Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF2246 PGA1_c22780 glycine betaine transport ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Phaeo:GFF2246 Length = 352 Score = 278 bits (710), Expect = 2e-79 Identities = 138/261 (52%), Positives = 189/261 (72%) Query: 4 IEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSG 63 + + +YKIFG K L V+ G+ K ++L++ +GLN++++ + AG+I V+MGLSG Sbjct: 6 VRLSGLYKIFGARDKDVLHHVQGGMGKEELLAQHKHVLGLNNINVDMQAGEITVVMGLSG 65 Query: 64 SGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVL 123 SGKSTL+RH+NRLIEPT+GE++ G++++ L LR R ++SMVFQ FAL+PH+TVL Sbjct: 66 SGKSTLIRHLNRLIEPTAGEIIVQGEDVMQLSEDGLRHARQEKMSMVFQKFALLPHKTVL 125 Query: 124 QNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTD 183 +N VRG + KW++ VGLSG++ +P QLSGGM+QRVG+ARAL A+T Sbjct: 126 KNAGMPLSVRGEDEATCDREAAKWLERVGLSGFENHYPAQLSGGMQQRVGIARALTANTP 185 Query: 184 VILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVV 243 ++LMDEAFSALDPLIR DMQD LL+LQ+ L KTI+FITHDLDEAL++ + IL+DG VV Sbjct: 186 IMLMDEAFSALDPLIRTDMQDLLLELQKELHKTIIFITHDLDEALKLADHLVILKDGFVV 245 Query: 244 QVGTPNDILDNPANDYVARFV 264 Q G P IL NP + Y+ FV Sbjct: 246 QQGEPQHILLNPNDPYIEDFV 266 Lambda K H 0.323 0.139 0.397 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: 324 Number of extensions: 8 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: 275 Length of database: 352 Length adjustment: 27 Effective length of query: 248 Effective length of database: 325 Effective search space: 80600 Effective search space used: 80600 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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