Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PfGW456L13_1974 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974 Length = 488 Score = 585 bits (1509), Expect = e-172 Identities = 290/483 (60%), Positives = 370/483 (76%) Query: 2 TLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAER 61 +L+I G+W+ G G + NPV+ +VLW G A A QVE A +AAR AFP WAR + ER Sbjct: 3 SLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEER 62 Query: 62 HAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRS 121 +V+E FAA L+++ EL I ETGKP WEAATEVT+M+NKIAIS+++Y RTGE+ Sbjct: 63 ISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEKSG 122 Query: 122 EMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM 181 + D A LRH+PHGV+AVFGPYNFPGHLPNGHIVPALLAGN+++FKPSELTP E + Sbjct: 123 PLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTV 182 Query: 182 RLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILA 241 + W +AGLP GVLNL+QG RETG AL+A +DGL FTGS+ TG LH+Q +G+P+KILA Sbjct: 183 KCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKILA 242 Query: 242 LEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301 LEMGGNNPL++D+VAD+DAAV+ IQSAF++AGQRCTCARRLL+ GA GD+ LARLVAV Sbjct: 243 LEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLVAV 302 Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPG 361 S L+ G +D +P PF+G ++S AA+ ++ A + L A G LL QA ++LLTPG Sbjct: 303 SSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLTPG 362 Query: 362 IIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLE 421 I++++ VA PDEE+FGPLL+V RY F+ AI AN+T +GL+ GL+S ++ Q LE Sbjct: 363 ILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFWLE 422 Query: 422 ARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLN 481 +RAGIVNWNK LTGAAS+APFGG+GASGNHR SA+YAADYCA+P+ASLE+ SL LP+ L Sbjct: 423 SRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSALT 482 Query: 482 PGL 484 PG+ Sbjct: 483 PGV 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: 792 Number of extensions: 34 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