Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate H281DRAFT_04256 H281DRAFT_04256 phosphoglycerate mutase (EC 5.4.2.1)
Query= SwissProt::F4KI56 (238 letters) >FitnessBrowser__Burk376:H281DRAFT_04256 Length = 223 Score = 117 bits (292), Expect = 2e-31 Identities = 80/210 (38%), Positives = 109/210 (51%), Gaps = 10/210 (4%) Query: 25 TEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKE----ERPVAVYSSDL 80 T+I+ +RHGET WN RIQG I+ L VGL QA ++A R+ E R A+YSSDL Sbjct: 3 TQILFIRHGETDWNRIKRIQGHIDIPLAAVGLAQAQSLARRIADEVKHGARLDAIYSSDL 62 Query: 81 KRAKDTALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLE 140 +RA+ TA A P + L+ER G+ QG E A + P+ Y A + +++ Sbjct: 63 QRARQTAQPFADALGLPVHLR-EGLRERSYGAFQGHDSDEIAARFPDEY-AHWQTRDPGF 120 Query: 141 IPGGGESFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAIYLRI----TQASSAGKL 196 P GGES R + A+E + H G R+ V HGGVL + A L Sbjct: 121 TPPGGESQRAFYHRVLHAIEPLVAAHPGGRIACVAHGGVLDCVRRFACGLPLDAPRDYAL 180 Query: 197 LNASVNVVHLRDQKWIIDSWSDVSHLSSVG 226 LN SVNVV + + + SW D+SHL + G Sbjct: 181 LNTSVNVVDFDNGRATVVSWGDISHLDAPG 210 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: 172 Number of extensions: 9 Number of successful extensions: 5 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: 223 Length adjustment: 23 Effective length of query: 215 Effective length of database: 200 Effective search space: 43000 Effective search space used: 43000 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 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