Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 229 bits (583), Expect = 2e-64 Identities = 154/505 (30%), Positives = 252/505 (49%), Gaps = 25/505 (4%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 ++ + I K+F V+A ++ L + G I AL+GENGAGKSTLM +LSG T G I Sbjct: 34 VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDT--GII 91 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 H +G FR+ D+ GI +++Q LV +++AEN+ LG A W + + Sbjct: 92 HVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGA------WLSPVHMS 145 Query: 125 R---ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181 R EL + GL P + D+ +G++Q VEI K L + ++LILDEPTA L ++E Sbjct: 146 RVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQ 205 Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN- 240 L L G + I+HK+ EV +AD+I +LR G V + H+ E+ + + N Sbjct: 206 LFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVD--EFHESEVPGEAELANR 263 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGR++ + G+ +L V L ++ VRKGEV IAG+ G Sbjct: 264 MVGREVILEVAAEPLEPGDRVLHVDGLAG--------DGLKGLSFEVRKGEVFAIAGVAG 315 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 G+ E V G G+V + G P + GLAY+ EDR+ L L+ + Sbjct: 316 NGQRELVECVTG--LRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLD 373 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 ++ N L ++ +D A D ++ +LSGGN QK+V+ Sbjct: 374 LVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVG 433 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 + + P +++ + PT+G+D+ A E++ + ++ + GVL++S ++ E+L DR+ V Sbjct: 434 REFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAV 492 Query: 481 MNEGRIVAELPKGEASQESIMRAIM 505 M G + L + + ++ + +M Sbjct: 493 MYRGCFIGLLDRSDTNKVDAIGLMM 517 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: 590 Number of extensions: 28 Number of successful extensions: 11 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 Apr 09 2024. 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