Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012385743.1 BIND_RS14235 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000019845.1:WP_012385743.1 Length = 511 Score = 357 bits (917), Expect = e-103 Identities = 204/505 (40%), Positives = 313/505 (61%), Gaps = 17/505 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L NI K FPGV AL+ V LK++ +HAL+GENGAGKSTLMK+++G+Y G I Sbjct: 21 LLTAENIRKEFPGVLALDGVELKLRRSSVHALMGENGAGKSTLMKIIAGIYKPDA--GRI 78 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123 +G +F++ D+ + GI +IHQEL L+ +++AENI++ E + G + + Sbjct: 79 RLKGNEISFQSPLDALESGISMIHQELNLMDYMTVAENIWIRREPLNRFGFVDHDEMRRM 138 Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 T+ L +++ + P+ + D+ V +Q+VEIAKA+S +LI+DEPT++L E + + L Sbjct: 139 TQALFRRLRIDLDPDAEVRDLSVANRQIVEIAKAVSYGSDVLIMDEPTSALTEREVDHLF 198 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQE-EISEDVIIRNMV 242 ++ + R QG+ + ITHK+NE+ ++AD+ ++ RDG + T H +++ D IIR MV Sbjct: 199 EIIRDLRAQGIGIVYITHKMNELFEIADEFSIFRDGRYIST---HAACDVTCDDIIRMMV 255 Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302 GR+L +P +VPIG+ L VKN V +N +R GE++GIAGL+G+G Sbjct: 256 GRELTQMFPKEEVPIGDVALSVKNVGL-------DGVFQGVNFDLRAGEILGIAGLIGSG 308 Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362 R+ A ++FG + +G + I G V + + A+ +A++TEDRK G +L+ +IL Sbjct: 309 RSSLAATLFGVTPA--TSGSIAIAGNDVVIDSPATAMRHQMAFLTEDRKVSGCLLSLSIL 366 Query: 363 HNTTLANLAGVSKASIIDDIKEMKVASDFRTR-LRIRSSGIFQETVNLSGGNQQKVVLSK 421 N LA L + KE+ A D R LR+++ + + NLSGGNQQKV++ + Sbjct: 367 ENLQLAVLQDKYVTNGFVHEKELFSACDEMARKLRVKTPNLQEIIGNLSGGNQQKVLIGR 426 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 WL + P +LILDEPTRGIDVGAK EI+ ++ +LA +G +++ISSEMPE+LG DRI VM Sbjct: 427 WLLNKPRILILDEPTRGIDVGAKAEIHRLVTELAREGVAIILISSEMPEVLGMSDRIMVM 486 Query: 482 NEGRIVAELPKGEASQESIMRAIMR 506 +EGR+ L + EA+Q IM R Sbjct: 487 HEGRMTGILDRSEATQVKIMELASR 511 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: 632 Number of extensions: 41 Number of successful extensions: 10 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: 511 Length adjustment: 35 Effective length of query: 477 Effective length of database: 476 Effective search space: 227052 Effective search space used: 227052 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