Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_089216461.1 CHB69_RS13190 sugar porter family MFS transporter
Query= TCDB::P15729 (468 letters) >NCBI__GCF_900188185.1:WP_089216461.1 Length = 475 Score = 394 bits (1011), Expect = e-114 Identities = 207/463 (44%), Positives = 294/463 (63%), Gaps = 4/463 (0%) Query: 8 SQSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGS 67 ++++ N+ + I VA +GG LFG+D+ +NG L+ F D G +V LLG Sbjct: 4 ARTSVNMALISAIVAVATIGGLLFGYDSGAVNGTQEGLKTAFALDDAALGFTVGSLLLGC 63 Query: 68 ALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVI 127 A GAF AG +AD GR K M++AA LF + ++ GL F+ R GG+ VGAASV+ Sbjct: 64 AAGAFFAGRLADLMGRRKVMLIAAALFVVGALIQGLTTVHALFVVARFAGGMAVGAASVL 123 Query: 128 APAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRW 187 +P YI+EV+PA++RGRL ++QQ+ I++G+ A + N+ + AG S + + G AWRW Sbjct: 124 SPLYISEVAPANIRGRLTTVQQVMIITGLTAAFVVNYMLQQAAGSSLGD--IAGRPAWRW 181 Query: 188 MFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEG-GDVPSRIEEIQATVS 246 M+ + IPA+++ V F IPESPR+LV G+ E+A +L ++ G + +I EI+A+ S Sbjct: 182 MYLAQAIPAVVFLVALFFIPESPRHLVGTGRDEQARGVLTRLFGSAEADRKIGEIRASFS 241 Query: 247 LDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLI 306 DH+PR +D+ + PIVW G+ L+ QQFVGINVIFYY LW+ G +E +L Sbjct: 242 EDHRPRLADVTAPGTIFRPIVWAGLLLATFQQFVGINVIFYYGETLWKLAGVSEAVALER 301 Query: 307 TVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATV-VNGQPTLT 365 +I+G ++I V I +DK GRKPLLL+GS+GM +TLG ++ F GA G L Sbjct: 302 NIISGVVSIAACFVTILVIDKIGRKPLLLIGSVGMAVTLGAMTWAFSGAAQDAAGNLALA 361 Query: 366 GAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTT 425 AG +ALV+ANLYV F SWGP++WV+LGEMF N+IR +AL+VA QW ANF++ + Sbjct: 362 PGAGWVALVSANLYVIFFNVSWGPVMWVMLGEMFPNQIRGSALAVAGLAQWGANFLVVQS 421 Query: 426 FPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 FP + +GL Y LY SA IS F + F+KETKGK LE+M Sbjct: 422 FPLMASGLGLSNTYLLYTISAVISFFLVKSFIKETKGKELEEM 464 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: 588 Number of extensions: 32 Number of successful extensions: 4 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: 475 Length adjustment: 33 Effective length of query: 435 Effective length of database: 442 Effective search space: 192270 Effective search space used: 192270 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