Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate AO356_10195 AO356_10195 taurine transporter ATP-binding subunit
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10195 Length = 264 Score = 196 bits (498), Expect = 4e-55 Identities = 101/257 (39%), Positives = 153/257 (59%), Gaps = 5/257 (1%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 +++ + R+ G L + + + LGPSG GK++LL ++AG ++G Sbjct: 1 MALLQLERISAQYPGAAEPVLADISLTLGPKQLLVALGPSGSGKTSLLNLIAGFVEPSAG 60 Query: 64 RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKV 123 ++ LDG PV+GP AERG+VFQ L PW + N+ FGL G+P+ +++ RA +A V Sbjct: 61 QITLDGTPVKGPSAERGVVFQDDALLPWQDVLANVGFGLELAGVPKEKREARAREMLALV 120 Query: 124 GLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWE 183 L GFEQ QLSGG +QR +ARALA DP++LLMDEPFGALD TR MQELLL +W+ Sbjct: 121 DLAGFEQRRVWQLSGGQKQRVGLARALAADPRVLLMDEPFGALDAFTREQMQELLLQVWQ 180 Query: 184 AERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPH-----PRHYTIKTSPEF 238 K V +THDI+EA+F+A + + + PG+I L++D +IK+ P F Sbjct: 181 RTAKPVFLITHDIEEAVFLATDLILLAPNPGQIVERLSLDFGQRYGAGESARSIKSDPRF 240 Query: 239 MDLKARLTEEIRAESMA 255 ++ + + ++ ++ A Sbjct: 241 IETREHVLAKVFSQRSA 257 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: 207 Number of extensions: 9 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: 259 Length of database: 264 Length adjustment: 25 Effective length of query: 234 Effective length of database: 239 Effective search space: 55926 Effective search space used: 55926 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