Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase
Query= curated2:Q1QTQ7 (489 letters) >NCBI__GCF_000745975.1:WP_035241269.1 Length = 485 Score = 208 bits (530), Expect = 3e-58 Identities = 153/480 (31%), Positives = 236/480 (49%), Gaps = 41/480 (8%) Query: 5 QQLLIDGAWVDGDAAR-FAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFA 63 Q I W++ D+ + A T+P +GE L T A + A+ AA + P W ++ A Sbjct: 12 QACFIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPAWRSKTAA 71 Query: 64 ERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGER 123 +R A++ R+ + L ++E LA + E GKPL E+R G++A + + + E Sbjct: 72 QRSAILRRWHDLLMENQEDLALLMTAEQGKPLAESR-------GEIAYAASFFEWFAEEA 124 Query: 124 ARDIGD--------ARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSE 175 R GD R V+ +P GV+A P+NFP + AL AG +V KP+ Sbjct: 125 KRIYGDIIPQTIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPAT 184 Query: 176 QTPMTADLTLQCWLEAGLPAGVINLVQGAAE-VGQALAGSADIDGLLFTGSAKVGGLLHR 234 TP +A + EAG+P GV N+V G++ +G L + + L FTGS +VG L + Sbjct: 185 ATPFSALAIAKLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQ 244 Query: 235 QFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAV 294 G + ++ ++ELGGN P +V D D +AAV L + + GQ C CA RL V G V Sbjct: 245 DCAGTMKRV-SMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAG-V 302 Query: 295 GDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRR 354 D + L A+A L+V E L ++A + + +D + +G + L+ +R Sbjct: 303 YDQFCEKLARAVATLKVGNGIEE-GVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKR 361 Query: 355 LQAGTSLLSPG-LIDVT-GCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIG 412 G + SP L DVT V EE FGP + ++ E + ANDT YGL+A Sbjct: 362 HALGGTFFSPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFT 421 Query: 413 ---------GERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYAAD 463 GE+ ++ L+ I +GI+ +++ APFGG+ +SGN R + Y D Sbjct: 422 RDMARTWRVGEKLEYG--LIGINSGII--------SNAVAPFGGVKESGNGREGSKYGLD 471 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: 603 Number of extensions: 27 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: 489 Length of database: 485 Length adjustment: 34 Effective length of query: 455 Effective length of database: 451 Effective search space: 205205 Effective search space used: 205205 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