Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_074201782.1 BUQ81_RS07630 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8ZPV0 (492 letters) >NCBI__GCF_900141795.1:WP_074201782.1 Length = 458 Score = 129 bits (325), Expect = 2e-34 Identities = 124/417 (29%), Positives = 185/417 (44%), Gaps = 25/417 (5%) Query: 53 WARQ-PFAARQAIVEKFAALLEAHKAELTEVIARETGKPRWEAATEVTAMINKIAISIKA 111 WA+Q P R ++ A LL K EL E+ RE GK EA EV K A Sbjct: 41 WAQQTPLETRCELLRNVAELLRVKKRELAELATREMGKRIGEAEAEV----EKCAWVCDF 96 Query: 112 YHARTGAQKS-ELVDGAAT---LRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIF 167 Y + A + E+V+ AT + ++P GV+ P+NFP PAL+AGN ++ Sbjct: 97 YADQAPAMLADEVVETEATRSLVVYQPLGVILAVMPWNFPYWQVFRAAAPALVAGNGVVL 156 Query: 168 KPSELTPWTGETVIKLWERAGLPAGVLNLVQGGRETGQALSSLDDLDGLLFTGSASTGYQ 227 K + P + L++ AG P + + + D+ G+ TGS G Sbjct: 157 KHASNVPLCALAIEGLFKEAGFPEDLFQSLMITSAQVERAICHPDVRGVTLTGSEPAGRA 216 Query: 228 LHRQLSGQPEKILALEMGGNNPLIIEDAANIDAAVHLTLQSAFITAGQRCTCARRLLVKQ 287 + ++G+ K LE+GG++P +I A++D V + L++ FI GQ C A+R LV + Sbjct: 217 V-ASIAGRELKKTVLELGGSDPFVILPDADLDEVVPMALKARFINMGQSCIAAKRFLVDK 275 Query: 288 GAQGDAFLARL-VDVAGRLQPGRWDDDPQPFIGGLISAQAAQHV------MEAWRQREAL 340 D F+AR V + PG DP +G + + + + + Sbjct: 276 -TMHDEFVARFKVAIEDYFVPGD-PMDPATTLGPMARRDLMEELHNQVIRAQDYGATVET 333 Query: 341 GGRTLLAPRKVKEGTSLLTPGIIELTGVADVPDEEVFGPLLNVWRYAHFDEAIRLANNTR 400 GG+TL P T LLT +T EE+FGP+ V Y A+ LAN TR Sbjct: 334 GGQTLDRPGAYYAPT-LLT----NVTTSNPAFQEELFGPVATVTTYTEPSHALGLANATR 388 Query: 401 FGLSCGLVSTDRAQFEQLLLEARAGIVNWNKPLTGAASTAPFGGVGASGNHRPSAWY 457 FGL + +TD A E + + G N + + PFGG+ SG R + Y Sbjct: 389 FGLGGSVWTTDIATGEAIARGMQCGCAFVN-DMVRSDPRLPFGGIKDSGYGRELSVY 444 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: 471 Number of extensions: 27 Number of successful extensions: 4 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: 458 Length adjustment: 33 Effective length of query: 459 Effective length of database: 425 Effective search space: 195075 Effective search space used: 195075 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: 51 (24.3 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