Align Proline dehydrogenase; PRODH; Proline oxidase; TtPRODH; EC 1.5.5.2 (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Query= SwissProt::Q72IB8 (307 letters) >MicrobesOnline__882:208845 Length = 1006 Score = 122 bits (307), Expect = 3e-32 Identities = 104/335 (31%), Positives = 158/335 (47%), Gaps = 51/335 (15%) Query: 24 IKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLEL 83 I+ +G+ R+++ G+ +EA+K L ++G +DLLGE +EEE+ A+ +G E+ Sbjct: 109 IRSNIEGMARQFIIGDNSKEAVKGLAKLRKDGFTFTVDLLGEATVSEEESEAYAQGYHEV 168 Query: 84 VWALA----------------GKPW---PKY-ISLKLTQL-------GLDLSEDLALALL 116 V A+A G W PK +S+K + L ++ S L+ L Sbjct: 169 VDAIAREQEKWKALPGNGPVEGFDWGATPKVNVSIKPSALYSQAKPVDVEGSVRGILSRL 228 Query: 117 REVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREE----GFSQVGIVLQSYLYRTEKD 172 + R+ G F+ +DME E TL L++ LR + + + IVLQ+YL TEKD Sbjct: 229 VPIYRKVVAMGGFLCIDMEQLKYKEMTLELFKRLRSDPEFRHYPHLSIVLQAYLRDTEKD 288 Query: 173 LLDLLPYRPN------LRLVKGAYREPKEV----------AFPDKRLIDAEYLHLGKLAL 216 L DLL + + +RLVKGAY + + V + DK D Y L L Sbjct: 289 LDDLLHWARSEKLPIGIRLVKGAYWDYETVIAKQNGWEIPVWTDKPESDIAYEKLAHRIL 348 Query: 217 KEG--LYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRA 274 + +Y A A+H+ R IA + A+ +P R+EFQ LYG+ ++ L VR Sbjct: 349 ENSDIVYFACASHNVRTIAAVMETALALNVPEHRYEFQVLYGMAEPVRKGLKNVAGRVRL 408 Query: 275 YVPYGR--DWYPYLTRRIAERPENLLLVLRSLVSG 307 Y PYG YL RR+ E N + +S G Sbjct: 409 YCPYGELIPGMAYLVRRLLENTANESFLRQSFAEG 443 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: 635 Number of extensions: 33 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: 1006 Length adjustment: 36 Effective length of query: 271 Effective length of database: 970 Effective search space: 262870 Effective search space used: 262870 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: 53 (25.0 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