Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate PfGW456L13_403 3'(2'),5'-bisphosphate nucleotidase (EC 3.1.3.7)
Query= BRENDA::Q8NS80 (260 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_403 Length = 275 Score = 96.3 bits (238), Expect = 6e-25 Identities = 75/236 (31%), Positives = 110/236 (46%), Gaps = 11/236 (4%) Query: 8 LALALELAELADSITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIATARPADSIL 67 +A +ELA A L F + V++K D +PV+ ADLA + + P+ +L Sbjct: 8 MAPVIELALQAGEAILP-FWRTGTAVTAKADDSPVTAADLAAHHLILAGLTALDPSIPVL 66 Query: 68 GEEFGG---DVEFSG-RQWIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPALA 123 EE DV R W++DP+DGTK ++ G + IAL++NG+ V GV+S P Sbjct: 67 SEEDANIPQDVRAGWQRWWLVDPLDGTKEFISGSEEFTVNIALIENGRVVFGVVSMPTNG 126 Query: 124 RRWWASEGAGAWRTFNGSSPRKLSVSQVSKLDDASLSFSS---LSGWAERDLRDQFVSLT 180 R + G GAWR G +P + V ++ +S S ER L SL Sbjct: 127 RFYVGGAGLGAWRGDKGGTPVAIKVRDALAPGESFTVVASRRHSSPEQERLLAGLSASLG 186 Query: 181 DTTWRLRGYGDFFSYCLVAEGAVDIAAE-PEVSLWDLAPLSILVTEAGGKFTSLAG 235 + +L G +CL+AEGA D S WD A ++ AGG+ L+G Sbjct: 187 EL--QLANIGSSLKFCLLAEGAADCYPRLAPTSQWDTAAAQGVLEGAGGEVLELSG 240 Lambda K H 0.315 0.133 0.396 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: 195 Number of extensions: 13 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: 260 Length of database: 275 Length adjustment: 25 Effective length of query: 235 Effective length of database: 250 Effective search space: 58750 Effective search space used: 58750 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: 47 (22.7 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