Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_011913471.1 PST_RS11845 cystine ABC transporter permease
Query= TCDB::P48244 (228 letters) >NCBI__GCF_000013785.1:WP_011913471.1 Length = 222 Score = 94.7 bits (234), Expect = 1e-24 Identities = 68/219 (31%), Positives = 109/219 (49%), Gaps = 21/219 (9%) Query: 10 PSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVL 69 P LL W T+ L++ ++ G L +R+ L+ L+ Y++ R TPL + + Sbjct: 14 PFLLKGAWWTVVLSLSGMFFGLLLGFGLALLRLYAFWPLQWLARVYVSFFRGTPLLVQLF 73 Query: 70 FCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQAE 129 +GL Q LG+ L + A++GF L + + AE LR+ I ++ GQ E Sbjct: 74 MIYYGLPQ-LGIQL-----------DPLPAALIGFSLNMAAYTAEILRAAIASIDRGQWE 121 Query: 130 AARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGE----ASLLMK 185 AA S+G+G T I PQA R A+ PLGN+ I+L K+T +A+ I V E A L+ Sbjct: 122 AAASIGMGRAQTLYRAILPQAARTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITA 181 Query: 186 ATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224 T E +F ++ A+ + +L + G+L R+ Sbjct: 182 RTFE-----IFTMYLAAALIYWLLASVLAYFQGRLEHRV 215 Lambda K H 0.327 0.139 0.397 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: 120 Number of extensions: 6 Number of successful extensions: 2 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: 228 Length of database: 222 Length adjustment: 22 Effective length of query: 206 Effective length of database: 200 Effective search space: 41200 Effective search space used: 41200 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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