Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate Synpcc7942_0564 Synpcc7942_0564 ATPase
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__SynE:Synpcc7942_0564 Length = 237 Score = 129 bits (323), Expect = 7e-35 Identities = 75/228 (32%), Positives = 134/228 (58%), Gaps = 9/228 (3%) Query: 1 MIELKNVNKYYG----THHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56 ++ ++N++ +YG VL ++ + GE +++ GPSG GK+T + + GL V +G Sbjct: 6 VVSIRNLDHFYGHDSLQKQVLFDVGFDLNPGEIVLLTGPSGCGKTTLLTLIGGLRSVQAG 65 Query: 57 EVVVNNLVLN---HKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113 + V L+ + ++E+ R+ +FQ NL +T QN+ + + E Sbjct: 66 TLSVLGQELHGASQRQRVEV-RRNIGYIFQAHNLLRFLTASQNVQMTLDLQADLNWDERI 124 Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173 + + L+ VGL D + YP LSGGQ+QRVAIAR+L + +L DEPT+ALD ++ ++ Sbjct: 125 ARSHQMLEAVGLGDHLDYYPENLSGGQKQRVAIARALVGRPKLVLADEPTAALDRQSGRD 184 Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPS 221 V+D+M++++ + T+++VTH+ ++ADRI+ MEDG +V+ + S Sbjct: 185 VVDLMQQLAKEQGCTILLVTHDNRIL-DIADRILEMEDGRLVKGGLTS 231 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: 135 Number of extensions: 6 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: 237 Length adjustment: 23 Effective length of query: 219 Effective length of database: 214 Effective search space: 46866 Effective search space used: 46866 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