Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate WP_092482535.1 BM299_RS05910 alpha-ribazole phosphatase
Query= SwissProt::F4KI56 (238 letters) >NCBI__GCF_900115975.1:WP_092482535.1 Length = 211 Score = 108 bits (270), Expect = 8e-29 Identities = 74/208 (35%), Positives = 124/208 (59%), Gaps = 22/208 (10%) Query: 27 IVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKEERPVAVYSSDLKRAKDT 86 + L+RHGET WN RIQG+ + L++ G +QA A++ RL +E A +SS+L RA++T Sbjct: 5 VFLIRHGETQWNKDFRIQGKSDVPLSDNGTRQAEALSNRLAGQEF-AAFFSSNLSRARET 63 Query: 87 ALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLEIPGGGE 146 A +IA+ P V + DL+E + G +G+ +E + + SA+++S + IP GGE Sbjct: 64 AAIIARPHNQP-VQVLNDLQELNFGHWEGMTIEEIRRQYRQESSAWWASPLETRIP-GGE 121 Query: 147 SFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAI-----------YLRITQASSAGK 195 + +LA+RS+ A++ I +++ ++V+VV HGG +R+I Y R+ Q Sbjct: 122 NLAELAERSVRAIKTIIERYPRQQVVVVAHGGTIRSIVGTVLGFDLNQYWRLRQD----- 176 Query: 196 LLNASVNVVHLRD-QKWIIDSWSDVSHL 222 NAS++++ +K II ++DVSHL Sbjct: 177 --NASLSIIEFYQWEKGIIMLYNDVSHL 202 Lambda K H 0.315 0.132 0.387 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: 141 Number of extensions: 9 Number of successful extensions: 4 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: 238 Length of database: 211 Length adjustment: 22 Effective length of query: 216 Effective length of database: 189 Effective search space: 40824 Effective search space used: 40824 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: 46 (22.3 bits)
This GapMind analysis is from Apr 10 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