Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 142 bits (357), Expect = 1e-38 Identities = 83/248 (33%), Positives = 142/248 (57%), Gaps = 18/248 (7%) Query: 8 LEIRNLHKRYGDLE--VLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQIL 65 L++ + K++ + +K I + +G V +I+G +GSGK+T L+ I LE+P +G+I+ Sbjct: 4 LQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIV 63 Query: 66 VSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGK 125 SG+ + NG +Q+ E+G +FQ + L+P M++L+NV EA L + Sbjct: 64 FSGQTI-----VNGKSALPANQR------EVGVIFQEYALFPQMTLLENVREA----LHQ 108 Query: 126 SKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALD 185 A +IA LA G+ D +YP QLS GQ+QRAA+AR LA +PK++L D+P +LD Sbjct: 109 ESRNARQIAMDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLD 168 Query: 186 PEMVQEVLNVIRALAE-EGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENP 244 E+ IR + + G T ++ +H A ++ + LH+G++++ GTP ++++ P Sbjct: 169 TRFKNEISEDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKP 228 Query: 245 QSARCKQF 252 +A F Sbjct: 229 ANAYVANF 236 Lambda K H 0.317 0.133 0.367 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: 191 Number of extensions: 10 Number of successful extensions: 4 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: 257 Length of database: 345 Length adjustment: 26 Effective length of query: 231 Effective length of database: 319 Effective search space: 73689 Effective search space used: 73689 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: 48 (23.1 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