Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized)
to candidate WP_017222570.1 A923_RS0115365 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= BRENDA::Q97XA5 (470 letters) >NCBI__GCF_000276805.1:WP_017222570.1 Length = 1038 Score = 161 bits (407), Expect = 1e-43 Identities = 137/457 (29%), Positives = 211/457 (46%), Gaps = 34/457 (7%) Query: 9 VRSPSNLKV-IGTVKRMSKDEVRGEIEEAYKGFEIISRMPLYKRTAILRKISEILEREQE 67 V +P + ++ +G V + EV ++ A F S +P+ +R A L I+++LE Sbjct: 580 VSAPYDRRIHVGQVLWSTPAEVTTALDTAADYFPTWSAVPVAERAACLNNIADLLEENLA 639 Query: 68 RLARLLAMEAGKPISDSRVEVLRASRLFR----QAAEEVGIVLEGKNYRVDAYEYPPGNE 123 L L EAGK I DS EV A R QA E + + A + Sbjct: 640 ELVALCHKEAGKTIHDSLDEVREAVDFCRYYAMQATENFSVAKNQVRFDGIAQQV----- 694 Query: 124 NRIVLSTREPIGVVTAILPFNFPINSFAHKVAPALAVGNSVVVKPSINTPLAAVEMKKIL 183 TR+ GV I P+NFP+ F +VA AL GN+V+ KP+ T L A +++ Sbjct: 695 ------TRQGQGVFVCISPWNFPLAIFLGQVAAALVAGNTVIAKPAEQTSLIAARTMELM 748 Query: 184 VEAGLPDSAVRVVTGYSSEIGDEIITHPLVGLITLTGSTQTGLKIASKAISLGKR----- 238 +EAG P A+ ++ G + +G + + + TGST+T I SL KR Sbjct: 749 LEAGFPKEAIHLLPGSGAVVGSLLTADERIAGVVFTGSTETAQVINR---SLAKRDTNVA 805 Query: 239 -IIMELGGSDPIIILEDANIERASSIAVRARFEYAGQNCNAGKRIIVRQEVYDKFVKAFN 297 +I E GG + +I+ A E+ +R+ F AGQ C+A + + V+++V D+ Sbjct: 806 TLIAETGGQNTMIVDSTALPEQVVRDVMRSAFASAGQRCSALRVLFVQEDVADRITTLIQ 865 Query: 298 EKAKALKVGEPLDETTDVGPVINKESVENLNSVLEDAKVKGGRVEILNRGPES--GSFF- 354 K L VG P TDVGPVI+ + L + ++ + V + E G F Sbjct: 866 GAMKELHVGLPQQHHTDVGPVIDLLAKNKLQAHIDIMRATSKLVGEVTLSEECNFGDFIA 925 Query: 355 PLTMVTNPSLDMLVLKSEVFGPIVPIVSVKSDE--EAIRIANSTEYGLQSAIFTNDVNRA 412 P+ N S+D L++E FGPI+ IV K+ E + I N+T +GL I + + Sbjct: 926 PIAFEIN-SIDQ--LENEQFGPILHIVRYKAAELNKVISEINATGFGLTMGIHSRNERTY 982 Query: 413 LKLSRELKFGAVIIN-DSTRLRWDSLPFGGFKKTGIG 448 + R+++ G IN D PFGG +G G Sbjct: 983 TDIERQIRVGNCYINRDQVGAVVGVQPFGGQGLSGTG 1019 Lambda K H 0.316 0.135 0.366 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: 875 Number of extensions: 44 Number of successful extensions: 3 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: 470 Length of database: 1038 Length adjustment: 39 Effective length of query: 431 Effective length of database: 999 Effective search space: 430569 Effective search space used: 430569 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 (21.6 bits) S2: 54 (25.4 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