Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate BWI76_RS10280 BWI76_RS10280 polar amino acid ABC transporter permease
Query= TCDB::P48245 (273 letters) >FitnessBrowser__Koxy:BWI76_RS10280 Length = 241 Score = 101 bits (252), Expect = 1e-26 Identities = 73/232 (31%), Positives = 117/232 (50%), Gaps = 13/232 (5%) Query: 22 WTTYILP----GLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIP 77 W ++ P G W TL + S++ +V+G L L + + R + + FR P Sbjct: 7 WQYFLSPEFVQGAWMTLLITLCSLLCGVVLGLVLALLQEAPFRAGKGLAFFYLWLFRGTP 66 Query: 78 VLILMIFAYQMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAI 137 VL +IF Y + + + S AF V L++ G+ +AEILRSG+ ++ GQ+ A + Sbjct: 67 VLFQIIFVYNVLPGFGLRFS---AFTCAVLALSLNEGAYMAEILRSGLQAVKSGQRTAGM 123 Query: 138 ALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNR 197 ALGM+S Q I+LPQA +LP + +QM+ LK SAL I E++ Q+AS + Sbjct: 124 ALGMTSGQIMRKIVLPQAARIVLPPMGNQMISMLKSSALVSVIAVQELLLVANQTASASF 183 Query: 198 NYLAALFVVALIMIVLNFSLTALASRIE-----RQLRA-GRARKNIVAKVPE 243 Y AL + ++L S +E +Q R+ + R N + K+P+ Sbjct: 184 RYFEALCAAGIYYLLLTSLFMVFQSWLESVLDPKQRRSKSQKRLNRLFKLPK 235 Lambda K H 0.323 0.136 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: 166 Number of extensions: 12 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: 273 Length of database: 241 Length adjustment: 24 Effective length of query: 249 Effective length of database: 217 Effective search space: 54033 Effective search space used: 54033 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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