Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component (characterized)
to candidate WP_009563564.1 RSPH17029_RS18145 amino acid ABC transporter substrate-binding protein
Query= reanno::Smeli:SMc02118 (341 letters) >NCBI__GCF_000015985.1:WP_009563564.1 Length = 345 Score = 344 bits (883), Expect = 2e-99 Identities = 174/338 (51%), Positives = 229/338 (67%), Gaps = 5/338 (1%) Query: 6 LTALVGAAVVGIGT--HAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFDVDY 63 L+ L + G GT A S TL VK +G V CGV+ GFAAPD+ G WSGF+VD+ Sbjct: 9 LSVLAALLLAGAGTAAFAQSGDTLAAVKERGEVLCGVHPARHGFAAPDSQGKWSGFEVDF 68 Query: 64 CKAIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRPVNY 123 C AIAAA+FGD +KV++ LS+++RFPA+QSGEVDVLARN T +++RDTALG NF P + Sbjct: 69 CHAIAAAVFGDANKVRFVALSSQQRFPAIQSGEVDVLARNVTATLSRDTALGLNFAPPIF 128 Query: 124 YDGQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLEEVN 183 Y G GF+VR ++ +L GAA+C+ G+TTE N+A F A L Y PVV E +++ Sbjct: 129 YTGTGFLVRAADGIEKVEDLDGAAICMAPGSTTERNVAQIFAARGLSYTPVVIENNKQLV 188 Query: 184 AAYDAGRCDVYTTDQSGLYSLR-LTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDIVS 242 AY GRCD T D++ L +R P DH++LP I SKEPLA AVRQGDD+W+D+V Sbjct: 189 DAYVTGRCDALTKDKAALPGVRAFDTEVPGDHVLLPGIYSKEPLAMAVRQGDDKWYDLVK 248 Query: 243 WVHYALVQAEEFGVTQANLEEMKKSTNPDVQRFLGVEADSKIGTDLGLTNEWAVNIVKAV 302 WV YA AEE GVTQAN++EMK S +PD+Q LGV D+ GT LG+ N+WA IVK V Sbjct: 249 WVTYATFNAEELGVTQANVDEMKASDDPDIQTLLGVIGDN--GTKLGVPNDWAYAIVKQV 306 Query: 303 GNYGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPV 340 GNY +++ R+ G +P+ ++R N LW +GGL Y P+ Sbjct: 307 GNYEDIYMRHFGPDTPVALDRDQNQLWTEGGLLYGFPM 344 Lambda K H 0.317 0.134 0.399 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: 390 Number of extensions: 16 Number of successful extensions: 3 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: 341 Length of database: 345 Length adjustment: 29 Effective length of query: 312 Effective length of database: 316 Effective search space: 98592 Effective search space used: 98592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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