Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter
Query= TCDB::O05176 (512 letters) >FitnessBrowser__HerbieS:HSERO_RS22465 Length = 518 Score = 435 bits (1118), Expect = e-126 Identities = 232/505 (45%), Positives = 338/505 (66%), Gaps = 5/505 (0%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M+ +LEM+ I K+F GV+AL +++K++ GE L GENGAGKSTLMK+LSGVYP GT+ Sbjct: 1 MSEYLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTW 60 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVA-SNGVISWQQ 119 EGEI ++G ++ D+E GI+IIHQEL LVP LS+AENIF+G+E+ G +++ Sbjct: 61 EGEILWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPA 120 Query: 120 TFNRTRELLKKVGLKESPETL-ITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178 + R EL++++ + + L ++ G G QQLVEIAKAL+K +LLILDEP++SL S+ Sbjct: 121 MYRRAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASE 180 Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVII 238 LL ++ + + +G+ + I+HKL+EV +V D I+V+RDG + T +E+ D II Sbjct: 181 IGVLLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTP--MQEMDVDKII 238 Query: 239 RNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298 MVGR++ YP R+ IGE +LE +N Y + R+ + D++ +VR+GE++GIAGL Sbjct: 239 TQMVGREITAMYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGL 298 Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358 +GAGRTE ++FG +Y R G VL++GKP D S+ K+I GL V EDRKH G+V + Sbjct: 299 VGAGRTELVSAIFG-AYRGRYEGQVLLEGKPADTSSPLKSIRRGLCMVPEDRKHHGIVPD 357 Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418 ++ N TL L S+ S ID E+K D R+R++++ F +LSGGNQQK V Sbjct: 358 LDVGQNITLTVLNRFSRGSRIDGSAELKTIQDEIGRMRVKTATPFLPITSLSGGNQQKAV 417 Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478 L+K L + P VLILDEPTRG+DVGAK EIY +I++LA G ++M+SSE+ E+LG DR+ Sbjct: 418 LAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAIIMVSSELAEVLGVSDRV 477 Query: 479 YVMNEGRIVAELPKGEASQESIMRA 503 V+ EGR+ + SQE+++ A Sbjct: 478 LVIGEGRLRGDFVNDNLSQETVLAA 502 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: 653 Number of extensions: 34 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: 518 Length adjustment: 35 Effective length of query: 477 Effective length of database: 483 Effective search space: 230391 Effective search space used: 230391 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