP+VPV + + A+ I EK Sbjct: 343 EDVVCGGQAEPAERYLAPTVVRSA-PDGPFMAEEIFGPVLPLVPVDSAEAAVGLITAGEK 401 Query: 358 PLALYVFSHNHKLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFD 417 PLALYVFS + + + TSSGG++ N ++H + PFGGVG+SG GAYHG+HSF+ Sbjct: 402 PLALYVFSEDPAVRELFARRTSSGGLSYNAPLLHLSHPGLPFGGVGASGTGAYHGRHSFE 461 Query: 418 TFSHQRPCLLKSLKREGANKLRYPP 442 TFSH+R L K + ++ YPP Sbjct: 462 TFSHRRAVLDKP-QAPDTLRVVYPP 485 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: 533 Number of extensions: 21 Number of successful extensions: 4 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: 506 Length adjustment: 34 Effective length of query: 451 Effective length of database: 472 Effective search space: 212872 Effective search space used: 212872 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: 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