Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate WP_012385980.1 BIND_RS15555 periplasmic binding protein/LacI transcriptional regulator
Query= uniprot:D8IZC6 (316 letters) >NCBI__GCF_000019845.1:WP_012385980.1 Length = 309 Score = 281 bits (719), Expect = 1e-80 Identities = 147/303 (48%), Positives = 206/303 (67%), Gaps = 4/303 (1%) Query: 13 LLLAAAAQPAMAAD---KPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSS 69 +L+AAAA M A K LKS+G+++ + NP+FVA+AKGA + A KINP+ K+ + Sbjct: 4 VLVAAAAVALMTAHASAKDLKSIGLSLASMDNPYFVAMAKGATASAQKINPNVKINTLDF 63 Query: 70 KYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAGADVTV 129 YDLN Q QI++ IA+ VDLI+LN D + PA+++A AGI V+AVD AA GAD+T+ Sbjct: 64 DYDLNKQATQIDSLIASGVDLILLNPGDPAALEPAIQRAHAAGIPVIAVDAAAKGADITI 123 Query: 130 MSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSPGIKILSDNQ 189 +DN AG +C+++ +KL GKGNV+I NGP VS+V +RV GCK +P I +LS +Q Sbjct: 124 TTDNRQAGEIACQYIVDKLGGKGNVIIQNGPQVSSVRERVEGCKKALANAPEIAVLSSDQ 183 Query: 190 NAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKWISGVDGAPD 249 NA GS GM M + L+ KIDAVF IND AIG++ A ++ R+D+ I+ VDGAPD Sbjct: 184 NAKGSHRHGMNVMQDHLSQFAKIDAVFTINDRQAIGSDFAAQRLHRNDL-IITSVDGAPD 242 Query: 250 AERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKLITRDNVADY 309 E ALK + AS +QDPY +A +V +G ++NG+ P+Q V L+ KL+TR+NVA+Y Sbjct: 243 IEVALKAKNTCIHASASQDPYAIAQLAVDLGNDLLNGKKPEQDVILIAPKLVTRENVAEY 302 Query: 310 QGW 312 +GW Sbjct: 303 KGW 305 Lambda K H 0.314 0.129 0.360 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: 253 Number of extensions: 6 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: 316 Length of database: 309 Length adjustment: 27 Effective length of query: 289 Effective length of database: 282 Effective search space: 81498 Effective search space used: 81498 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 (22.0 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