Align histidinol-phosphatase (EC 3.1.3.15); inositol-phosphate phosphatase (EC 3.1.3.25) (characterized)
to candidate Synpcc7942_2582 Synpcc7942_2582 myo-inositol-1(or 4)-monophosphatase
Query= BRENDA::G7J7Q5 (326 letters) >FitnessBrowser__SynE:Synpcc7942_2582 Length = 273 Score = 100 bits (250), Expect = 3e-26 Identities = 79/265 (29%), Positives = 129/265 (48%), Gaps = 22/265 (8%) Query: 68 DVANKAANAAGDVIRKYFRKNNFDIIHKNDLSPVTIADQSAEEAMVSVILDNFPSHAVYG 127 DVA +AA AAG + +++ + +T AD++AE A++SV+ + P HAV Sbjct: 14 DVATEAALAAGAELDRFWGRLTQIEEKGRPGDLLTEADRAAEAAVLSVLERHCPDHAVLA 73 Query: 128 EEKGWRCKQDSADYVWVLDPIDGTKSFITGKPLFGTLIALLQNGTPILGIIDQPVLKERW 187 EE GW + ++ W +DP+DGT ++ G P GT IALL PI+G+ P LKE + Sbjct: 74 EESGWSGDRQQ-EFSWAVDPLDGTTNYAHGYPFCGTSIALLYQNQPIVGVFYAPYLKELF 132 Query: 188 IGITGKRTTLNGQEVSTRTCADLSQAYLYTTSPHLFSGDAEEA-------FIRVRDKVK- 239 G TLN Q + L+++ L T F+ D E F R+ + Sbjct: 133 RAAQGLGATLNRQPIRVSKTEKLAKSLLVTG----FAYDRCEVEDNNYAEFCRLTHVTQG 188 Query: 240 IPLYGCDCYAYALLSSGFVDLVVESGLKPYDFLALIPVIEGSGGVITDWKGHQLRWEASP 299 + G + ++ G +D E GL P+D A + +++ +GG++T ++ SP Sbjct: 189 VRRGGSAALDLSYVACGRLDGYWERGLSPWDLAAGVVLVQEAGGLVT-------AYDRSP 241 Query: 300 LSIATSFNVVAAGDKQIHQQALDSL 324 I S + A + QIH + ++L Sbjct: 242 FDI--SSGRILATNGQIHAELSETL 264 Lambda K H 0.319 0.135 0.407 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: 178 Number of extensions: 9 Number of successful extensions: 3 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: 326 Length of database: 273 Length adjustment: 27 Effective length of query: 299 Effective length of database: 246 Effective search space: 73554 Effective search space used: 73554 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 (21.7 bits) S2: 48 (23.1 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