Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate 3607252 Dshi_0667 heavy metal translocating P-type ATPase (RefSeq)
Query= SwissProt::Q21YU0 (237 letters) >FitnessBrowser__Dino:3607252 Length = 729 Score = 45.8 bits (107), Expect = 2e-09 Identities = 67/270 (24%), Positives = 99/270 (36%), Gaps = 67/270 (24%) Query: 9 GLIIQGFAPPLRLSDFKLIAFDMDSTLINIECVDEIADAVGRK----------------- 51 GL+I+ RL++ + FD TL + + E AD + + Sbjct: 429 GLLIKSGTALERLAEVDEVVFDKTGTLTLGQPILENADRIAARDLAVARALAQGSAHPLA 488 Query: 52 REVAAITEAAMRGEITDYKE-----------------SLRQRVALLQG---VTEVQMNQI 91 R +AA E+T+ +E V QG T +++ Q Sbjct: 489 RAIAATDAGGASAEVTELREVPGYGVEGRWQDQPVRLGRADWVGAAQGDVTATWLRIGQA 548 Query: 92 YQERMQFN----PGAAELVAACKAAGLKVLLVSGGFTHFTDRVAQRLGIDYTRSNVLQIE 147 +F PGAAE VAA +A GLKV L+SG RVA+ LGI R+ Sbjct: 549 APVAFEFKDALRPGAAEAVAALQARGLKVSLLSGDAPGAVARVARELGITDYRAE----- 603 Query: 148 NGVLTGRMVDQPWGDICDGAEKRKMLLETCALLGIAPKQAIAVGDGANDLPMMREAGLSV 207 C EK + G A + + VGDG ND + A SV Sbjct: 604 ----------------CRPEEKAAHV----TARGEAGYKVLMVGDGLNDTAALAAAHASV 643 Query: 208 A-FHAKSAVRELANVSIESGGLDRLLELFQ 236 + A A R +++ + L L ++ Q Sbjct: 644 SPASALDAARVASDIVLLGQDLSPLADMLQ 673 Lambda K H 0.321 0.137 0.390 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: 383 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 237 Length of database: 729 Length adjustment: 31 Effective length of query: 206 Effective length of database: 698 Effective search space: 143788 Effective search space used: 143788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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