Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate 5210675 Shew_3103 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P51648 (485 letters) >FitnessBrowser__PV4:5210675 Length = 474 Score = 294 bits (752), Expect = 5e-84 Identities = 168/429 (39%), Positives = 248/429 (57%), Gaps = 13/429 (3%) Query: 23 RLQQLEALRRMVQEREKDILTAIAADLC-KSEFNVYSQEVITVLGEIDFMLENLPEWVTA 81 R QL AL++ + ++ I+ A+ AD +S + +++ + I++ L+ L W+ Sbjct: 35 REAQLIALKQALLSHQQAIVEALNADYGHRSPDDSRISDIMPCVNNINYTLKKLKGWMKP 94 Query: 82 KPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLIGAIAAGNAVIIKPSELSE 141 +L + +Q QPLGVV II WN+P +L+I PLI A+AAGN +IK SE + Sbjct: 95 SRRHAGILLAPAKVEVQYQPLGVVGIIVPWNFPVMLSIGPLITALAAGNRAMIKLSEFTP 154 Query: 142 NTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFYTGNTAVGKIVMEAAAKHL 201 T ++L ++L D+ V+ G E FDH+ +TG+T VG+ VM AAA +L Sbjct: 155 ETNRVLRQMLAGLFDETQVAVVEGEAEVAAAFSALPFDHLLFTGSTTVGRYVMRAAADNL 214 Query: 202 TPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIAPDYILCEASLQNQIVWKI 261 TPVTLELGGKSP I D LD R+ +GK +N GQ C+APDY+L V Sbjct: 215 TPVTLELGGKSPVIIAPDMPLDTAVERMIYGKCLNAGQICVAPDYVLLPKGQSQAFVQAF 274 Query: 262 KETVKEFYGENIKESPDYERIINLRHFKRILSLLEGQKIAFGGE-TDEATRYIAP----- 315 K+ YGE I ++PDY IIN R F R+ ++L+ I G + T +T + P Sbjct: 275 INRFKQMYGE-IGQNPDYGAIINQRQFDRLQAVLQ-DAIDLGAQVTPTSTETMTPGSRKL 332 Query: 316 --TVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREKPLALYVFSHNHKLIKR 373 ++T V+ + KVMQEEIFGP+LPIV ++++AI+++N+R +PLALY+ S + +R Sbjct: 333 PVQLITGVNEQMKVMQEEIFGPLLPIVEYDSLEQAIDYVNDRPRPLALYIMSFDSDTQQR 392 Query: 374 MIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFDTFSHQRPCLLKSLKRE 433 ++++T SGGV N+ + H + PFGG+G SGMG YHGK F T SH + L + Sbjct: 393 LLNQTHSGGVCINETVFHVAADDAPFGGIGPSGMGHYHGKEGFLTMSHAKTILSRGKLNT 452 Query: 434 GANKLRYPP 442 G KL +PP Sbjct: 453 G--KLVHPP 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: 507 Number of extensions: 15 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