Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_068170492.1 HTA01S_RS10485 aldehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >NCBI__GCF_001592305.1:WP_068170492.1 Length = 492 Score = 195 bits (495), Expect = 3e-54 Identities = 152/459 (33%), Positives = 226/459 (49%), Gaps = 13/459 (2%) Query: 12 AGQGETLESLDPV-GQGVVWSGRGADATQVDAAVCAAREAFP--AWARRPLEQRIELLER 68 A G+T + + PV G+ + RG A +DAAV A R AF W+ QR ++ + Sbjct: 22 ARDGQTFDCISPVDGRVLTQVARGGQA-DIDAAVAAGRAAFEDRRWSGMAPAQRKRVMIK 80 Query: 69 FAATLKSRADELARVIGEETGKPL-WESATEVTSMVNKVAISVQAFRERTGEKSGPLADA 127 FA L + ADELA + GKP+ + A +V S N + +A + E + A+A Sbjct: 81 FADQLLAHADELALTETLDMGKPVKYARAVDVNSAANCIRWYGEAVDKVYDEIAPTGANA 140 Query: 128 TAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLKAWIQ 187 A++ +P GVV + P+N+P + I PAL AGN VV KPSE +P A + + Sbjct: 141 LALITREPVGVVGIIVPWNYPMIMAAWKIAPALAAGNSVVLKPSEKSPLTALRLAELALA 200 Query: 188 AGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILALEMG 246 AG+P GV N+V G G E G LA H +D + FTGS+R G +H G K E+G Sbjct: 201 AGIPPGVFNVVPGFGTEAGSPLALHMDVDCIAFTGSTRVGKQIHVMAGQSNLKRAWTELG 260 Query: 247 GNNP-LVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAVSAT 305 G +P +V + DLD AV + S F + G+ C RL V + + DA L + + + Sbjct: 261 GKSPNIVFADCPDLDRAVEAAVGSIFFNQGESCNAPSRLFV-EASIKDAFLEKALKLVPQ 319 Query: 306 LRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLL--AMTQPIDGAALLTPGI 363 + G MGA++ +++++ +GAQ + A+ P+ G + P I Sbjct: 320 YQPGN-PLDKGTVMGAIVDQMQLDNVMRYIGLGQSEGAQLIAGGALASPVAGGCYVQPTI 378 Query: 364 LD-VSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFLVE 422 D V+ EE FGP+L V ++D A +R AN + YGL AG+ + + Sbjct: 379 FDGVTPQMTIAREEIFGPVLAVQSFTDAADVVRAANNSVYGLQAGVWTRDINKAHGVARA 438 Query: 423 SRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAAD 461 RAG V+ N Q + PFGG SG R + +A D Sbjct: 439 LRAGTVHVN-QYDEDDITVPFGGFKQSGVGRDKSLHAFD 476 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: 575 Number of extensions: 26 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: 492 Length adjustment: 34 Effective length of query: 453 Effective length of database: 458 Effective search space: 207474 Effective search space used: 207474 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 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