Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_090446352.1 BLS63_RS15725 succinate-semialdehyde dehydrogenase I
Query= SwissProt::Q8ZPV0 (492 letters) >NCBI__GCF_900100495.1:WP_090446352.1 Length = 485 Score = 189 bits (481), Expect = 1e-52 Identities = 148/466 (31%), Positives = 223/466 (47%), Gaps = 17/466 (3%) Query: 4 WINGDWITGQ-GERRRKTNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQ 62 ++NG W G R NP S EI+ + + A AA+AA P W R Sbjct: 16 YVNGQWCEADSGARTEIRNPASGEIIGSVPNLGRGETRRAIAAAQAAQPAWRALTAKERA 75 Query: 63 AIVEKFAALLEAHKAELTEVIARETGKPRWEAATEVTAMINKIA-ISIKAYHARTGAQKS 121 + ++ +L+ A++ +L ++ E GKP EA E+ + I + +A A + Sbjct: 76 NRLRQWFSLIMANQEDLARIMTAEQGKPLAEARGEIAYAASFIEWFAEEAKRAYGDVIPA 135 Query: 122 ELVDGAATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETVI 181 D ++ GV A P+NFP + PAL AG ++ KP+ TP++ + Sbjct: 136 HATDKRILVQKEAVGVTAAITPWNFPSAMITRKAGPALAAGCAMLLKPAPQTPFSALALA 195 Query: 182 KLWERAGLPAGVLNL----VQGGRETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPE 237 L E AG+PAG+ ++ V R+ G L + L FTGS + G +L +Q + + Sbjct: 196 ALAECAGIPAGLFSVLPADVDASRDVGGELCENPIVRKLSFTGSTAVGIRLMQQCAPTLK 255 Query: 238 KILALEMGGNNPLIIEDAANIDAAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLAR 297 K L+LE+GGN P I+ D A++DAAV + S + AGQ C CA RL V+ G AF A+ Sbjct: 256 K-LSLELGGNAPFIVFDDADLDAAVEGAIISKYRNAGQTCVCANRLYVQDGVY-QAFAAK 313 Query: 298 LVDVAGRLQPGRWDDDPQPFIGGLISAQAAQHVMEAWRQREALGGRTLLAPRKVKEGTSL 357 L +L+ G ++ G LI+A+A V R+AL L G + Sbjct: 314 LAAAVAKLKVGNGMEEGVT-TGPLINAEAVAKVER--HLRDALDKGATLVAGGNSLGGNF 370 Query: 358 LTPGIIE-LTGVADVPDEEVFGPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTDRAQFE 416 P I+ +T V EE FGPL ++R++ E IR AN+T FGL+ + D + Sbjct: 371 FEPTIVSGVTAEMAVAREETFGPLAPLFRFSDEAEVIRQANDTEFGLAAYFYARDLGRVF 430 Query: 417 QLLLEARAGIVNWNKPLTGAAST--APFGGVGASGNHRPSAWYAAD 460 ++ G+V N TG ST APFGG+ +SG R + Y D Sbjct: 431 RVAEALEYGMVGIN---TGLISTEVAPFGGMKSSGLGREGSKYGLD 473 Lambda K H 0.319 0.134 0.411 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: 509 Number of extensions: 28 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: 492 Length of database: 485 Length adjustment: 34 Effective length of query: 458 Effective length of database: 451 Effective search space: 206558 Effective search space used: 206558 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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