Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate AO356_10720 AO356_10720 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8ZPV0 (492 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10720 Length = 480 Score = 189 bits (480), Expect = 2e-52 Identities = 143/463 (30%), Positives = 223/463 (48%), Gaps = 14/463 (3%) Query: 4 WINGDWITGQ-GERRRKTNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQ 62 +I+G W+ G+ + TNP + E+L AA+ A +AA A P W R Sbjct: 14 FIDGAWVDADNGQTIKVTNPATGEVLGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 Query: 63 AIVEKFAALLEAHKAELTEVIARETGKPRWEAATEVTAMINKIA-ISIKAYHARTGAQKS 121 + ++ LL ++ +L ++ E GKP EA E+ + I + +A Sbjct: 74 NKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIPG 133 Query: 122 ELVDGAATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETVI 181 D + +P GV A P+NFP + PAL AG T++ KP+ TP++ ++ Sbjct: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALALV 193 Query: 182 KLWERAGLPAGVLNLVQGGR-ETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPEKIL 240 +L RAG+P GVL++V G + G L+S + L FTGS G QL + + +K+ Sbjct: 194 ELAHRAGIPQGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKV- 252 Query: 241 ALEMGGNNPLIIEDAANIDAAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLARLVD 300 +LE+GGN P I+ D A++D AV + S + GQ C CA RL + Q + DAF +L Sbjct: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYI-QDSVYDAFAEKLKV 311 Query: 301 VAGRLQPGRWDDD---PQPFIGGLISAQAAQHVMEAWRQREALGGRTLLAPRKVKEGTSL 357 +L+ G DD P I G A+ +H+ +A + G T+L+ K EG Sbjct: 312 AVAKLKIGNGLDDGTTTGPLIDGKAVAKVQEHIADAVSK-----GATVLSGGKAMEGNFF 366 Query: 358 LTPGIIELTGVADVPDEEVFGPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTDRAQFEQ 417 + + A V EE FGPL ++R+ E I ++N+T FGL+ + D + + Sbjct: 367 EPTILTNVPKNAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRVFR 426 Query: 418 LLLEARAGIVNWNKPLTGAASTAPFGGVGASGNHRPSAWYAAD 460 + G+V N L + APFGG+ ASG R + Y + Sbjct: 427 VAEALEYGMVGVNTGLI-SNEVAPFGGIKASGLGREGSKYGIE 468 Lambda K H 0.319 0.134 0.411 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: 531 Number of extensions: 30 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: 492 Length of database: 480 Length adjustment: 34 Effective length of query: 458 Effective length of database: 446 Effective search space: 204268 Effective search space used: 204268 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 (21.7 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