Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_023433101.1 N177_RS14415 aldehyde dehydrogenase
Query= curated2:B0T8I8 (484 letters) >NCBI__GCF_000496075.1:WP_023433101.1 Length = 492 Score = 199 bits (506), Expect = 2e-55 Identities = 155/466 (33%), Positives = 222/466 (47%), Gaps = 16/466 (3%) Query: 6 FIDGVWRAGAGAQATSVDPTTGEVIWRQATASTAEVAAAVEAARKAF--PAWADRSREER 63 +IDG + G SVDP TGE A+ A+V AV AA +AF P+W+ + +R Sbjct: 9 YIDGAFCEGGAGSFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSRLTATQR 68 Query: 64 IAVLRRYKDVLVARTGTFAEALSRETGKALWETKAELGSMAGKVEASIKAYDERTGEHAN 123 +L R D++ AE +R+TGK + ET A++ +A D+ G H Sbjct: 69 GKLLYRLADLVAENAQALAELETRDTGKIIRETSAQIAYVADYYRYYAGLADKIEGAHLP 128 Query: 124 -DMAFGRAVLRHRAHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLL 182 D LR GV+A + P+N L + PAL AG TVV K SE+ P Sbjct: 129 IDKPDMETYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDGPAPLLAF 188 Query: 183 VEALEEAGVPAGVINLVQG-GREVGQALIDQE-IDGLLFTGSAAAGAFFRRHFADRPDVI 240 +++AG P GV+N++ G G + G AL + + FTG A RH A+ + Sbjct: 189 ARLVDQAGFPPGVVNILTGFGDQCGSALASHPLVARIAFTGGPATARHIVRHSAENLAAV 248 Query: 241 LALELGGNNPLVVWDAGDPEAVAALIVQSAFITTGQRCSCARRLIVSDDAAGRAVIDAVA 300 LELGG +P+VV++ D ++VA +V F TGQ C RLIV A+++ + Sbjct: 249 -TLELGGKSPVVVFEDADLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKD-ALLERLV 306 Query: 301 ALSERLVIGPWNGGQEPFMGPLISDRAAAM---ALAGAKAMPGQTLRAMTSVDGLSRA-F 356 + + IG QE MGPL + R +A + A G+ + DG + Sbjct: 307 QKARAIRIGD-PQAQETEMGPLATARQLRHIEDVIARSLAAGGRLVTGGGRPDGFPAGHY 365 Query: 357 VSPGLVDVTGETVP--DEELFAPLLQVRRVGSFEEAIAAANATRYGLSAGLVSNETAHWD 414 P ++D T+P +EELF P+L V EA+ AN T YGL++G+ + Sbjct: 366 FEPTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGVFTASLTRAH 425 Query: 415 RFLTRIRAGVVNWNRPTTGAAGTMPFGGLGNSGNHRPSAYYAA-DY 459 R + IRAGVV W + MPFGG G SG+ R AA DY Sbjct: 426 RMIRAIRAGVV-WVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDY 470 Lambda K H 0.318 0.134 0.395 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: 620 Number of extensions: 33 Number of successful extensions: 6 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: 484 Length of database: 492 Length adjustment: 34 Effective length of query: 450 Effective length of database: 458 Effective search space: 206100 Effective search space used: 206100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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