Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate Pf1N1B4_5979 Ureidoglycolate/malate/sulfolactate dehydrogenase family (EC 1.1.1.-)
Query= BRENDA::Q9I492 (334 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5979 Length = 335 Score = 480 bits (1235), Expect = e-140 Identities = 240/334 (71%), Positives = 278/334 (83%), Gaps = 1/334 (0%) Query: 1 MIRMTLDEVRELAVRILRRHAFSEAHVQAVADTLVAGERDECASHGIWRLLGCIATLKAG 60 MIR+TL + RELA IL + F+ AH QAVA T++AGERD CASHG++R+LGC+ +L+AG Sbjct: 1 MIRLTLIQARELAESILLHNGFNLAHAQAVAATVIAGERDGCASHGLYRILGCVNSLRAG 60 Query: 61 KVSADAEPELHDIAPGLLRVDAHGGFSQCAFRLGLPHLLEKARSQGIAAMAVNRCVHFSA 120 KVSADAEP++ D AP ++RVDA GGFSQ AF+ GL L EK R+ GIAA+A+NRCVHFSA Sbjct: 61 KVSADAEPQVIDQAPSIVRVDAGGGFSQLAFQAGLGLLAEKTRANGIAALAINRCVHFSA 120 Query: 121 LWVEVEALTEAGLVALATTPSHAWVAPAGGRKPIFGTNPIAFGWPRPDGPPFVFDFATSA 180 LWVE+E LT GLVALA PSHAWVAPAGGR P+FGTNPIAFGWPR PFVFDFATSA Sbjct: 121 LWVEIEQLTAVGLVALACNPSHAWVAPAGGRVPVFGTNPIAFGWPRAGQDPFVFDFATSA 180 Query: 181 VARGEIQLHERAGKPIPLGWGVDEQGEPTTDASAAL-RGAMLTFGGHKGSALAAMVELLA 239 +ARG+I+LH RAGK IP GWGVD +G P+TDA+ L GAMLTFGGHKGSALAAMVEL+A Sbjct: 181 IARGDIELHRRAGKAIPEGWGVDAEGRPSTDANVVLDSGAMLTFGGHKGSALAAMVELIA 240 Query: 240 GPLIGDLTSAESLAYDEGSRSSPYGGELLIAIDPRRMLGASAEEHLARAETLFEGIVEQG 299 GPLIGDLTSAESLAYD GS+SSPY GEL+IA+DPRR LGA+ EEHLARAE LF+GI QG Sbjct: 241 GPLIGDLTSAESLAYDAGSKSSPYHGELIIALDPRRFLGAATEEHLARAEVLFQGIEGQG 300 Query: 300 ARLPSQRRFEARERSARDGVTIPEALHRELLALL 333 ARLPSQRR+ AR RS +GV IPEAL+ +L ALL Sbjct: 301 ARLPSQRRYAARARSVVEGVQIPEALYNDLKALL 334 Lambda K H 0.320 0.136 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: 395 Number of extensions: 13 Number of successful extensions: 2 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: 334 Length of database: 335 Length adjustment: 28 Effective length of query: 306 Effective length of database: 307 Effective search space: 93942 Effective search space used: 93942 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 (21.8 bits) S2: 49 (23.5 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