Align Proline dehydrogenase; PRODH; Proline oxidase; TtPRODH; EC 1.5.5.2 (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= SwissProt::Q72IB8 (307 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 118 bits (295), Expect = 7e-31 Identities = 100/342 (29%), Positives = 152/342 (44%), Gaps = 56/342 (16%) Query: 22 RLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLL 81 + I+ +G+ R ++ GE +EA+K L +EG +DLLGE +EEEA A++ G L Sbjct: 106 KFIRSNIEGMARTFIIGENTKEAIKGLAKLRKEGFAFTVDLLGEATVSEEEADAYRDGYL 165 Query: 82 ELVWALAGK--PWPKYISLKLTQLGLDLSEDLA--------------------------- 112 E++ A++ + W + G D S+D Sbjct: 166 EVLDAISREHAKWAPLTDSTGSTTGPDASQDWGHTPKVNVSIKPSALYSQAKPGDVEGSV 225 Query: 113 ---LALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALRE----EGFSQVGIVLQSY 165 L+ L + R+ G F+ +DME E TL L++ LR + + IVLQ+Y Sbjct: 226 QGILSRLVPIYRKIVEMGGFLCIDMEQLKYREMTLELFKRLRTMPEFRDYPHLSIVLQAY 285 Query: 166 LYRTEKDLLDLLPYRP------NLRLVKGAYREPKEV----------AFPDKRLIDAEYL 209 L TE DL +LL + +RLVKGAY + + V + K D Y Sbjct: 286 LRCTEHDLDELLAWGRAERLPFGIRLVKGAYWDYETVMAKQNGWEIPVWTRKPESDICYE 345 Query: 210 HLGKLALKEG--LYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAR 267 L + L+ +Y A A+H+ R I+ + A+ +P R+EFQ LYG+ ++ L Sbjct: 346 KLARRILENNDLVYFACASHNVRTISTVMETARALNVPAHRYEFQVLYGMAEPVRKGLKN 405 Query: 268 EGYTVRAYVPYGR--DWYPYLTRRIAERPENLLLVLRSLVSG 307 VR Y PYG YL RR+ E N + +S V G Sbjct: 406 VAGRVRLYCPYGELIPGMAYLVRRLLENTANESFLRQSFVDG 447 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: 627 Number of extensions: 34 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 307 Length of database: 1013 Length adjustment: 36 Effective length of query: 271 Effective length of database: 977 Effective search space: 264767 Effective search space used: 264767 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