Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF789 PS417_04010 glycine/betaine ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__WCS417:GFF789 Length = 385 Score = 181 bits (459), Expect = 2e-50 Identities = 93/231 (40%), Positives = 152/231 (65%), Gaps = 7/231 (3%) Query: 37 SGCTV-GLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLG 95 +G TV +NDVSL + G+I V +G SG GKST ++ INRLI+PTSG++L +G++ DL Sbjct: 14 NGKTVTAVNDVSLTVNEGEICVFLGPSGCGKSTTLKMINRLIKPTSGKILINGEDTTDLD 73 Query: 96 AKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSG 155 LR R + V Q L P+ T+ +N+V ++ G K + + + + L Sbjct: 74 EVTLR----RNIGYVIQQIGLFPNMTIEENIVVVPKLLGWDKQKCHDRARELMSMIKLEP 129 Query: 156 --YDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNL 213 Y ++P +LSGG +QR+G+ RALAAD ++LMDE F A+DP+ R +Q++ ++QR L Sbjct: 130 KQYLHRYPRELSGGQQQRIGVIRALAADAPLLLMDEPFGAVDPINREMIQNEFFEMQRAL 189 Query: 214 AKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 KT++ ++HD+DEA+++G +IAI R G+++Q+ P+ +L +PA+++V+ FV Sbjct: 190 NKTVIMVSHDIDEAIKLGDKIAIFRAGKLLQIDHPDTLLAHPADEFVSNFV 240 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: 257 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 275 Length of database: 385 Length adjustment: 28 Effective length of query: 247 Effective length of database: 357 Effective search space: 88179 Effective search space used: 88179 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