Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate WP_094508947.1 CEV31_RS17420 carbohydrate ABC transporter permease
Query= reanno::Smeli:SMc04257 (305 letters) >NCBI__GCF_002252445.1:WP_094508947.1 Length = 278 Score = 130 bits (326), Expect = 5e-35 Identities = 87/288 (30%), Positives = 142/288 (49%), Gaps = 14/288 (4%) Query: 20 KPRRTLSRRNIIVYGTLIVV-ALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPW 78 +P R LSR +I T++++ A+ LLP +V S K +I FA + F+P Sbjct: 3 RPPRFLSRYEVIFANTVVILLAIMTLLPFLWFVVMSFKPADQI-----FAGVDGLFFKPT 57 Query: 79 VKAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTIL 138 ++ + GL + R WNS+ + S ++++ I YAL+ K ++ Sbjct: 58 LENYE----GLVTERFMRSMWNSIVTSTVSTVLALVIGIPGAYALSRASLKRDRSLSLLI 113 Query: 139 IVGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFK 198 + P P +V R +G+ T TGLIIV+ F + ++ L RN+F P EL + Sbjct: 114 LASRMAPPVAFAIPYFLVYRNLGILDTKTGLIIVYLTFNLALVVWLMRNFFDATPRELEE 173 Query: 199 AARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNN 258 AA +DGA W + +I+LPMS P V +L WNDF F + TR V++ N Sbjct: 174 AAWIDGASLWGTFIRIVLPMSGPAVVTTGMLCFLYSWNDFFFALTLTRNNAMTAPVEVVN 233 Query: 259 IVNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLF-VRGIAAGAVKG 305 +N +G + + T++ + P+ ++ + R + V G+ AGAVKG Sbjct: 234 FMN-YEGWEWGKIAAGGTLI--MAPVLIFSLLMRKYLVAGMTAGAVKG 278 Lambda K H 0.329 0.145 0.450 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: 232 Number of extensions: 10 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: 305 Length of database: 278 Length adjustment: 26 Effective length of query: 279 Effective length of database: 252 Effective search space: 70308 Effective search space used: 70308 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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