Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF2520 PGA1_c25590 putative glycine betaine/L-proline transport system, ATP binding subunit
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Phaeo:GFF2520 Length = 350 Score = 302 bits (774), Expect = 6e-87 Identities = 153/262 (58%), Positives = 194/262 (74%), Gaps = 1/262 (0%) Query: 4 IEIRNVYKIFGHDAKKALTMVED-GLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLS 62 I+IRN+YKIFG + L MV + G+ K+ +L +GL D+S+ I AG+I VIMGLS Sbjct: 6 IQIRNLYKIFGANPGTVLPMVRNQGMGKSQLLEEHKHVLGLQDISIDIQAGEISVIMGLS 65 Query: 63 GSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTV 122 GSGKSTL+RH+NRLIEPT+GE+L DG +++DL LR R R +SMVFQ FAL+PH+TV Sbjct: 66 GSGKSTLIRHLNRLIEPTAGEILLDGQDVMDLDPVQLREMRQRSMSMVFQKFALLPHKTV 125 Query: 123 LQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADT 182 L+N RVRG + KW+D VGLSG++ ++P QLSGGM+QRVG+ARAL ADT Sbjct: 126 LENAETALRVRGDDRATCEAAARKWLDRVGLSGFENRYPSQLSGGMQQRVGIARALTADT 185 Query: 183 DVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQV 242 D++L+DEAFSALDPLIR DMQD LL+LQ L KTIVFITHDLDEAL++ + IL+DG V Sbjct: 186 DIMLLDEAFSALDPLIRTDMQDLLLELQTELHKTIVFITHDLDEALKLADHLVILKDGAV 245 Query: 243 VQVGTPNDILDNPANDYVARFV 264 VQ G P I+ NPA+ Y+ FV Sbjct: 246 VQQGPPQGIVMNPADPYIEAFV 267 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: 331 Number of extensions: 13 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: 275 Length of database: 350 Length adjustment: 27 Effective length of query: 248 Effective length of database: 323 Effective search space: 80104 Effective search space used: 80104 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