Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_090439664.1 BLS63_RS03170 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_900100495.1:WP_090439664.1 Length = 478 Score = 238 bits (607), Expect = 3e-67 Identities = 168/468 (35%), Positives = 236/468 (50%), Gaps = 17/468 (3%) Query: 5 FIDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 +I G WV G+ ++ V E A A A VE+A+A+AR AF AWS + AR Sbjct: 8 YIGGQWVAGSDYSRNINPSDLSDLVGEYAQADAAQVEQAIAAARAAFPAWSTSAIQARSD 67 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124 + + + ++ R+E L +++ RE GK L EA EV+ + GE A + Sbjct: 68 ALDKVGSEILARREELGSLLAREEGKTLAEAIGEVSRAGNIFKFFAGECLRQAGELLASV 127 Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 GV+V + P GV+ + P+NFP +P I PAL GN VVFKP++L PG A A E Sbjct: 128 RPGVSVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAYGNCVVFKPADLVPGCAWAIAE 187 Query: 184 IWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242 I AG PAGV NLV G + G L H Q+DG+ FTGS G + R V Sbjct: 188 IIARAGFPAGVFNLVMGSGRVVGETLVQHPQVDGVSFTGSVGVGRSIAAVCVARGAKV-Q 246 Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302 LEMGG NP V+ + D++ AV ++QSAF S GQRCT + R++V G DRFV +A+ Sbjct: 247 LEMGGKNPQVILDDADLNTAVELSVQSAFYSTGQRCTASSRLIVTAG-IHDRFVEAMAER 305 Query: 303 ASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEM-----KQRDPALG 357 + + +G V+S + R +G+G + + G Sbjct: 306 MRSLRVG-HALERGVDIGPVVSQAQLEQ----DLRYIGIGRDEGARLVCGGERVSCATEG 360 Query: 358 FVNAAIL--DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQA 415 + A L D T + EE FGP+A I++ D ++A+A ANDT FGLSAG+ + Sbjct: 361 YFLAPTLFADSTAAMRINREEIFGPVANILKVADYEEALAMANDTEFGLSAGICTTSLKY 420 Query: 416 WHTFRRAIRAGIVNWNRPTNGASSAAPFGG-AGRSGNHRPSAYYAADY 462 + F+R +AG+V N PT G PFGG G S R YA ++ Sbjct: 421 ANHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEF 468 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: 503 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 487 Length of database: 478 Length adjustment: 34 Effective length of query: 453 Effective length of database: 444 Effective search space: 201132 Effective search space used: 201132 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