Align Extracellular solute-binding protein, family 7 (characterized, see rationale)
to candidate WP_092345287.1 BLU87_RS04925 TRAP transporter substrate-binding protein DctP
Query= uniprot:Q48AL6 (362 letters) >NCBI__GCF_900107645.1:WP_092345287.1 Length = 385 Score = 204 bits (520), Expect = 2e-57 Identities = 109/319 (34%), Positives = 176/319 (55%), Gaps = 9/319 (2%) Query: 32 KKYRWKLAETWGPNFPIFGDATKNMAKMVKEMSNGRLTIRIDSSNKHKSALGIFDFVKSG 91 +K++WK+ W +F D ++ A VK S GRL I++ S+ + A+ FD V G Sbjct: 51 EKFKWKMVMPWSKGL-LFYDVAQHFADSVKLASGGRLDIKLFSAGELVGAMESFDAVSKG 109 Query: 92 QYQMGHSASYYWKGKNFNTMFFTTVPFGMIASEQHAWFYYGGGMELMKKVYDQYGIMSFP 151 Q +GH YWKGKN + F +VP G+ A + W + GG+E+M+++Y +Y + + P Sbjct: 110 QADIGHDWPGYWKGKNEAFVAFASVPMGLDAEGYNIWLFERGGLEMMQEMYGRYNLFALP 169 Query: 152 GGNTGNQMGGWFKKEINSVEDLKGLKMRIPGFAGEVLAKLGAKPTNIPSGELYTALERNT 211 GGN G ++G + K+ + +ED KG+++R G+ ++L LGA T +P GE+Y ALER Sbjct: 170 GGNVGQELGLFSNKKASKIEDFKGMRVRTAGWYMDILTNLGASVTPLPGGEVYLALERGV 229 Query: 212 IDALEWVGPSLDLRMGFHKIAPY-YYTGWHEPGTELQFMVNQKAYNSLPKDLQKILTVAM 270 IDA E+ P+++ MGF I Y G H+P + F +NQ +YN LP DL+ IL +A Sbjct: 230 IDAAEFSTPAMNYPMGFDDITKYVIQPGVHQPSCQSAFFINQDSYNKLPDDLKWILDIAA 289 Query: 271 KAAAY--DMYSQSMHASGVNLASLKKDYPNVQMRSFPKPVMEAIVQANDELLEEFAAKDP 328 K + +++ ++A V L K ++ + S + A +A+ E LE AK P Sbjct: 290 KETQLWSNAWAEDLNAKAVKLFKEKVEFVRMDEAS-----ITAFAKASHEYLEGLKAKYP 344 Query: 329 MTAEILKSLNDYKHQIRAW 347 +++ S + +K W Sbjct: 345 DVKKVMDSQDQFKADFADW 363 Lambda K H 0.318 0.133 0.402 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: 347 Number of extensions: 12 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: 362 Length of database: 385 Length adjustment: 30 Effective length of query: 332 Effective length of database: 355 Effective search space: 117860 Effective search space used: 117860 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 (21.7 bits) S2: 50 (23.9 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