Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_090218033.1 CV091_RS10640 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_002796795.1:WP_090218033.1 Length = 483 Score = 186 bits (473), Expect = 1e-51 Identities = 141/455 (30%), Positives = 220/455 (48%), Gaps = 20/455 (4%) Query: 6 IDGAWVDGAGPVFASRNPGT-NERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 I G+W G + +RNP ++ V A AS+D ++ + A+ A A W+A ++ + Sbjct: 9 IAGSWTVGVDEI-ENRNPSDLSDLVGMFAQASSDQLDATLDQAKIAQAEWAAYGIERKYN 67 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124 ++ ++ R E L T++ RE GKPL E + EV + GE + Sbjct: 68 VLMAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAETLRQIGENADSV 127 Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 +G+ + +R G VA+ P+NFP + I PAL GN VV+KP+ P A A E Sbjct: 128 REGIEIDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANATPASAVALTE 187 Query: 184 IWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242 I +P G+ +LV G ++ G L ++D + FTGS G + + + Sbjct: 188 IIERQDIPKGLFSLVMGAGREIGQRLVESSKVDAISFTGSVPVGKGIASA-AIQNLTKVQ 246 Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302 +EMG N L V + DID AV A+ AF GQ+CT + R++V A D FV++L Sbjct: 247 MEMGSKNALAVMDDADIDLAVSLALGGAFGGTGQKCTASSRLVV-HSAVHDEFVSKLVAG 305 Query: 303 ASKITAS-VFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEM-----KQRDPAL 356 A + +A Q +G V++ + + +A V LG S E+ + P Sbjct: 306 AKAMKVGHALEAGTQ--IGPVVTEQQLNENLA----YVDLGKSEGAELLCGGQRLEMPHQ 359 Query: 357 GF-VNAAI-LDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQ 414 G+ +N I + TN + EE F PLA +++ + D+A++ NDT FGL++G++ Sbjct: 360 GYYMNPGIFIGTTNDMRINREEMFAPLAAVIKVSGYDEALSVVNDTNFGLTSGIVTKSLA 419 Query: 415 AWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRS 449 + FRR + G V N PT G PFGG G S Sbjct: 420 RANHFRRNAQTGCVMVNLPTAGTDYHVPFGGRGDS 454 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: 441 Number of extensions: 21 Number of successful extensions: 3 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: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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 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