Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate WP_041938828.1 FRAAL_RS04200 HAD-IB family hydrolase
Query= reanno::psRCH2:GFF3795 (217 letters) >NCBI__GCF_000058485.1:WP_041938828.1 Length = 293 Score = 103 bits (258), Expect = 3e-27 Identities = 70/218 (32%), Positives = 107/218 (49%), Gaps = 5/218 (2%) Query: 4 ALFDLDNTLLAGDSDHAWGEYLCQRGIVDASQYKARNDAFYQDYLAGNLDVHAYQNFCQE 63 A FD+DNT++AG S + L R D+ L G+ + ++ + Sbjct: 41 AFFDVDNTMMAGASIFYFARGLAARDFFDSRDLLRFGWQHVTYRLRGHENPDGMRDARET 100 Query: 64 LL----GRSEMPQLQQWHDEFMRDFIEPIVLSKGEALLRQHLEAGDKVVIITATNRFITG 119 L GRS + ++ ++ +E + + + S AL +QHL+AG +V ++TAT + Sbjct: 101 ALAFVAGRS-VAEIVRYGEEIYDERMAEQIYSGAHALAQQHLDAGQRVWLVTATPVELAS 159 Query: 120 PIAARLGVDTLLATECEMRDGRYTGRLTDIPCFQEGKVQRIERWLAETEQSLEDSYFYSD 179 IA RL + L T E+ DG YTG L + K + ++ L + YSD Sbjct: 160 VIARRLSLTGALGTVSEVTDGTYTGHLVGGLLHGQAKAEAVQALAEREGLDLSRCWAYSD 219 Query: 180 SRNDLPLLQRVTHPVAVDPDPLLRQIATERGWQIISLR 217 S NDLP+L V HPVA++PDP L+ +A ER W I R Sbjct: 220 SINDLPMLSLVGHPVAINPDPDLKTVAREREWPIKDFR 257 Lambda K H 0.322 0.138 0.422 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: 142 Number of extensions: 4 Number of successful extensions: 2 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: 217 Length of database: 293 Length adjustment: 24 Effective length of query: 193 Effective length of database: 269 Effective search space: 51917 Effective search space used: 51917 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: 46 (22.3 bits)
This GapMind analysis is from Apr 10 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