Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate GFF1143 PGA1_c11580 octopine permease ATP-binding protein P
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__Phaeo:GFF1143 Length = 259 Score = 203 bits (517), Expect = 2e-57 Identities = 105/247 (42%), Positives = 157/247 (63%), Gaps = 12/247 (4%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60 ++E++ ++K YG V+K ++++ G+ + +IG SGSGKST +RC N LE+ G+++ Sbjct: 7 VLEIRGLHKSYGELEVIKGVDITAHRGDVVSLIGSSGSGKSTLLRCCNLLEDSQEGDILF 66 Query: 61 NNLVLNHKN-----------KIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSK 109 +N ++ R +MVFQ FNL+ HMT+LQN+ AP+ + + + Sbjct: 67 KGEPINWSGTGLARRPSDAKQVLRIRTNLSMVFQQFNLWAHMTILQNVMEAPLTVLGRDR 126 Query: 110 KEAEETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPE 169 E E+ A KYL VG+ DK + YPA LSGGQQQR AIAR+LC + +LFDEPTSALDPE Sbjct: 127 AEVEDAARKYLTKVGIGDKCDAYPAQLSGGQQQRAAIARALCMEPEALLFDEPTSALDPE 186 Query: 170 TIQEVLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKT 229 QEV+ V+K+++ + TM++VTH+M A +V+ I+F+ G I EE P E F + ++ Sbjct: 187 LEQEVVKVIKDLAAEGR-TMIIVTHDMNMAADVSSHIVFLHKGLIEEEGCPDEVFGSTRS 245 Query: 230 ERARLFL 236 ER R FL Sbjct: 246 ERLRGFL 252 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: 144 Number of extensions: 7 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: 259 Length adjustment: 24 Effective length of query: 218 Effective length of database: 235 Effective search space: 51230 Effective search space used: 51230 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