Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 320 bits (819), Expect = 1e-91 Identities = 179/502 (35%), Positives = 290/502 (57%), Gaps = 14/502 (2%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M+ +LE+R I KTF +AL+ +L+V G +H LVGENGAGKSTL+KVL+G++ Sbjct: 1 MSTPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDA- 59 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 G + +G + E +GI IHQE L ++ E +F G+E ++ + Sbjct: 60 -GSLLLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQ 118 Query: 121 FNRTRELLKKV-GLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDS 179 LL GL+ LI ++ +QQ+V+I +AL ++L+ DEP+ +L + + Sbjct: 119 QREAARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREV 178 Query: 180 EALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIR 239 E LL ++ R+ G+ + I+H L E+ + D++TVLR+G V + + + I R Sbjct: 179 ERLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQ--ITR 236 Query: 240 NMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLM 299 MV R++ + YP VP G +L+V+ + I++ VR+GE+VG+ GL+ Sbjct: 237 LMVNREVGELYPKVAVPAGALLLDVRGLGR-------ARAYQGIDLQVRRGEIVGLTGLV 289 Query: 300 GAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLND 359 G+G E S+FG + +G+V +DG+P+ + + R+A+ G+A + E+R+ G+ L+ Sbjct: 290 GSGAKELLRSLFGLAPPD--SGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDL 347 Query: 360 NILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVL 419 ++ NTTLA L+ + ++ +E + RLRI++ G + LSGGNQQKV L Sbjct: 348 SVQENTTLAALSRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVAL 407 Query: 420 SKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIY 479 +KW + +LDEP+ GIDVGAK EIY +I +L +G GVL++SS++PEL+G CDRI+ Sbjct: 408 AKWFARCSSLYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIH 467 Query: 480 VMNEGRIVAELPKGEASQESIM 501 VM+ G I A GEA+ + ++ Sbjct: 468 VMHRGAIAARFAAGEANSDRLL 489 Score = 65.1 bits (157), Expect = 6e-15 Identities = 60/232 (25%), Positives = 104/232 (44%), Gaps = 15/232 (6%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRI-TGDVLIDGKPVDVSTVR 336 + L ++ V G V G+ G GAG++ + G HR G +L+DG+P + R Sbjct: 19 RALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGI---HRPDAGSLLLDGQPHGHFSPR 75 Query: 337 KAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVAS---DFRT 393 + G+ ++ ++R +L L ++D + + A+ D Sbjct: 76 QVERLGIGFIHQER-----LLPARFTVGEALFFGHERRFGPLLDRRSQQREAARLLDDYF 130 Query: 394 RLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQ 453 LR+ ++ + E LS QQ V + + L P VL+ DEP+ + + I+ + Sbjct: 131 GLRLPANALIGE---LSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLRIVQR 187 Query: 454 LAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 L DG ++ IS + E+ CDR+ V+ GR VAE+ S E I R ++ Sbjct: 188 LRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMV 239 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: 38 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: 512 Length adjustment: 35 Effective length of query: 477 Effective length of database: 477 Effective search space: 227529 Effective search space used: 227529 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