Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate 351430 BT1902 pyrroline-5-carboxylate reductase (NCBI ptt file)
Query= reanno::Btheta:353283 (257 letters) >FitnessBrowser__Btheta:351430 Length = 266 Score = 253 bits (646), Expect = 3e-72 Identities = 134/256 (52%), Positives = 172/256 (67%), Gaps = 1/256 (0%) Query: 1 MKIAIIGAGNMGGSIARGLAKGSLIADSDIIVSNPSAGKLEKLKEEFPGISTTLSNTEAA 60 MKI IIGAGN+G ++A LAKG L + DII+S P KLE L ++FP I N A Sbjct: 1 MKITIIGAGNIGSAVAACLAKGHLYNEKDIIISTPHTDKLENLHKQFPAIRIMTENQYAI 60 Query: 61 TGADVVILAVKPWFVESVMRELKLKSKQTLVSVAAGISFEELAHFVIAPEMPMFRLIPNT 120 + AD++ILAVKP V+ V+ L+ Q LVS+ GIS LAH + EMP+FR++PN Sbjct: 61 SEADIIILAVKPCIVDEVLSPLRFSRTQILVSLVTGISISHLAH-LSETEMPIFRVVPNI 119 Query: 121 AISELESMTLIAARNTNDEQNLFMLRLFNEMGMAMLIPEDKIAATTALTSCGIAYVLKYI 180 AI+E S+TLI +R E + + F E G + E ++ +ALTS GIA+ LKYI Sbjct: 120 AITEHSSLTLITSRKAGKEHQQLIKQTFEEGGKCLFAEEKQLDIISALTSSGIAFALKYI 179 Query: 181 QAAMQAGIEMGIRPKDAMEMVAQSVKGAAALILNNDTHPSVEIDKVTTPGGITIKGINEL 240 AAMQAGIE+GI +DAM M A S++GA LILN+DTHP +EI+K TPGG TIKG+NEL Sbjct: 180 HAAMQAGIELGISAEDAMRMTAYSMEGATELILNHDTHPLLEIEKAATPGGATIKGLNEL 239 Query: 241 EHNGFTSAVIKAMKAS 256 EH GFTSAVI A+K+S Sbjct: 240 EHRGFTSAVIHAIKSS 255 Lambda K H 0.316 0.131 0.353 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: 194 Number of extensions: 8 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: 257 Length of database: 266 Length adjustment: 25 Effective length of query: 232 Effective length of database: 241 Effective search space: 55912 Effective search space used: 55912 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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