Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 303 bits (777), Expect = 8e-87 Identities = 192/504 (38%), Positives = 287/504 (56%), Gaps = 14/504 (2%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L +R ++K F GV+AL+ V+ V+ GEIHAL+GENGAGKSTL+K L+GVY G + Sbjct: 12 LLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDA--GTV 69 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 EG R + +++ + I ++QE+ L+P LS+AEN+FLG + G++ R Sbjct: 70 TLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRA 129 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 R +L GL + V QQ+V IA+A+ S K+LILDEPTASL+ + L Sbjct: 130 RAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFK 189 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 ++ R++G+ + +TH L++V + D+ITVLR+G V + E+ ++ M+GR Sbjct: 190 VMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVG--ERRTAELPRLDLVAMMLGR 247 Query: 245 DLEDRY----PPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 +LE PP D + + + Y + + ++ +R GEVVG+AGL+G Sbjct: 248 ELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARS----VEPFDLDIRPGEVVGLAGLLG 303 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 +GRTE A VFG R G+ +DG+ V + R AI G + EDRK G+V + Sbjct: 304 SGRTETARLVFGMDRADR--GEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALS 361 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 + N LA A I ++ ++A F L IR+ Q LSGGNQQK +L+ Sbjct: 362 VRENIILALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLA 421 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 +WL + P +LILDEPTRGIDVGA EI +I +L ADG +L++SSE+ E++ R+ V Sbjct: 422 RWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVV 481 Query: 481 MNEGRIVAELPKGEASQESIMRAI 504 + + R VAEL GE + + I+ AI Sbjct: 482 LRDRRHVAELRGGEVAVDRIVAAI 505 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: 598 Number of extensions: 31 Number of successful extensions: 8 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: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 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