Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 287 bits (734), Expect = 7e-82 Identities = 187/503 (37%), Positives = 285/503 (56%), Gaps = 36/503 (7%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L+ R + K F AL+ V+L ++ GE+HAL+G+NGAGKSTL+K+L+GV G + Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPD--RGSV 69 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGV--ISWQQTFN 122 +G V +++ GI ++QE+ L P LS+AEN++ G + I W+Q + Sbjct: 70 ELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRD 129 Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182 R LL+++ L+ + + V +Q+V IA+AL S ++LILDEPT+SL+E + L Sbjct: 130 GARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVREL 189 Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242 ++ + R +GM + +TH L++V V+D+ITVLRDG V + ++ ++ MV Sbjct: 190 FRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVG--EYAVADLPPAALVNAMV 247 Query: 243 GRDLE-------DRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGI 295 GRDL +R PP D P ++ + R LH +++ VR+GE++G+ Sbjct: 248 GRDLPTVAGADAERAPPPDAP---PAIDAQGLGC-------RGKLHPVDLQVRRGEMLGL 297 Query: 296 AGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGL 355 GL+G+GRTE A +FG R G++ I G+ V++ A+ GLA E+RK G+ Sbjct: 298 GGLLGSGRTELARLLFGLDRAER--GELRIGGERVELKHPADAVVRGLALCPEERKTDGI 355 Query: 356 VLNDNILHNTTLANLA-----GVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLS 410 V ++ N LA A G+S+A ++ ++A L I+++ I LS Sbjct: 356 VAELSVRENIVLALQARQGWRGMSRA------RQDELARQLVQALGIKAADIETPVGLLS 409 Query: 411 GGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPE 470 GGNQQKV+L++WL + P +LILDEPTRGIDV AK E+ + + A G VL IS+E E Sbjct: 410 GGNQQKVMLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGE 469 Query: 471 LLGNCDRIYVMNEGRIVAELPKG 493 L CDRI VM E R ELP G Sbjct: 470 LTRWCDRIAVMRERRKAGELPGG 492 Score = 61.6 bits (148), Expect = 6e-14 Identities = 54/226 (23%), Positives = 102/226 (45%), Gaps = 6/226 (2%) Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAI 339 L +++ +R GEV + G GAG++ + G R G V +DG+ + ST +A Sbjct: 28 LDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDR--GSVELDGRVIAPSTPMEAQ 85 Query: 340 DAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRS 399 G+ V ++ + L N ++ N + +ID + A +L + Sbjct: 86 RDGIGTVYQE---VNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGARSLLRQLHLEL 142 Query: 400 SGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGK 459 + + +Q V +++ L + VLILDEPT +D G E++ +I QL G Sbjct: 143 D-VDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFRVIAQLRERGM 201 Query: 460 GVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 +L ++ + ++ DRI V+ +G V E + +++ A++ Sbjct: 202 AILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMV 247 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: 579 Number of extensions: 39 Number of successful extensions: 10 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: 505 Length adjustment: 34 Effective length of query: 478 Effective length of database: 471 Effective search space: 225138 Effective search space used: 225138 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