Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component (characterized)
to candidate SMc00676 SMc00676 amino acid-binding periplasmic signal peptide protein
Query= reanno::Smeli:SMc02118 (341 letters) >FitnessBrowser__Smeli:SMc00676 Length = 331 Score = 402 bits (1033), Expect = e-117 Identities = 190/320 (59%), Positives = 243/320 (75%), Gaps = 2/320 (0%) Query: 22 ASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFDVDYCKAIAAAIFGDGSKVKYT 81 A AATLD VK +G ++CGV+ G+ GF+APD G WSGFD+D+C+A+AAA G KVKY Sbjct: 14 AQAATLDVVKQRGELRCGVSQGVLGFSAPDDKGEWSGFDIDFCRAVAAATLGSPDKVKYV 73 Query: 82 PLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRPVNYYDGQGFMVRKELDVKSAL 141 PLS KERF ALQSGEVD+L+R TTW+++RDT LG +F VNYYDGQ FMVR ++ VKS Sbjct: 74 PLSTKERFTALQSGEVDLLSRQTTWTLSRDTDLGMSFVGVNYYDGQAFMVRGDIGVKSVK 133 Query: 142 ELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLEEVNAAYDAGRCDVYTTDQSGL 201 ELSGA+VC +TGTTTE N+ADYF AN ++Y + FEK ++ A+++GRCDVY+TD S L Sbjct: 134 ELSGASVCTETGTTTEQNMADYFSANKIEYQVIAFEKADQTIQAFNSGRCDVYSTDASAL 193 Query: 202 YSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDIVSWVHYALVQAEEFGVTQANL 261 YS RLTL+ PD +VLPE+ISKEPL PAVRQGDDQWF +V W +A+++AEE G+T+ N Sbjct: 194 YSQRLTLNDPDRFVVLPEVISKEPLGPAVRQGDDQWFKVVRWTLFAMIEAEELGITRENA 253 Query: 262 EEMKKSTNPDVQRFLGVEADSKIGTDLGLTNEWAVNIVKAVGNYGEVFDRNIGAGSPLKI 321 + +S +RFLG+ D++ G LGL +WA V AVGNYGE+F+R++G S L+I Sbjct: 254 ASLLESGTAAQKRFLGI--DNEAGKALGLDPKWAYQTVAAVGNYGEIFERHLGKESALRI 311 Query: 322 ERGLNALWNKGGLQYAPPVR 341 +RGLN LWN GGL YAPPVR Sbjct: 312 DRGLNKLWNNGGLIYAPPVR 331 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: 379 Number of extensions: 15 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: 341 Length of database: 331 Length adjustment: 28 Effective length of query: 313 Effective length of database: 303 Effective search space: 94839 Effective search space used: 94839 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