Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate AZOBR_RS23480 AZOBR_RS23480 glycine/betaine ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__azobra:AZOBR_RS23480 Length = 398 Score = 281 bits (719), Expect = 2e-80 Identities = 144/262 (54%), Positives = 186/262 (70%) Query: 2 ADIEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGL 61 A I + V +IFG ++AL +++ GL K +I R+G TVG+ D S ++ AG+IFVIMGL Sbjct: 3 AKIAVNGVTRIFGRHPRQALDLLKAGLSKEEIFKRTGQTVGVLDASFEVEAGEIFVIMGL 62 Query: 62 SGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRT 121 SGSGKSTLVR +NRLI+PT+GE+ DG +I L L R R + MVFQSFAL+PH Sbjct: 63 SGSGKSTLVRMLNRLIDPTAGEIRIDGRDITKLSRAELTELRRRDLGMVFQSFALLPHLR 122 Query: 122 VLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAAD 181 V +N +G + G S R+ + +D VGL Y FP +LSGGM+QRVGLARALA + Sbjct: 123 VWENAAFGLEIAGESLKARRDKAQQALDAVGLGAYAESFPRELSGGMQQRVGLARALANE 182 Query: 182 TDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQ 241 V+LMDEAFSALDPLIR +MQD+LL+LQ +TIVFI+HDLDEA+RIG +AI+ GQ Sbjct: 183 PSVLLMDEAFSALDPLIRTEMQDELLRLQAERQRTIVFISHDLDEAIRIGDRLAIMEGGQ 242 Query: 242 VVQVGTPNDILDNPANDYVARF 263 ++QVG P++IL PANDYV F Sbjct: 243 IIQVGRPDEILKQPANDYVRSF 264 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: 339 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: 275 Length of database: 398 Length adjustment: 28 Effective length of query: 247 Effective length of database: 370 Effective search space: 91390 Effective search space used: 91390 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: 49 (23.5 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