Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 211 bits (537), Expect = 5e-59 Identities = 162/472 (34%), Positives = 241/472 (51%), Gaps = 43/472 (9%) Query: 5 INGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAV 64 I+G W+ G+ + V NP G ++ D AA+ A AA A P WA + ER A+ Sbjct: 16 IDGQWVRGEASFDVL-NPADGTLIAAVADLGAAETTLAIDAAHRALPAWAARTAKERGAI 74 Query: 65 VERFAALLESNKAELTAIIARETGKPRWEAATEVT---AMINKIAISIKAYHVRTGEQRS 121 + R++ L+ ++ +L ++ E GKP EA EV + I+ A K + T + Sbjct: 75 LRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAYGHTIP--T 132 Query: 122 EMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM 181 MP + +P GV A P+NFP + + PAL AG T++ KP+ TP S A+ Sbjct: 133 PMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLSALAIA 192 Query: 182 RLWQQAGLPPGVLNLVQGGR--ETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKI 239 RL +AG+P GVLN+V R E G+ L + L FTGS G L++Q +G +K Sbjct: 193 RLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCAGTMKK- 251 Query: 240 LALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLV 299 L+LE+GGN P I+ + AD++AAV I S + AGQ C CA RL+++SG DAF ARL Sbjct: 252 LSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIH-DAFAARLA 310 Query: 300 --AVSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSL 357 + ++ PG + IG LI+E+A +VV L +QAG + Sbjct: 311 EKVAALKVGPGTGEGVQ---IGPLINEKALTKVVG-------------LVSGAVQAGAEV 354 Query: 358 LTPGIIEMTG---------VAGVPD-----EEVFGPLLRVWRYDTFDEAIRMANNTRFGL 403 LT G + G V P+ EE+FGP+ + +++T EA+ +AN T FGL Sbjct: 355 LTGGDVHGLGGHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGL 414 Query: 404 SCGLVSPEREKFDQLLLEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSA 455 + S + + ++ + AG+V N+ L + APFGG+ SG R A Sbjct: 415 AAYFYSRDVGRCWRVAEQIEAGMVGINEGLI-STEVAPFGGVKESGLGREGA 465 Lambda K H 0.318 0.134 0.412 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: 587 Number of extensions: 27 Number of successful extensions: 5 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: 492 Length of database: 485 Length adjustment: 34 Effective length of query: 458 Effective length of database: 451 Effective search space: 206558 Effective search space used: 206558 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 (21.7 bits) S2: 52 (24.6 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