Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Phaeo:GFF385 Length = 509 Score = 285 bits (728), Expect = 4e-81 Identities = 165/498 (33%), Positives = 286/498 (57%), Gaps = 19/498 (3%) Query: 14 LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73 +E+ GI+K+F V+A +++++V P +IH ++GENGAGKSTL+ L+G Y+ D G + Sbjct: 6 IELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIH 65 Query: 74 GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAI 133 GK + ++ A+ GI MV Q LV +V++N+ LG + K + K + Sbjct: 66 GKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDGGLLKPSLSKARKSLKDL 125 Query: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIR 193 E ++++DP AR+ + V Q +EI KA A I+I+DEPT LT E + LF I+ Sbjct: 126 AAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILD 185 Query: 194 KLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQR 253 +L+ G I+ I+HK+ EI + D V+V+R G+ AT A + + + +MVGR + R Sbjct: 186 RLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVGRKVLLR 245 Query: 254 FPDKENKPGEVILEVRNLTSLRQPS---IRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310 PG+ ILE+ NL+ + + ++++ + GEILGIAG+ G +++++E L Sbjct: 246 VDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLG 305 Query: 311 GIREKSAGTITLHGKQI------NNHNANEAINHGFALVTEERRSTGI----YAYLDIGF 360 G+RE G+I L+G + ++ A A + A V E+R+ G+ +A+ ++ F Sbjct: 306 GMRE-GQGSIRLNGAPLPLSGAGSDARARRAAH--VAHVPEDRQREGLIMDFHAWENVAF 362 Query: 361 NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420 + Y+ + L++N+ +++DT+ + V+ P + SGGNQQK+++ R Sbjct: 363 G--YHHAPEYQRGL-LMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVARE 419 Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480 + PE+L++ +PTRG+D+GA I++ I EL +GK I+++S E+ E+L + DR+ VM Sbjct: 420 IERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMF 479 Query: 481 NGLVSGIVDTKTTTQNEI 498 +G++ G T + E+ Sbjct: 480 DGMIMGERPADQTDEKEL 497 Score = 77.8 bits (190), Expect = 9e-19 Identities = 57/229 (24%), Positives = 107/229 (46%), Gaps = 21/229 (9%) Query: 280 RDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHG 339 +D+S + G I GI G GA ++ ++ L+G + G + +HGK+ ++ AI+ G Sbjct: 22 KDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIHGKRTEIPDSQAAISAG 81 Query: 340 FALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKV-GLLDNSRMKSDTQWVIDSMRVKTP 398 +V + + L+ N +N + G D +K S++ Sbjct: 82 IGMVFQHFK--------------LVENFTVLENIILGAEDGGLLKPSLSKARKSLKDLAA 127 Query: 399 GHR------TQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAEL 452 + +I + G QQ+V I + L Q +IL+LDEPT + ++++++ L Sbjct: 128 EYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILDRL 187 Query: 453 AKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501 +GK II+I+ ++ E++ TD + VM G ++ V T T+ + L Sbjct: 188 RAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAEL 236 Score = 68.2 bits (165), Expect = 7e-16 Identities = 58/258 (22%), Positives = 119/258 (46%), Gaps = 15/258 (5%) Query: 2 VSSTTPSSGEYLLEMSGINK-SFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF 60 V + G+ +LE+ ++ GV + N++L VR I + G G G+S L++ L Sbjct: 246 VDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLG 305 Query: 61 GIYQKDSGTILFQGKEI-------DFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGR 113 G+ ++ G+I G + D + + A + Q L++ +N+ G Sbjct: 306 GM-REGQGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWENVAFGY 364 Query: 114 YPT----KGMFVDQDKMYRETKAIFDELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNA 168 + +G+ ++ + +T+A + D+ DP S Q I +A+ N Sbjct: 365 HHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVAREIERNP 424 Query: 169 KIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWI 228 +++++ +PT + + + I +L+++G I+ +S ++EEI L D V V+ DG + Sbjct: 425 ELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGMIM 484 Query: 229 ATEPLAGLTMDKIIAMMV 246 P A T +K + +++ Sbjct: 485 GERP-ADQTDEKELGLLM 501 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: 616 Number of extensions: 32 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 506 Length of database: 509 Length adjustment: 34 Effective length of query: 472 Effective length of database: 475 Effective search space: 224200 Effective search space used: 224200 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