Align succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase
Query= BRENDA::Q0K2K1 (483 letters) >FitnessBrowser__HerbieS:HSERO_RS05645 Length = 493 Score = 538 bits (1386), Expect = e-157 Identities = 269/486 (55%), Positives = 352/486 (72%), Gaps = 7/486 (1%) Query: 1 MELQHTALLRSHCLIDGEWTGAQSGAELAVCNPATGERIGSVPLAGAAEAEQAVRAAERA 60 + LQ L+ LI +W GA G +L V +PATG+ SVP GAA+A AV AA A Sbjct: 4 LTLQRQDLMPGAQLIGADWRGAADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAA 63 Query: 61 LPAWRAQTGKARAAVLRRWADLMLAHQEDLARLMTAEQGKPLPEARGEVAYAASFLEWFG 120 AWRA K RA +++RW DL+LAHQ+DL RL++ EQGKPL EA+GEVAYAAS++EWFG Sbjct: 64 FAAWRATPAKQRAGIIKRWNDLLLAHQDDLGRLISREQGKPLAEAKGEVAYAASYVEWFG 123 Query: 121 EEAKRVDGEVLASPRSSQKMLVLREPVGVCAAITPWNFPAAMITRKVGPALAAGCTIIVK 180 EEA R +G+++ +P + ++M+ L+EPVGV AAITPWNFPAAMI RK+ PALAAGCT++ K Sbjct: 124 EEATRANGDIIPAPVTGRRMMALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCK 183 Query: 181 PAEQTPLTALALAVLGEQAGVPRGVLQVVTGD---AVQIGGVLCASPVVRKLSFTGSTAI 237 PAE TPLT+LAL L ++AGVP GV+ +VT ++ V A VRK+SFTGSTA+ Sbjct: 184 PAEDTPLTSLALVRLAQEAGVPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAV 243 Query: 238 GKLLMAQCAGTVKKLSLELGGNAPLIIFDDADLDRAVEGILASKFRNSGQTCVCANRIYV 297 GK L A T+KKLSLELGGNAP I+FDDAD+D A++G++A+KFRN GQTCV NRIYV Sbjct: 244 GKHLARHSADTLKKLSLELGGNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYV 303 Query: 298 HDRVYDEVARRLVSAVEQLRPGHGVDSGVTQGPLIDADAVAKVEAHIADALAQGATVLTG 357 ++VYD +L + V L+ G D GP+I+A A+AK++ H+ DA+A+GA V+TG Sbjct: 304 QEKVYDAFVDKLGARVAALKVGPATDPASQIGPMINARAIAKIDQHVRDAIARGARVITG 363 Query: 358 GQRHALGG----TFFAPTVLANATASMRVAREETFGPLAPLFRFTSEAEVVAMANDTESG 413 G+R G ++APTVLA+ T +M+ + EETFGP+AP+ RF +E EV+A AN T G Sbjct: 364 GKRLQGPGFGSDNYYAPTVLADVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFG 423 Query: 414 LAAYFFSRDMAKIWRVAQGLEYGMVGINTGLISNEVAPFGGVKQSGLGREGSRHGIDEYL 473 LAAYF+S D+ +I RV LE G+VG+N G ++ E APFGGVK+SG GREGS HG+D+YL Sbjct: 424 LAAYFYSTDVRRIHRVTDALESGIVGVNEGALAAEAAPFGGVKESGYGREGSVHGLDDYL 483 Query: 474 ETKYLC 479 TKY+C Sbjct: 484 HTKYVC 489 Lambda K H 0.319 0.133 0.390 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: 691 Number of extensions: 24 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: 483 Length of database: 493 Length adjustment: 34 Effective length of query: 449 Effective length of database: 459 Effective search space: 206091 Effective search space used: 206091 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 (21.8 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