Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012759468.1 RLEG_RS20700 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000023185.1:WP_012759468.1 Length = 513 Score = 372 bits (954), Expect = e-107 Identities = 203/502 (40%), Positives = 316/502 (62%), Gaps = 15/502 (2%) Query: 2 ANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYE 61 A +L + K FPGV AL++V ++K +HAL+GENGAGKSTLMK+L+G+Y + Sbjct: 20 AEYLLSAEGVRKEFPGVVALDDVQFRLKRASVHALMGENGAGKSTLMKILAGIYTPD--K 77 Query: 62 GEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQT 120 G+I +G ++ D+ + GI +IHQEL L+P +++AENI++ E + G I Sbjct: 78 GDIRLKGIEIQLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRLGFIDHGVM 137 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 T EL ++ + P+ + + V +Q+VEIAKA+S + +LI+DEPT++L E + E Sbjct: 138 HRMTEELFTRLNIAIDPDIEVRHLSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVE 197 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 L ++ + R QG+ + ITHK+NE+ ++AD+ +V RDG + T +++ D IIR Sbjct: 198 HLFRIIRDLRAQGIGIVYITHKMNELFEIADEFSVFRDGRYIGTHA--STDVTRDDIIRM 255 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGR++ +P +VPIGE +L VK+ + V ++++ VR GE++G+AGL+G Sbjct: 256 MVGREITQMFPKEEVPIGEVVLSVKDLCL-------KGVFNNVSFEVRAGEILGVAGLVG 308 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 +GR+ A ++FG + +G + + GKPV +S+ +AI +A++TEDRK G +L + Sbjct: 309 SGRSNVAETLFGVTPAS--SGSIELYGKPVTISSPTEAIRNRMAFLTEDRKDTGCLLILD 366 Query: 361 ILHNTTLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVL 419 IL N +A L K + D +LR+++ +++ NLSGGNQQKV++ Sbjct: 367 ILENMQIAVLQDRYVKGGFVQQGAVEATCEDMAKKLRVKTPNLYERVENLSGGNQQKVLI 426 Query: 420 SKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIY 479 +WL +NP +LILDEPTRGIDVGAK EI+ ++ ++A DG V+MISSEMPE+LG DRI Sbjct: 427 GRWLLTNPRILILDEPTRGIDVGAKAEIHRLVTEMARDGVAVVMISSEMPEVLGMSDRIM 486 Query: 480 VMNEGRIVAELPKGEASQESIM 501 VM+EGR+ L + EA+Q +M Sbjct: 487 VMHEGRVTGFLNRDEATQIKVM 508 Score = 69.7 bits (169), Expect = 2e-16 Identities = 56/227 (24%), Positives = 105/227 (46%), Gaps = 9/227 (3%) Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAI 339 L D+ +++ V + G GAG++ + G + GD+ + G + + + A+ Sbjct: 39 LDDVQFRLKRASVHALMGENGAGKSTLMKILAGIYTPDK--GDIRLKGIEIQLKSPLDAL 96 Query: 340 DAGLAYVTEDRKHLG-LVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIR 398 + G+A + ++ + + + +NI N G ID ++ + TRL I Sbjct: 97 ENGIAMIHQELNLMPFMTVAENIWIRREPKNRLG-----FIDHGVMHRMTEELFTRLNIA 151 Query: 399 SSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADG 458 E +LS N+Q V ++K + N DVLI+DEPT + ++ II L A G Sbjct: 152 IDPDI-EVRHLSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVEHLFRIIRDLRAQG 210 Query: 459 KGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 G++ I+ +M EL D V +GR + + +++ I+R ++ Sbjct: 211 IGIVYITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDIIRMMV 257 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: 621 Number of extensions: 36 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: 513 Length adjustment: 35 Effective length of query: 477 Effective length of database: 478 Effective search space: 228006 Effective search space used: 228006 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 24 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