Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate Pf6N2E2_2051 Amino acid ABC transporter, permease protein
Query= TCDB::P48245 (273 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2051 Length = 220 Score = 85.9 bits (211), Expect = 7e-22 Identities = 60/203 (29%), Positives = 103/203 (50%), Gaps = 7/203 (3%) Query: 30 LWGTLKSAVFSVILALVMGTALGLGRISEIRILR-WFCAVI---IETFRAIPVLILMIFA 85 LW ++V +LA+V+GT +GL + R W A ++ R PV +L++ Sbjct: 18 LWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLVLAC 77 Query: 86 YQMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSSRQ 145 + M AF A V GLT++ GS +AEI+R + +LP+GQ EA+ A+G++ Q Sbjct: 78 FYMAPALGWQIG---AFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQ 134 Query: 146 TTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRNYLAALFV 205 + +LLPQA+ +LP ++ +K S L IG E++ S Q + L Sbjct: 135 SLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLF 194 Query: 206 VALIMIVLNFSLTALASRIERQL 228 + ++N+++ L IE+++ Sbjct: 195 AGFLFFIINYAIELLGRHIEKRV 217 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: 142 Number of extensions: 9 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: 220 Length adjustment: 24 Effective length of query: 249 Effective length of database: 196 Effective search space: 48804 Effective search space used: 48804 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