Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate BWI76_RS13425 BWI76_RS13425 1-pyrroline dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >FitnessBrowser__Koxy:BWI76_RS13425 Length = 475 Score = 180 bits (457), Expect = 8e-50 Identities = 152/473 (32%), Positives = 222/473 (46%), Gaps = 28/473 (5%) Query: 3 SLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEER 62 +L I G+ +AG GEA NP T + + S ATA QVE+AV+AA QAF W++ T R Sbjct: 4 NLLINGKLVAGEGEAVPVFNPATGEEIVSIAEATAAQVEAAVEAADQAFISWSQTTPRSR 63 Query: 63 ISVLEAFAAALKNHADELAHTIGEETGKPLWEAAT-EVTSMVNKIAISVQSYRERTGEKS 121 L A A + HA LA GKPL E+ ++ + + R G + Sbjct: 64 AECLLALANVIDEHAQTLAKLESLNCGKPLHCVINDELPAVADVFRFFAGAARCLPGMAA 123 Query: 122 GP-LGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTP----K 176 G L T+++R P GVVA P+N+P + + PAL AGN V+ KPSE+TP K Sbjct: 124 GEYLEGHTSMIRRDPVGVVASIAPWNYPLMMAAWKLAPALAAGNCVVIKPSEITPLTALK 183 Query: 177 VAELTVKCWIEAGLPAGVLNLLQGARET-GIALAANPGIDGLFFTGSSRTGNHLHQQFAG 235 + EL + + PAGVLN+L G T G L A+ + + TGS TG H+ A Sbjct: 184 LGELAKEIF-----PAGVLNVLFGRGATVGDPLTAHAKVRMVSLTGSIATGAHIIGHTAS 238 Query: 236 RPDKILALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSL 295 K +E+GG P++V AD+DA V + F +AGQ CT A R+ G + D L Sbjct: 239 -SIKRTHMELGGKAPVIVFDDADIDAVVEGVRTFGFYNAGQDCTAACRIYAQAGIY-DQL 296 Query: 296 LARLVAVSSTLSVGAFDQQPAPF--MGSVVSLGAAKALMDAQEHL-----LANGAVALLE 348 + +L A ++L +G + + + S L A +DA L +A G+ A Sbjct: 297 VEKLGAAVASLKMGPPEDETTELGPLSSQAHLDRVSAAVDAARALPHIQVIAGGSKA--- 353 Query: 349 MTQPQAQSALLTPGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGL 408 L G A+ R E+FGP++ + + D E A++ AND+ YGLA+ + Sbjct: 354 PGNGYYYQPTLLAGARQEDAIVQR---EVFGPVVSITSFTDEEQALSWANDSQYGLASSV 410 Query: 409 LSDSEARYQQFWLESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAAD 461 + R + + G W S P GG SG + + Y + Sbjct: 411 WTRDVGRAHRLSARLQYG-CTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLE 462 Lambda K H 0.316 0.132 0.388 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: 546 Number of extensions: 25 Number of successful extensions: 4 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: 488 Length of database: 475 Length adjustment: 34 Effective length of query: 454 Effective length of database: 441 Effective search space: 200214 Effective search space used: 200214 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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