Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate CCNA_00857 CCNA_00857 glucose/fructose transport protein
Query= TCDB::P15729 (468 letters) >FitnessBrowser__Caulo:CCNA_00857 Length = 478 Score = 452 bits (1162), Expect = e-131 Identities = 233/458 (50%), Positives = 315/458 (68%), Gaps = 4/458 (0%) Query: 13 NVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSALGAF 72 N+ FV I VA +GGF+FG+D+ VING L+ F L TGL+V L+G A+GAF Sbjct: 21 NMTFVAAIVAVATIGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLNVGAILIGCAIGAF 80 Query: 73 GAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYI 132 AG +AD GR MI++A+LF +S+IG+G + FI +R++GG+GVGAASV+ P YI Sbjct: 81 AAGRLADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLCPVYI 140 Query: 133 AEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTE 192 +EV+PA++RGRL S+QQ+ I++G+ A ++N+ +A AG S WL G AWRWMFW + Sbjct: 141 SEVTPANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWL-GLPAWRWMFWMQ 199 Query: 193 LIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEG-GDVPSRIEEIQATVSLDHKP 251 +IPA ++ +C IPESPRYLVA+G+ +A AIL ++ G G ++EEI+A++S DHKP Sbjct: 200 IIPAGVFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVEEIRASLSADHKP 259 Query: 252 RFSDLLSRRGGLLPIV-WIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVIT 310 FSDLL L ++ W G+ L+ QQ VGIN++FYY SVLW+SVGFTE+ SL I +++ Sbjct: 260 TFSDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTEDDSLKINILS 319 Query: 311 GFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGI 370 G ++IL L+AI +DK GRKPLLL+GS GM +TLG+L+ F AT VNG TL G+ Sbjct: 320 GTLSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATTVNGALTLGDQIGL 379 Query: 371 IALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLL 430 AL+ ANLYV F SWGP++WV+LGEMF N++R +AL+V QWIANF IS +FP L Sbjct: 380 TALIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPALA 439 Query: 431 DTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 L YG YA SA +S F + V ET+GK LE M Sbjct: 440 -AASLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAM 476 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: 643 Number of extensions: 32 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: 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