Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate H281DRAFT_03178 H281DRAFT_03178 succinate semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >FitnessBrowser__Burk376:H281DRAFT_03178 Length = 486 Score = 202 bits (514), Expect = 2e-56 Identities = 153/463 (33%), Positives = 220/463 (47%), Gaps = 12/463 (2%) Query: 5 YIAGEWL-AGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEERI 63 Y+AGEW A G FE +NP T +V+ + + A+ AA A+P W T ++R Sbjct: 17 YLAGEWQGADDGSTFEVVNPATGEVVATVPRMGTAETRRAIDAANAAWPAWRASTAKQRA 76 Query: 64 SVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK-SG 122 +L + + +AD+LA + E GKPL EA E+ + + + + G+ Sbjct: 77 VILRKWHDLMLENADDLALILTTEQGKPLAEAKGEIQYAASFLEWFAEEGKRLNGDTIPT 136 Query: 123 PLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTV 182 P D V+ +P GV A P+NFP + + PAL AG ++ KP+E TP A Sbjct: 137 PANDKRIVVTKEPVGVCAAITPWNFPAAMITRKVGPALAAGCPIIVKPAEATPLSALALA 196 Query: 183 KCWIEAGLPAGVLNLLQG-ARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKIL 241 AG+P GV N++ G + G + NP + L FTGS+ G L Q A K+ Sbjct: 197 VLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRLLMAQCAPTVKKV- 255 Query: 242 ALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLVA 301 +LE+GGN P +V ADLDAAV I S + ++GQ C C R V + D+ A+L A Sbjct: 256 SLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDKVY-DAFAAKLRA 314 Query: 302 VSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLTP 361 L+VG + G +++ A + E LA GA + + P Sbjct: 315 AVEQLTVGR-GTEAGVTQGPLINEAAVLKVESHIEDALAKGARVVTGGKRHALGHGFFEP 373 Query: 362 GIL-DVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420 IL DV+ +E FGPL + R++ E IA ANDT +GLA+ S R + Sbjct: 374 TILADVTPDMKVARDETFGPLAPLFRFSSDEEVIALANDTEFGLASYFYSRDIGRVWRVA 433 Query: 421 LESRAGIVNWNKQLTGAASS--APFGGVGASGNHRASAYYAAD 461 G+V N TG S+ APFGGV SG R ++Y D Sbjct: 434 EALEYGMVGIN---TGLISNEVAPFGGVKQSGLGREGSHYGID 473 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: 514 Number of extensions: 26 Number of successful extensions: 6 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: 486 Length adjustment: 34 Effective length of query: 454 Effective length of database: 452 Effective search space: 205208 Effective search space used: 205208 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 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