Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate PP_0213 PP_0213 succinate-semialdehyde dehydrogenase (NADP+)
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__Putida:PP_0213 Length = 480 Score = 249 bits (636), Expect = 2e-70 Identities = 159/475 (33%), Positives = 232/475 (48%), Gaps = 25/475 (5%) Query: 41 YIGGEWVDTKE-RMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRS 99 YI GEW+D + + + A EV+GT K G AE A+EAA KA W+ ++RS Sbjct: 14 YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73 Query: 100 RLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEV 159 L + LM + +L + E GK EA ++A A FIE++A A R + Sbjct: 74 AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTI-- 131 Query: 160 VPYPGEDNESFYV----PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVV 215 PG + + P+G I PWNFP A+ T +A G T++ KPA Sbjct: 132 ---PGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYS 188 Query: 216 GAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRL 275 + E+ H AG P GV++ + G EVG L + R ++FTGS E+G ++ E + Sbjct: 189 ALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK- 247 Query: 276 APGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAY 335 K+ +E GG IV + AD D A EG ++S Y GQ C A+R+ + G Y Sbjct: 248 -----DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVY 302 Query: 336 EPVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEG 394 + E++ +L +G EE GP++ + KV +IE ++G VL G +L Sbjct: 303 DAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI- 361 Query: 395 EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKR 454 EG F PT+ +VP A +A+EE FGP+ + R KD AE + ++NDT +GL Y+R Sbjct: 362 EGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDM 421 Query: 455 EHLEWARREFHVGNLYFNRKITGALVG-VQPFGGFKLSG---TNAKTGALDYLRL 505 + G + N TG + V PFGG K SG +K G DYL + Sbjct: 422 SRVFRVAEALEYGMVGIN---TGLISNEVAPFGGIKASGLGREGSKYGIEDYLEI 473 Lambda K H 0.319 0.137 0.403 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: 553 Number of extensions: 32 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: 516 Length of database: 480 Length adjustment: 34 Effective length of query: 482 Effective length of database: 446 Effective search space: 214972 Effective search space used: 214972 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