Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate 202778 SO3683 coniferyl aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P51648 (485 letters) >FitnessBrowser__MR1:202778 Length = 474 Score = 299 bits (765), Expect = 2e-85 Identities = 169/448 (37%), Positives = 261/448 (58%), Gaps = 15/448 (3%) Query: 5 VRRVRQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLC-KSEFNVYSQEVIT 63 ++R R ++L+ + R ++L L+ + ++ ++ A++ D +S + +++ Sbjct: 17 LQRQRASYLAAPNPDYAIRKERLTRLKTALLNYQQPLVEALSQDYGHRSTDDSLISDIMP 76 Query: 64 VLGEIDFMLENLPEWVTAKPVKKNVLTMLDEAYIQP--QPLGVVLIIGAWNYPFVLTIQP 121 V+ I++ L+NL +W+ KP +++ +L A ++ QPLGV+ II WN+P +L+I P Sbjct: 77 VVNNINYSLKNLKKWL--KPSRRHAGILLAPAQVKVHYQPLGVIGIIVPWNFPVMLSIGP 134 Query: 122 LIGAIAAGNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHI 181 L+ AIAAGN ++K SE + T K++ +LL + D+ ++ G + + FDH+ Sbjct: 135 LVTAIAAGNHAMLKLSEFTPATNKVIKQLLTEVFDESHVAIVEGEADVAAQFSALPFDHL 194 Query: 182 FYTGNTAVGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTC 241 +TG+T VG+ VM AAA +LTPVTLELGGKSP I D L+I R+ +GK +N GQ C Sbjct: 195 LFTGSTTVGRHVMRAAANNLTPVTLELGGKSPVIIAPDMPLEIAVERMIYGKCLNAGQIC 254 Query: 242 IAPDYILCEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLLE----- 296 +APDY+LC + N + + YGE + ++ DY IIN R F R++++LE Sbjct: 255 VAPDYVLCPNAKVNDFIQAYQAKFLAMYGE-VAKNKDYGSIINARQFDRLMAVLEDAKTK 313 Query: 297 GQKI--AFGGETDEATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINE 354 G KI A D R I ++T ++MQEEIFGP+LPI+ +DEAI +IN Sbjct: 314 GAKIISASNEAIDSLNRKIPTQLITHTTEDMQLMQEEIFGPLLPIIGYDTLDEAIRYINL 373 Query: 355 REKPLALYVFSHNHKLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKH 414 R +PLALYV S + ++++ +T SGGV N+ + H + PFGG+G SGMG YHGK Sbjct: 374 RARPLALYVMSFDEANQQKILQQTHSGGVCINETVFHVAADDAPFGGIGPSGMGHYHGKE 433 Query: 415 SFDTFSHQRPCLLKSLKREGANKLRYPP 442 F TFSH + L S R K +PP Sbjct: 434 GFLTFSHAKTVL--SRGRFNTGKFVHPP 459 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: 546 Number of extensions: 23 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: 474 Length adjustment: 34 Effective length of query: 451 Effective length of database: 440 Effective search space: 198440 Effective search space used: 198440 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