Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate GFF827 PS417_04200 aldehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__WCS417:GFF827 Length = 481 Score = 224 bits (571), Expect = 5e-63 Identities = 160/465 (34%), Positives = 233/465 (50%), Gaps = 9/465 (1%) Query: 4 HYIAGQWLAGQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRI 63 +YI GQW+AG + V+ AD TQV+AA+ AAR AFPAW+ ++ R Sbjct: 9 NYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQARH 68 Query: 64 ELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEKSGP 123 + L++ + + +R +EL ++ E GK L E+ EVT N +G+ Sbjct: 69 DALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPS 128 Query: 124 LADATAV-LRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTL 182 + V + + GVV + P+NFP +P I PAL GNCVV KP+EL P A Sbjct: 129 VRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALA 188 Query: 183 KAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKIL 241 + +AG PAGV NLV G GR G L +DG+ FTGS G + + K+ Sbjct: 189 EIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQAKV- 247 Query: 242 ALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVA 301 LEMGG NP ++ + ADL AV +QSAF S GQRCT + RL+V G D +A + Sbjct: 248 QLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGI-HDQFVAAMAE 306 Query: 302 VSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLA---MTQPIDGAAL 358 +++VG + +G V+S + + LK + +GA+ + +T +G L Sbjct: 307 RMKSIKVGHALKSGTD-IGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYL 365 Query: 359 LTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQ 418 D A EE FGP+ V+R +D+ AA+ AN T++GL+AG+ + S + Sbjct: 366 APTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANH 425 Query: 419 FLVESRAGIVNWNKQLTGAASSAPFGG-IGASGNHRPSAYYAADY 462 F S+AG+V N G PFGG G+S R YA ++ Sbjct: 426 FKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEF 470 Lambda K H 0.318 0.134 0.396 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: 570 Number of extensions: 29 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: 481 Length adjustment: 34 Effective length of query: 453 Effective length of database: 447 Effective search space: 202491 Effective search space used: 202491 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 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