Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate WP_086510783.1 BZY95_RS15420 carbohydrate ABC transporter permease
Query= TCDB::Q97UY9 (287 letters) >NCBI__GCF_002151265.1:WP_086510783.1 Length = 292 Score = 121 bits (304), Expect = 2e-32 Identities = 87/284 (30%), Positives = 137/284 (48%), Gaps = 23/284 (8%) Query: 15 YLALAIVSVIWLIPVYAMLINGFKSNFEVLS--------TPVLVPPTKITFEAYVSVLLS 66 Y L + ++ +L+P+ MLI K E+ P L P K EA + Sbjct: 20 YAVLLLAALFYLLPLAVMLITSVKPLAEITPGTLLSLPREPTLAPWGKAWGEACTGMRCE 79 Query: 67 -LAKPLINSLIIVIPTSFISAFLGAMGAYFFYTLSYSFSRASSAISDVLFSLISLATFIP 125 + NS+ IV+P IS +GA+ Y + ++ S++LF+L+ FIP Sbjct: 80 GIGVYFFNSIAIVVPAVLISTAIGALNGY-------ALTKWRFKGSELLFALMLFGCFIP 132 Query: 126 QEATLLPLTRLIVSMGLLDSYIGIIFALLIFYIPTGALLMSMFISVIPRSLIEAAKMDGT 185 + LLP+ + + +GL S G+I +IF I L F +P L+ AAK+DG Sbjct: 133 FQVVLLPMAQTLGWLGLSSSRAGLILVHVIFGIAFTTLFFRNFYVAVPTELVSAAKLDGA 192 Query: 186 GDLKIFMKIVFPLSMPGFISTLIFIIIQAWNNFFIPLVLV---TTPGMKLTSIAVLSYSG 242 G +IF +I+ P+S P + ++I+ Q WN+F + T P + V + +G Sbjct: 193 GFFRIFWRILLPVSAPIIVVSVIWQFTQIWNDFLFGVAFSAHNTQPVTVALNNLVNTSTG 252 Query: 243 AYGTLYNDTFAAGMVASIIPLAIFVFLGRYFIRGLMALGGGGKG 286 A YN AA M+A++ L ++V G+YF+RGL A G KG Sbjct: 253 A--REYNVDMAAAMIAALPTLIVYVLAGKYFVRGLTA--GSVKG 292 Lambda K H 0.330 0.144 0.417 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: 254 Number of extensions: 19 Number of successful extensions: 4 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: 287 Length of database: 292 Length adjustment: 26 Effective length of query: 261 Effective length of database: 266 Effective search space: 69426 Effective search space used: 69426 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 Apr 09 2024. 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