Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate CCNA_00857 CCNA_00857 glucose/fructose transport protein
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__Caulo:CCNA_00857 Length = 478 Score = 270 bits (690), Expect = 8e-77 Identities = 158/458 (34%), Positives = 255/458 (55%), Gaps = 18/458 (3%) Query: 19 SMGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVG 78 +M FV I A +GG ++GYD+ VI+G L+ ++LS GL + +I+IG +G Sbjct: 21 NMTFVAAIVAVATIGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLNVGAILIGCAIGAF 80 Query: 79 ISGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYI 138 +G L+D +GRR +++ +ALLF ISAI + ++ II R+IGGLG+G S L YI Sbjct: 81 AAGRLADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLCPVYI 140 Query: 139 TEAAPPAIRGSLSSLYQLFTILGISATYFINLAVQR---SGTYE-WGVHTGWRWMLAYGM 194 +E P IRG LSS+ Q+ I G++ + N A+ S T E W WRWM + Sbjct: 141 SEVTPANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWLGLPAWRWMFWMQI 200 Query: 195 VPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGS 254 +P+ +FFL LL +PESPR+L GK +A IL+R+ G ++++ I SL + + Sbjct: 201 IPAGVFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVEEIRASLSADHKPT 260 Query: 255 LSQLFKPGLRKALVI---GILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVG 311 S L P +K VI G++LA+F Q++G+N + YYG +++ +GF ++ + G Sbjct: 261 FSDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTEDDSLKINILSG 320 Query: 312 VVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELT----------SGIM 361 + ++ ++A+ LIDK+GRK L+ IGSA MA+ + ++ F T G+ Sbjct: 321 TLSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATTVNGALTLGDQIGLT 380 Query: 362 MIVLILGFVAAFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMID 421 ++ +V F +S GP+ W+M+ E+FPN +R A + W AN+AI P + Sbjct: 381 ALIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPALA- 439 Query: 422 SFGLAYTFWIFAVINILCFLFVVTICPETKNKSLEEIE 459 + L T+ +A+ ++ F V + ET+ K LE ++ Sbjct: 440 AASLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAMQ 477 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: 546 Number of extensions: 37 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: 478 Length adjustment: 33 Effective length of query: 431 Effective length of database: 445 Effective search space: 191795 Effective search space used: 191795 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