Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate N515DRAFT_2925 N515DRAFT_2925 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= TCDB::S6EX81 (469 letters) >FitnessBrowser__Dyella79:N515DRAFT_2925 Length = 480 Score = 260 bits (665), Expect = 6e-74 Identities = 164/477 (34%), Positives = 252/477 (52%), Gaps = 22/477 (4%) Query: 3 FMRKADFELYRDADKHYN-----QVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGV 57 F RK DF DAD + + L ALG+G +I T IF + GQ AA+ AGP V Sbjct: 6 FARKTDFS---DADDCHGGPSLRRTLGKWGITALGIGAVIGTGIFVVTGQAAAEHAGPAV 62 Query: 58 VFSYLLAALVAGFVALAYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVA 117 + S++LAA+ +GF AL YAE +T++P +GS+YS+ GE W GW ++ EY I+ + Sbjct: 63 LISFMLAAICSGFTALCYAEFATLIPISGSSYSYAYATLGELVAWFIGWNMVLEYGISAS 122 Query: 118 FVGSGFSANLQQLLAPLGFHLPKVLANP--------FGTDGGVVDIISLLVILLSAIIVF 169 V + ++ LL +G HLP L T G ++++ ++ ++L + + Sbjct: 123 AVAASWTGYFTSLLDHVGIHLPVALTEAPLAFKDGHLVTTGHLLNLPAVAIVLALTWLCY 182 Query: 170 RGASDAGRISQILVVLKVAAVIAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGV 229 G ++ ++ ++V LKV +I ++ G + PAN+HPFIP + G G+SGI G Sbjct: 183 VGIRESSGLNVLMVALKVGLIIVVVVAGYRYVDPANWHPFIPAEQ-EPGKYGWSGIMRGA 241 Query: 230 SMIFLAYIGFDSIAANSAEAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAG 289 +M+F AYIGF++ + + E KNPQK +P G + SL+I VL+ A+ VL G+ PY+ G Sbjct: 242 AMVFFAYIGFEATSTAAQECKNPQKDLPFGTLVSLVICTVLYLAMAAVLTGLIPYTE-LG 300 Query: 290 NAAPVGWALQ-QSGYSVLSEVVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGK 348 + PV A++ L VV A+ G+ +L M++A R+ RDGLLP + Sbjct: 301 TSEPVVTAIRNHPELGWLRLVVEIGAMIGLSSVILVMIIAQPRIFMIMSRDGLLPPVFNR 360 Query: 349 MNARN-LPANGVWTLAIVAIVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKD 407 ++ ++ P I ++ A FP LA L S GTLIAF+ V G+ L R + Sbjct: 361 IHPKHRTPHLNTVITGIGIAILAAVFPLDLLADLTSMGTLIAFVAVCAGVLIL-RYTAPE 419 Query: 408 LPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSR 464 LP +++P + G L + + + L IW IG+ IYF YG R SR Sbjct: 420 LPR-LFRVPAAWFVCTAGVFSCLALLYFMAWFNWLLMIIWTAIGLAIYFGYGMRHSR 475 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: 617 Number of extensions: 34 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: 480 Length adjustment: 33 Effective length of query: 436 Effective length of database: 447 Effective search space: 194892 Effective search space used: 194892 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