Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 186 bits (472), Expect = 2e-51 Identities = 149/472 (31%), Positives = 226/472 (47%), Gaps = 24/472 (5%) Query: 1 MSTHYIAGQWLAGQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLE 60 M H I G+ + T+ +L+P V+ +V AV AA+EAFP WA P Sbjct: 1 MIKHLINGRQVES-ASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPAS 59 Query: 61 QRIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK 120 QR +LL + + DE+A++ +TG+ W + +V + A + F + Sbjct: 60 QRAKLLRKVGDLINQHVDEIAKLESLDTGQSYWRTK---KMLVPRAADNFYFFADTCCHV 116 Query: 121 SG---PLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKV 177 G P D ++P GVV + P+N P P L GN V K SEL+P Sbjct: 117 DGETYPTNDHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLS 176 Query: 178 AELTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQ 236 A+ + ++AG+PAGV N+V G G G AL H + G+ FTGS+ TGN + Q GG Sbjct: 177 ADRLGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRI-IQSGG- 234 Query: 237 PQKILALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALL 296 K ++E+GG +P ++ + D + AV I + + + G+ CT R+LV G + D + Sbjct: 235 -LKKYSMELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLY-DRFV 292 Query: 297 ARLVAVSATLRVG-RFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDG 355 A L + + VG DE A +G +I+ + + E I +GA+ + +G Sbjct: 293 AALAERTRKVVVGDPLDE--ATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEG 350 Query: 356 AA-------LLTPGIL-DVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAG 407 A + P +L DV EE FGP+ VIR+ D A A++ ANAT YGLA+ Sbjct: 351 LAPHLKNGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASY 410 Query: 408 LLSDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYA 459 + +++ R + AG+V N Q PFGGI SG R +Y+ Sbjct: 411 VWTENGARAIRMAEGIEAGLVFVNSQNVRDLRQ-PFGGIKGSGTGREGGHYS 461 Lambda K H 0.318 0.134 0.396 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: 556 Number of extensions: 30 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: 487 Length of database: 485 Length adjustment: 34 Effective length of query: 453 Effective length of database: 451 Effective search space: 204303 Effective search space used: 204303 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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