Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Dsui_1833 Dsui_1833 nitrate transport ATP-binding subunits C and D
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__PS:Dsui_1833 Length = 266 Score = 204 bits (518), Expect = 2e-57 Identities = 108/249 (43%), Positives = 160/249 (64%), Gaps = 6/249 (2%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 V I+AV + F+T KG+ AL+ VD +R +F+ ++G SGCGKSTLL ++AGL T G Sbjct: 5 VQIEAVGQTFDTKKGKFV-ALRDVDLSIRQGEFIALIGHSGCGKSTLLNLIAGLTRPTDG 63 Query: 64 RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRE---RGMPEAQQKERAAYFI 120 ++ DG + GPG ERG+VFQ+++L PWLT N+ + +A+ K+R + Sbjct: 64 ALICDGREIAGPGPERGVVFQNHSLLPWLTCFDNVYLAVERVFAAKEGKAKLKQRTHDAL 123 Query: 121 AKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLG 180 A VGL E FP ++SGGM+QR IARAL+ PK+LLMDEPFGALD TR +Q+ L+ Sbjct: 124 ALVGLTHAETKFPHEISGGMKQRVGIARALSMQPKVLLMDEPFGALDALTRAKLQDELMK 183 Query: 181 IWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTE-LAVDLPHPRH-YTIKTSPEF 238 I +A + TV+ VTHD+DEA+ +++R+ + + P E L+VDLP PR+ + P++ Sbjct: 184 ICDATQATVVMVTHDVDEAVLLSDRIVMMTNGPAATIGEILSVDLPRPRNRLALANDPKY 243 Query: 239 MDLKARLTE 247 + +A + E Sbjct: 244 IAARAAVLE 252 Lambda K H 0.322 0.136 0.394 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: 174 Number of extensions: 5 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: 259 Length of database: 266 Length adjustment: 25 Effective length of query: 234 Effective length of database: 241 Effective search space: 56394 Effective search space used: 56394 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: 47 (22.7 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