Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= TCDB::P48244 (228 letters) >FitnessBrowser__psRCH2:GFF3103 Length = 394 Score = 79.3 bits (194), Expect = 1e-19 Identities = 42/126 (33%), Positives = 71/126 (56%) Query: 101 VLGFILYTSTFVAESLRSGINTVHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGN 160 V+ +YT+ F+ E++RSGI +V GQ EAA SLGL G R +I PQA+R + PL + Sbjct: 266 VVALSVYTAAFIGETVRSGIQSVSHGQTEAAASLGLRPGQVLRLVIVPQALRVIVPPLTS 325 Query: 161 TLIALTKNTTIASVIGVGEASLLMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKL 220 + L KN+++A+ IG + L T+ N AI ++ +++ + L + Sbjct: 326 QYLNLAKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETMAITMSVYLAISISISLLMNWY 385 Query: 221 SERLAV 226 ++R+A+ Sbjct: 386 NKRIAL 391 Score = 37.0 bits (84), Expect = 5e-07 Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 4/68 (5%) Query: 16 FWVTIKLTIY-SAIG---AMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLFC 71 FWV + T+ S IG A + G IL R+S ++R L+T YI RN P L++ F Sbjct: 85 FWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEIFRNIPPLLLIFFV 144 Query: 72 SFGLYQNL 79 F + L Sbjct: 145 YFAVISPL 152 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: 240 Number of extensions: 17 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: 228 Length of database: 394 Length adjustment: 27 Effective length of query: 201 Effective length of database: 367 Effective search space: 73767 Effective search space used: 73767 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