Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate SMc02780 SMc02780 succinate-semialdehyde dehydrogenase [NADP+] protein
Query= reanno::SB2B:6938906 (486 letters) >FitnessBrowser__Smeli:SMc02780 Length = 484 Score = 188 bits (478), Expect = 3e-52 Identities = 146/459 (31%), Positives = 219/459 (47%), Gaps = 14/459 (3%) Query: 9 WLAGEGKE-MQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQAIVEA 67 W+ + K ++ NPA GE+I + A + A+ AA Q EW + R A++ Sbjct: 19 WIEADPKNAIEVNNPATGEIIGRVPKLGAADTRTAIEAAARVQKEWAARTAKERSAVLRR 78 Query: 68 YRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNEGAAGR 127 + + NK +L ++ E GKP E E I + G V + Sbjct: 79 WFELMIENKDDLGRILTMEQGKPLAEATGEIVYGASFIEWFAEEARRVYGDLVPGHQKDK 138 Query: 128 AVLRHK-PHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMLKLWEK 186 +L K P GVVA P+NFP + PAL AG +V KP+ TP A + L E+ Sbjct: 139 RILVMKQPIGVVAAITPWNFPNAMITRKAGPALAAGCAMVLKPAAQTPFSAIAIAVLAER 198 Query: 187 AGLPAGVINLVQGEV-ETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILALEMG 245 AG+P G+ +++ G E G + S+P + L FTGS+ G L++Q A K L LE+G Sbjct: 199 AGMPKGLFSVITGSAREIGAEMTSNPTVRKLTFTGSTEVGAELYRQSAATIKK-LGLELG 257 Query: 246 GNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKG---AEGDKLLAGLVEAV 302 GN P IV +D AA+ + + F ++GQ C CA R+YV+ G A DK L +AV Sbjct: 258 GNAPFIVFDDADLDAAVEGALIAKFRNNGQTCVCANRIYVQDGVYEAFSDK----LAQAV 313 Query: 303 KAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLV-EMTHLQAGTGLVSPG 361 +K G D +G +I + A K + + + L GA+ + H GT + Sbjct: 314 AKLKTGNGMED-GVILGPLIDQPALKKVEEHVADALAKGARVVQGGRRHSLGGTFYEATV 372 Query: 362 LIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLAR 421 L DVT+ + + EE FGP+ + R+ + I ANDT +GL++ A D A Sbjct: 373 LADVTQAMAVAREETFGPVAPLFRFKDESDVIAQANDTEFGLASYFYAKDLARVFRVAEA 432 Query: 422 IRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAAD 460 + G+V N + ++ APFGGV SG R + Y + Sbjct: 433 LEYGMVGVNTGLI-STAEAPFGGVKLSGLGREGSKYGIE 470 Lambda K H 0.317 0.133 0.393 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: 581 Number of extensions: 23 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: 486 Length of database: 484 Length adjustment: 34 Effective length of query: 452 Effective length of database: 450 Effective search space: 203400 Effective search space used: 203400 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