Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::P73721 (252 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 129 bits (325), Expect = 7e-35 Identities = 78/243 (32%), Positives = 133/243 (54%), Gaps = 9/243 (3%) Query: 8 LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEV 67 L+ +++ K F ++ + V+ I ++ +++G SG GKST LR L E + GR+ + Sbjct: 20 LLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYL 79 Query: 68 AGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRA 127 G D++ L + M+FQ + LFPH+TV QN+ ++ ++ A+ R Sbjct: 80 DGQDITD-------LPPYERPINMMFQSYALFPHMTVEQNIAFGLKQD-KMSKADISQRV 131 Query: 128 LTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEV-L 186 L V + A P QLSGGQ+QRVA+AR L +P++LL DEP ALD +L ++ L Sbjct: 132 QEMLKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQL 191 Query: 187 NVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFL 246 V++ L G+T +VTH+ + A ++ R+ + G I + G P +++ +P S + F+ Sbjct: 192 EVVEILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFI 251 Query: 247 SRI 249 + Sbjct: 252 GTV 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: 7 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: 252 Length of database: 378 Length adjustment: 27 Effective length of query: 225 Effective length of database: 351 Effective search space: 78975 Effective search space used: 78975 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: 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