Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 379 bits (973), Expect = e-109 Identities = 211/501 (42%), Positives = 311/501 (62%), Gaps = 16/501 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L+++ I K FPGVKAL L V G + ALVGENGAGKST+MKVL+G+Y G + Sbjct: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDA--GTL 61 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123 + G F S++ GI IIHQEL L+P L+IAENIFLG E + G I W+ + Sbjct: 62 LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121 Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 +LL K+ L+ + L+ D+ +G QQ+VEIAK LS K++I+DEPT +L ++++E+L Sbjct: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243 ++ E ++QG + I+H++ E+ ++ D +TV RDG + + ++ED +I MVG Sbjct: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREV--ASLTEDSLIEMMVG 239 Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 R LED+YP D G+ L+V N ++D++ T+RKGE++G++GLMGAGR Sbjct: 240 RKLEDQYPHLDKAPGDIRLKVDNLCG--------PGVNDVSFTLRKGEILGVSGLMGAGR 291 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 TE ++G R +G V +DG V + + + G+ Y++EDRK GLVL ++ Sbjct: 292 TELMKVLYGAL--PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349 Query: 364 NTTLANLAGVSKAS-IIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKW 422 N +L L S+A + E + SDF +++ + Q LSGGNQQKV +++ Sbjct: 350 NMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARG 409 Query: 423 LFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMN 482 L + P VLILDEPTRG+DVGAK EIY +INQ ADG ++++SSEMPE+LG DRI VM+ Sbjct: 410 LMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMH 469 Query: 483 EGRIVAELPKGEASQESIMRA 503 EG + E + +A+QE +M A Sbjct: 470 EGHLSGEFTREQATQEVLMAA 490 Score = 70.5 bits (171), Expect = 1e-16 Identities = 58/225 (25%), Positives = 106/225 (47%), Gaps = 15/225 (6%) Query: 285 VTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLA 344 + V G V+ + G GAG++ M V Y R G +L GK + + + +AG+ Sbjct: 25 LNVYPGRVMALVGENGAGKSTM-MKVLTGIYT-RDAGTLLWLGKETTFTGPKSSQEAGIG 82 Query: 345 YVTEDRKHLG-LVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASD---FRTRLRIRSS 400 + ++ + L + +NI N G D K M +D + LR +S Sbjct: 83 IIHQELNLIPQLTIAENIFLGREFVNRFGKI------DWKTMYAEADKLLAKLNLRFKSD 136 Query: 401 GIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKG 460 + + LS G+QQ V ++K L V+I+DEPT + ++ +I +L + G+G Sbjct: 137 KLVGD---LSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKSQGRG 193 Query: 461 VLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 ++ IS M E+ CD + V +G+ +AE +++S++ ++ Sbjct: 194 IVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMV 238 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: 647 Number of extensions: 37 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 501 Length adjustment: 34 Effective length of query: 478 Effective length of database: 467 Effective search space: 223226 Effective search space used: 223226 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