Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011372993.1 SUDEN_RS07140 ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_000012965.1:WP_011372993.1 Length = 237 Score = 127 bits (319), Expect = 2e-34 Identities = 78/221 (35%), Positives = 127/221 (57%), Gaps = 7/221 (3%) Query: 4 LKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEV----- 58 +KN K V+ N + + +GE + +I PSG+GK+T + + + E +SGE+ Sbjct: 13 VKNFGKNDSLVKVIDNASFEINKGELVALIAPSGAGKTTLLMMIGCVLEPTSGEIWLGEE 72 Query: 59 VVNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFK 118 VV N K+ I R+ +FQ L P + V++N+TL P ++ K S+KEA++ A + Sbjct: 73 VVYNNKWIAKDTRRIRREKIGFIFQAHYLIPFLNVIENITLLP-QVNKVSEKEAKQKAME 131 Query: 119 YLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVM 178 L+ + + DKA+ P+ LSGGQ QRVAIAR+L IL DEPT+ALD V+ ++ Sbjct: 132 LLEYLEIADKAHAMPSQLSGGQNQRVAIARALANNPEIILADEPTAALDAHRSISVIKML 191 Query: 179 KEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENI 219 K+I+ + N ++ VTH+ D+I+ +++ IV E + Sbjct: 192 KKIAIEQNVAIITVTHDERIL-PYFDKIMKIQNRGIVFEEL 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: 128 Number of extensions: 9 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 Apr 09 2024. 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