Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate CCNA_01242 CCNA_01242 amino acid permease
Query= TCDB::S6EX81 (469 letters) >FitnessBrowser__Caulo:CCNA_01242 Length = 531 Score = 253 bits (645), Expect = 1e-71 Identities = 158/511 (30%), Positives = 263/511 (51%), Gaps = 52/511 (10%) Query: 3 FMRKADFELYRDA-DKHYNQVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSY 61 F++K+ + ++A + L + ++LGVG II IF L GQVA+ AGP ++ S+ Sbjct: 7 FLKKSIASIQKEAAHSQLKRTLGPINLMSLGVGAIIGAGIFVLTGQVASANAGPAIMLSF 66 Query: 62 LLAALVAGFVALAYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGS 121 ++A + L YAE+++ MP +GSAY++ GE F WI GW L+ EY +A + V Sbjct: 67 IVAGIACALAGLCYAELASTMPVSGSAYTYAYGTLGEVFAWIMGWLLVLEYGVAASTVAV 126 Query: 122 GFSANLQQLLAPLGFHLPKV-----------------LANPFGTD----GGVVDIISLLV 160 G+S + L LG + P + +A P G G +++++ + Sbjct: 127 GWSGYVVSTLHALGINFPMIQVAGADAPMWATPLIQAVAAPGGGTMFAMTGTLNLVAAIG 186 Query: 161 ILLSAIIVFRGASDAGRISQILVVLKVAAVIAFIIVGITVIKPANYHPFIPPHNPKTGFG 220 I + + ++ G S++ ++ +VV+KV ++ FI VG I PAN+HPFIP + G Sbjct: 187 IAMVSALLVVGVSESANVNNAIVVIKVIVLVTFIAVGAQYINPANWHPFIPEPTGQPGEF 246 Query: 221 GFSGIWSGVSMIFLAYIGFDSIAANSAEAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVG 280 G GI+ G ++IF AY+GF++++ +AEAKNP + +P GI+G+L+I +++ AV V+ G Sbjct: 247 GIGGIFRGAAIIFFAYVGFEAVSTAAAEAKNPSRDVPIGILGALIICTLIYMAVAAVMTG 306 Query: 281 MHPYSAYAGNAAPVGWALQQSG---------------YSVLSEVVTAIALAGMFIALLGM 325 + P+ A + AP+ A+ + G ++LS + A+ G+ +L + Sbjct: 307 VVPFRELA-SPAPIAVAIDRMGLEWADIPYAAAEGGKLNLLSFAIKIGAITGLSSVMLVL 365 Query: 326 VLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAIVIGAFFPFAFLAQLISA 384 +R+ Y RDGLLPK +++ + P G L +V + +F P + L L+S Sbjct: 366 CYGQTRIFYTMARDGLLPKVFAEIHPKFRTPWLGTILLGVVIAIAASFLPISLLGDLVSL 425 Query: 385 GTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFIGSLFV----FWGLDVQA 440 GT +AF V L + LR + DLP +K+P A G LF+ F + V A Sbjct: 426 GTAVAFSIVCLSVIYLRIKH-PDLPR-PFKVPGGIFTAAAGIAACLFLPYQNFQPMIVHA 483 Query: 441 K-------LYSGIWFLIGILIYFAYGNRRSR 464 + G + +G +IY AYG S+ Sbjct: 484 MNDNPLPLMILGGYAAVGAIIYIAYGYWHSK 514 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: 655 Number of extensions: 34 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: 531 Length adjustment: 34 Effective length of query: 435 Effective length of database: 497 Effective search space: 216195 Effective search space used: 216195 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: 52 (24.6 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