Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate PfGW456L13_4772 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
Query= TCDB::P48245 (273 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4772 Length = 223 Score = 109 bits (272), Expect = 6e-29 Identities = 64/209 (30%), Positives = 111/209 (53%), Gaps = 8/209 (3%) Query: 27 LPGLWG----TLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILM 82 LPGLW TLK VI +++GT L L R+S ++L + FR+IP+L+++ Sbjct: 12 LPGLWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPLLLVI 71 Query: 83 IFAY---QMFAQYNIVPSSQL-AFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIA 138 + Y ++ + + AFA+ + M+ + EI+R+G+ S+PKGQ AA A Sbjct: 72 TWFYLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQA 131 Query: 139 LGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRN 198 LGMS Q I+LPQA M P L+ Q +I +D++L Y +G ++ + + S + Sbjct: 132 LGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGDIIGR 191 Query: 199 YLAALFVVALIMIVLNFSLTALASRIERQ 227 L L+ +++F+ + L R++++ Sbjct: 192 SNEFLIFAGLVYFIISFAASQLVKRLQKR 220 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: 146 Number of extensions: 11 Number of successful extensions: 3 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: 223 Length adjustment: 24 Effective length of query: 249 Effective length of database: 199 Effective search space: 49551 Effective search space used: 49551 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: 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