Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate Ga0059261_1486 Ga0059261_1486 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P51648 (485 letters) >FitnessBrowser__Korea:Ga0059261_1486 Length = 468 Score = 262 bits (670), Expect = 2e-74 Identities = 152/437 (34%), Positives = 229/437 (52%), Gaps = 16/437 (3%) Query: 7 RVRQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLC-KSEFNVYSQEVITVL 65 R R AF++ P+ R +L MV++ A++ D +S +V+ + Sbjct: 7 RQRAAFMAELPVPIDLRRDRLRRAVAMVKDNAARFCDALSEDFGHRSPRQSMITDVVASV 66 Query: 66 GEIDFMLENLPEWVTA--KPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLI 123 + + + W KPV + + A+++ QP GVV II WN+P L + PL Sbjct: 67 SPLKHAEKMVTRWARREKKPVMFPLGLLGARAWVEYQPKGVVGIIAPWNFPVNLVMSPLA 126 Query: 124 GAIAAGNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFY 183 G AAGN ++K SE + TA + +L P+Y D ++GG E FDH+ + Sbjct: 127 GVFAAGNRAMVKTSEFTPATAALFEELCPRYFDPAELAFVSGGPEVGQAFSALPFDHLLF 186 Query: 184 TGNTAVGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIA 243 TG T +G+ ++ AAA +LTPVTLELGGKSP + + +L R+ GK +N GQ CIA Sbjct: 187 TGATGIGRHILHAAADNLTPVTLELGGKSPAILGRSANLAQATERVAMGKMLNAGQICIA 246 Query: 244 PDYILCEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLLEGQKIAFG 303 PDY++ A + V + Y + +PDY IIN RHF R+ + ++ + A G Sbjct: 247 PDYLMVAAEQEQAAVDGLVRAASAMY-PTLLSNPDYTTIINDRHFARLTAAIDDAR-AKG 304 Query: 304 GE-----------TDEATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFI 352 E R + ++ + VMQEEIFGP+LP+ ++D AI + Sbjct: 305 AEVIAVNPANEDFAASNARKLPLHIIRNATDDMTVMQEEIFGPLLPVRKYDSIDGAIGEV 364 Query: 353 NEREKPLALYVFSHNHKLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHG 412 N R++PLALY F ++ +R++D T SGGV+ +D I H ++ PFGG+G SGMGAYHG Sbjct: 365 NRRDRPLALYYFGNDEAERRRVLDRTISGGVSLDDTIFHVSMEELPFGGIGPSGMGAYHG 424 Query: 413 KHSFDTFSHQRPCLLKS 429 + F TFSH + +S Sbjct: 425 EPGFRTFSHAKSVFKQS 441 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: 475 Number of extensions: 20 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: 468 Length adjustment: 33 Effective length of query: 452 Effective length of database: 435 Effective search space: 196620 Effective search space used: 196620 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