Align ABC transporter permease (characterized, see rationale)
to candidate HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__HerbieS:HSERO_RS08275 Length = 308 Score = 242 bits (618), Expect = 7e-69 Identities = 134/304 (44%), Positives = 196/304 (64%), Gaps = 13/304 (4%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 L QQ++NGL LG++YALIA+GYTMVYGII +INFAHGE+ MI + + + G G Sbjct: 8 LTQQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVTLTAI-GVQSG 66 Query: 64 APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123 P ++L A I++ +V + +E+VAYRPLR PRL PLI+AIGMSI LQ I Sbjct: 67 YPLPLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQ 126 Query: 124 KPNYKPYPTMLPSS-PFEIGGAF---ITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 P ++ + F++G F I ++++I+GVT V + +L + + +GRA RA Sbjct: 127 GARDMSVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIARSRMGRACRA 186 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 AE+ +A+L+G+ + VIS TF++GA+LAA+ G++ A G +GF+ G+KAFTAA Sbjct: 187 CAEDMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFIAGIKAFTAA 246 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 V GGIG++ GA++GG+LLGL E +GY L S Y D+ +F +L++IL RP+G Sbjct: 247 VLGGIGSIPGAMLGGVLLGLAETFAAGY--------LPSEYKDVVSFGLLVLILLFRPTG 298 Query: 300 LLGE 303 LLG+ Sbjct: 299 LLGK 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: 290 Number of extensions: 18 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