Align ABC transporter permease (characterized, see rationale)
to candidate RR42_RS14420 RR42_RS14420 branched-chain amino acid transporter permease subunit LivH
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Cup4G11:RR42_RS14420 Length = 308 Score = 255 bits (651), Expect = 1e-72 Identities = 137/302 (45%), Positives = 198/302 (65%), Gaps = 13/302 (4%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAP 65 QQ++NGL LG++YALIA+GYTMVYGII +INFAHGE+ MIGA + + GA G P Sbjct: 10 QQLVNGLTLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIGAYVGLVTLTAI-GASAGYP 68 Query: 66 GWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKP 125 ++L A +++ +V F +E+VAYRPLR PRL PLI+AIGMSI LQ I Sbjct: 69 LPLVLGAALLVSVLVTGLYGFAVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGA 128 Query: 126 NYKPYPTMLPSS-PFEIGGAF---ITPTQILILGVTAVALASLVYLVNHTNLGRAMRATA 181 P ++ + F++G F + +++LI+GVT V + +L + H+ +GRA RA A Sbjct: 129 RDMSVPVLISGAIEFQMGSDFTVTVPYSRLLIVGVTLVLMLALTLFIGHSRMGRACRACA 188 Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241 E+ R+A+L+G+ + VIS TF++GA+LAA+ G++ G +GF+ G+KAFTAAV Sbjct: 189 EDMRMANLLGIDTNRVISFTFVLGAMLAAVGGVLIGLTIGKLNPYIGFVAGIKAFTAAVL 248 Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLL 301 GGIG++ GA++GG+LLGL E SGY + + Y D+ AF +L++IL RP+GLL Sbjct: 249 GGIGSIPGAMLGGVLLGLAETFASGY--------MPAEYKDVVAFGLLVLILLFRPTGLL 300 Query: 302 GE 303 G+ Sbjct: 301 GK 302 Lambda K H 0.327 0.142 0.419 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: 278 Number of extensions: 14 Number of successful extensions: 4 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: 309 Length of database: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 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: 48 (23.1 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