Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate 3609638 Dshi_3021 aldehyde dehydrogenase (RefSeq)
Query= curated2:Q9AAL5 (472 letters) >FitnessBrowser__Dino:3609638 Length = 485 Score = 199 bits (505), Expect = 2e-55 Identities = 149/444 (33%), Positives = 206/444 (46%), Gaps = 13/444 (2%) Query: 10 DPYTGEAIADFAVNDARSIDAACHSARAAF-AEWAMTPLAERRAIALRFAETVRARREEI 68 DP G +A A A ID A +ARAA +W ER R V + + Sbjct: 33 DPSDGTPLAQIARGGAAEIDRAVAAARAALDGDWGRMSATERGRCLTRLGALVAGEVDRL 92 Query: 69 ATLIARETGKPMWEALTEADSVAAKVAISIRAQDERAGERSEPMADATARLAHRPHGVLA 128 A + AR+ GKP+ +A +A ++A + A D+ GE + T PHGV Sbjct: 93 AEMEARDVGKPLSQARADALALARYLEFYGGAADKVMGETIPYQSGYTVYTLREPHGVTG 152 Query: 129 VIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHVLTIVIG 188 I P+N+PM + + AL GNA V KP+E L AAGLP L +V G Sbjct: 153 HIVPWNYPMQIIGRSVGAALAMGNACVLKPAEDACLTALAFARLAEAAGLPPGALNVVTG 212 Query: 189 -GGEAGEALVRHEALDGVLFTGGVQAGRAIHRALADAPHKILALELGGNAPLVVWDVADI 247 G EAG AL H +D + FTG V G + +A A + LELGG +P +V+ AD+ Sbjct: 213 LGAEAGAALSDHPGVDHLSFTGSVPVGAEV-QATAARHITPVTLELGGKSPQIVFADADL 271 Query: 248 EAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQSPA--P 305 +AA +V+ AGQ C+ A R+++ DA+ + + L +G PA P Sbjct: 272 DAALPFLVKGGVQNAGQTCSAAARILVQTDV-FDAVADRMAEAYRALTVGPALSDPAVGP 330 Query: 306 FMGPVIDAHAAAQVLAAQ-DRMTADGGRPLRLAAVREARSALLSPGLIE--LTDAPLRDE 362 + P A +A + AQ D++ A G L + P L+ D PL + Sbjct: 331 LISPKQKARVSAMLAQAQPDQILATG----HLLPEAPEGGCYVLPHLLGGIAADHPLAQQ 386 Query: 363 EIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPTT 422 EIFGP+ + R A+ALAN T FGL AG+ + D A R +RAG V N Sbjct: 387 EIFGPVQILMRFETEQEAIALANGTEFGLVAGIWTRDGARQMRMPKRLRAGQVFVNTYGA 446 Query: 423 GASSAAPFGGVGGSGNHRPSAYYA 446 G PFGGVG SG+ R + A Sbjct: 447 GGGVELPFGGVGKSGHGREKGFEA 470 Lambda K H 0.320 0.135 0.400 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: 630 Number of extensions: 36 Number of successful extensions: 5 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: 472 Length of database: 485 Length adjustment: 34 Effective length of query: 438 Effective length of database: 451 Effective search space: 197538 Effective search space used: 197538 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: 51 (24.3 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