Align D-xylose-proton symporter (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter
Query= CharProtDB::CH_109760 (491 letters) >FitnessBrowser__Pedo557:CA265_RS23325 Length = 443 Score = 313 bits (802), Expect = 8e-90 Identities = 183/476 (38%), Positives = 271/476 (56%), Gaps = 45/476 (9%) Query: 3 TQYNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVA 62 +++N++YI I+L+A GG LFG+D AVISG++ L F GF Sbjct: 4 SKFNTAYITFISLLAAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWE--------GFATG 55 Query: 63 SALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAW-PELGFTSINPDNTVPVY 121 S +G ++G + GY S+ +GR+ L IAA +F S + A P F Sbjct: 56 SLALGAMVGCLIAGYVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDF------------ 103 Query: 122 LAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCV 181 F++ R GIGVG+ASMLSPMYIAELAP RG+LV+ NQ I+ G L+ + Sbjct: 104 -------FIVSRFFSGIGVGMASMLSPMYIAELAPPKFRGRLVAINQLTIVLGILITNLI 156 Query: 182 NYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILR 241 NY + +G+ D WR+MF IP+ +FL+ + +PESPRWL+ +GK E+A +L Sbjct: 157 NYTLRNTGE------DAWRWMFGLGAIPSGIFLIGISILPESPRWLVQKGKNEKALKVLN 210 Query: 242 KIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGV--GVIVIGVMLSIFQQFVGINVVLYY 299 KI + A A++ I+ +L + + ++IG+ L+IFQQF GIN V Y Sbjct: 211 KIGNHEFAADALKNIEQTLQRKSNVEHESIFNKMYFPAVMIGIGLAIFQQFCGINTVFNY 270 Query: 300 APEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSL 359 AP++F+++G S D LLQT+ +G +N+ FT+ A+ VDK GRKPL +IGA G+A+ ++ L Sbjct: 271 APKLFESIGTSQDDQLLQTVFIGAVNVIFTISAMFLVDKIGRKPLMLIGAGGLAV-LYVL 329 Query: 360 GTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLAN 419 + +V+ +L + +A+S PV WVL+SEIFPN +R KA A+ W A Sbjct: 330 ISQLLASGSTMVSWF-LLSAIGVYAVSLAPVTWVLISEIFPNKVRVKATTWAILCLWGAY 388 Query: 420 YFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELE 475 + + +TFP++ WL ++IY + L + +WKFV ETKGKTLEE+E Sbjct: 389 FVLVFTFPIL--FDWLKESI-----FYIYAAICTLGCIGIWKFVKETKGKTLEEIE 437 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: 583 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: 491 Length of database: 443 Length adjustment: 33 Effective length of query: 458 Effective length of database: 410 Effective search space: 187780 Effective search space used: 187780 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