Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component (characterized)
to candidate GFF3104 Psest_3163 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain
Query= reanno::Smeli:SMc02118 (341 letters) >FitnessBrowser__psRCH2:GFF3104 Length = 342 Score = 445 bits (1145), Expect = e-130 Identities = 216/337 (64%), Positives = 264/337 (78%), Gaps = 3/337 (0%) Query: 6 LTALVGAAVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFDVDYCK 65 L L A+++GI A + ATLD V+ KGFVQCG++ GL GF+ DA G + G DVD C+ Sbjct: 8 LAVLGAASLLGISGLAQAGATLDAVQKKGFVQCGISDGLPGFSFADAKGKYQGIDVDICR 67 Query: 66 AIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRPVNYYD 125 A+AAA+FGD SKVKY+PL+AKERF ALQSGEVDVL+RNTTW+ +RD A+G NF V YYD Sbjct: 68 AVAAAVFGDASKVKYSPLTAKERFTALQSGEVDVLSRNTTWTSSRDAAMGLNFTGVTYYD 127 Query: 126 GQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLEEVNAA 185 GQGF+V KEL V SA EL GA VC+Q GTTTELNL+DYF+AN +Y P+ ++ +E + Sbjct: 128 GQGFLVNKELGVSSAKELDGATVCIQAGTTTELNLSDYFRANGHKYTPITYDTSDESAKS 187 Query: 186 YDAGRCDVYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDIVSWVH 245 ++GRCDV T+DQS LY+ R+ L+KP D++VLPE+ISKEPL PAVRQGD++WFDIV W Sbjct: 188 LESGRCDVLTSDQSQLYAQRIKLAKPADYVVLPEVISKEPLGPAVRQGDEEWFDIVRWTL 247 Query: 246 YALVQAEEFGVTQANLEEMKKST-NPDVQRFLGVEADSKIGTDLGLTNEWAVNIVKAVGN 304 +A++ AEE GVT AN+EEM KST NPDV R LG A+ + G DL L +WAV IVK VGN Sbjct: 248 FAMLNAEELGVTSANVEEMAKSTKNPDVARLLG--AEGEYGKDLKLPKDWAVQIVKQVGN 305 Query: 305 YGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPVR 341 YGE+FDRN+GAGS LKIERGLNALWN GGLQYAPPVR Sbjct: 306 YGEIFDRNVGAGSELKIERGLNALWNNGGLQYAPPVR 342 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: 421 Number of extensions: 20 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: 342 Length adjustment: 29 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 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 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