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 Ac3H11_2553 Cell division transporter, ATP-binding protein FtsE (TC 3.A.5.1.1)
Query= TCDB::Q9HU32 (257 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2553 Length = 265 Score = 238 bits (608), Expect = 7e-68 Identities = 126/252 (50%), Positives = 165/252 (65%), Gaps = 6/252 (2%) Query: 4 ATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63 A P + IR L K +G VL GI V+ ++G SGSGKSTFLRC N LE P G Sbjct: 15 AEPIVRIRGLRKAFGSHVVLNGIDFDVLPSQVVVVIGPSGSGKSTFLRCCNGLEQPEGGS 74 Query: 64 ILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVL 123 + + G L ++G ++ +N LR E+G VFQ+FNL+PH+S+LDNV PR++ Sbjct: 75 VEICGRTL----VQDGRMLP--DHDLNALREEVGMVFQSFNLFPHLSVLDNVTLGPRKLR 128 Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 G S+ EA E A+ LL KVG+A K + PA LSGGQ+QR AIAR LAM+P+V+LFDEPTSA Sbjct: 129 GLSRKEAEERAQALLTKVGLAHKAPAMPASLSGGQKQRVAIARALAMEPRVMLFDEPTSA 188 Query: 184 LDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFEN 243 LDPE+V EVL V++ LA EG TM++VTHEM FAR+V VV + G + E G P +F N Sbjct: 189 LDPELVGEVLQVMKLLASEGMTMMVVTHEMDFAREVGDVVVVMDGGGIIEAGAPATIFTN 248 Query: 244 PQSARCKQFMSS 255 P R + F+ + Sbjct: 249 PTQERTRSFLQA 260 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: 174 Number of extensions: 4 Number of successful extensions: 2 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: 265 Length adjustment: 25 Effective length of query: 232 Effective length of database: 240 Effective search space: 55680 Effective search space used: 55680 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