Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Cup4G11:RR42_RS04800 Length = 529 Score = 254 bits (648), Expect = 7e-72 Identities = 171/508 (33%), Positives = 274/508 (53%), Gaps = 25/508 (4%) Query: 6 LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65 L + +I+K +PGV A ++V+L V GEIHA++GENGAGKSTLMK++ G G++H Sbjct: 9 LALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDA--GDMH 66 Query: 66 YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVI-------SWQ 118 + GA +D+ ++GI ++ Q +L L++AENI LG S + + Sbjct: 67 FNGARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHAGTNMK 126 Query: 119 QTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178 Q + RE + GL P + + VG++Q VEI +AL +LLILDEPT+ L Sbjct: 127 QLAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQA 186 Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVII 238 + L L + +G + + I+HKL+E+R++ TV+R G D QE + + Sbjct: 187 VQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAAS--LS 244 Query: 239 RNMVGRDLEDRYPPRDVPI----GETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVG 294 R M+G + PPR+ + G L V+ + + H L I++ +R GE+VG Sbjct: 245 RLMIGGE-----PPREARVQTEPGVCRLAVRELSL-PRSHAFATELAGISLDLRAGEIVG 298 Query: 295 IAGLMGAGRTEFAMSVFGKSYGHRITGDVL-IDGKPVDVSTVRKAIDAGLAYVTEDRKHL 353 IAG+ G G+ E ++ G+ R D + +D KPV R+ AGLA+V E+R Sbjct: 299 IAGVSGNGQQELLAALSGEDV--RAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGR 356 Query: 354 GLVLNDNILHNTTLANL-AGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGG 412 G V ++ N L++ A + +I +A RLR+++SG +LSGG Sbjct: 357 GAVPGMSLAANILLSHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHALAKSLSGG 416 Query: 413 NQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELL 472 N QK ++ + + S P VLI+ +PT G+DVGA +I+ + L A G +L++S E+ EL Sbjct: 417 NLQKFIVGREIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELF 476 Query: 473 GNCDRIYVMNEGRIVAELPKGEASQESI 500 CDR++V+ +GR+ +P +A++E + Sbjct: 477 AICDRLHVIAKGRLSPSIPTRDATREQV 504 Score = 70.5 bits (171), Expect = 1e-16 Identities = 62/239 (25%), Positives = 105/239 (43%), Gaps = 24/239 (10%) Query: 282 DINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDA 341 D+++ V GE+ + G GAG++ +FG GD+ +G + A + Sbjct: 26 DVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPD--AGDMHFNGARAAIHNPHDARNL 83 Query: 342 GLAYVTEDRKHLGLVLNDNILHNTTL-----------ANLAGVSKASIIDDIKEMKVASD 390 G+A V + H L + N L + AG + + + I+E + Sbjct: 84 GIAMVFQ---HFSLFDTLTVAENIALGLPRGSKTAAGSPHAGTNMKQLAEQIRETAL--- 137 Query: 391 FRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTI 450 R L + + + LS G +Q+V + + L + P +LILDEPT + A ++ Sbjct: 138 -RYGLPLEPN---RHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAVQTLFIT 193 Query: 451 INQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSGE 509 + QLAA+G +L IS ++ E+ C VM GR+ + S S+ R +M GE Sbjct: 194 LRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSR-LMIGGE 251 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: 546 Number of extensions: 32 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: 529 Length adjustment: 35 Effective length of query: 477 Effective length of database: 494 Effective search space: 235638 Effective search space used: 235638 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