Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 14504 b0366 taurine transporter subunit (NCBI)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Keio:14504 Length = 255 Score = 196 bits (499), Expect = 3e-55 Identities = 99/225 (44%), Positives = 145/225 (64%), Gaps = 5/225 (2%) Query: 23 ALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERGMV 82 AL+ ++ + + + +LGPSGCGK+TLL ++AG G + L G +EGPGAERG+V Sbjct: 16 ALEDINLTLESGELLVVLGPSGCGKTTLLNLIAGFVPYQHGSIQLAGKRIEGPGAERGVV 75 Query: 83 FQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSGGMQQ 142 FQ+ L PW ++ N+ FGL+ G+ + Q+ E A + KVGL G E+ + QLSGG +Q Sbjct: 76 FQNEGLLPWRNVQDNVAFGLQLAGIEKMQRLEIAHQMLKKVGLEGAEKRYIWQLSGGQRQ 135 Query: 143 RTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDEAIFM 202 R IARALA +P++LL+DEPFGALD TR MQ LLL +W+ K VL +THDI+EA+FM Sbjct: 136 RVGIARALAANPQLLLLDEPFGALDAFTRDQMQTLLLKLWQETGKQVLLITHDIEEAVFM 195 Query: 203 ANRVAVFSARPGRIKTELAVDLPH-----PRHYTIKTSPEFMDLK 242 A + + S+ PGR+ L ++ +IK+ P+F+ ++ Sbjct: 196 ATELVLLSSGPGRVLERLPLNFARRFVAGESSRSIKSDPQFIAMR 240 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: 178 Number of extensions: 4 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: 255 Length adjustment: 24 Effective length of query: 235 Effective length of database: 231 Effective search space: 54285 Effective search space used: 54285 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