Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate AO353_08475 AO353_08475 phosphoserine phosphatase
Query= reanno::psRCH2:GFF3795 (217 letters) >FitnessBrowser__pseudo3_N2E3:AO353_08475 Length = 218 Score = 327 bits (839), Expect = 8e-95 Identities = 156/217 (71%), Positives = 179/217 (82%) Query: 1 MRLALFDLDNTLLAGDSDHAWGEYLCQRGIVDASQYKARNDAFYQDYLAGNLDVHAYQNF 60 MRLALFDLDNTLL GDSDHAWG+YLC+RG++DA YK RND FYQDYLAG LD Y NF Sbjct: 1 MRLALFDLDNTLLGGDSDHAWGDYLCERGLLDAVAYKTRNDEFYQDYLAGKLDQAEYLNF 60 Query: 61 CQELLGRSEMPQLQQWHDEFMRDFIEPIVLSKGEALLRQHLEAGDKVVIITATNRFITGP 120 C E+LGR+EM L +WH ++MRD IEP+VLSKG LL +H AGDK+VIITATNRF+TGP Sbjct: 61 CLEILGRTEMTLLDEWHRDYMRDCIEPLVLSKGLELLARHRAAGDKLVIITATNRFVTGP 120 Query: 121 IAARLGVDTLLATECEMRDGRYTGRLTDIPCFQEGKVQRIERWLAETEQSLEDSYFYSDS 180 IA RLGV+TL+ATECEM DGRYTGR TD+PC++EGKV R+ RWL ET SLEDSYFYSDS Sbjct: 121 IAQRLGVETLIATECEMVDGRYTGRSTDVPCYREGKVTRLNRWLEETGMSLEDSYFYSDS 180 Query: 181 RNDLPLLQRVTHPVAVDPDPLLRQIATERGWQIISLR 217 NDL LL+ V +PVAVDPDP LR A +RGW I+SLR Sbjct: 181 MNDLALLEEVANPVAVDPDPNLRAEAQKRGWPIMSLR 217 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: 233 Number of extensions: 11 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: 217 Length of database: 218 Length adjustment: 22 Effective length of query: 195 Effective length of database: 196 Effective search space: 38220 Effective search space used: 38220 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: 45 (21.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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