Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate BPHYT_RS28770 BPHYT_RS28770 aldehyde dehydrogenase
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__BFirm:BPHYT_RS28770 Length = 480 Score = 220 bits (560), Expect = 1e-61 Identities = 166/467 (35%), Positives = 232/467 (49%), Gaps = 16/467 (3%) Query: 5 FIDGAWVDGAGPVFASR-NPG-TNERVWEGASASADDVERAVASARRAFAAWSALDLDAR 62 F+ G WVDG FA NP T++ + A ASAD ++A+ASAR AF WS R Sbjct: 7 FVGGEWVDGND--FAPNVNPSDTSDVIGHFARASADQTQKAIASARSAFRTWSLSTPQQR 64 Query: 63 CTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRA 122 ++ + + ++ RK L ++ RE GK L EA EV A ++ R G + Sbjct: 65 FDLLDQAGSTILARKNELGKLLAREEGKTLAEAVGEVGR-AGQIFKFFAGEALRVGGEIL 123 Query: 123 P-MADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180 P + G+ V + P GV+ + P+NFP +P I PAL GN VV KP+EL PG Sbjct: 124 PSVRPGLTVEVTREPVGVIGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGSVWE 183 Query: 181 TVEIWRDAGLPAGVLNLVQGEKD-TGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239 V+I +AG PAGV+NLV G G L +D + FTGS TG + + + Sbjct: 184 LVKIIAEAGAPAGVINLVMGMGSIVGEILVMSADVDAVSFTGSVGTGQAIAAKCVATGK- 242 Query: 240 VLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFV-AR 298 LEMGG NP+VV + D+D AV I AF S GQRCT + R++V G DRFV A Sbjct: 243 KFQLEMGGKNPMVVLDDADLDVAVEACINGAFYSTGQRCTASSRLIVTSG-IHDRFVEAM 301 Query: 299 LADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPALGF 358 LA + S + DA Q +G V+ A+ + G S + GF Sbjct: 302 LARMRSLKIGNALDASTQ--IGPVVDAKQLEQDERYIELARNEGGSVFGGERVTSATEGF 359 Query: 359 --VNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAW 416 A + + T + EE FGP+A +++ + ++A+A AND+ FGLSAG+ Sbjct: 360 FLAPALVTNTTPAMTINREEVFGPVASVIKVANYEEALAVANDSPFGLSAGICTMSLAHA 419 Query: 417 HTFRRAIRAGIVNWNRPTNGASSAAPFGG-AGRSGNHRPSAYYAADY 462 F+R ++AG+V N T G PFGG G S R YA ++ Sbjct: 420 SHFKRHVQAGMVMINTATAGVDYHVPFGGRKGSSLGPREQGTYAREF 466 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: 534 Number of extensions: 24 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: 480 Length adjustment: 34 Effective length of query: 453 Effective length of database: 446 Effective search space: 202038 Effective search space used: 202038 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 17 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