Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate GFF202 PS417_01025 glutamine ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__WCS417:GFF202 Length = 258 Score = 237 bits (604), Expect = 2e-67 Identities = 119/239 (49%), Positives = 170/239 (71%), Gaps = 2/239 (0%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEV-V 59 +IE + NK++G VLK I+LSV+ GE +VI+GPSG GKST +RC+NGLE SG + Sbjct: 4 LIEFQGFNKFFGEAQVLKGIDLSVQRGEVVVILGPSGCGKSTLLRCLNGLEVAHSGSLRF 63 Query: 60 VNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119 N +L+ + R+ MVFQ ++L+PHM+VL N+ L P+K+Q++ +EA E A K Sbjct: 64 AGNELLDKQTDWRQVRQDIGMVFQSYHLFPHMSVLDNILLGPLKVQQRDPREAREQAEKL 123 Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179 L+ VGL +K + +P LSGGQQQR+AI RSLC +LFDE T+ALDPE ++EVL+V++ Sbjct: 124 LERVGLAEKRDAFPRQLSGGQQQRIAIVRSLCMNPQVMLFDEVTAALDPEMVKEVLEVIQ 183 Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGK 238 ++ + T+++VTHEM FA+ VADR++FME G I+E+N P FF+NP+T RA+ FL K Sbjct: 184 GLA-RDGMTLLIVTHEMAFARAVADRVVFMEAGRILEQNTPEAFFTNPQTARAQQFLEK 241 Lambda K H 0.317 0.133 0.372 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: 161 Number of extensions: 5 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: 242 Length of database: 258 Length adjustment: 24 Effective length of query: 218 Effective length of database: 234 Effective search space: 51012 Effective search space used: 51012 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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