Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 336 bits (861), Expect = 1e-96 Identities = 198/507 (39%), Positives = 310/507 (61%), Gaps = 9/507 (1%) Query: 4 TILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGE 63 T+L++ ++K+FPGV+AL+ V+L V GE+HAL+GENGAGKSTL+K+LS + A G Sbjct: 2 TLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADA--GT 59 Query: 64 IHYEGAVRNFR-AINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFN 122 + + G V + R A + +GI I+QE L P LS+AEN++LG E G++ W + Sbjct: 60 VTFAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119 Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182 + LL +GL +P+ + + V +QQ+VEIAKA++ + +L+I+DEPTA+L+ + + L Sbjct: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242 ++ + + ++ I ++H+L EV+ + D+ TV+RDG V + D E+++ ++R MV Sbjct: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVAD--MVRLMV 237 Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302 GR +E R P G +L+V+ + L ++ R GE+VG+AGL+GAG Sbjct: 238 GRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAG 297 Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362 RT+ A +FG G VL+D KP+ + + R AI AG+ V EDRK G L+ +I Sbjct: 298 RTDLARLIFGAD--PIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIR 355 Query: 363 HNTTLANLAGVSK-ASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421 N +L +L +S +D+ E + +R +LRI+ + LSGGNQQKV+L + Sbjct: 356 RNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 + P VLI+DEPTRGID+GAK E++ +++ LA G V++ISSE+ E++ DRI V Sbjct: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475 Query: 482 NEGRIVAELPKGEASQESIMRAIMRSG 508 EG IVA+L A++E +M A M +G Sbjct: 476 REGVIVADLDAQTATEEGLM-AYMATG 501 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: 609 Number of extensions: 29 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 512 Length of database: 515 Length adjustment: 35 Effective length of query: 477 Effective length of database: 480 Effective search space: 228960 Effective search space used: 228960 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