Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Koxy:BWI76_RS14860 Length = 510 Score = 390 bits (1001), Expect = e-113 Identities = 198/488 (40%), Positives = 318/488 (65%), Gaps = 5/488 (1%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 LL + GI+K + AL+NV + +HALMGENGAGKSTL+K L G Q+DSG I Sbjct: 9 LLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFI 68 Query: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GMFVDQDKMYRETK 131 G+ ID + ++A + GI+++HQELN V +V +N++LG+ PT +D+ +M+RE K Sbjct: 69 DGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMHREAK 128 Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 + ++ DIDP+A +G+LS+ + QM+EIA+A S NAK++++DEPT++L+ E L+ + Sbjct: 129 EKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRL 188 Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 I ++++ G G+VYISH+MEE++QL + VTV RDG WI TE L ++ I+ MMVGR + Sbjct: 189 IAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVGRQIV 248 Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311 + + PG+V+LEVR+L + VSF++ GE++ ++GLVG+ RT++ LFG Sbjct: 249 DLYQHEPRTPGDVLLEVRDLAG---SATGPVSFEVSAGEVVSMSGLVGSGRTEVARLLFG 305 Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371 +S G++ L G++ + AI G +VTE+R++ G++ + N IS++ N+ Sbjct: 306 ADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNFV 365 Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431 G++ +++ + +R++ + +LSGGNQQK + RWLL +L+LD Sbjct: 366 -AGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILD 424 Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491 EPTRG+D+GAK EIY+LI LA+ GK I++ISS++PE +GI+DR+LVM G + + + Sbjct: 425 EPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSC 484 Query: 492 TTTQNEIL 499 + T+ E++ Sbjct: 485 SATEEEVM 492 Score = 91.7 bits (226), Expect = 6e-23 Identities = 57/224 (25%), Positives = 115/224 (51%), Gaps = 6/224 (2%) Query: 278 SIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAIN 337 ++ +V FDL GE+ + G GA ++ +++ L G ++ +G I + G+ I+ +A Sbjct: 24 ALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFIDGQAIDIRTPRDARK 83 Query: 338 HGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKT 397 +G A++ +E + + + N + + + G+LD RM + + ++ + Sbjct: 84 YGIAIIHQELNTV---PDMTVAENLFLG--QEPTSFAGILDRKRMHREAKEKLNRINADI 138 Query: 398 PGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGK 457 + +GSLS G QQ V I R + ++L+LDEPT + ++Y+LIA++ + G Sbjct: 139 DP-QAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRLIAQMRQDGV 197 Query: 458 GIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501 G++ IS M E+ + +R+ V +G G + + +I+R+ Sbjct: 198 GMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRM 241 Score = 63.5 bits (153), Expect = 2e-14 Identities = 59/252 (23%), Positives = 114/252 (45%), Gaps = 17/252 (6%) Query: 10 GEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69 G+ LLE+ + S G V+ +V + ++ G G+G++ + + LFG + G+ Sbjct: 259 GDVLLEVRDLAGSATGP-----VSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGS 313 Query: 70 ILFQGKEIDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLGRYPTKGMFVDQDKM 126 + G+E A+ +GI MV ++ L L SV N+ + FV + Sbjct: 314 VRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDN---FVAGGVV 370 Query: 127 YRET--KAIFDELD-IDIDPRA---RVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL 180 R+T A+ +++ + + A V LS Q +A+ +++++I+DEPT + Sbjct: 371 KRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILDEPTRGV 430 Query: 181 TEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDK 240 ++ +I +L G I+ IS + E + D V V+R G+ + P T ++ Sbjct: 431 DIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEEE 490 Query: 241 IIAMMVGRSLNQ 252 ++ G +Q Sbjct: 491 VMLHATGTFTSQ 502 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: 601 Number of extensions: 35 Number of successful extensions: 8 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: 510 Length adjustment: 34 Effective length of query: 472 Effective length of database: 476 Effective search space: 224672 Effective search space used: 224672 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