Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate RR42_RS01585 RR42_RS01585 amino acid permease
Query= TCDB::S6EX81 (469 letters) >FitnessBrowser__Cup4G11:RR42_RS01585 Length = 464 Score = 290 bits (743), Expect = 5e-83 Identities = 164/452 (36%), Positives = 254/452 (56%), Gaps = 15/452 (3%) Query: 16 DKHYNQVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAY 75 D +VL D + +G+G II T IF L G A AGP + S+++AAL GF AL Y Sbjct: 18 DDGLKKVLGPVDLILMGIGAIIGTGIFVLTG-TGALTAGPALTVSFVIAALACGFAALCY 76 Query: 76 AEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLG 135 AE ++ +P +GS Y++ GE W+ GW LL EY +A + V G+S Q L+A G Sbjct: 77 AEFASAIPVSGSIYTYSYATLGEIVAWMIGWDLLLEYGLATSAVSVGWSGYFQSLMAGFG 136 Query: 136 FHLPKVLANPFGTDGGVVDIISL---LVILLSAIIVFRGASDAGRISQILVVLKVAAVIA 192 HLP +L G GV + +L +++LL +V G ++ R++ ++V +K+A V+ Sbjct: 137 IHLPAMLTAAPGAVPGVQTLFNLPAAVIMLLITWVVSYGVRESARLNNVMVAVKIAVVLL 196 Query: 193 FIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAKNP 252 FI VG+ +KPAN+HPF P G G+++ +++F A+IGFD++ + + E +NP Sbjct: 197 FIGVGVWHVKPANWHPFAP--------FGLDGVFNAAALVFFAFIGFDAVTSAAEEVRNP 248 Query: 253 QKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVVTA 312 ++ +P GIIGSL + VL+ V ++ G+ P++ +AG PV ALQ +G + ++ V Sbjct: 249 RRDLPIGIIGSLAVCTVLYVTVAAIMTGIVPFAKFAGIDHPVSLALQYAGENWVAGFVDL 308 Query: 313 IALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMN-ARNLPANGVWTLAIVAIVIGA 371 A+ GM +L M +R+++A RDGLLP+ L ++ P WT+ IV I A Sbjct: 309 GAILGMTTVILVMTFGQTRIIFAMSRDGLLPERLSTVHPVHATPFFATWTVGIVFAFIAA 368 Query: 372 FFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFIGSLF 431 F P LA+LI+ GTL AF +++ + LR+ + DLP A ++ P PV+P L LF Sbjct: 369 FVPLNVLAELINIGTLSAFTLISVAVLVLRKTR-PDLPRA-FRCPGVPVVPLLSVGFCLF 426 Query: 432 VFWGLDVQAKLYSGIWFLIGILIYFAYGNRRS 463 + L + W IG+ IYF Y R + Sbjct: 427 LMAHLQALTWVAFLAWLAIGLAIYFLYARRNA 458 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: 676 Number of extensions: 40 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: 464 Length adjustment: 33 Effective length of query: 436 Effective length of database: 431 Effective search space: 187916 Effective search space used: 187916 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