Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate WP_013449840.1 SULKU_RS12970 phenylacetaldehyde dehydrogenase
Query= curated2:Q9AAL5 (472 letters) >NCBI__GCF_000183725.1:WP_013449840.1 Length = 481 Score = 198 bits (504), Expect = 3e-55 Identities = 138/446 (30%), Positives = 216/446 (48%), Gaps = 16/446 (3%) Query: 10 DPYTGEAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETVRARREEIA 69 +P TGE A + A I+ A +A AA WA T E+ A+ L+ A+ +R +EI Sbjct: 25 NPATGEVFAKVHLASAEDIEEAISTAYAASKLWAKTTPREKEAVLLKAADIFESRTDEIR 84 Query: 70 TLIARETGKPMWEALTEADSVAAKVAISIRAQDERAGER---SEPMADATARLAHRPHGV 126 T++ RE+G +A+ E VA + ++ G+ ++P + RP GV Sbjct: 85 TILMRESGSVYAKAMFEIGLVADILRVAAGEARRVFGQTFTSNDP--GVLSYSTRRPLGV 142 Query: 127 LAVIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHVLTIV 186 +A I PFN PM L+ A+ AGNA V KPS TP CG + GE+++ AGLPD VL I+ Sbjct: 143 IAGISPFNAPMILSTKKFAMAIAAGNAFVLKPSSHTPICGLIFGEIFKEAGLPDGVLNII 202 Query: 187 -IGGGEAGEALVRHEALDGVLFTGGVQAGRAIHRALADAPH-KILALELGGNAPLVVWDV 244 G+ GE + + TG + G+ + A + A H K +ELGG +P +V Sbjct: 203 PCSSGDLGETFQTDPRIAMITLTGSTRVGKLV--AASAAMHLKKCTVELGGKSPTIVLGD 260 Query: 245 ADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQSPA 304 AD++ A S ++ GQ C R+I+ E D E + L +G P + P+ Sbjct: 261 ADVDYAVDTATFSIFLHQGQICMAGSRIIVEENIY-DEFCEKFAAKVKTLKVGNP-EDPS 318 Query: 305 PFMGPVIDAHAAAQVLAAQDRMTADGGRPLRLAAVREARSALLSPGLIE--LTDAPLRDE 362 +GP+I+ + D A G L + RE P ++ + + E Sbjct: 319 TIIGPLIEEAQCRFIDGLIDDAVAKGA---TLLSGREHEGCFYKPTVVSNVTEEMVIFHE 375 Query: 363 EIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPTT 422 E FGP + +A D D + LAN + +GL++ +I+D+ + R + +G+V+ N PT Sbjct: 376 EAFGPAAAIIKARDLDHVIELANNSNYGLSSSIITDNLSAALRLSEEIESGMVHINGPTI 435 Query: 423 GASSAAPFGGVGGSGNHRPSAYYAAD 448 + PFGGV SG R ++A + Sbjct: 436 QDEAHIPFGGVKESGMGREGGHFAIE 461 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: 539 Number of extensions: 27 Number of successful extensions: 4 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: 481 Length adjustment: 33 Effective length of query: 439 Effective length of database: 448 Effective search space: 196672 Effective search space used: 196672 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 24 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