Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__Pedo557:CA265_RS23325 Length = 443 Score = 315 bits (807), Expect = 2e-90 Identities = 171/443 (38%), Positives = 261/443 (58%), Gaps = 12/443 (2%) Query: 22 FVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISG 81 ++ IS A GG L+G+D AVISG++ FL+ + L+P+ EG S+ +G +VG I+G Sbjct: 10 YITFISLLAAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWEGFATGSLALGAMVGCLIAG 69 Query: 82 FLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEA 141 ++SD +GR+ LM AA +F S++ A++ + I++R G+G+GM S LS YI E Sbjct: 70 YVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMASMLSPMYIAEL 129 Query: 142 APPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGVHTGWRWMLAYGMVPSVIFF 201 APP RG L ++ QL +LGI T IN ++ +G WRWM G +PS IF Sbjct: 130 APPKFRGRLVAINQLTIVLGILITNLINYTLRNTG------EDAWRWMFGLGAIPSGIFL 183 Query: 202 LVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGSLSQLFKP 261 + + ++PESPRWL + GK +ALK+L +I A + LKNIE +L+ + +F Sbjct: 184 IGISILPESPRWLVQKGKNEKALKVLNKIGNHEFAADALKNIEQTLQRKSNVEHESIFNK 243 Query: 262 GLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEVIFTVIA 321 A++IGI LA+F Q G+N + Y P++F+ +G Q+ + T +G V VIFT+ A Sbjct: 244 MYFPAVMIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQDDQLLQTVFIGAVNVIFTISA 303 Query: 322 VLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIV-LILGFVAAFCVSVGPI 380 + L+DK+GRK LM IG+ +A+ +LI L SG M+ +L + + VS+ P+ Sbjct: 304 MFLVDKIGRKPLMLIGAGGLAVLYVLISQL----LASGSTMVSWFLLSAIGVYAVSLAPV 359 Query: 381 TWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWIFAVINILCF 440 TW++ISEIFPN +R +A A + LWGA + + P++ D + F+I+A I L Sbjct: 360 TWVLISEIFPNKVRVKATTWAILCLWGAYFVLVFTFPILFDWLKES-IFYIYAAICTLGC 418 Query: 441 LFVVTICPETKNKSLEEIEKLWI 463 + + ETK K+LEEIE + I Sbjct: 419 IGIWKFVKETKGKTLEEIEDIQI 441 Lambda K H 0.327 0.142 0.425 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: 501 Number of extensions: 23 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: 464 Length of database: 443 Length adjustment: 33 Effective length of query: 431 Effective length of database: 410 Effective search space: 176710 Effective search space used: 176710 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