Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate BWI76_RS21205 BWI76_RS21205 MFS transporter
Query= TCDB::P15729 (468 letters) >FitnessBrowser__Koxy:BWI76_RS21205 Length = 478 Score = 287 bits (735), Expect = 5e-82 Identities = 182/469 (38%), Positives = 267/469 (56%), Gaps = 22/469 (4%) Query: 8 SQSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQ-TDSLLTGLSVSLALLG 66 +Q+ + +V I VAA GG LFG+D VI GA + F TD +G ++S AL+G Sbjct: 4 AQTHLKMGYVWTICLVAACGGLLFGYDWVVIGGAKPFYEAWFSITDPAQSGWAMSSALVG 63 Query: 67 SALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASV 126 GA +G AD+ GR +IL+AVLF+ S+ G+ + + F+ +R++GG+G+G AS Sbjct: 64 CVFGALISGWCADKLGRKLPLILSAVLFSASAWGTAVASSFDMFVVYRIVGGVGIGLASA 123 Query: 127 IAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIA-LMAGGSAQ----NPWLFG 181 ++P YIAEVSPA RGR ++ QL IV G+ A L N IA +A G+ Q W G Sbjct: 124 LSPLYIAEVSPAEKRGRFVAVNQLTIVIGVLAAQLINLMIAEPVATGATQQMIVETW-NG 182 Query: 182 AAAWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGDVPSRI-EE 240 WRWMF EL+PAL + V F +PESPR+L+ G+ E+A A L ++ D RI + Sbjct: 183 QMGWRWMFGAELVPALAFLVLMFFVPESPRWLMKAGKPERARAALERIGSADYADRILRD 242 Query: 241 IQATVSLD-HKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFT 299 I T+ D HK + LL+ + + PIV IGM L+ QQ+ GINVIF Y+ ++ S GF Sbjct: 243 IAHTLEKDNHKVSYGALLAPQ--VKPIVIIGMVLAVFQQWCGINVIFNYAQEIFASAGFD 300 Query: 300 EEKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVN 359 +L V TG +N++ TL A+ VDK GR+ L+L+G+ G+T+ +++ + A + Sbjct: 301 INSTLKSIVATGVVNLVFTLAALPLVDKIGRRKLMLLGASGLTLIYVLIAGAY--AMGIM 358 Query: 360 GQPTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIAN 419 G P L IA+ + + P+ WVLL E+F N++R A+S+ WIA Sbjct: 359 GWPVLLLVLAAIAI---------YALTLAPVTWVLLAEIFPNRVRGLAMSLGTLALWIAC 409 Query: 420 FIISTTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 F+++ TFP L +G ++ LY A +I V ETKG TLE + Sbjct: 410 FLLTYTFPLLNAGLGAAGSFLLYGVICAAGYLYILRNVPETKGVTLEAL 458 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: 570 Number of extensions: 30 Number of successful extensions: 5 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: 478 Length adjustment: 33 Effective length of query: 435 Effective length of database: 445 Effective search space: 193575 Effective search space used: 193575 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