Align D-xylose-proton symporter (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)
Query= CharProtDB::CH_109760 (491 letters) >FitnessBrowser__Btheta:353923 Length = 460 Score = 324 bits (831), Expect = 4e-93 Identities = 186/483 (38%), Positives = 283/483 (58%), Gaps = 43/483 (8%) Query: 5 YNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASA 64 YN +++SI LV+ +GGLLFGYD VI G F +++S ++ G ++ A Sbjct: 4 YNKKFVYSICLVSAMGGLLFGYDWVVIGGAKPFYELYF----GIADSP--TMQGLAMSVA 57 Query: 65 LIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAG 124 L+GC+IG + G ++R+GR+ L I+A +F + SA+ F+ + Sbjct: 58 LLGCLIGAMVAGMMADRYGRKPLLLISAFIF----LSSAYATGAFSVFS----------- 102 Query: 125 YVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYF 184 F+ R +GGIG+G+AS LSPMYIAE+AP IRGKLVS NQ I+ G L N+ Sbjct: 103 ---WFLAARFLGGIGIGIASGLSPMYIAEVAPTSIRGKLVSLNQLTIVLGILGAQIANWL 159 Query: 185 IARSGDA---------SWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQ 235 IA A SW GWR+MF PA +FL+L +PESPRWL +GK+E+ Sbjct: 160 IAEPIPADFTPADICASWNGQMGWRWMFWGAAFPAAVFLLLACFIPESPRWLAMKGKREK 219 Query: 236 AEGILRKIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGVG---VIVIGVMLSIFQQFVG 292 A +L +I GN A Q +Q ++ + + GG L+F V+V+GV++++FQQ+ G Sbjct: 220 AWSVLSRIGGNRYAEQELQMVEQT-SASKSEGGLKLLFSRPFRKVLVLGVIVAVFQQWCG 278 Query: 293 INVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGM 352 NV+ YA E+F++ G S L ++ GV N+ FT +AI TV++ GR+ L ++GA G+ Sbjct: 279 TNVIFNYAQEIFQSAGYSLGDVLFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGGL 338 Query: 353 AIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAV 412 A LGT ++ Q G ++ ++ +A +AMS GP+ WVLL+EIFPN +RG A+A Sbjct: 339 AGIYLVLGTCYFFQVSGFFMVVLVVLAIACYAMSLGPITWVLLAEIFPNRVRGVAMATCT 398 Query: 413 AAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLE 472 A W+ ++ +++TFP++ N+ L ++ ++WIY + V LF + +PETKGK+LE Sbjct: 399 FALWVGSFTLTYTFPLL--NTALGSY----GTFWIYSAICVFGFLFFLRALPETKGKSLE 452 Query: 473 ELE 475 LE Sbjct: 453 TLE 455 Lambda K H 0.326 0.140 0.433 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: 630 Number of extensions: 29 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: 491 Length of database: 460 Length adjustment: 33 Effective length of query: 458 Effective length of database: 427 Effective search space: 195566 Effective search space used: 195566 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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