Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_011840414.1 RSPH17029_RS02745 inositol monophosphatase family protein
Query= reanno::Phaeo:GFF2154 (250 letters) >NCBI__GCF_000015985.1:WP_011840414.1 Length = 266 Score = 306 bits (785), Expect = 2e-88 Identities = 151/247 (61%), Positives = 186/247 (75%) Query: 1 MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF 60 MA AAR A L +FRS GL +D K + FDPVT+ADR E+ MR++L+ RP D I GEE Sbjct: 19 MAAAARDATLLHFRSRGLSADTKEADRFDPVTVADRLCEERMRAILARRRPRDGIFGEEM 78 Query: 61 GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE 120 G G SG TWVLDPIDGTR ++ GTPTWGVLI++ DA GP G++DQPYIGERF G Sbjct: 79 GVQAGDSGLTWVLDPIDGTRSYLCGTPTWGVLISVADASGPIYGLIDQPYIGERFEGGFG 138 Query: 121 GASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCYA 180 A + GP G L TRA +LSEA L +TFPEVGT E AAF+R+S QVRLTRYG DCYA Sbjct: 139 LARVRGPRGEDRLATRAARALSEAILMSTFPEVGTAVEEAAFRRLSRQVRLTRYGTDCYA 198 Query: 181 YALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELHA 240 YALLAAGQ DLV+EAGL YD+QAP+AVI+AAGG++T+W+G +GG+V+AA+ E+HA Sbjct: 199 YALLAAGQIDLVVEAGLQPYDVQAPMAVIEAAGGLMTDWEGRRNPQGGRVIAASCPEVHA 258 Query: 241 AALALIQ 247 AAL +++ Sbjct: 259 AALEILR 265 Lambda K H 0.317 0.134 0.392 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: 239 Number of extensions: 5 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: 250 Length of database: 266 Length adjustment: 24 Effective length of query: 226 Effective length of database: 242 Effective search space: 54692 Effective search space used: 54692 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 16 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