Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 228 bits (581), Expect = 4e-64 Identities = 160/467 (34%), Positives = 235/467 (50%), Gaps = 13/467 (2%) Query: 5 FIDGAWVDGAGPV-FASRNPGT-NERVWEGASASADDVERAVASARRAFAAWSALDLDAR 62 +I+G W++ A S NP +E V + ADD +RAV +AR+A+ +W + AR Sbjct: 10 YINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKVPAPAR 69 Query: 63 CTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKR- 121 + R LL++ KE LA +I RE GKP+ EAR +V S G+ Sbjct: 70 AEYIFRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEGRRLFGQTTP 129 Query: 122 APMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARAT 181 + M + A+ P GV A+ P+NFP +P +PAL+ GNTV+ KP+E P A Sbjct: 130 SEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACATKL 189 Query: 182 VEIWRDAGLPAGVLNLVQG-EKDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIV 240 +EI+ AGLP GV+NLV G ++ G AL H ID + FTGSS TG + + GR Sbjct: 190 IEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETC-GRTHKR 248 Query: 241 LALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLA 300 + LEMGG N VV E D++ A+ A+ AF + GQRCT R+++ R ++F L Sbjct: 249 VCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRD-IKEKFTTMLR 307 Query: 301 DVASKITASVFDADPQPFMGAVISARAASRL-----VAAQARLVGLGASPIIEMKQRDPA 355 + S++ +P+ +G +I+ R R+ +A + L I+ Q Sbjct: 308 ERTSQLRLGA-GTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEGQLKQG 366 Query: 356 LGFVNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQA 415 F + +VT + EE FGP+ ++ + ++AIA NDT +GLS+ + D Sbjct: 367 YFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINR 426 Query: 416 WHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGN-HRPSAYYAAD 461 R I GI N PT GA PFGG ++GN HR + A D Sbjct: 427 AFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALD 473 Lambda K H 0.320 0.134 0.402 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: 513 Number of extensions: 23 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: 487 Length of database: 498 Length adjustment: 34 Effective length of query: 453 Effective length of database: 464 Effective search space: 210192 Effective search space used: 210192 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 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