Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 305 bits (781), Expect = 3e-87 Identities = 187/509 (36%), Positives = 293/509 (57%), Gaps = 17/509 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L + KT+ L V+L ++ GE+ AL GENGAGKSTL K++SG+ T G + Sbjct: 16 VLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTT--GHM 72 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 Y G + ++E +G+ ++ QEL L+P L++AEN+FL N + G IS ++ Sbjct: 73 TYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQLA 132 Query: 125 RELLKKVGLKE-SPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 + +VGL P+T + ++G+G QQ+VEIA+ L +LILDEPTA L + L Sbjct: 133 TAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLF 192 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243 + R +G+ + I+H+L E+++VA +I VLRDG V D + S ++ MVG Sbjct: 193 TQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLV--CDEPIQRYSSAELVNLMVG 250 Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 R+L + +G +L+V + + +++ VR GE+ GI+GL+GAGR Sbjct: 251 RELGEHIDLGRRQLGAPLLKVDKLCRGDK-------VREVSFEVRAGEIFGISGLIGAGR 303 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKP--VDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361 TE ++G +G + + P V + + + A+ AG+A +TEDRK GL+L +I Sbjct: 304 TELLRLIYGADRAD--SGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSI 361 Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421 N L NL VS+A ++D E +A +RIRS+G Q LSGGNQQKVV+ + Sbjct: 362 SANIALGNLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGR 421 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 WL + VL+ DEPTRGIDVGAK++IY ++ +LA GK ++++SS++ EL+ CDRI V+ Sbjct: 422 WLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVL 481 Query: 482 NEGRIVAELPKGEASQESIMRAIMRSGEK 510 + GR++ + SQ+ ++ A +K Sbjct: 482 SAGRLIDTFARDHWSQDQLLAAAFAGYQK 510 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: 623 Number of extensions: 31 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: 524 Length adjustment: 35 Effective length of query: 477 Effective length of database: 489 Effective search space: 233253 Effective search space used: 233253 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