Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate CCNA_00435 CCNA_00435 amino acid transporter
Query= TCDB::S6EX81 (469 letters) >FitnessBrowser__Caulo:CCNA_00435 Length = 483 Score = 251 bits (642), Expect = 3e-71 Identities = 144/463 (31%), Positives = 253/463 (54%), Gaps = 14/463 (3%) Query: 15 ADKHY-NQVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVAL 73 AD H + L+ +ALGVG I+ T I+TL G V A AGPGV+ S+L+A V AL Sbjct: 25 ADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPGVILSFLIAGAVCACAAL 83 Query: 74 AYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAP 133 YAE+ST++P +GSAY++ GE W GW+L+ EY + A V G+SA+ L Sbjct: 84 CYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAHGLFKM 143 Query: 134 LGFHLPKVLANPFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAF 193 +GF +LA P GG++++ ++ + + A ++ G ++ ++ +LV +K+ A+I F Sbjct: 144 IGFP-DALLAGPH--QGGLINMPAVFISMAVAGLLALGTRESATVNMVLVFVKIIALIVF 200 Query: 194 IIVGITVIKPANYHPFIP----PHNPKTGFGGFS--GIWSGVSMIFLAYIGFDSIAANSA 247 +++ + A++ PF+P H P+ + G+ + S+IF A+ GFD+++ + Sbjct: 201 VVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFYGFDAVSTAAE 260 Query: 248 EAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLS 307 E KNP++ + GI+GS+ + ++ V V +G ++ + AP+ + L+ + ++ Sbjct: 261 ETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFILESLNHGKIA 320 Query: 308 EVVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVA 366 ++V A+ + +L + SR+ + RDGLLP+ L K+NA+ P ++A Sbjct: 321 QLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPVMMTLLTGVLA 380 Query: 367 IVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGF 426 VI +A+L +AGTL AF+ V + LR R+ + P +P++ G Sbjct: 381 AVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPN--RPRVFSTPLWPIVAPAGI 438 Query: 427 IGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSRKSEEK 469 +G L++F L + +LY LIG ++Y AYG R+S ++++ Sbjct: 439 LGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLAQQE 481 Lambda K H 0.328 0.143 0.433 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: 632 Number of extensions: 41 Number of successful extensions: 5 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: 469 Length of database: 483 Length adjustment: 33 Effective length of query: 436 Effective length of database: 450 Effective search space: 196200 Effective search space used: 196200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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