Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_040658978.1 ON16_RS02070 ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >NCBI__GCF_000307265.1:WP_040658978.1 Length = 519 Score = 318 bits (815), Expect = 3e-91 Identities = 184/498 (36%), Positives = 291/498 (58%), Gaps = 12/498 (2%) Query: 11 EYLLEMSGINKSFP-GVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69 EY+++M GI K +P G+ A V+L VR IHALMGENGAGKSTL+K LFG+ Q SG Sbjct: 4 EYVVQMKGITKVYPNGIAANQGVDLNVRKGEIHALMGENGAGKSTLMKMLFGLEQPTSGE 63 Query: 70 ILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GMFVDQDKMYR 128 I G++++ S A+ G+ MVHQ LV +V +NM LG P K G+F+D K Sbjct: 64 IWVNGEKVNLTSPTVAIAKGVGMVHQHFMLVPSLTVAENMVLGMVPKKSGLFIDSGKAIE 123 Query: 129 ETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHL 188 TK ++ ++ +DP ARV + V Q +EI KA AKI+I+DEPT+ LT +E L Sbjct: 124 ITKEYAEKFNLHVDPTARVCDIPVGMKQKVEILKALVRGAKILILDEPTAVLTTQETTEL 183 Query: 189 FTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGR 248 F + LKE+G I++ISHK+ EI Q+ D +T+LR G+ + + +KI +MVGR Sbjct: 184 FKELMSLKEQGYTIIFISHKLAEIMQITDRMTILRGGRSMGVYETKDESPEKISRLMVGR 243 Query: 249 SLNQRFPDKENKPGEVILEVRNLTSLRQ---PSIRDVSFDLHKGEILGIAGLVGAKRTDI 305 + + + +PGE +L VR+L + + + VSFDL +GEILGIAG+ G + ++ Sbjct: 244 DVVLKVEKGKAQPGESVLRVRDLEYINEWGKKMLDKVSFDLRQGEILGIAGVEGNGQKEL 303 Query: 306 VETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGF--NSL 363 V+ LF + +AG++ ++G + + + G +LV E+R +Y D G +L Sbjct: 304 VDMLFHLNTPNAGSVEVNGASVLGQSQRKIREMGVSLVPEDRM---LYGIADSGTIEENL 360 Query: 364 ISNIRNYK--NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWL 421 IS+ K NK L D + ++ +I+ V Q+ LSGGN QKV++ R Sbjct: 361 ISDRCGTKRLNKGPLFDMKAIHNECDQLIEDYTVLCKSGAQQVKMLSGGNIQKVVVAREF 420 Query: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481 P++++ D+PTRGIDVGA I + + EL++ G ++++S+++ E++ ++D ++VM Sbjct: 421 SNNPKLIIADQPTRGIDVGATEFIRRKLVELSRSGVAVLLVSADLNEVMELSDSLIVMYG 480 Query: 482 GLVSGIVDTKTTTQNEIL 499 G +S + + +E++ Sbjct: 481 GRISAYFEDTSDLSDEVM 498 Score = 84.0 bits (206), Expect = 1e-20 Identities = 61/243 (25%), Positives = 126/243 (51%), Gaps = 11/243 (4%) Query: 263 EVILEVRNLTSLRQPSI---RDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGT 319 E +++++ +T + I + V ++ KGEI + G GA ++ +++ LFG+ + ++G Sbjct: 4 EYVVQMKGITKVYPNGIAANQGVDLNVRKGEIHALMGENGAGKSTLMKMLFGLEQPTSGE 63 Query: 320 ITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGL-LD 378 I ++G+++N + AI G +V + + L + N ++ + K GL +D Sbjct: 64 IWVNGEKVNLTSPTVAIAKGVGMVHQHFM---LVPSLTVAENMVLGMV---PKKSGLFID 117 Query: 379 NSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGID 438 + + T+ + + ++ + G +QKV I + L+ +IL+LDEPT + Sbjct: 118 SGKAIEITKEYAEKFNLHVDP-TARVCDIPVGMKQKVEILKALVRGAKILILDEPTAVLT 176 Query: 439 VGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEI 498 E+++ + L ++G II IS ++ E++ ITDR+ ++ G G+ +TK + +I Sbjct: 177 TQETTELFKELMSLKEQGYTIIFISHKLAEIMQITDRMTILRGGRSMGVYETKDESPEKI 236 Query: 499 LRL 501 RL Sbjct: 237 SRL 239 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: 611 Number of extensions: 28 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 506 Length of database: 519 Length adjustment: 35 Effective length of query: 471 Effective length of database: 484 Effective search space: 227964 Effective search space used: 227964 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 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