Align The glucose uptake porter, GluP (characterized)
to candidate BWI76_RS21205 BWI76_RS21205 MFS transporter
Query= TCDB::Q0SE66 (483 letters) >FitnessBrowser__Koxy:BWI76_RS21205 Length = 478 Score = 303 bits (776), Expect = 9e-87 Identities = 183/460 (39%), Positives = 267/460 (58%), Gaps = 25/460 (5%) Query: 26 IAVVAALGGLLFGYDSAVINGAVSAIEGKFQV-DSALLGFAIASALLGAAAGAMLAGRIA 84 I +VAA GGLLFGYD VI GA E F + D A G+A++SAL+G GA+++G A Sbjct: 16 ICLVAACGGLLFGYDWVVIGGAKPFYEAWFSITDPAQSGWAMSSALVGCVFGALISGWCA 75 Query: 85 DRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIAEISPA 144 D+ GR + + +AV+F SA GT A++ +M V +RIVGG+G+GLAS ++P YIAE+SPA Sbjct: 76 DKLGRKLPLILSAVLFSASAWGTAVASSFDMFVVYRIVGGVGIGLASALSPLYIAEVSPA 135 Query: 145 RVRGRLGSLQQLAIVTGIFVSLLVDYALA--AIAGGSQE---ELWFGLEAWRWMFLAMCV 199 RGR ++ QL IV G+ + L++ +A G +Q+ E W G WRWMF A V Sbjct: 136 EKRGRFVAVNQLTIVIGVLAAQLINLMIAEPVATGATQQMIVETWNGQMGWRWMFGAELV 195 Query: 200 PALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRSTLARETQPSI 259 PALA+ +L +PESPR+L+ G+ AR L + D + I TL ++ + Sbjct: 196 PALAFLVLMFFVPESPRWLMKAGKPERARAALERIGSADYADRILRDIAHTLEKDNH-KV 254 Query: 260 RDLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSVV 319 A + PIV IG+ L+VFQQ+ GINVIF Y+ ++ + GFD S+L+ V T VV Sbjct: 255 SYGALLAPQVKPIVIIGMVLAVFQQWCGINVIFNYAQEIFASAGFDINSTLKSIVATGVV 314 Query: 320 NIATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQG 379 N+ TL A+ +D++GRR L+++G++G+ + +A + G+ G Sbjct: 315 NLVFTLAALPLVDKIGRRKLMLLGASGLTLIYVLIAGAYA---------------MGIMG 359 Query: 380 PIALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPSM 439 L+ + + ++ PV WVLL E FPNR+R A+SL A W A +L+T TFP + Sbjct: 360 WPVLLLVLAAIAIYALTLAPVTWVLLAEIFPNRVRGLAMSLGTLALWIACFLLTYTFP-L 418 Query: 440 KDFSLGISYGF--YAVCAVLSLVFVLRWVKETKGVELEAM 477 + LG + F Y V +++LR V ETKGV LEA+ Sbjct: 419 LNAGLGAAGSFLLYGVICAAGYLYILRNVPETKGVTLEAL 458 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: 588 Number of extensions: 27 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: 483 Length of database: 478 Length adjustment: 34 Effective length of query: 449 Effective length of database: 444 Effective search space: 199356 Effective search space used: 199356 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 17 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