Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Dsui_2121 Dsui_2121 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__PS:Dsui_2121 Length = 269 Score = 214 bits (544), Expect = 2e-60 Identities = 110/245 (44%), Positives = 163/245 (66%), Gaps = 5/245 (2%) Query: 16 AKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGP 75 A G+ L+ V EV + F+T+LGPSG GKSTLLR++AGL+ T GR+ GA + GP Sbjct: 20 AYGEGDTILRRVALEVPEGQFLTLLGPSGSGKSTLLRLIAGLEAPTDGRLAWQGATITGP 79 Query: 76 GAERGMVFQSYTLFPWLTIEQNIRFGLRER--GMPEAQQKERAAYFIAKVGLRGFEQHFP 133 G +R +VFQ+Y+LFPWL +E N+ + + + A+++E+A ++ +VGL +P Sbjct: 80 GIDRAVVFQNYSLFPWLKVEDNVALAVAKAHPKLSRAERREKARDYLGRVGLADAAGKYP 139 Query: 134 KQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWE--AERKTVLF 191 QLSGGMQQR AIARALA + +LLMDEPFGALD R +Q+LLL +W+ + R+T++F Sbjct: 140 FQLSGGMQQRAAIARALALEAPVLLMDEPFGALDPINRGKLQDLLLEVWQSTSPRRTIVF 199 Query: 192 VTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYT-IKTSPEFMDLKARLTEEIR 250 VTHD+DEA+++ +RVAV A PGR+ ++ V PR+ + SP F L+ + E + Sbjct: 200 VTHDVDEALYLGDRVAVLGASPGRVLAQIEVPFERPRNRARLFASPAFHALREDIAERLD 259 Query: 251 AESMA 255 A+ ++ Sbjct: 260 ADVLS 264 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: 201 Number of extensions: 8 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: 269 Length adjustment: 25 Effective length of query: 234 Effective length of database: 244 Effective search space: 57096 Effective search space used: 57096 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