Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)
Query= TCDB::P15729 (468 letters) >FitnessBrowser__Keio:18059 Length = 491 Score = 325 bits (834), Expect = 2e-93 Identities = 194/489 (39%), Positives = 289/489 (59%), Gaps = 53/489 (10%) Query: 13 NVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHF--------QTDSLLTGLSVSLAL 64 N ++ I+ VA LGG LFG+DTAVI+G V +L F + L G V+ AL Sbjct: 6 NSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASAL 65 Query: 65 LGSALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLP---FT--------------- 106 +G +G G ++R GR ++ +AAVLF +S +GS P FT Sbjct: 66 IGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGY 125 Query: 107 IWDFIFWRVLGGIGVGAASVIAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFI 166 + +F+ +R++GGIGVG AS+++P YIAE++PAH+RG+L S Q AI+ G + N+FI Sbjct: 126 VPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFI 185 Query: 167 ALMAGGSAQNPWLFGAAAWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAIL 226 A S WL WR+MF +E IPALL+ + + +PESPR+L+++G+ E+A IL Sbjct: 186 ARSGDAS----WL-NTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGIL 240 Query: 227 WKVEGGDVPSR-IEEIQATVSLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVI 285 K+ G + ++ ++EI+ SLDH + L G + ++ IG+ LS QQFVGINV+ Sbjct: 241 RKIMGNTLATQAVQEIKH--SLDHGRKTGGRLLMFG--VGVIVIGVMLSIFQQFVGINVV 296 Query: 286 FYYSSVLWRSVGFTEEKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITL 345 YY+ +++++G + + +LL T+I G IN+ T++AI VDKFGRKPL ++G++GM I + Sbjct: 297 LYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGM 356 Query: 346 GILSVVFGGATVVNGQPTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRA 405 L F T A GI+AL++ YV +F SWGP+ WVLL E+F N IR Sbjct: 357 FSLGTAF-----------YTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRG 405 Query: 406 AALSVAAGVQWIANFIISTTFPPLLDTVGL------GPAYGLYATSAAISIFFIWFFVKE 459 AL++A QW+AN+ +S TFP + L G +Y +Y ++ F+W FV E Sbjct: 406 KALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPE 465 Query: 460 TKGKTLEQM 468 TKGKTLE++ Sbjct: 466 TKGKTLEEL 474 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: 623 Number of extensions: 33 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: 468 Length of database: 491 Length adjustment: 34 Effective length of query: 434 Effective length of database: 457 Effective search space: 198338 Effective search space used: 198338 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