Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= TCDB::O05176 (512 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 224 bits (572), Expect = 4e-63 Identities = 159/494 (32%), Positives = 254/494 (51%), Gaps = 31/494 (6%) Query: 6 LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65 L++ ITK +PG A + ++L ++ GEIHAL+GENGAGKSTLMK++ GV GEIH Sbjct: 9 LQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDA--GEIH 66 Query: 66 YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125 ++G R + + GI ++ Q +L LS+AENI L + + +Q + R Sbjct: 67 WQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAG---TPKQLEPKIR 123 Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185 E+ ++ G+ P+ L+ + +G++Q VEI + L + ++LLILDEPT+ L +++ L Sbjct: 124 EVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVT 183 Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG-- 243 L +G + + I+HKLNEVR + TVLR G + +C E S+ + R MVG Sbjct: 184 LRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRV--SGECIPAECSDLELARLMVGDA 241 Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 LE YP + +E +W H L ++++ VR GE+VGIAG+ G G+ Sbjct: 242 EGLEAEYPKSEGRAPFLRVERLSW---HNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQ 298 Query: 304 TEFAMSVFG-------KSYGHRITGDVLIDGKPVDVSTVRKAIDA--GLAYVTEDRKHLG 354 E + G ++ R GD DV+ +R G+A+V +R G Sbjct: 299 DELLALLSGEQRLQAAQAMRIRFLGD--------DVAHLRPGARRRHGMAFVPAERLGHG 350 Query: 355 LVLNDNILHN--TTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGG 412 V + ++ N T G+ + +I + A R +++ +LSGG Sbjct: 351 AVPSMSLADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGG 410 Query: 413 NQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELL 472 N QK +L + + P +LI PT G+DVGA I+ + +L G +L+IS ++ EL Sbjct: 411 NLQKFILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELF 470 Query: 473 GNCDRIYVMNEGRI 486 DRI +++GR+ Sbjct: 471 QISDRIAALSDGRL 484 Score = 63.5 bits (153), Expect = 2e-14 Identities = 54/227 (23%), Positives = 105/227 (46%), Gaps = 11/227 (4%) Query: 283 INVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAG 342 I+++++ GE+ + G GAG++ ++G + G++ G+ V + +A + G Sbjct: 27 IDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPD--AGEIHWQGERVTMRDPAQARERG 84 Query: 343 LAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGI 402 + V + H L ++ N LA A ++ K +V+ + L + Sbjct: 85 IGMVFQ---HFSLFETLSVAENIALALGAKAGTPKQLEP-KIREVSQRYGMPLEPQ---- 136 Query: 403 FQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVL 462 + +LS G +Q+V + + L + +LILDEPT + E++ + +LAA+G +L Sbjct: 137 -RLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSIL 195 Query: 463 MISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSGE 509 IS ++ E+ C V+ GR+ E E S + R ++ E Sbjct: 196 FISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDAE 242 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: 548 Number of extensions: 25 Number of successful extensions: 9 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: 518 Length adjustment: 35 Effective length of query: 477 Effective length of database: 483 Effective search space: 230391 Effective search space used: 230391 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