Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_1958 Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1958 Length = 245 Score = 259 bits (662), Expect = 4e-74 Identities = 135/243 (55%), Positives = 172/243 (70%), Gaps = 3/243 (1%) Query: 20 LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79 +I ++ ++K YG VL + + +GE +V+CGPSGSGKSTLI+ IN LE Q+G I V Sbjct: 1 MIELKNVSKWYGPVQVLNECSATINKGEVVVVCGPSGSGKSTLIKTINALEPFQKGEITV 60 Query: 80 DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMY 139 DG+ L + ++RS +GMVFQHF LFPH+SV DN +A V G S +A++R Sbjct: 61 DGVKLHDPSTNLPKLRSRVGMVFQHFELFPHLSVTDNLTIAQIKVLGRSADEAKKRGLKM 120 Query: 140 LSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLV 199 L +VG+ + K+P QLSGGQQQRVAIARAL M P +MLFDEPTSALDPEMV EVLDV+V Sbjct: 121 LERVGLIAHKDKFPGQLSGGQQQRVAIARALSMDPIVMLFDEPTSALDPEMVGEVLDVMV 180 Query: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLE-GGQIIEDSPPQVFFNQP--RTERAKAFLA 256 LA GMTM+CVTHEMGFAR+V+ RV+F++ GG+I+ED FFN P R R K FL Sbjct: 181 GLANEGMTMMCVTHEMGFARKVSNRVIFMDVGGKILEDCSKDEFFNNPDARQPRTKDFLN 240 Query: 257 QIL 259 +IL Sbjct: 241 KIL 243 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: 194 Number of extensions: 4 Number of successful extensions: 2 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: 245 Length adjustment: 24 Effective length of query: 236 Effective length of database: 221 Effective search space: 52156 Effective search space used: 52156 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: 46 (22.3 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