Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_015886756.1 NGR_RS03080 NAD-dependent succinate-semialdehyde dehydrogenase
Query= curated2:Q1QTQ7 (489 letters) >NCBI__GCF_000018545.1:WP_015886756.1 Length = 484 Score = 207 bits (528), Expect = 5e-58 Identities = 162/473 (34%), Positives = 230/473 (48%), Gaps = 35/473 (7%) Query: 4 KQQLLIDGAWVDGDAARFAKT-DPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62 +Q +I G W+ + + DP S L T + A+ AA AF W +++ Sbjct: 10 RQAGVIGGEWIGAASGDVVEVFDPASQAVLGTVPDMGTAETRAAIEAAETAFGPWKKKTH 69 Query: 63 AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEV--GAMIGKVAISITAYHERT 120 AER A++ER+ + H E LA + E GKPL EAR E+ GA A+ + Sbjct: 70 AERAALLERWHALMIEHLEDLALILTLEQGKPLDEARGEIRYGA----------AFVKWF 119 Query: 121 GERARDIG---------DARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVF 171 E AR IG D R V+ GV A+ P+NFP + + PAL AG VV Sbjct: 120 AEEARRIGGHTIPSPTPDRRIVVLKEAVGVCAIVTPWNFPNAMITRKVAPALAAGCTVVI 179 Query: 172 KPSEQTPMTADLTLQCWLE-AGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVG 229 KPSE TP +A L L E AG+PAGV+N+V G +G + + + + FTGS +VG Sbjct: 180 KPSEFTPFSA-LALGVLAERAGIPAGVVNIVTGMPTAIGNEIMANETVRKISFTGSTRVG 238 Query: 230 GLLHRQFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIV 289 LL R V K L+LELGGN P +V D D + AV + S F +GGQ C CA R++V Sbjct: 239 SLLMRGAADSV-KRLSLELGGNAPFIVFDDADLDLAVEGAIASKFRNGGQTCVCANRILV 297 Query: 290 PHGAVGDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPL 349 G V D + L + + ++V P +EP + + A D + +D +A+G + Sbjct: 298 QSG-VYDAFAEKLAARVNAMKV-GPGTEPGVAIGPMINAAAIDKIDRHVEDALAKGAKIA 355 Query: 350 SRMRRLQAGTSLLSPGLID--VTGCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLS 407 +R R L G +P ++ T + EE FGP+ + + +EAI +AN T +GL+ Sbjct: 356 ARGRSLPVGRQYTAPLVLTGATTEMLLASEETFGPVAPLFCFETEEEAITIANGTPFGLA 415 Query: 408 AGLIGGERADWDDFLLRIRAGIVNWNRQTTGASSD--APFGGIGDSGNHRPSA 458 A + G+V N TGA S APFGG+ SG R A Sbjct: 416 AYFYTENLKRSWRVAEALEFGMVGLN---TGAISTEVAPFGGVKQSGLGREGA 465 Lambda K H 0.319 0.135 0.409 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: 639 Number of extensions: 34 Number of successful extensions: 7 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: 489 Length of database: 484 Length adjustment: 34 Effective length of query: 455 Effective length of database: 450 Effective search space: 204750 Effective search space used: 204750 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 Apr 09 2024. 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