Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate GFF1143 PGA1_c11580 octopine permease ATP-binding protein P
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__Phaeo:GFF1143 Length = 259 Score = 211 bits (537), Expect = 1e-59 Identities = 109/257 (42%), Positives = 161/257 (62%), Gaps = 10/257 (3%) Query: 12 VSTTDVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQ 71 ++ T +EI ++K YG+ V++ +++ RG+ + + G SGSGKST++RC N LE+ Q Sbjct: 1 MTDTTPVLEIRGLHKSYGELEVIKGVDITAHRGDVVSLIGSSGSGKSTLLRCCNLLEDSQ 60 Query: 72 KGKIVVDGIELT----------NDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIW 121 +G I+ G + +D K++ +R + MVFQ FNL+ H+TIL+N AP+ Sbjct: 61 EGDILFKGEPINWSGTGLARRPSDAKQVLRIRTNLSMVFQQFNLWAHMTILQNVMEAPLT 120 Query: 122 VRKMPKKEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPT 181 V + E E A +L +V I ++ YP QLSGGQQQR AIAR+LCM P+ LLFDEPT Sbjct: 121 VLGRDRAEVEDAARKYLTKVGIGDKCDAYPAQLSGGQQQRAAIARALCMEPEALLFDEPT 180 Query: 182 SALDPEMVKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFF 241 SALDPE+ +EV+ + LA EG TMI VTH+M A V++ ++F+ +G I E+ P E F Sbjct: 181 SALDPELEQEVVKVIKDLAAEGRTMIIVTHDMNMAADVSSHIVFLHKGLIEEEGCPDEVF 240 Query: 242 DNPQHERTKLFLSQILH 258 + + ER + FL+ H Sbjct: 241 GSTRSERLRGFLASTRH 257 Lambda K H 0.322 0.136 0.397 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: 162 Number of extensions: 5 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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