Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_066326767.1 BLR17_RS06040 sugar porter family MFS transporter
Query= TCDB::P15729 (468 letters) >NCBI__GCF_900100165.1:WP_066326767.1 Length = 439 Score = 265 bits (678), Expect = 2e-75 Identities = 155/456 (33%), Positives = 255/456 (55%), Gaps = 28/456 (6%) Query: 15 KFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSV-SLALLGSALGAFG 73 K ++ S VA+ GFLFGFDT VI+GA ALQ + + G V ++AL G+ +GA Sbjct: 3 KKIMSWSIVASFAGFLFGFDTVVISGADKALQILWDSSDFFHGSVVMAMALWGTVIGAIF 62 Query: 74 AGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIA 133 G ++ GR T+++ +LF++S++GS L W F F+R +GG+G+GA+++ APAYI+ Sbjct: 63 GGIPTNKIGRKSTLLIIGILFSISALGSSLANGPWIFAFFRFIGGLGIGASTIAAPAYIS 122 Query: 134 EVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTEL 193 E++PA RGRL L Q IV GI A LSN+ ++ + G AWRWM ++ Sbjct: 123 EIAPAKDRGRLVGLYQFNIVFGILTAFLSNYLLSDI-----------GENAWRWMLGIQV 171 Query: 194 IPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGDVPSRIEEIQATVSLDHKPRF 253 P+++Y V AF IPESPR+L+ Q Q ++A IL K+ + ++ I +S D+K Sbjct: 172 FPSVVYTVLAFYIPESPRWLLTQSQIDEARVILNKINSKE---DVQSIIDNISEDNKNTS 228 Query: 254 SD-LLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVITGF 312 SD + + P++ + + ++A Q GIN YY+ ++ G + +LL ++ GF Sbjct: 229 SDENIFMKKYSFPLILVFL-IAAFNQLSGINAFLYYAPRIFEEAGLGAKTALLSSIGIGF 287 Query: 313 INILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIA 372 +N++ TL+ + +D+ GR+ L++ GS+G +L ++++ F + TG A I Sbjct: 288 VNLIFTLIGVYLIDRLGRRKLMIFGSLGYIFSLSMVAISF--------YLSWTGMAVPIF 339 Query: 373 LVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDT 432 L +++ S G ++WV + E+F N +RA+ S + V W+ II + P L Sbjct: 340 LF---VFIASHAIGQGAVIWVFISEIFPNHLRASGQSFGSSVHWVLAAIIPSMVPILFSN 396 Query: 433 VGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 G+G + +A + F+ F + ETKG +LE M Sbjct: 397 FGVGNVFSFFAIMMVFQLVFVLFMMPETKGVSLESM 432 Lambda K H 0.325 0.140 0.430 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: 559 Number of extensions: 33 Number of successful extensions: 6 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: 468 Length of database: 439 Length adjustment: 33 Effective length of query: 435 Effective length of database: 406 Effective search space: 176610 Effective search space used: 176610 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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