Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_043919874.1 jaqu_RS15290 ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_000877395.1:WP_043919874.1 Length = 376 Score = 152 bits (383), Expect = 1e-41 Identities = 89/246 (36%), Positives = 137/246 (55%), Gaps = 13/246 (5%) Query: 7 PLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLE 66 PLIS + K +G + +T +I+P++ +++GPSGCGK+T +R L E +SGGR+ Sbjct: 17 PLISCQDVTKRYGEFTAIERLTLDIFPREFFALLGPSGCGKTTLMRMLGGFEDVSGGRIT 76 Query: 67 VAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAK-- 124 + G D++G +++ V M+FQ + LFPHLTV NL + R MA+ + Sbjct: 77 IDGQDMAGIPPNKR-------AVNMMFQSYALFPHLTVWDNLAFG---LKRSDMAKDQIG 126 Query: 125 DRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGE 184 DR L V L A P QLSGGQKQRVA+AR L P++LL DEP ALD +L + Sbjct: 127 DRVEAMLKLVQLQKFAKRKPHQLSGGQKQRVALARALAKGPKLLLLDEPLGALDKKLRQQ 186 Query: 185 VLNVMKQLAEE-GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLR 243 + + E+ G T +VTH+ + A V++R+ ++G I + P ++ P S + Sbjct: 187 TQFELMDIQEKTGTTFVIVTHDQEEAMTVASRIAVMDEGRIVQVDTPGRIYEAPNSVYVA 246 Query: 244 AFLSRI 249 F+ + Sbjct: 247 DFIGDV 252 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: 225 Number of extensions: 12 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: 376 Length adjustment: 27 Effective length of query: 225 Effective length of database: 349 Effective search space: 78525 Effective search space used: 78525 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 24 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