Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__HerbieS:HSERO_RS08275 Length = 308 Score = 298 bits (763), Expect = 1e-85 Identities = 148/300 (49%), Positives = 212/300 (70%), Gaps = 6/300 (2%) Query: 6 QQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP 65 QQL+NGL+LG+IY L+AIGYTMVYGIIGMINFAHG+I+M+ + L+ L + +G P Sbjct: 10 QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVT-LTAIGVQSGYP 68 Query: 66 VAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQGP 125 + +LL L+V++L+T L+ WT+ERVAYRPLRG RL PLI+AIGMSI L N++Q+ QG Sbjct: 69 LPLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGA 128 Query: 126 RNKPIPPMVSSVYQFG-----NISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180 R+ +P ++S +F +++ +++I+ +T VL+ + R+ +GRA RA Sbjct: 129 RDMSVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIARSRMGRACRACA 188 Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240 +D MA LLG++ ++ IS TFV+GA LAAV G + + G + GF G+KAFTAAVL Sbjct: 189 EDMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFIAGIKAFTAAVL 248 Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300 GGIGS+PGA+ GG+L+GL E+ + Y YKDV +F +L +L+F+PTG+LG+P+VEKV Sbjct: 249 GGIGSIPGAMLGGVLLGLAETFAAGYLPSEYKDVVSFGLLVLILLFRPTGLLGKPDVEKV 308 Lambda K H 0.329 0.143 0.421 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: 364 Number of extensions: 19 Number of successful extensions: 3 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: 300 Length of database: 308 Length adjustment: 27 Effective length of query: 273 Effective length of database: 281 Effective search space: 76713 Effective search space used: 76713 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 (21.8 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