Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Pf6N2E2_368 Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_368 Length = 485 Score = 206 bits (523), Expect = 2e-57 Identities = 157/463 (33%), Positives = 226/463 (48%), Gaps = 16/463 (3%) Query: 9 IDGAWVDGD-AARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFAERQA 67 +DG W+ D AA DP +G +L A + A+ AA +A+P W R AER A Sbjct: 18 VDGQWIGADNAATLDVIDPATGHSLARVPAMQGVETRRAIEAAERAWPAWRARPAAERAA 77 Query: 68 VVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGER-ARD 126 ++ER+ + + + + LA + E GKPL EA+ E+ G GE Sbjct: 78 LLERWYQAMMDNLDDLALIMTCEQGKPLSEAKGEIRYGAGFAKWFAEEARRVYGETIPAP 137 Query: 127 IGDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTADLTLQ 186 GD R + +P GV A P+NFP + PAL AG V+ KPS+ TP++A Sbjct: 138 SGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCPVIVKPSDLTPLSALALAV 197 Query: 187 CWLEAGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVGGLLHRQFGGQVDKILA 245 G+PAGV N+V G A +G+ L G+ + + FTGS VG LL RQ + K L+ Sbjct: 198 LAERVGIPAGVFNVVTGMPAGIGEELTGNPTVRKISFTGSTAVGRLLMRQSAEHI-KRLS 256 Query: 246 LELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLIDALTSA 305 LELGGN P +V D D E AV I+ S F + GQ C CA R++V G + + L Sbjct: 257 LELGGNAPFIVFDDADLEQAVAGIMLSKFRNAGQTCVCANRILVQDG-IYERFAARLVEE 315 Query: 306 IAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRRLQAGTSLLSPG 365 + +L+V E L ++ A + + DD +++G R L + + + P Sbjct: 316 VGKLKVGNGL-EAGVMIGPLINLAAVNKVARHIDDALSQGARLLCG-GVPEGDSQFVQPT 373 Query: 366 LIDV--TGCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGE-RADWDDFL 422 ++ G + +EE FGP+ + R+ ++A+ALAN T YGL A + R W F Sbjct: 374 VLGEAHAGMLLANEETFGPVAPLMRFTTEEQALALANATPYGLGAYYFTQDLRRSW-RFG 432 Query: 423 LRIRAGIVNWNRQTTGASS--DAPFGGIGDSGNHRPSAYYAAD 463 + G+V N TG S APFGGI SG R + Y D Sbjct: 433 EALEFGMVGLN---TGIISMEVAPFGGIKQSGLGREGSKYGLD 472 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: 640 Number of extensions: 37 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: 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 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