Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate H281DRAFT_00987 H281DRAFT_00987 glycine betaine/proline transport system ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Burk376:H281DRAFT_00987 Length = 429 Score = 277 bits (708), Expect = 3e-79 Identities = 136/260 (52%), Positives = 193/260 (74%) Query: 4 IEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSG 63 + ++N+ KIFG ++A ++ GL + +I ++G V +NDVSL + AG+IFV+MGLSG Sbjct: 38 LTVKNLSKIFGPRPERAAELIRQGLGRNEIFEQTGNMVAVNDVSLSVKAGEIFVVMGLSG 97 Query: 64 SGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVL 123 SGKSTLVR +NRLIEPTSG+V+ +G +I + LR R ++++MVFQSFAL+P+RTVL Sbjct: 98 SGKSTLVRLLNRLIEPTSGQVILEGRDIAPMSTPELRDVRRKKMAMVFQSFALLPNRTVL 157 Query: 124 QNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTD 183 N+ YG V G+ K + +I + VGL Y+ P +LSGGM+QRVGLARALA + Sbjct: 158 DNIAYGLEVAGLKKAERYDIARAALTRVGLGSYEKLLPGELSGGMQQRVGLARALAVNPS 217 Query: 184 VILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVV 243 V+LMDEAFSALDPLIR +MQ +LL+LQ+ +TIVFI+HD++EA++IG I I++DG ++ Sbjct: 218 VLLMDEAFSALDPLIRFEMQSELLRLQKEEQRTIVFISHDIEEAIKIGGRIGIMKDGCLI 277 Query: 244 QVGTPNDILDNPANDYVARF 263 QVGTP +++ +PA+DYV F Sbjct: 278 QVGTPAELIQSPADDYVRDF 297 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: 342 Number of extensions: 6 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: 429 Length adjustment: 29 Effective length of query: 246 Effective length of database: 400 Effective search space: 98400 Effective search space used: 98400 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