Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 407 bits (1047), Expect = e-118 Identities = 222/498 (44%), Positives = 324/498 (65%), Gaps = 14/498 (2%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 IL+++ ++K FPGV AL+ ++L ++ GE+HA+ GENGAGKSTLMK++SG Y A +G I Sbjct: 22 ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHAD--DGVI 79 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 YEG F + +D++ GI IIHQEL LVP LS+AENI+L E + ++ Sbjct: 80 CYEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNANA 139 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 + L+++GL SP TL+ + + +QQ+VEIAKALS ++LI+DEPT+SL ES++ L Sbjct: 140 QRCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFR 199 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 ++ E R G+ + I+H+L+E+ ++ D++TVLRDG + T D I+E I+ MVGR Sbjct: 200 IIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINE--IVARMVGR 257 Query: 245 DLEDRYPPRD-VPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 L+D YPPR+ VP + ++ V++ Q D ++ +RKGE++G AGLMGAGR Sbjct: 258 ALDDAYPPRESVPTEQVLMRVRDL-----QRTD--TFGPLSFDLRKGEILGFAGLMGAGR 310 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 TE A ++FG +G + + PV + + R+AI G+AY++EDRK GL L+ + Sbjct: 311 TEVARAIFGAE--RLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAA 368 Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 N TL+N+ +S + +E +A + L IR+ + Q NLSGGNQQK+V+SKWL Sbjct: 369 NITLSNVRAISSRGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWL 428 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 + +L DEPTRGIDVGAKY IY ++++LAADG GV++ISSE+PELLG DRI V +E Sbjct: 429 YRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHE 488 Query: 484 GRIVAELPKGEASQESIM 501 G I A L + SQE I+ Sbjct: 489 GLITAVLETRQTSQEEIL 506 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: 627 Number of extensions: 33 Number of successful extensions: 10 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: 515 Length adjustment: 35 Effective length of query: 477 Effective length of database: 480 Effective search space: 228960 Effective search space used: 228960 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