Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate BPHYT_RS01785 BPHYT_RS01785 amino acid permease
Query= TCDB::S6EX81 (469 letters) >FitnessBrowser__BFirm:BPHYT_RS01785 Length = 463 Score = 286 bits (732), Expect = 1e-81 Identities = 165/451 (36%), Positives = 257/451 (56%), Gaps = 15/451 (3%) Query: 21 QVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMST 80 + L D LGVG II T IF L G A Q AGP ++ S+L+AA+ GF ALAYAE ++ Sbjct: 24 KALGALDLTFLGVGAIIGTGIFVLTGTGAVQ-AGPALMISFLIAAIACGFAALAYAEFAS 82 Query: 81 VMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPK 140 +P AGS Y++ GE WI GW L+ EY +A + V G+S LQ LL+ G LP Sbjct: 83 TIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAVSVGWSGYLQSLLSGFGVSLPV 142 Query: 141 VLANPFGTDGG---VVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAFIIVG 197 L G G + ++ + LV++ ++ G ++ RI+ ++V +KV V+ I VG Sbjct: 143 ALTAAPGALPGHDTLFNLPAFLVMMAITALLSVGVRESARINNVMVAIKVVVVLLVIGVG 202 Query: 198 ITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAKNPQKTMP 257 + + PAN+HPF+P G++G++ +++F A+IGFDS+++ + E K+P++ +P Sbjct: 203 VFHVTPANWHPFMP--------NGWNGVFGAAAVMFFAFIGFDSVSSAAEEVKDPKRDLP 254 Query: 258 RGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVVTAIALAG 317 GII SL + VL+ AV V+ G+ P + +A + PV +ALQ +G ++ + A+ G Sbjct: 255 IGIIASLGVCAVLYVAVAAVVTGIVPSAQFANISHPVSYALQVAGEKWVAGFIDLGAVLG 314 Query: 318 MFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAIVIGAFFPFA 376 M +L M +R+++A RDGLLP+ L +++ R P W + I +IGA P Sbjct: 315 MLTVILVMAYGQTRVIFAMSRDGLLPERLSRVHPRFATPFFTTWLVGIFFGLIGALVPLN 374 Query: 377 FLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFIGSLFVFWGL 436 LA+LI+ GTL AF V++ + LR+ DLP A ++ P PV+P L LF+ L Sbjct: 375 VLAELINIGTLAAFSMVSIAVLVLRKTH-PDLPRA-FRCPGVPVVPVLAVAACLFLMVNL 432 Query: 437 DVQAKLYSGIWFLIGILIYFAYGNRRSRKSE 467 + +W L+G++IYF Y R S+ S+ Sbjct: 433 QAVTWVAFVVWLLVGMVIYFGYSRRHSKLSK 463 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: 651 Number of extensions: 44 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: 463 Length adjustment: 33 Effective length of query: 436 Effective length of database: 430 Effective search space: 187480 Effective search space used: 187480 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