Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate WP_042120002.1 RHE_RS28105 histidine phosphatase family protein
Query= SwissProt::F4KI56 (238 letters) >NCBI__GCF_000092045.1:WP_042120002.1 Length = 191 Score = 75.1 bits (183), Expect = 9e-19 Identities = 63/180 (35%), Positives = 92/180 (51%), Gaps = 28/180 (15%) Query: 24 VTEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKE-ER---PVAVYSSD 79 +T I L+RHGET WNAAGR QGQ +S L E G +QA RL +E ER + V+ S Sbjct: 1 MTTIFLLRHGETVWNAAGRFQGQKDSPLTERGQQQADEAGRRLARELERHPGQIDVHVSP 60 Query: 80 LKRAKDTALMIAKTCFCP-EVIEVPDLKERHVGSLQGLYWKE------GAEKEPEAYSAF 132 L R K+TA IA+ + P + P L E +GS G+ E G + +A++ F Sbjct: 61 LGRTKETAARIAR--YVPLRSRDEPRLMEVTIGSWDGMSHYEIHMEYPGMLEGADAFNWF 118 Query: 133 FSSQNDLEIPGGGESFDQLADRSMDALEQIAKKHKGERVIVVTH---GGVLRAIYLRITQ 189 F S + GE+FD R + L Q+ I ++H G ++R +YL +++ Sbjct: 119 FRSPD-------GETFDAACARIKEWLSQLR-----STTIAISHGLTGRLIRGMYLGLSR 166 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: 126 Number of extensions: 4 Number of successful extensions: 1 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: 191 Length adjustment: 22 Effective length of query: 216 Effective length of database: 169 Effective search space: 36504 Effective search space used: 36504 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 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