Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase
Query= BRENDA::P51648 (485 letters) >FitnessBrowser__SynE:Synpcc7942_0489 Length = 459 Score = 401 bits (1031), Expect = e-116 Identities = 202/435 (46%), Positives = 289/435 (66%), Gaps = 2/435 (0%) Query: 8 VRQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLCKSEFNVYSQEVITVLGE 67 ++ F G +R L FRL +L+ L ++V + E ++L A+A+DL K Y+ E+ V + Sbjct: 16 LQATFDRGDTRTLAFRLARLQDLAKLVADNEAELLQALASDLRKPALEAYASEIYFVRDQ 75 Query: 68 IDFMLENLPEWVTAKPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLIGAIA 127 I ++L W+ + +++ +AY Q +PLGVVLIIG WNYPF L I PLIGAIA Sbjct: 76 IKLTCKHLRRWMQPEKQSISLMQQPGQAYRQAEPLGVVLIIGPWNYPFQLLITPLIGAIA 135 Query: 128 AGNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFYTGNT 187 AGN ++KPSEL+ T+ ++ +L+ D D V+ G + L+ Q FDHIF+TG T Sbjct: 136 AGNCAVLKPSELAPATSSLIQRLISDRFDPDYIRVLEGDASVSQALITQPFDHIFFTGGT 195 Query: 188 AVGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIAPDYI 247 A+G+ VM AAA++LTPVTLELGGKSPC +D D DLD+ RRI WGK+ N GQTCIAPDY+ Sbjct: 196 AIGRKVMAAAAENLTPVTLELGGKSPCIVDTDIDLDVAARRIAWGKFFNAGQTCIAPDYL 255 Query: 248 LCEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLLEGQKIAFGGETD 307 L + ++ + + + +++FYGE+ ++S DY RI++ RH++R+ SLL I GG+ D Sbjct: 256 LVQRTVAEPFIEALIDNIQQFYGEDPQQSADYARIVSDRHWQRLNSLLVDGTIRHGGQVD 315 Query: 308 EATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREKPLALYVFSHN 367 + RYIAPT++TDV+ + ++QEEIFGP+LPI+ +DEAI I + KPLALY+FS + Sbjct: 316 RSDRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQLDEAIAQIRAQPKPLALYLFSRD 375 Query: 368 HKLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFDTFSHQRPCLL 427 ++ +R++ ETS+G V ND I+ + FGGVG SGMG YHGK SF+TFSH + L Sbjct: 376 RQVQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPSGMGGYHGKASFETFSHYKLVLK 435 Query: 428 KSLKREGANKLRYPP 442 + + A LRYPP Sbjct: 436 RPFWLDLA--LRYPP 448 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: 542 Number of extensions: 17 Number of successful extensions: 1 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: 459 Length adjustment: 33 Effective length of query: 452 Effective length of database: 426 Effective search space: 192552 Effective search space used: 192552 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