Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__Dino:3608624 Length = 333 Score = 151 bits (381), Expect = 2e-41 Identities = 90/236 (38%), Positives = 133/236 (56%), Gaps = 4/236 (1%) Query: 2 IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN 61 + L NV K +G V+ +++ V EGE +VI+GPSG GKST +R + GLE VSSGEV ++ Sbjct: 4 LTLDNVKKSFGKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSGEVRID 63 Query: 62 NLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKYLK 121 V+N +E + AMVFQ++ LYPHM+V N+ +K+ K K E + K Sbjct: 64 GRVVN---TLEPMDRDIAMVFQNYALYPHMSVFDNMAYG-LKIAKVPKAEIADRVAVAAK 119 Query: 122 VVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMKEI 181 ++ L P LSGGQ+QRVA+ R++ K LFDEP S LD + ++ +K + Sbjct: 120 LLQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKAL 179 Query: 182 SHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLG 237 + T + VTH+ A +ADR+I M G + P E ++NP+T F+G Sbjct: 180 QRELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIG 235 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: 160 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: 333 Length adjustment: 26 Effective length of query: 216 Effective length of database: 307 Effective search space: 66312 Effective search space used: 66312 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: 47 (22.7 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