Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 347 bits (890), Expect = e-100 Identities = 209/501 (41%), Positives = 300/501 (59%), Gaps = 17/501 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 + EMR I K FPGVKAL++V+ + GE+H L+GENGAGKS+LMKVL GVY A GE Sbjct: 10 LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADA--GEF 67 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN--GVISWQQTFN 122 +++G+ + D+ +GI +I QE +LVP L IA+NIFLG E G + + Sbjct: 68 YHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHA 127 Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182 R +L +G++ S T + +GV +QQ+VEIAKALS++ ++L+LDEPTA+L++ ++E L Sbjct: 128 EARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKL 187 Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242 ++ + G++ I I+H++ EV + D+IT+LRDG V C + + D ++ MV Sbjct: 188 FAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGA--CLPGDATPDELVARMV 245 Query: 243 GRDLEDRYP-PRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGA 301 GR ++ Y R GE L+V+N +A + DIN+ VR GE+VG+AGL+G+ Sbjct: 246 GRKVDMSYSRERSAQPGEVALDVRNVSA-------DSGIADINLQVRAGEIVGLAGLVGS 298 Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361 GR+E A +VFG + G++ I GK + R A + G A + E RK GL L + Sbjct: 299 GRSEVARAVFGADPIRQ--GEIYIFGKRLTGGPDR-ARELGAALIPESRKSEGLALIRTV 355 Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421 N LA L A K +A RLRI + Q LSGGNQQK+V+ K Sbjct: 356 RDNLLLAGLRRAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGK 415 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 WL + + I DEPTRGIDVGAK EI+ +I+ L G GVL+ISSE+PE++ CDR YVM Sbjct: 416 WLVAEAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVM 475 Query: 482 NEGRIVAELPKGEASQESIMR 502 GRI E+ E ++E I++ Sbjct: 476 RGGRIAGEVAHAEMTEERILQ 496 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: 607 Number of extensions: 37 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: 502 Length adjustment: 34 Effective length of query: 478 Effective length of database: 468 Effective search space: 223704 Effective search space used: 223704 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