Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate GFF1457 HP15_1422 amino acid ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__Marino:GFF1457 Length = 240 Score = 213 bits (541), Expect = 4e-60 Identities = 112/241 (46%), Positives = 168/241 (69%), Gaps = 4/241 (1%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60 MI ++NV+K +G VLK ++L VK+GE + +IG SGSGKST + C+N +E ++ G+++V Sbjct: 1 MISVQNVHKSFGDLEVLKGVSLDVKKGEVVSVIGGSGSGKSTLLYCINAIEPINKGKILV 60 Query: 61 NNLVLNHK--NKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFK 118 +++ ++ K NK ++ R+ MVFQ +N +PHMTVL+N LAP ++K SK+EA E A K Sbjct: 61 DDVDVHAKETNKDKL-RQKLGMVFQQWNSFPHMTVLENAALAPRIVKKMSKEEAIEIAKK 119 Query: 119 YLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVM 178 L+ VGL DK +VYP +SGGQQQR+AIAR+L K Y+L DE TSALDPE + EVLD + Sbjct: 120 ELEHVGLGDKFDVYPTKMSGGQQQRLAIARALAMKPDYMLLDEVTSALDPELVGEVLDTL 179 Query: 179 KEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGK 238 + ++ + TM+ VTHEMGFA++V+DR+ + +G I E + ++P+ + FL K Sbjct: 180 RLLA-EEGMTMICVTHEMGFARDVSDRVAYFHEGVIAEIGEARQVITDPQNPLTQKFLSK 238 Query: 239 I 239 + Sbjct: 239 V 239 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: 136 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: 240 Length adjustment: 23 Effective length of query: 219 Effective length of database: 217 Effective search space: 47523 Effective search space used: 47523 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