Align The glucose uptake porter, GluP (characterized)
to candidate WP_058857557.1 AS188_RS02770 sugar porter family MFS transporter
Query= TCDB::Q0SE66 (483 letters) >NCBI__GCF_001482365.1:WP_058857557.1 Length = 471 Score = 557 bits (1435), Expect = e-163 Identities = 285/457 (62%), Positives = 351/457 (76%), Gaps = 4/457 (0%) Query: 21 SVPVRIAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASALLGAAAGAMLA 80 S +RI+++AA GG LFGYDSAVINGAVSAI+ +F V LGFA+ASALLGAAAGA Sbjct: 17 SAVLRISIIAAFGGFLFGYDSAVINGAVSAIQEEFGVSPGPLGFAVASALLGAAAGAFFG 76 Query: 81 GRIADRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIAE 140 GRIADR GR+ M+ AAV+FL+SAIG G + E L+ +R+VGG+GVG+AS+IAPAYIAE Sbjct: 77 GRIADRLGRVPVMKIAAVLFLVSAIGCGVVESFEWLIFWRVVGGVGVGVASIIAPAYIAE 136 Query: 141 ISPARVRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEAWRWMFLAMCVP 200 I+PA VRGRLGSLQQ+ IV GIF+SL VD LAA+AGGS E LW+GLEAWRWMF+A VP Sbjct: 137 IAPASVRGRLGSLQQMGIVLGIFISLAVDAWLAALAGGSGEPLWWGLEAWRWMFMAEAVP 196 Query: 201 ALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRSTLARETQPSIR 260 ALAY + + TIPESPRYL+A+GR EAR +L L GE ++ I+ TL E +P + Sbjct: 197 ALAYLIGAFTIPESPRYLVAEGRADEARAVLTDLQGEASATERVRLIQQTLRTERKPRMS 256 Query: 261 DLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSVVN 320 DLKG GL PIVW+GIGL+ QQFVGINVIFYYS+VLWQ+VGF E S ITVITSV N Sbjct: 257 DLKGRMAGLKPIVWVGIGLAALQQFVGINVIFYYSNVLWQSVGFTEADSFTITVITSVTN 316 Query: 321 IATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQGP 380 + T++AIA ++RVGRR LL+IGS GM + L T+A IF TA +VDG P L GP Sbjct: 317 VVVTVVAIALVERVGRRRLLLIGSGGMTLMLGTLAVIFATA--PLVDG--APVLGPTAGP 372 Query: 381 IALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPSMK 440 +ALVAANLFVV FG+SWGP++WVLLGE FPN+IR AAL++A QW ANW++TVTFP++ Sbjct: 373 VALVAANLFVVFFGVSWGPMMWVLLGEMFPNQIRGAALAVAGFVQWIANWVVTVTFPALA 432 Query: 441 DFSLGISYGFYAVCAVLSLVFVLRWVKETKGVELEAM 477 SLG++YG YA A++SL+F +R V+ET G+ELE M Sbjct: 433 AASLGLAYGLYAFFALVSLLFTIRMVRETTGIELEDM 469 Lambda K H 0.324 0.138 0.405 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: 746 Number of extensions: 29 Number of successful extensions: 2 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: 483 Length of database: 471 Length adjustment: 33 Effective length of query: 450 Effective length of database: 438 Effective search space: 197100 Effective search space used: 197100 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