Align The major glucose (or 2-deoxyglucose) uptake transporter, GlcP (characterized)
to candidate WP_066326777.1 BLR17_RS06000 sugar porter family MFS transporter
Query= TCDB::Q7BEC4 (472 letters) >NCBI__GCF_900100165.1:WP_066326777.1 Length = 439 Score = 239 bits (611), Expect = 1e-67 Identities = 155/459 (33%), Positives = 249/459 (54%), Gaps = 41/459 (8%) Query: 24 IFI-AAAAAMGGFLFGYDSSVINGAVEAIRDRYDVGSAVLAQVI-AVALIGCAIGAATAG 81 IFI A A++ GFLFG+D+ VI+GA + ++ ++ A V+ +AL G IGA G Sbjct: 4 IFIWALVASLAGFLFGFDTVVISGADKKLQTLWNSSDAFHGTVVMGMALWGTVIGAIFGG 63 Query: 82 RIADRIGRIRCMQIAAVLFTVSAVGSALPFALWDLAMWRIIGGFAIGMASVIGPAYIAEV 141 +RIGR + +LF SA+GSAL + A +R +GG +G +++ PAYI+E+ Sbjct: 64 IPTNRIGRKNTLLWIGILFFFSAIGSALANGPYVFAAFRFVGGLGVGASTIAAPAYISEI 123 Query: 142 SPPAYRGRLGSFQQAAIVIGIAVSQLVNWGLLNAAGGDQRGELMGLEAWQVMLGVMVIPA 201 +P RG+L +F Q IV+GI ++ L N+ L N +G +W+ M+GV P+ Sbjct: 124 APAKDRGKLVAFYQFNIVLGILIAFLSNYLLRN----------VGENSWRWMMGVQAFPS 173 Query: 202 VLYGLLSFAIPESPRFLISVGKRERAKKILEEVEGKDVDFDARVTEIEHAMHREEKSSFK 261 +Y +L F+IP+SPR+L+S + E AK +L+ + G + DF+ +I + ++ Sbjct: 174 FIYSVLIFSIPKSPRWLLSKNRDEEAKSVLQRM-GLEADFEEMKKDI------DADNANA 226 Query: 262 DLLGGSFFFK----PIVWIGIGLSVFQQFVGINVAFYYSSTLWQSVGVDPADSFFYSFTT 317 L S F K P++ + ++ F Q GIN YYS+ ++Q G+ + + S Sbjct: 227 ALANDSIFLKKYRTPLI-LAFLIAFFNQLSGINAFLYYSNRIFQEAGLGESTALLSSIGI 285 Query: 318 SIINIVGTVIAMIFVDRVGRKPLALIGSVGMVIGLALEAWAFSFDLVDGKLPATQGWVAL 377 ++N+V T++ + +DR+GRK L IGSVG +I L L A AF QG + Sbjct: 286 GVVNLVFTLLGVFLIDRLGRKILMYIGSVGYIISLTLVAMAFFLH--------WQGIMVP 337 Query: 378 IAAHVFVLFFALSWGVVVWVFLGEMFPNRIRAAALGVAASAQWIANWAITASFPSLADWN 437 + +F+ A+ G V+WVF+ E+FPN +RA+ ++ WI + A PSL + Sbjct: 338 VFLFLFIAAHAIGQGAVIWVFISEIFPNHLRASGQAFGSTTHWI----LAAIIPSLIPFL 393 Query: 438 LS--GTYVIYTIFAAL---SIPFVLKFVKETKGKALEEM 471 S G V++ FA + + FV + ETKG +LEE+ Sbjct: 394 FSTIGAGVVFLFFAIMMVFQLFFVAFLMPETKGISLEEL 432 Lambda K H 0.326 0.139 0.426 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: 655 Number of extensions: 41 Number of successful extensions: 7 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: 472 Length of database: 439 Length adjustment: 33 Effective length of query: 439 Effective length of database: 406 Effective search space: 178234 Effective search space used: 178234 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