Align succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)
to candidate RR42_RS26155 RR42_RS26155 succinate-semialdehyde dehydrogenase
Query= BRENDA::Q0K2K1 (483 letters) >FitnessBrowser__Cup4G11:RR42_RS26155 Length = 487 Score = 815 bits (2106), Expect = 0.0 Identities = 409/481 (85%), Positives = 437/481 (90%) Query: 1 MELQHTALLRSHCLIDGEWTGAQSGAELAVCNPATGERIGSVPLAGAAEAEQAVRAAERA 60 + LQ LLRS CLIDGEWTGA GA L V NPAT + +G+VP GAAE QAV AA RA Sbjct: 5 LTLQRPGLLRSACLIDGEWTGAAGGAVLMVHNPATHDVVGTVPRCGAAETRQAVEAAARA 64 Query: 61 LPAWRAQTGKARAAVLRRWADLMLAHQEDLARLMTAEQGKPLPEARGEVAYAASFLEWFG 120 LPAWR TGKARAAVLRRWADLML HQEDLA+LMTAEQGKPL EARGE+AYAASFLEWFG Sbjct: 65 LPAWRDLTGKARAAVLRRWADLMLVHQEDLAQLMTAEQGKPLAEARGEIAYAASFLEWFG 124 Query: 121 EEAKRVDGEVLASPRSSQKMLVLREPVGVCAAITPWNFPAAMITRKVGPALAAGCTIIVK 180 EEAKRVDG+VL+SPR+ QKMLVLR+PVGVCAAITPWNFPAAMITRK GPALAAGCT+IVK Sbjct: 125 EEAKRVDGDVLSSPRAGQKMLVLRQPVGVCAAITPWNFPAAMITRKAGPALAAGCTMIVK 184 Query: 181 PAEQTPLTALALAVLGEQAGVPRGVLQVVTGDAVQIGGVLCASPVVRKLSFTGSTAIGKL 240 PAEQTPLTALALA L E+AGVPRGVLQVVTGD VQIGGVLC SPVVRKLSFTGSTAIGKL Sbjct: 185 PAEQTPLTALALAALAEEAGVPRGVLQVVTGDPVQIGGVLCESPVVRKLSFTGSTAIGKL 244 Query: 241 LMAQCAGTVKKLSLELGGNAPLIIFDDADLDRAVEGILASKFRNSGQTCVCANRIYVHDR 300 LMAQCAGTVKKLSLELGGNAPLI+F+DADLDRAV+GILASKFRNSGQTCVCANRIYVHD Sbjct: 245 LMAQCAGTVKKLSLELGGNAPLIVFEDADLDRAVDGILASKFRNSGQTCVCANRIYVHDA 304 Query: 301 VYDEVARRLVSAVEQLRPGHGVDSGVTQGPLIDADAVAKVEAHIADALAQGATVLTGGQR 360 VYDEVA RLV AV LRPGHG+DS VTQGPLIDADAVAKVE+HIADALA GA VLTGG+R Sbjct: 305 VYDEVASRLVRAVSALRPGHGIDSDVTQGPLIDADAVAKVESHIADALAHGARVLTGGKR 364 Query: 361 HALGGTFFAPTVLANATASMRVAREETFGPLAPLFRFTSEAEVVAMANDTESGLAAYFFS 420 HALGGTFF PTV+A ATA+MRVAREETFGPLAPLFRF + EV+AMANDTESGLAAYFFS Sbjct: 365 HALGGTFFEPTVVAGATAAMRVAREETFGPLAPLFRFKGDQEVIAMANDTESGLAAYFFS 424 Query: 421 RDMAKIWRVAQGLEYGMVGINTGLISNEVAPFGGVKQSGLGREGSRHGIDEYLETKYLCM 480 +DMA++WRVA+ LEYGMVGINTGLISNEVAPFGGVKQSGLGREGS +GIDEYLE KYLC+ Sbjct: 425 KDMARVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSSYGIDEYLEMKYLCL 484 Query: 481 E 481 E Sbjct: 485 E 485 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: 840 Number of extensions: 13 Number of successful extensions: 1 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: 487 Length adjustment: 34 Effective length of query: 449 Effective length of database: 453 Effective search space: 203397 Effective search space used: 203397 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