Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 410 bits (1054), Expect = e-119 Identities = 222/502 (44%), Positives = 325/502 (64%), Gaps = 14/502 (2%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 ++ IL+++ ++K FPGV AL+ ++L + GE+HA+ GENGAGKSTLMK++SG Y A Sbjct: 19 VSREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRAD-- 76 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 EG + Y GA F + +D++ GI IIHQEL LVP LS+AENI+L E + ++ Sbjct: 77 EGVVRYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTL 136 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 + + L+++GL SP TL+ + + +QQ+VEIAKALS ++LI+DEPT+SL ES++ Sbjct: 137 NSNAQRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETV 196 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 L ++ E R G+ + I+H+L+E+ ++ D++TVLRDG + T D ++E I+ Sbjct: 197 QLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNE--IVAR 254 Query: 241 MVGRDLEDRYPPRD-VPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLM 299 MVGR L+D YPPR P + +L V++ V ++ +RKGE++G AGLM Sbjct: 255 MVGRPLDDAYPPRQSTPSNQILLRVRDLQR-------TGVFGPLSFELRKGEILGFAGLM 307 Query: 300 GAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLND 359 GAGRTE A ++FG +G + + +PV + + R+AI G+AY++EDRK GL L+ Sbjct: 308 GAGRTETARAIFGAERPD--SGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSM 365 Query: 360 NILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVL 419 + N TLAN+ +S + +E +A + L IR+ + Q NLSGGNQQK+V+ Sbjct: 366 PVSANITLANVRAISSRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVI 425 Query: 420 SKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIY 479 SKWL+ +L DEPTRGIDVGAKY IY ++++LAADG GV++ISSE+PELLG DRI Sbjct: 426 SKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIA 485 Query: 480 VMNEGRIVAELPKGEASQESIM 501 V +EGRI A L + SQE I+ Sbjct: 486 VFHEGRITAVLETRQTSQEEIL 507 Lambda K H 0.316 0.135 0.374 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: 618 Number of extensions: 29 Number of successful extensions: 9 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: 512 Length of database: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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