Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase
Query= TCDB::P0A9S7 (255 letters) >FitnessBrowser__SynE:Synpcc7942_0513 Length = 250 Score = 142 bits (358), Expect = 7e-39 Identities = 90/243 (37%), Positives = 132/243 (54%), Gaps = 19/243 (7%) Query: 15 FGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHLEGLPG 74 +G L VN V+L + E+V L+GPNGAGKTT F TG +P G + L + L LP Sbjct: 20 YGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLDETELTRLPM 79 Query: 75 QQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRRAQSEALDRA 134 Q AR+G+ Q +FR +TV+ENLL+ Q TG+ E R Sbjct: 80 TQRARLGIGYLAQEASIFRHLTVVENLLLVLQQ---TGI------------RGREQRQRV 124 Query: 135 ATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVT---QPEILMLDEPAAGLNPKETKE 191 L L + A+ Q ++ G++RR EIAR + P+ L+LDEP AG++P E Sbjct: 125 EELLSEFRLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAVAE 184 Query: 192 LDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRNNPDVIRAY 251 + E+IA LR IL+ +H+++ + I+DR Y++ G LA G+ E++ +NP V + Y Sbjct: 185 VQEIIARLR-AQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQYY 243 Query: 252 LGE 254 LGE Sbjct: 244 LGE 246 Lambda K H 0.320 0.137 0.395 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: 170 Number of extensions: 8 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: 255 Length of database: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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 (21.8 bits) S2: 46 (22.3 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