Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012046544.1 BBTA_RS31430 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000015165.1:WP_012046544.1 Length = 507 Score = 375 bits (964), Expect = e-108 Identities = 222/505 (43%), Positives = 317/505 (62%), Gaps = 13/505 (2%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M+ ILEMR ++K+F G+KAL+ V+L V GE+HAL+GENGAGKSTLMK+LSG Y Sbjct: 1 MSGPILEMRGVSKSFFGIKALQKVDLTVYAGEVHALMGENGAGKSTLMKILSGAYRPDP- 59 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 GEI +G GI II+QEL+L P L++AENI+LG EV+ +G+++ Sbjct: 60 GGEIRIDGHPVRIEGPLGGRAAGISIIYQELSLAPNLTVAENIYLGREVSQSGLLARGAM 119 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 +L ++G + TL+ ++ +G++QLVEIA+AL K+LI+DEPT SL+ +SE Sbjct: 120 REGVGPILTRLGADFAASTLVAELSMGQRQLVEIARALHARSKILIMDEPTTSLSAGESE 179 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 L L+ + R +G+ I I+H+++EV + D++TVLRDG V +LD + EI D I+R Sbjct: 180 KLFALIRQLRAEGLAIIYISHRMDEVYALGDRVTVLRDGRLVGSLD--KPEIRADSIVRM 237 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGRD+ Y P + V HR + ++TV GEVVG+AGL+G Sbjct: 238 MVGRDVSSFYKKDHDPHAKRDRPVLTAVDLGDGHR----VKGCSLTVHAGEVVGLAGLIG 293 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 AGRTE A + G + ++TG V +DG+ +++ T R A+DAG+AY+TEDRK LGL L+ + Sbjct: 294 AGRTELAHLIIGAT--PKMTGHVTLDGERIEIETPRDALDAGIAYLTEDRKALGLFLDMS 351 Query: 361 ILHNTTLANLAGVSK-ASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVL 419 N LA + ++ ++D K A + + L IR+ LSGGNQQKV+L Sbjct: 352 CADNINLAVIGRDARLGGVLDRDKARLRADEAFSALGIRAPNPGVTVGGLSGGNQQKVLL 411 Query: 420 SKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIY 479 S+ L + P VLILDEPTRG+DVGAK EIY+II+ LA G +L+ISS++PE+LG CDR+ Sbjct: 412 SRLLATAPKVLILDEPTRGVDVGAKSEIYSIIDNLAKSGTAILVISSDLPEILGICDRVL 471 Query: 480 VMNEGRIVAELPKGEA---SQESIM 501 VM G++ EL + +QE IM Sbjct: 472 VMRCGQLAGELQQSATTPITQEDIM 496 Score = 89.7 bits (221), Expect = 2e-22 Identities = 66/230 (28%), Positives = 115/230 (50%), Gaps = 11/230 (4%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337 + L +++TV GEV + G GAG++ M + +Y G++ IDG PV + Sbjct: 19 KALQKVDLTVYAGEVHALMGENGAGKSTL-MKILSGAYRPDPGGEIRIDGHPVRIEGPLG 77 Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLR- 396 AG++ + ++ L L N + N L VS++ ++ + TRL Sbjct: 78 GRAAGISIIYQE---LSLAPNLTVAENIYLGR--EVSQSGLLARGAMREGVGPILTRLGA 132 Query: 397 -IRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLA 455 +S + E LS G +Q V +++ L + +LI+DEPT + G +++ +I QL Sbjct: 133 DFAASTLVAE---LSMGQRQLVEIARALHARSKILIMDEPTTSLSAGESEKLFALIRQLR 189 Query: 456 ADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 A+G ++ IS M E+ DR+ V+ +GR+V L K E +SI+R ++ Sbjct: 190 AEGLAIIYISHRMDEVYALGDRVTVLRDGRLVGSLDKPEIRADSIVRMMV 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: 648 Number of extensions: 35 Number of successful extensions: 11 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: 507 Length adjustment: 34 Effective length of query: 478 Effective length of database: 473 Effective search space: 226094 Effective search space used: 226094 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