Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_245300279.1 B1812_RS18275 sulfate/molybdate ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_002117405.1:WP_245300279.1 Length = 353 Score = 164 bits (415), Expect = 3e-45 Identities = 95/240 (39%), Positives = 134/240 (55%), Gaps = 10/240 (4%) Query: 38 GCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAK 97 G L DVSL I G++ ++G SGSGK+TL+R I L P G V FD N L + Sbjct: 9 GSYPALRDVSLDIAGGELVALLGPSGSGKTTLLRVIAGLNSPHRGAVFFDALNATSLSVQ 68 Query: 98 ALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRG-VSKDDAREIGMK---WIDTVGL 153 RRV VFQ++AL H +V NV +G + R S+ REI + ++ V L Sbjct: 69 E------RRVGFVFQNYALFKHMSVADNVAFGLKARPRASRPPKREIAARVAELLELVQL 122 Query: 154 SGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNL 213 G ++P QLSGG +QRV LARALA + V+L+DE F ALD +R D++ L ++ + Sbjct: 123 EGLGQRYPAQLSGGQRQRVALARALAIEPRVLLLDEPFGALDARVRKDLRRWLREIHKRT 182 Query: 214 AKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQRRHERPQT 273 T VF+THD DEA+ + + +L G++ Q G+P + D PA+ +V FV P T Sbjct: 183 GLTTVFVTHDQDEAMELADRVVVLNQGRIEQAGSPAALYDRPASAFVLSFVGEAVALPVT 242 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: 227 Number of extensions: 12 Number of successful extensions: 3 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: 353 Length adjustment: 27 Effective length of query: 248 Effective length of database: 326 Effective search space: 80848 Effective search space used: 80848 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 Apr 09 2024. 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