Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate WP_084704737.1 BS73_RS17900 carbohydrate ABC transporter permease
Query= TCDB::Q97UY9 (287 letters) >NCBI__GCF_000744815.1:WP_084704737.1 Length = 247 Score = 106 bits (265), Expect = 4e-28 Identities = 75/252 (29%), Positives = 123/252 (48%), Gaps = 13/252 (5%) Query: 32 MLINGFKSNFEVLSTPVLVPPTKITFEAYVSVLLSLAKPLINSL---IIVIPTSFISAFL 88 M+I + + E+ L P + +V V + PL ++L +IV + + L Sbjct: 1 MVITSLRPSNELRDNTFL--PHHFQWSTFVDVWKNQQVPLGDNLRVTLIVAACATVLVLL 58 Query: 89 GAMGAYFFYTLSYSFSRASSAISDVLFSLISLATFIPQEATLLP-LTRLIVSMGLLDSYI 147 ++ A ++ + R LF L+ L T + Q A+L+ L R LLD+ Sbjct: 59 VSLPAAYYTARNRYRGRR-------LFLLLVLVTQMFQPASLVVGLYREFSQFNLLDTIW 111 Query: 148 GIIFALLIFYIPTGALLMSMFISVIPRSLIEAAKMDGTGDLKIFMKIVFPLSMPGFISTL 207 +I F + +++ +I IP L EAA +DGTG L ++ PL+MPG ++ + Sbjct: 112 VLILVNAAFNLAFAIWILTAYIGSIPAELEEAAMIDGTGRLGAMFRVTLPLAMPGVVTAM 171 Query: 208 IFIIIQAWNNFFIPLVLVTTPGMKLTSIAVLSYSGAYGTLYNDTFAAGMVASIIPLAIFV 267 IF I AWN F + L L TTP + ++ + S+ GAYG +N FA ++A I + +F Sbjct: 172 IFTFISAWNEFIMGLTLTTTPSHQPLTVGIDSFIGAYGVAWNQMFAGSVIAIIPVIILFA 231 Query: 268 FLGRYFIRGLMA 279 F+ R + GL A Sbjct: 232 FIERRVVSGLTA 243 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: 216 Number of extensions: 14 Number of successful extensions: 1 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: 247 Length adjustment: 25 Effective length of query: 262 Effective length of database: 222 Effective search space: 58164 Effective search space used: 58164 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 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