Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate AO353_10020 AO353_10020 amino acid ABC transporter permease
Query= TCDB::P48245 (273 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10020 Length = 278 Score = 100 bits (250), Expect = 3e-26 Identities = 65/209 (31%), Positives = 107/209 (51%), Gaps = 5/209 (2%) Query: 27 LPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILMIFAY 86 L G TL + S++ + ++G L R+S+ + + FR P+LI ++ Y Sbjct: 72 LQGAALTLFLCLCSIVASSLLGFITALARLSKSAVAFGIASFYASFFRGTPLLIQILLIY 131 Query: 87 QMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSSRQT 146 Q IVP A AA + L++ G+ ++EI R+GI +P GQ+EA++ALGM Sbjct: 132 LGLPQLGIVPG---AIAAGIIALSLNYGAYLSEIFRAGIVGVPHGQREASLALGMRESVI 188 Query: 147 TWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRNYLAALFVV 206 W + LPQA+ ++P +Q + LKDS+L +G EV+ + Y+ L Sbjct: 189 FWRVTLPQAMRTIIPPTTNQFISMLKDSSLISVMGVWEVMFLAQSYGRSSYRYIEMLSTA 248 Query: 207 ALIMIVLNFSLTALASRIERQLRAGRARK 235 A+I +L+ L + +R+ER G+A K Sbjct: 249 AIIYWLLSIGLELIQARMERHY--GKAYK 275 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: 177 Number of extensions: 10 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: 278 Length adjustment: 25 Effective length of query: 248 Effective length of database: 253 Effective search space: 62744 Effective search space used: 62744 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