Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::P48244 (228 letters) >MicrobesOnline__882:206399 Length = 337 Score = 103 bits (258), Expect = 3e-27 Identities = 71/225 (31%), Positives = 117/225 (52%), Gaps = 23/225 (10%) Query: 12 LLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLFC 71 LL W+T+++++ + I ++ G + R+S LR L+ YI +R +PL + V Sbjct: 127 LLEGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLLVQVFLW 186 Query: 72 SF-------GLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVH 124 F L++ +GL+ V+ ++T +VAE +R+GI +VH Sbjct: 187 YFVVGTLLNALFEKVGLSAIPP----------LWYGVMALAIFTGAYVAEIVRAGIQSVH 236 Query: 125 FGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASLLM 184 GQ EAARSLG+ + + R +I PQA R + PL I+L K++++ VI V E L Sbjct: 237 RGQMEAARSLGMSYAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRE---LT 293 Query: 185 KATIENHANML--FVVFAIFAVGFMILTLPMGLGLGKLSERLAVK 227 KAT E L F ++ + A+ +++LT + L + L ER AV+ Sbjct: 294 KATREVVTTSLQPFELWIVCALLYLVLTFTLSLCVQYL-ERRAVR 337 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: 160 Number of extensions: 8 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: 337 Length adjustment: 25 Effective length of query: 203 Effective length of database: 312 Effective search space: 63336 Effective search space used: 63336 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: 47 (22.7 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