Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_090445639.1 BLS63_RS14235 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_900100495.1:WP_090445639.1 Length = 476 Score = 221 bits (564), Expect = 3e-62 Identities = 163/471 (34%), Positives = 225/471 (47%), Gaps = 15/471 (3%) Query: 1 MTELFIDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLD 60 M + I G W+DG G TN+ V A ASADD + A+A+A A W+A Sbjct: 1 MHKNLIAGRWLDGTGVRENLSPSDTNDLVGLYAQASADDTQSAIAAAEHAQPLWAAKPPQ 60 Query: 61 ARCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEK 120 R + A ++ R+E L T++ RE GK L EA EV GE Sbjct: 61 QRADALDFIGAEILLRREELGTLLAREEGKTLPEAIAEVVRAGQIFKFFAGEALRIPGEH 120 Query: 121 RAPMADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVAR 179 + G+ V + +P GV+ + P+NFP +P I PAL GN VVFKP++L PG A Sbjct: 121 LDSVRPGIEVDVLRQPVGVIGIIAPWNFPIAIPAWKIAPALAYGNAVVFKPADLVPGSAW 180 Query: 180 ATVEIWRDAGLPAGVLNLVQGEKD-TGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPE 238 A EI AGLP G NLV G G L ++ L FTGSSDTG + G R Sbjct: 181 ALSEIIHRAGLPDGTFNLVMGRGSVVGQTLVESPRVKALSFTGSSDTGRRILHSAGAR-F 239 Query: 239 IVLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRG---AFGDRF 295 L LEMGG NPLVV D++ A+ A+Q A+ S GQRCT + R +V +G F + Sbjct: 240 AKLQLEMGGKNPLVVLNDADLEQAIECAVQGAYFSTGQRCTASSRFIVEKGIYRRFSEGV 299 Query: 296 VARL--ADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRD 353 ARL V + A P G A + ++ ++ G P+ QRD Sbjct: 300 QARLQALQVGHALHADT-QIGPVAEQGQYEQNLAYVDIGLSEGAVLACGGRPL----QRD 354 Query: 354 PALGFVNAAI-LDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADD 412 +++ A+ +D + EE FGP+A + D + A+ AN + +GLSAG+ Sbjct: 355 TQGYYMSPALFVDAEAQMRIAQEEIFGPIACAIPADDYEHALQLANASPYGLSAGICTTS 414 Query: 413 EQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGA-GRSGNHRPSAYYAADY 462 + F+R + +G+V N PT G PFGG G S R YAA++ Sbjct: 415 LKYAAHFKRHMHSGMVMINTPTAGVDYHVPFGGTKGSSYGSREQGRYAAEF 465 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: 554 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: 487 Length of database: 476 Length adjustment: 34 Effective length of query: 453 Effective length of database: 442 Effective search space: 200226 Effective search space used: 200226 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