Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 3608829 Dshi_2221 ABC transporter related (RefSeq)
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Dino:3608829 Length = 259 Score = 247 bits (630), Expect = 2e-70 Identities = 134/254 (52%), Positives = 173/254 (68%), Gaps = 7/254 (2%) Query: 1 MTSPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPI 60 MT PT P+I L K +GAL+VL+GV+ DV+S+IG SG GKST LRC N LE Sbjct: 1 MTEPTVPVIEIRDLHKAYGALEVLKGVSIRAERGDVVSLIGSSGSGKSTLLRCCNLLEDS 60 Query: 61 SGGRLEVAG--VDLSGAKIDQ-----KHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPR 113 G + G V +G+ +D+ K + ++R + MVFQ FNL+ H+T+L+N++ AP Sbjct: 61 QRGDVLFCGEPVTWTGSGLDRRPADKKQVIRIRTNLSMVFQQFNLWAHMTILENVMEAPV 120 Query: 114 KVLRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEP 173 VL P E + RA LDKVG+G K D YP QLSGGQ+QR AIARGL M+P+ LLFDEP Sbjct: 121 TVLGEPPKEVEARARALLDKVGIGDKCDAYPAQLSGGQQQRAAIARGLAMEPKALLFDEP 180 Query: 174 TSALDPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEV 233 TSALDPEL EV+ V+K LA EG TM +VTH+M+ A +VS+ V F +QG+IEEEG P+ + Sbjct: 181 TSALDPELEQEVVKVIKDLAAEGRTMLIVTHDMRLAADVSDHVVFLHQGLIEEEGPPDIL 240 Query: 234 FRNPKSDRLRAFLS 247 F PKS RL+ FLS Sbjct: 241 FGQPKSARLKQFLS 254 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: 203 Number of extensions: 9 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