Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__HerbieS:HSERO_RS08275 Length = 308 Score = 243 bits (620), Expect = 4e-69 Identities = 140/313 (44%), Positives = 203/313 (64%), Gaps = 35/313 (11%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPGLP 65 QQ++NGL LG++YALIA+GYTMVYG++ +INFAHG+I M+ + VGL L + V G P Sbjct: 10 QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVTLTAIG-VQSGYP 68 Query: 66 GIVQLVIAIVGAIPVCIVVSLL----IERIAYRPLRNAPRLAPLITAIGVSILLQTLAMM 121 L + + GA+ V ++V+ L +ER+AYRPLR PRL PLI+AIG+SI LQ + Sbjct: 69 ----LPLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQI 124 Query: 122 IWGRSPLPFPQVMPSDPVHIAGAL-----------ISPTQIMLLALAVLAMVGLVLIVEK 170 G + S PV I+GAL I ++++++ + ++ MV L L + + Sbjct: 125 GQGARDM-------SVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIAR 177 Query: 171 TKMGRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFV 230 ++MGRA RA AE+ +A L+G+D NKVI TF +GA LAA+ GV+ A +GF+ Sbjct: 178 SRMGRACRACAEDMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFI 237 Query: 231 PGLKAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLI 290 G+KAF+AAVLGGIG+I GAMLGG+LLGL E+ AGY L S Y+D+ +F +L+ Sbjct: 238 AGIKAFTAAVLGGIGSIPGAMLGGVLLGLAETFAAGY--------LPSEYKDVVSFGLLV 289 Query: 291 IVLTLRPSGIMGE 303 ++L RP+G++G+ Sbjct: 290 LILLFRPTGLLGK 302 Lambda K H 0.328 0.144 0.416 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: 317 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