Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate BPHYT_RS30285 BPHYT_RS30285 succinate-semialdehyde dehydrogenase
Query= BRENDA::P25526 (482 letters) >FitnessBrowser__BFirm:BPHYT_RS30285 Length = 490 Score = 541 bits (1393), Expect = e-158 Identities = 271/486 (55%), Positives = 347/486 (71%), Gaps = 6/486 (1%) Query: 1 MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60 + L + L R Q LI+G W A +G VTNPA G+ + V GA + RAA DAA RA Sbjct: 3 LALTRNELIRPQNLIDGAWTGAADGARFAVTNPATGETIVEVADSGAADARAATDAAARA 62 Query: 61 LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120 PAWR +ERA ILR W L++ + DDLA+LM++EQGKPLAEA+GE++Y AS++ WFA Sbjct: 63 FPAWRDTLPRERAEILRRWHALIVANTDDLAKLMSMEQGKPLAEARGEVAYGASYVAWFA 122 Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180 +E RIYGD IP Q KR+ +K+P+GV AAITPWNFP AMI RK PALAAGCT+V K Sbjct: 123 DEATRIYGDLIPQQQRGKRMSAVKEPVGVIAAITPWNFPLAMIARKIAPALAAGCTVVAK 182 Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVTGS----AGAVGNELTSNPLVRKLSFTGSTE 236 PA TP +ALALA LA AG+P GV N+++ S AV + L ++ VRK++FTGST Sbjct: 183 PAEDTPLTALALAVLAQEAGLPDGVLNMLSASREQGIAAVADWL-ADSRVRKITFTGSTP 241 Query: 237 IGRQLMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLY 296 +G+ L + A +KK+SLELGGNAPFIVFDDADLD AV G +A+KFRN GQTCVC NR+Y Sbjct: 242 VGKHLARESAGTLKKLSLELGGNAPFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVY 301 Query: 297 VQDGVYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVC 356 VQ GVY+RFA+ L + V L + D IGP+I+E+A+ K+ H+ DA++ GA+V+ Sbjct: 302 VQAGVYERFADLLAKRVGALKVAPATDPQAQIGPMINERAIQKIARHVEDAVKHGAKVLV 361 Query: 357 GGK-AHERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLA 415 GGK E G N++ PT+L D + VS EETFGP+APLFRF +EA+ I +NDT FGLA Sbjct: 362 GGKRLTELGPNYYAPTVLTDARDDMLVSCEETFGPVAPLFRFNEEAEAIRLSNDTPFGLA 421 Query: 416 AYFYARDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEI 475 AYFY +D+ R+ RV LE G++GIN G +S+E APFGG+K SG GREGSKYG++DY+ I Sbjct: 422 AYFYTQDVRRINRVAAQLEAGVIGINEGAVSSEAAPFGGVKESGYGREGSKYGLDDYMSI 481 Query: 476 KYMCIG 481 KYMC G Sbjct: 482 KYMCQG 487 Lambda K H 0.318 0.135 0.395 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: 675 Number of extensions: 18 Number of successful extensions: 3 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: 482 Length of database: 490 Length adjustment: 34 Effective length of query: 448 Effective length of database: 456 Effective search space: 204288 Effective search space used: 204288 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 (21.7 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