Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate HSERO_RS17565 HSERO_RS17565 glutamate/aspartate ABC transporter permease GltJ
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__HerbieS:HSERO_RS17565 Length = 241 Score = 87.4 bits (215), Expect = 4e-22 Identities = 44/130 (33%), Positives = 78/130 (60%) Query: 241 LSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALR 300 ++ +F +L L +T A + E +R GI S+P GQ A ALGLT QT +++P A+R Sbjct: 103 MTQQFVMAMLCLGMFTAARVCEQVRSGIESLPRGQKGAGLALGLTLGQTYLFVLLPMAMR 162 Query: 301 VIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVI 360 +++P L S+++ KNS++A +G +L A + ++ T +P E F+ + L Y+ IN + Sbjct: 163 IVLPPLTSEFLNIFKNSAVASTIGLLELAAQGRQLVDYTAQPYEAFIAVTLAYMLINICV 222 Query: 361 SAGMNGLQQR 370 + M L+++ Sbjct: 223 MSLMRILERK 232 Score = 45.4 bits (106), Expect = 2e-09 Identities = 26/77 (33%), Positives = 39/77 (50%) Query: 74 TADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTP 133 T +Y L+ GL ++ + IL V+GT G+ N L + YV + RN P Sbjct: 16 TGQTYLDWLLSGLGVTVALGLSAWILALVLGTFLGILRTLPNRALSGFAACYVELFRNVP 75 Query: 134 LLLQLIVWYFPILLSLP 150 LL+Q+ +WYF + LP Sbjct: 76 LLVQIFIWYFAMPELLP 92 Lambda K H 0.326 0.140 0.445 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: 219 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 241 Length adjustment: 27 Effective length of query: 350 Effective length of database: 214 Effective search space: 74900 Effective search space used: 74900 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