Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease
Query= TCDB::S6EX81 (469 letters) >NCBI__GCF_002117405.1:WP_085770386.1 Length = 488 Score = 259 bits (663), Expect = 1e-73 Identities = 154/438 (35%), Positives = 241/438 (55%), Gaps = 13/438 (2%) Query: 29 LALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMSTVMPFAGSA 88 + +G+G +I IF L G VAA AGPGV S+L+A + +G AL YAE ++++P AGSA Sbjct: 35 VGIGLGGLIGVGIFVLTGVVAATQAGPGVALSFLIAGVASGAAALCYAEFASMLPVAGSA 94 Query: 89 YSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPKVLANPFGT 148 Y++ + GE WI GW LL EY + VA V G+S L+ LLA G P+ A GT Sbjct: 95 YTYAYAVLGELPAWIIGWDLLLEYALVVAVVSIGWSGYLRALLALFGVAPPEWAAGAPGT 154 Query: 149 -DGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAFIIVGITVIKPANYH 207 DG ++D+ ++L A+++ R + +V+LK+AAVI I+ I PAN+ Sbjct: 155 GDGHILDLFAMLGAFGVALLLTLRVEWGARFNTAMVLLKIAAVIVVILAAAPHINPANWR 214 Query: 208 PFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAKNPQKTMPRGIIGSLLIA 267 PF+P GF G+ G +++F A G+D++ EA PQ+ +PR ++ SL+++ Sbjct: 215 PFMP--------FGFGGVVEGAAVVFFAVFGYDTLTTAGEEALEPQRDLPRAVLLSLVVS 266 Query: 268 VVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVVTAIALAGMFIALLGMVL 327 + L+ ++L L G+ Y NAAPV A G + VV+A A+ G+ +L +L Sbjct: 267 LTLYILMSLALTGIARYDT-LDNAAPVASAFAALGMGWATLVVSAAAVVGILSVMLAFLL 325 Query: 328 AGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAIVIGAFFPFAFLAQLISAGT 386 +R+ +A RDGLLP + + + P + ++ AFFP +A+L++ GT Sbjct: 326 GCARIWFAMSRDGLLPAWFARPHPQFATPYRPTLIAGGLCALVSAFFPIREVAELVNIGT 385 Query: 387 LIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLYSGI 446 L AF+ + L + +LR + D+P ++ P P LP +G SL++ L A + Sbjct: 386 LSAFVVICLAVIALRHTR-PDVPRG-FRAPLSPYLPLIGVGFSLWLLSKLPAIAWERFVV 443 Query: 447 WFLIGILIYFAYGNRRSR 464 W +IG+ +YF YG R SR Sbjct: 444 WLIIGLAVYFLYGRRHSR 461 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: 652 Number of extensions: 42 Number of successful extensions: 6 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: 488 Length adjustment: 34 Effective length of query: 435 Effective length of database: 454 Effective search space: 197490 Effective search space used: 197490 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 Apr 09 2024. 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