Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_036136362.1 N800_RS06835 amino acid permease
Query= TCDB::S6EX81 (469 letters) >NCBI__GCF_000768355.1:WP_036136362.1 Length = 491 Score = 281 bits (720), Expect = 3e-80 Identities = 163/458 (35%), Positives = 253/458 (55%), Gaps = 20/458 (4%) Query: 21 QVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMST 80 +VLT R + LGVG II IF + G AA +AGP V+ S+++AA+ GF L YAE ++ Sbjct: 35 RVLTARHLVMLGVGAIIGAGIFVMTGTAAANYAGPAVILSFVMAAVACGFAGLCYAEFAS 94 Query: 81 VMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPK 140 +MP +GSAYS+ GE W GW L+ EY A + V G+S L L G +P Sbjct: 95 MMPVSGSAYSYTYSTLGEVVAWFIGWNLVLEYLFAASSVAVGWSGYLNSFLTTHGAGVPA 154 Query: 141 VLA----------NPFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAV 190 LA + F + G +V++ ++L++ + + +RG + + ++ ++V +KV + Sbjct: 155 ALAQAPFHYSAETSSFVSTGSIVNLPAVLIVAAISGLCYRGITQSAWVNALIVAIKVTVI 214 Query: 191 IAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAK 250 +AF+ I P N+ PFIP + T F G G+ G +++F AYIGFD+++ + EAK Sbjct: 215 VAFLGFAAQYINPDNWQPFIPENEGGTRF-GTEGVVRGAAVVFFAYIGFDAVSTAAGEAK 273 Query: 251 NPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVV 310 NPQ+ MP GI+GSL + VL+ AV L G+ PY A PV AL+ Y L + Sbjct: 274 NPQRDMPIGILGSLAVCTVLYIAVAATLTGLLPY-PQLDTAKPVATALE--AYPTLGWLK 330 Query: 311 TAI---ALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVA 366 A+ A+AG+ +L M++ R+ YA +DGL+PK G+++ + P G + +VA Sbjct: 331 MAVEIGAIAGLSSVILVMLMGQPRIFYAMAKDGLMPKIFGRVHPKFQTPYVGTVIVGVVA 390 Query: 367 IVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGF 426 ++ P FL L+S GTL+AF V G+ LR + DL + +++P V+ +LG Sbjct: 391 AIMAGLLPLDFLGDLVSMGTLLAFATVCAGVLILRYTR-PDL-QRPFRVPGAIVVCSLGV 448 Query: 427 IGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSR 464 + L++FW W +IG +IYF YG R S+ Sbjct: 449 LSCLYLFWQPFKDHWQVMLGWTVIGFVIYFGYGYRNSK 486 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: 672 Number of extensions: 42 Number of successful extensions: 8 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: 491 Length adjustment: 34 Effective length of query: 435 Effective length of database: 457 Effective search space: 198795 Effective search space used: 198795 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 24 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