Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__Dino:3607155 Length = 483 Score = 218 bits (555), Expect = 4e-61 Identities = 157/474 (33%), Positives = 226/474 (47%), Gaps = 23/474 (4%) Query: 2 TELFIDGAWVDGAGPVFASRNPG-TNERVWEGASASADDVERAVASARRAFAAWSALDLD 60 T+L+IDGAW +G + +RNP T + + A A A ++ A+A+ARRA AW A + Sbjct: 5 TQLYIDGAWTEGTAQI-ENRNPSDTTDLIGMYAQADAGQLDTALAAARRAQPAWWAAGIQ 63 Query: 61 ARCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEK 120 R ++ L+ R + + ++ RE GKPL E + EV + G+ Sbjct: 64 KRHDVLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQHGDL 123 Query: 121 RAPMADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVAR 179 + G+ + +R GVVA+ P+NFP P I PAL GN VV+KP+ + P A Sbjct: 124 AESVRPGIEIDVRREAVGVVAIISPWNFPVATPAWKIAPALAFGNAVVWKPANVTPASAI 183 Query: 180 ATVEIWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPE 238 A EI +P G+ NLV G +D G L ++D + FTGS G + + Sbjct: 184 ALTEIIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAA-AVQNM 242 Query: 239 IVLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVAR 298 + +EMG NPL+V + D+D AV HA SAF GQ+CT A R++V A D FV + Sbjct: 243 TKVQMEMGSKNPLIVMDDCDLDLAVAHAASSAFGGTGQKCTAASRLIV-HSAVHDAFVEK 301 Query: 299 L--ADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPAL 356 L A A K+ ++ D +G V+S ++ +G+G E+ L Sbjct: 302 LVAAARAMKVGHALEDGTQ---LGPVVSESQLNQ----NMEYIGVGKDEGAELLCGGDRL 354 Query: 357 GFVN-------AAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLL 409 A N + EE F P+ + R D+A+ARANDT FGL+AG++ Sbjct: 355 EMATDGYFMAPAVFAGTANDMRINREEMFAPITAVQRVDSYDEALARANDTQFGLTAGIM 414 Query: 410 ADDEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSG-NHRPSAYYAADY 462 FR +RAG V N PT G PFGG G S R YAA++ Sbjct: 415 TTSLARASHFRAHMRAGCVMVNLPTAGTDYHVPFGGRGASSFGPREQGSYAAEF 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: 526 Number of extensions: 20 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: 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 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