Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456 Length = 518 Score = 369 bits (947), Expect = e-106 Identities = 210/505 (41%), Positives = 314/505 (62%), Gaps = 11/505 (2%) Query: 11 EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--G 68 +YLL+M+GI K+F GVKAL+ +++KVRP L GENGAGKSTL+K L +Y + G Sbjct: 3 DYLLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDG 62 Query: 69 TILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPT-KGMFVDQDKMY 127 IL+ G+ + S E GI ++HQEL LV SV +N+++G T G ++ M Sbjct: 63 EILWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMI 122 Query: 128 RETKAIFDELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186 +A+ EL + D++ V Q++EIAKA + A+++I+DEP+S+LT E+ Sbjct: 123 HRAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIE 182 Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMV 246 L IIR LK +G VYISHK++E+ +CD ++V+RDG+ IAT +A +++ KII MV Sbjct: 183 VLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQMV 242 Query: 247 GRSLNQRFPDKENKPGEVILEVRNLT-----SLRQPSIRDVSFDLHKGEILGIAGLVGAK 301 GR ++ +P + + GEVI E R+ T + R+ + D+SF L +GEILGIAGLVGA Sbjct: 243 GREMSNLYPTEPHDVGEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAG 302 Query: 302 RTDIVETLFGIRE-KSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGF 360 RT++V LFG + G + L+G+QI+ ++I G +V E+R+ GI L +G Sbjct: 303 RTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQ 362 Query: 361 NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420 N ++ + NY +K+ +D I M +KT I SLSGGNQQK ++ + Sbjct: 363 NITLAVLDNY-SKLTRIDAEAELGSIDKEISRMHLKTASPFLPITSLSGGNQQKAVLAKM 421 Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480 LLT+P +L+LDEPTRG+DVGAK+EIY+L+ LA +G II++SSE+ E+LG++DR+LV+ Sbjct: 422 LLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVIG 481 Query: 481 NGLVSGIVDTKTTTQNEILRLASLH 505 +G + G TQ ++L A H Sbjct: 482 DGQLRGDFINHELTQEQVLAAALSH 506 Lambda K H 0.318 0.136 0.384 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: 605 Number of extensions: 27 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: 506 Length of database: 518 Length adjustment: 35 Effective length of query: 471 Effective length of database: 483 Effective search space: 227493 Effective search space used: 227493 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 (21.7 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