Align Histidine biosynthesis bifunctional protein hisIE, chloroplastic; Protein HISTIDINE BIOSYNTHESIS 2; EC 3.5.4.19; EC 3.6.1.31 (characterized)
to candidate HSERO_RS20310 HSERO_RS20310 phosphoribosyl-AMP cyclohydrolase
Query= SwissProt::O82768 (281 letters) >FitnessBrowser__HerbieS:HSERO_RS20310 Length = 166 Score = 89.0 bits (219), Expect = 6e-23 Identities = 41/100 (41%), Positives = 64/100 (64%), Gaps = 1/100 (1%) Query: 56 LDRIKWDDKGLAVAIAQNVDTGAVLMQGFVNREALSTTISSRKATFFSRSRSTLWTKGET 115 L+++KWD+ GL IAQ V + VLM ++NREAL+ T+ +A ++SRSR LW KGE Sbjct: 8 LNKVKWDEVGLVPVIAQEVGSNDVLMFAWMNREALARTVEIGQAVYWSRSRKKLWHKGEE 67 Query: 116 SNNFINILDVYVDCDRDSIIY-LGTPDGPTCHTGEETCYY 154 S +F + ++ +DCD D ++ + G CHTG +C++ Sbjct: 68 SGHFQKVHEIRLDCDEDVVLLKVEQVAGIACHTGRHSCFF 107 Lambda K H 0.315 0.130 0.368 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: 119 Number of extensions: 5 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: 281 Length of database: 166 Length adjustment: 22 Effective length of query: 259 Effective length of database: 144 Effective search space: 37296 Effective search space used: 37296 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: 45 (21.9 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