Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__psRCH2:GFF3101 Length = 255 Score = 328 bits (842), Expect = 5e-95 Identities = 157/241 (65%), Positives = 198/241 (82%) Query: 20 LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79 +I+++G++K +G FHVL+DI+L VR+GERIVLCGPSGSGKST IRC+NRLE QQG I + Sbjct: 15 VIQMQGVHKWFGQFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVI 74 Query: 80 DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMY 139 +G++L + ++ +RS++GMVFQHFNLFPH++VL NC LAP VR L R+ AEE A Y Sbjct: 75 NGVELTSDLKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMWVRKLPRRQAEEIAMHY 134 Query: 140 LSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLV 199 L +V I QA+K+P QLSGGQQQRVAIARALCMKP+IMLFDEPTSALDPEMV EVLD +V Sbjct: 135 LERVRIPEQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMV 194 Query: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFLAQIL 259 LA +GMTMLCVTHEMGFAR VA+RV+F++ G+I+E + P++FF P +R K FL+QIL Sbjct: 195 SLAESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAEPEMFFTNPVNDRTKLFLSQIL 254 Query: 260 H 260 H Sbjct: 255 H 255 Lambda K H 0.322 0.137 0.395 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: 230 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: 260 Length of database: 255 Length adjustment: 24 Effective length of query: 236 Effective length of database: 231 Effective search space: 54516 Effective search space used: 54516 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