Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >MicrobesOnline__882:209027 Length = 368 Score = 161 bits (407), Expect = 2e-44 Identities = 87/225 (38%), Positives = 137/225 (60%), Gaps = 6/225 (2%) Query: 40 TVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKAL 99 T L+++ L+I G+ ++G SG GK+T++R I+ +P +G + G + D +A Sbjct: 20 TCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLKGQRMDDAPPEA- 78 Query: 100 RAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAK 159 R+V+ VFQ++AL PH +V +NV +G R++ KD+ + V L + + Sbjct: 79 -----RQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHLEAHADR 133 Query: 160 FPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVF 219 P QLSGG +QRV +ARA+ + V+L+DE FSALD +R MQ ++ LQR L T VF Sbjct: 134 RPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQLGITFVF 193 Query: 220 ITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 +THD +EA + + ++ DG++ Q+G+P +I + PAN YVARFV Sbjct: 194 VTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFV 238 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: 268 Number of extensions: 8 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: 368 Length adjustment: 27 Effective length of query: 248 Effective length of database: 341 Effective search space: 84568 Effective search space used: 84568 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