Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF4235 PS417_21695 succinylglutamate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__WCS417:GFF4235 Length = 488 Score = 592 bits (1527), Expect = e-174 Identities = 296/483 (61%), Positives = 365/483 (75%) Query: 2 TLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAER 61 +L+I G W+ GQG RNPV+ +VLW GN A A QVE A +AAR AFP WA+ ER Sbjct: 3 SLYIAGSWLAGQGELFESRNPVTQQVLWAGNGATAEQVESAVQAARQAFPAWAKRPLEER 62 Query: 62 HAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRS 121 +V+E FAA L+ ++ I ETGKP WE+ATEVT+M NKIAIS+++Y RTGE+ Sbjct: 63 ISVLETFAATLKRRADDIARCIGEETGKPLWESATEVTSMANKIAISVQSYRERTGEKSG 122 Query: 122 EMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM 181 + D A LRH+PHGV+AVFGPYNFPGHLPNGHIVPALLAGNT++FKPSELTP E + Sbjct: 123 PLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVLFKPSELTPKVAELTV 182 Query: 182 RLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILA 241 + W +AGLP GVLNL+QG RETG AL+A +DGL FTGS+ TG LH+Q SG+P+KILA Sbjct: 183 QCWVEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFSGRPDKILA 242 Query: 242 LEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301 LEMGGNNPL++DEVAD+DAAV+ IQSAF++AGQRCTCARRLL+ GA GDA LARLVAV Sbjct: 243 LEMGGNNPLVVDEVADVDAAVYTIIQSAFISAGQRCTCARRLLVPEGAWGDALLARLVAV 302 Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPG 361 S + G +D +P PF+G +IS AA+ ++ A + + A G LL Q +LLTPG Sbjct: 303 SSTIEVGAFDQQPAPFMGSVISLAAAKALMDAQELMLANGAVALLEMTQPQDQAALLTPG 362 Query: 362 IIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLE 421 II++TGV DEE+FGPLL+V RY F+ AI ANNT++GL+ GL+S ++ Q LE Sbjct: 363 IIDVTGVTEREDEELFGPLLQVIRYADFEAAIAEANNTQYGLAAGLLSDSEARYQQFWLE 422 Query: 422 ARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLN 481 +RAGIVNWNK LTGAASTAPFGG+GASGNHR SA+YAADYCA+P+ASLE+ SL LPATL Sbjct: 423 SRAGIVNWNKQLTGAASTAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPATLT 482 Query: 482 PGL 484 PG+ Sbjct: 483 PGI 485 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: 785 Number of extensions: 32 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: 492 Length of database: 488 Length adjustment: 34 Effective length of query: 458 Effective length of database: 454 Effective search space: 207932 Effective search space used: 207932 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