Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate AZOBR_RS14700 AZOBR_RS14700 C4-dicarboxylate ABC transporter permease
Query= TCDB::P74224 (445 letters) >FitnessBrowser__azobra:AZOBR_RS14700 Length = 433 Score = 218 bits (554), Expect = 4e-61 Identities = 136/438 (31%), Positives = 235/438 (53%), Gaps = 17/438 (3%) Query: 10 MMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGTLLA 69 ++ V L+ LG G VA +L GV + AL + P+ + M I+G + TL A Sbjct: 9 VVVVTMLLMLGTGIWVALALAGVGF----VAMALFTTRPVGM-VMATNIWGASTSWTLTA 63 Query: 70 IPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVAM 129 +P FI++G +L R+ I+ + + + G L G L I+ T+ AA +G AAT + Sbjct: 64 LPLFIWMGEILFRTRISSDMFKGLAPWTGWLPGRLMHVNIVGCTIFAAVSGSSAATAATI 123 Query: 130 GLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSLLPG 189 G +++P + R GY + G + +GTLG +IPPS+++IV VS+ LFI ++PG Sbjct: 124 GRMTIPELTRRGYDPMMIVGSLAGAGTLGLLIPPSIIMIVYGVAADVSIARLFIAGVIPG 183 Query: 190 LMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQV--MLPPLVLILLVLGS 247 +++ G F LYV + L PD P P E R Q L +I ++P ++LI VLGS Sbjct: 184 IVLTGLFMLYVGGWSLLNPDRVP--PREAR----QSLMEKIRDTGSLIPVMLLIAGVLGS 237 Query: 248 IFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAFSL 307 I+ GIA+PTEA +G +G++ LA ++W + + M+ IL G+ AF Sbjct: 238 IYAGIATPTEAAGIGVLGSLLLALVTGTMSWATFRDSVMGAAHTSCMIGFILAGA-AFLT 296 Query: 308 VFRGLEG-DRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEA 366 V G G R + + + ++ L + + ++G F+D + + + P+ + Sbjct: 297 VAMGYTGIPRLLAEWITSMQLTTASLLVVLTLFFIVMGCFLDGISMVVLTTSVILPMVQN 356 Query: 367 LNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVL 426 +DL+W+G+ + ++ + +TPP GF LF L+ + ++ T I + ++PF + ++++ Sbjct: 357 AGIDLLWFGIYIIIVVEMAQITPPVGFNLFVLQSMTGKNIFT--IAKASLPFFLMMIVMV 414 Query: 427 LLIIIFPALINWLPSLSV 444 L+ IFP +++WLPSL + Sbjct: 415 ALLWIFPGMVSWLPSLMI 432 Lambda K H 0.331 0.148 0.443 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: 534 Number of extensions: 30 Number of successful extensions: 3 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: 445 Length of database: 433 Length adjustment: 32 Effective length of query: 413 Effective length of database: 401 Effective search space: 165613 Effective search space used: 165613 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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