Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 402 bits (1034), Expect = e-116 Identities = 212/498 (42%), Positives = 326/498 (65%), Gaps = 10/498 (2%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 +L + I K F GVKALD+V+L+++ + A++GENGAGKSTL+K L G+Y GTI + Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRETK 131 G + F + ++A E GI+++HQELNL+ S+ +N++LGR P M +D KM++E Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120 Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 + L +++DP V L V Q Q++EIAKA S ++++IMDEPTS+++++EV LF I Sbjct: 121 QLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGI 180 Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 IR L+ G I YISHK++E+F + D VLRDG+ I + + G+T + +I MVGR + Sbjct: 181 IRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREIV 240 Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSI------RDVSFDLHKGEILGIAGLVGAKRTDI 305 + E +L V++LT ++ P I +D++F+L KGE+LGI GL+GA RT++ Sbjct: 241 IERSCSGRQFDETVLSVKHLT-VKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTEL 299 Query: 306 VETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLIS 365 +E LFG+ ITL GK EA++ G ALV E+R+ G+ +D+ NS ++ Sbjct: 300 MEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLT 359 Query: 366 NIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425 + + + GLLD+ + K Q + +++K HR + LSGGNQQKV++ +WL T+P Sbjct: 360 VVDSILSG-GLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRP 418 Query: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNG-LV 484 ++LMLDEPTRGID+ AK EIY+LI +LA +G G+I++SSE+PE+L ++DR+LVM+ G L Sbjct: 419 KVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLT 478 Query: 485 SGIVDTKTTTQNEILRLA 502 + I T+++EIL+ A Sbjct: 479 ANIPIDAQTSEDEILQAA 496 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: 602 Number of extensions: 28 Number of successful extensions: 8 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: 502 Length adjustment: 34 Effective length of query: 472 Effective length of database: 468 Effective search space: 220896 Effective search space used: 220896 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