Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate GFF1143 PGA1_c11580 octopine permease ATP-binding protein P
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Phaeo:GFF1143 Length = 259 Score = 243 bits (619), Expect = 4e-69 Identities = 127/250 (50%), Positives = 168/250 (67%), Gaps = 7/250 (2%) Query: 5 TAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEP----- 59 T P++ L K++G L+V++GV + DV+S+IG SG GKST LRC N LE Sbjct: 4 TTPVLEIRGLHKSYGELEVIKGVDITAHRGDVVSLIGSSGSGKSTLLRCCNLLEDSQEGD 63 Query: 60 --ISGGRLEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLR 117 G + +G L+ D K + ++R + MVFQ FNL+ H+T+LQN++ AP VL Sbjct: 64 ILFKGEPINWSGTGLARRPSDAKQVLRIRTNLSMVFQQFNLWAHMTILQNVMEAPLTVLG 123 Query: 118 IPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSAL 177 AE +D A YL KVG+G K D YP QLSGGQ+QR AIAR LCM+PE LLFDEPTSAL Sbjct: 124 RDRAEVEDAARKYLTKVGIGDKCDAYPAQLSGGQQQRAAIARALCMEPEALLFDEPTSAL 183 Query: 178 DPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNP 237 DPEL EV+ V+K LA EG TM +VTH+M A +VS+ + F ++G+IEEEG P+EVF + Sbjct: 184 DPELEQEVVKVIKDLAAEGRTMIIVTHDMNMAADVSSHIVFLHKGLIEEEGCPDEVFGST 243 Query: 238 KSDRLRAFLS 247 +S+RLR FL+ Sbjct: 244 RSERLRGFLA 253 Lambda K H 0.321 0.139 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: 179 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: 252 Length of database: 259 Length adjustment: 24 Effective length of query: 228 Effective length of database: 235 Effective search space: 53580 Effective search space used: 53580 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