Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_011424551.1 RHE_RS06210 D-ribose transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000092045.1:WP_011424551.1 Length = 524 Score = 390 bits (1003), Expect = e-113 Identities = 221/507 (43%), Positives = 328/507 (64%), Gaps = 19/507 (3%) Query: 2 ANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYE 61 A +LEMR+ITK FPGV AL+ ++LKV+ G +H LVGENGAGKSTLMK+LSG+Y Sbjct: 25 AGFVLEMRSITKAFPGVLALDGMSLKVRAGTVHVLVGENGAGKSTLMKILSGIYAIDG-- 82 Query: 62 GEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNE--VASNGVISWQQ 119 GEI + G + ++ + + GI +IHQEL+ V ++IAENIFLG E + GV+S Sbjct: 83 GEILFRGEKLDHQSAAAALERGISMIHQELSPVLDMTIAENIFLGREPTYSRTGVLSRFV 142 Query: 120 TFNR----TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLN 175 F+R T+ LL ++GLK SP+T + D+ + QL+EI KA+S+ L+I+DEPT++++ Sbjct: 143 DFDRMNSDTQTLLDRLGLKYSPQTKMRDLSIATMQLIEIVKAISREASLIIMDEPTSAIS 202 Query: 176 ESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISED 235 +++ L + + + G+ I ITHK++E+ ++AD ITV+RDG V + E ++ Sbjct: 203 DTEVAMLFRQIADLKAAGVAIIYITHKMDEIFQIADDITVMRDGQFVAAAPASEYEPAK- 261 Query: 236 VIIRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGI 295 +I MVGR + +P +VPIG+ +L V+N + RD V ++ VR GE+VG+ Sbjct: 262 -LISQMVGRTISSIFPKEEVPIGDIVLSVENLS------RDG-VFDNVGFEVRAGEIVGL 313 Query: 296 AGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGL 355 +GL+GAGRTE A +FG G V ++GKP+ +++ + AI G+A V+EDRK GL Sbjct: 314 SGLIGAGRTEVARVIFGLDAAD--AGVVRLNGKPLKLTSPKDAIANGIAMVSEDRKAEGL 371 Query: 356 VLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQ 415 VL ++ N +LANL + I + +E + L+I++ NLSGGNQQ Sbjct: 372 VLCRSVGENISLANLKKFASGIFISERQEETASQRMIKMLQIKTPDTAMIVENLSGGNQQ 431 Query: 416 KVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNC 475 K+VL+KWL + +LILDEPTRGIDVG+K EI+ ++ + A G ++MISSE+PE+LG Sbjct: 432 KIVLAKWLLGDLKLLILDEPTRGIDVGSKSEIHRLMTEFARQGLAIIMISSELPEILGMS 491 Query: 476 DRIYVMNEGRIVAELPKGEASQESIMR 502 DR+ VM+EGR+ EL + EA+QE+IMR Sbjct: 492 DRVVVMSEGRVTGELTRAEATQENIMR 518 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: 656 Number of extensions: 28 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 24 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