Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate BWI76_RS05890 BWI76_RS05890 haloacid dehalogenase
Query= reanno::Marino:GFF473 (218 letters) >FitnessBrowser__Koxy:BWI76_RS05890 Length = 220 Score = 142 bits (358), Expect = 5e-39 Identities = 77/216 (35%), Positives = 119/216 (55%) Query: 2 TLAIFDLDNTLLAGDSDHAWGEFLVEEGIVDAEEYRLANDRFYQEYLNGELDILHYLGFA 61 TL IFDLDNTL+ GDS W F+V EG V+ +Y R ++Y GE++I Y+ Sbjct: 4 TLTIFDLDNTLIKGDSSTLWSRFMVREGWVNDPDYLAREARLMEDYDRGEMNIADYVALI 63 Query: 62 LQPLASHNMEELLAWREAFMEKKVRPMMQATANTLLDSHREQGHTLMIITATNRFVTEPI 121 PL ++ A + ++V P + A L+ + + +G +++I+A+ + + + Sbjct: 64 QAPLIGVAKRDVDALLARCVREEVMPRVYPQAWDLIRTLQAKGEQMLVISASVSLLVQAV 123 Query: 122 AEALGIEHLIATEPELVNGRYTGEVAGTPSFQDGKVTRLDDWLSAHNRTLEGAWFYSDSH 181 A LGIE + + + +G Y+G +AGTPS+Q GKV RL+ WL+AH FY+DS Sbjct: 124 AAELGIEQALGIDVVMADGGYSGVIAGTPSYQQGKVVRLELWLAAHPDYSGEITFYTDSI 183 Query: 182 NDLPLLKKVDNPVAVDPDPTLAQYARDNGWKVMSLR 217 NDLPL + D V+P P LA + W V++ R Sbjct: 184 NDLPLCLRADRVRLVNPCPQLAAANAQHRWPVLAWR 219 Lambda K H 0.318 0.135 0.408 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: 149 Number of extensions: 4 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: 218 Length of database: 220 Length adjustment: 22 Effective length of query: 196 Effective length of database: 198 Effective search space: 38808 Effective search space used: 38808 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: 45 (21.9 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