Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate WP_011803054.1 PNAP_RS18455 carbohydrate ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >NCBI__GCF_000015505.1:WP_011803054.1 Length = 289 Score = 257 bits (657), Expect = 2e-73 Identities = 133/279 (47%), Positives = 188/279 (67%), Gaps = 11/279 (3%) Query: 1 MGRALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEA-- 58 + RALLY LL+ A FFL P Y+++ T+ K+ +I + P ++++R AW + Sbjct: 11 LSRALLYAVLLVAALFFLAPFYVMLATSFKDAEQIRSGNLLSPPASLNFDAWRLAWSSAC 70 Query: 59 -------FRPKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPY 111 +P F NSV +A+ A L+S G++NGYVL+ W FRGS LLF +LFG+F+P+ Sbjct: 71 TGVDCRGLQPYFWNSVSMAIPAVLISTAWGAVNGYVLSLWKFRGSELLFGFLLFGVFMPF 130 Query: 112 QSILIPLFQFMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAG 171 Q +L+P+ Q + +GL S+ GLVLVH + G+ TL FRNYY+ IP ELV AAR+DGAG Sbjct: 131 QVVLLPMSQVLGYLGLSSSIGGLVLVHCLAGMAGTTLFFRNYYTAIPKELVNAARMDGAG 190 Query: 172 FFGIFRHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLAG-GEAV 230 F+ IF ++LPLS P +V IWQFT IWN+FLF V + +S+PITV L +A +V Sbjct: 191 FWRIFWRIVLPLSTPILMVTLIWQFTNIWNDFLFGVAFSGADSKPITVGLNNMANTSSSV 250 Query: 231 K-WNLPMAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268 K +N+ MA A++A LPT+LVY+L G+YF++GL AG+VKG Sbjct: 251 KSYNVDMAAAVIAGLPTMLVYVLAGQYFVKGLTAGAVKG 289 Lambda K H 0.330 0.146 0.461 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: 309 Number of extensions: 10 Number of successful extensions: 3 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: 268 Length of database: 289 Length adjustment: 25 Effective length of query: 243 Effective length of database: 264 Effective search space: 64152 Effective search space used: 64152 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: 47 (22.7 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