Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__Keio:18059 Length = 491 Score = 334 bits (856), Expect = 4e-96 Identities = 186/478 (38%), Positives = 278/478 (58%), Gaps = 37/478 (7%) Query: 18 HSMGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLY--------SLSPFMEGLVISSI 69 ++ ++ I+ A LGGLL+GYDTAVISG + L ++ S + + G ++S Sbjct: 5 YNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASA 64 Query: 70 MIGGVVGVGISGFLSDRFGRRKILMTAALLFAISAIVSA------------------LSQ 111 +IG ++G + G+ S+RFGRR L AA+LF IS + SA L+ Sbjct: 65 LIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAG 124 Query: 112 DVSTLIIARIIGGLGIGMGSSLSVTYITEAAPPAIRGSLSSLYQLFTILGISATYFINLA 171 V +I RIIGG+G+G+ S LS YI E AP IRG L S Q I G Y +N Sbjct: 125 YVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYF 184 Query: 172 VQRSGTYEWGVHTGWRWMLAYGMVPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRIN 231 + RSG W GWR+M A +P+++F ++L VPESPRWL GK +A IL +I Sbjct: 185 IARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIM 244 Query: 232 GETVAKEELKNIENSLKI-EQMGSLSQLFKPGLRKALVIGILLALFNQVIGMNAITYYGP 290 G T+A + ++ I++SL + G +F G+ +VIG++L++F Q +G+N + YY P Sbjct: 245 GNTLATQAVQEIKHSLDHGRKTGGRLLMFGVGV---IVIGVMLSIFQQFVGINVVLYYAP 301 Query: 291 EIFKMMGFGQNAGFVTTCIVGVVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGT 350 E+FK +G + + T IVGV+ + FTV+A++ +DK GRK L IG+ MAI M +GT Sbjct: 302 EVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGT 361 Query: 351 SFYFELTSGIMMIVLILGFVAAFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANW 410 +FY + GI+ ++ +L +VAAF +S GP+ W+++SEIFPN +R +A IA W AN+ Sbjct: 362 AFYTQ-APGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANY 420 Query: 411 AIGQFVPMM------IDSFGLAYTFWIFAVINILCFLFVVTICPETKNKSLEEIEKLW 462 + PMM + F +++WI+ + +L LF+ PETK K+LEE+E LW Sbjct: 421 FVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALW 478 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: 593 Number of extensions: 37 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: 464 Length of database: 491 Length adjustment: 34 Effective length of query: 430 Effective length of database: 457 Effective search space: 196510 Effective search space used: 196510 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