Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008 Length = 485 Score = 324 bits (830), Expect = 5e-93 Identities = 192/484 (39%), Positives = 298/484 (61%), Gaps = 13/484 (2%) Query: 36 LVGENGAGKSTLMKVLSGVYPAGTYEGEIHYEGAVRNFRAIN-DSEDIGIIIIHQELALV 94 L+GENGAGKST++K+L+G PA +G + + G V +++GII I+QE L+ Sbjct: 1 LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60 Query: 95 PLLSIAENIFLGNEVASNGVISWQQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEI 154 +S+AEN++LG E +G + W+Q F+ + +L +GL +P T++ + V +QQ+VEI Sbjct: 61 ADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVEI 120 Query: 155 AKALSKSVKLLILDEPTASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQIT 214 AKAL+ + KL+I+DEPTA+L+ + + L ++ + + +G++ I ++HKLNEV+ D+ T Sbjct: 121 AKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRYT 180 Query: 215 VLRDGMTVKTLD-CHQEEISEDVIIRNMVGRDLEDRYPPRDVPIGETILEVKNWN---AY 270 + RDG + + D C ++S D I+R MVGRD+E P GE +L+V++ + A Sbjct: 181 IFRDGAYITSGDVC---DVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAAG 237 Query: 271 HQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPV 330 + L D++V VR GE+VG AGL+GAGRTE A +FG G + ++G+ V Sbjct: 238 GGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDE--GMIYVNGRQV 295 Query: 331 D-VSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSK-ASIIDDIKEMKVA 388 + R+ I AG+A V EDRK L+ +I N +L +L G+ + IDD E ++ Sbjct: 296 SPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLI 355 Query: 389 SDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIY 448 D++ RLRI+ S LSGGNQQKV+L++ + P VLI+DEPTRGIDVGAK E++ Sbjct: 356 QDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVH 415 Query: 449 TIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSG 508 ++ +A G V++ISSE+PE++ DRI EG+I + EA++E +M A M G Sbjct: 416 QLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLM-ARMAQG 474 Query: 509 EKNS 512 +S Sbjct: 475 VSSS 478 Score = 70.1 bits (170), Expect = 2e-16 Identities = 65/258 (25%), Positives = 123/258 (47%), Gaps = 32/258 (12%) Query: 5 ILEMRNITKTFPG------VKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAG 58 +L+++++++T G L ++++ V+ GEI G GAG++ L +V+ G G Sbjct: 225 MLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGA--DG 282 Query: 59 TYEGEIHYEG-AVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN----- 112 EG I+ G V F++ + G+ ALVP + FL + + N Sbjct: 283 CDEGMIYVNGRQVSPFKSPREGIAAGV-------ALVPEDRKQQACFLSHSIRWNMSLPS 335 Query: 113 --GVISWQQTFNRTRE------LLKKVGLKESPETL-ITDIGVGKQQLVEIAKALSKSVK 163 G+ W + E K++ +K S +++ I + G QQ V +A+ ++ K Sbjct: 336 LGGLQRWGMFIDDRAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPK 395 Query: 164 LLILDEPTASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVK 223 +LI+DEPT ++ + LL + G+ I+I+ +L EV V+D+I R+G Sbjct: 396 VLIVDEPTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITG 455 Query: 224 TLDCHQEEISEDVIIRNM 241 + +E +E++++ M Sbjct: 456 IVSA--DEATEELLMARM 471 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: 583 Number of extensions: 35 Number of successful extensions: 9 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: 485 Length adjustment: 34 Effective length of query: 478 Effective length of database: 451 Effective search space: 215578 Effective search space used: 215578 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