Align Proline dehydrogenase; PRODH; Proline oxidase; TtPRODH; EC 1.5.5.2 (characterized)
to candidate WP_073040272.1 BUB04_RS13170 L-glutamate gamma-semialdehyde dehydrogenase
Query= SwissProt::Q72IB8 (307 letters) >NCBI__GCF_900129305.1:WP_073040272.1 Length = 995 Score = 121 bits (303), Expect = 8e-32 Identities = 94/312 (30%), Positives = 144/312 (46%), Gaps = 49/312 (15%) Query: 34 RYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLEL--VWALAGKP 91 +++AG EAL E + +G+ DLLGE V + EE A+ L+L V A + Sbjct: 117 QFIAGADAREALPVLEKMRAQGLAFTADLLGEAVVSREEEEAYLERYLDLFDVLGTAARS 176 Query: 92 W-----------------------PKYISLKLTQLGLDLSEDLALALLREVLREAEPRGV 128 W P + ++ D S D A LR + R+A G Sbjct: 177 WKALGDGAGDLDWGWAPKLNVSIKPSAMYSQMNACAFDYSVDRAKDRLRPLFRKAMELGA 236 Query: 129 FVRLDMEDSPRVEATLRLYRALREE----GFSQVGIVLQSYLYRTEKDLLDLLPY-RPN- 182 FV LDME + TL LY++L EE G+ G+V+Q+YL +E DL DL+ + R N Sbjct: 237 FVCLDMEHTALKNITLALYKSLMEEPEFRGYPHTGVVIQAYLRDSEADLRDLIDWARKNR 296 Query: 183 ----LRLVKGAYREPKEV----------AFPDKRLIDAEYLHLGKLALKEGLYVAFA--T 226 +RLVKGAY + + + + +K DA + L +L ++ +V FA + Sbjct: 297 QPCTVRLVKGAYWDAEVIWARQNHWPVPVYTNKYDTDANFEKLARLLMENSAHVGFACAS 356 Query: 227 HDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGR--DWYP 284 H+ R +A + ++ + +P R E+Q LYG+ + L + G +R Y P G Sbjct: 357 HNIRSLAYVIELSKDLKVPEDRIEYQILYGMAEPVRTALKKAGLPLRLYTPIGEMIPGMA 416 Query: 285 YLTRRIAERPEN 296 YL RR+ E N Sbjct: 417 YLVRRLLENTSN 428 Lambda K H 0.323 0.141 0.407 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: 623 Number of extensions: 34 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: 307 Length of database: 995 Length adjustment: 35 Effective length of query: 272 Effective length of database: 960 Effective search space: 261120 Effective search space used: 261120 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 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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