Align GluB aka CGL1951, component of Glutamate porter (characterized)
to candidate WP_062734864.1 AYX06_RS05070 glutamate ABC transporter substrate-binding protein
Query= TCDB::P48242 (295 letters) >NCBI__GCF_001580365.1:WP_062734864.1 Length = 282 Score = 197 bits (502), Expect = 2e-55 Identities = 120/262 (45%), Positives = 158/262 (60%), Gaps = 21/262 (8%) Query: 18 ALAGVTLTACGDSSGGDGFLAAIENG----SVNVGTKYDQPGLGLRNPDNSMSGLDVDVA 73 A A +TLTACG GG E G SV +G KYDQPGLG R+ D +G DVDVA Sbjct: 14 AAAALTLTACG---GGGEQAGGGETGGSGESVRIGIKYDQPGLGFRDGDQ-YTGFDVDVA 69 Query: 74 EYVVNSIADDKGWDHPTIEWRESPSAQRETLIQNGEVDMIAATYSINAGRSESVNFGGPY 133 +YV N + G+ IEW ESPSA RE ++ N +VDMI ATYSI R ++V+F GPY Sbjct: 70 KYVANEL----GYAEDQIEWVESPSANRENMLANDQVDMIFATYSITEERDQTVDFAGPY 125 Query: 134 LLTHQALLVRQDDDRIETLEDLDNGLILCSVSGSTPAQKVKDVLPGVQLQEYDTYSSCVE 193 + Q LLVR DD I +DL+ G LCSV+GST AQKVK+ PG L E Y+ C+ Sbjct: 126 FVAGQDLLVRSDDTSITGPDDLE-GKNLCSVTGSTSAQKVKEDQPGANLVEQPGYADCLT 184 Query: 194 ALSQGNVDALTTDATILFGY--SQQYEGDFRVVEMEKDGEPFTDEYYGIGLKKDDQEGTD 251 AL G VDA+TTD IL G ++ +G F+VV G F++E YG+GL + + + Sbjct: 185 ALESGQVDAVTTDDIILAGLAATEANQGKFKVV-----GNTFSEERYGVGLPQGSDQ-CE 238 Query: 252 AINAALERMYADGTFQRLLTEN 273 A+N A+ +M +G ++ +T N Sbjct: 239 AVNEAITKMIDEGAWEEAVTAN 260 Lambda K H 0.312 0.133 0.378 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: 273 Number of extensions: 21 Number of successful extensions: 5 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: 295 Length of database: 282 Length adjustment: 26 Effective length of query: 269 Effective length of database: 256 Effective search space: 68864 Effective search space used: 68864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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