Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate HSERO_RS05195 HSERO_RS05195 xylose ABC transporter ATP-binding protein
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__HerbieS:HSERO_RS05195 Length = 518 Score = 394 bits (1012), Expect = e-114 Identities = 220/499 (44%), Positives = 320/499 (64%), Gaps = 12/499 (2%) Query: 13 LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--GSI 70 +LEMRGI KSFPGVKAL+NVNL VR IHA++GENGAGKSTL+K L G+Y S G I Sbjct: 4 ILEMRGIEKSFPGVKALNNVNLAVREGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGDI 63 Query: 71 VFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDT 130 V++G+ F +++ GI ++HQEL LV SVM+N++LG +G +D ++ Y Sbjct: 64 VYKGEVRAFKDIRDSEHLGIIIIHQELALVPLLSVMENLFLGNEQARGGVIDWEQSYVRA 123 Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 K + ++ + P +VG L V + Q+IEIAKA S K++I+DEPT+SL E + + L Sbjct: 124 KELLAKVGLKESPLTQVGDLGVGKQQLIEIAKALSKEVKLLILDEPTASLNESDSDALLE 183 Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPL--EGLDMDKIIAMMVGR 248 ++ +LK +G + ISHK+ EI ++ D IT+LRDG + T E + D+II MVGR Sbjct: 184 LLLELKRQGIASILISHKLNEISKVADSITVLRDGTTVDTFDCRAEPISEDRIIQHMVGR 243 Query: 249 SLNQRFPDKENKPGDVILEVR-----HLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRT 303 + R+P ++ + G+VI EVR H + +I+DV+ + GEI+GIAGL+GA RT Sbjct: 244 EMADRYPQRDPQIGEVIFEVRDWRVHHPLHTDRLAIKDVNMSVRAGEIVGIAGLMGAGRT 303 Query: 304 DIVETLFG--IREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFN 361 ++ +++FG +K +G LHGK+++ T +AI G A VTE+R+ G+ DI N Sbjct: 304 ELAKSIFGRAYGKKITGQAFLHGKEVDLSTIEKAIAKGIAYVTEDRKGDGLVLEEDIKKN 363 Query: 362 SLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWL 421 ++N+ + ++D +R MR++ ++ +LSGGNQQKV++ +WL Sbjct: 364 ISLANLGGVSERT-VIDEAREYKIAADFKQQMRIRCSSVLQKVVNLSGGNQQKVVLSKWL 422 Query: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481 +QPE+L+LDEPTRGIDVGAKFEIY +I++LA +GK II+ISSEMPELLG+ DRI VM+ Sbjct: 423 FSQPEVLILDEPTRGIDVGAKFEIYNIISKLAAEGKCIIMISSEMPELLGMCDRIYVMNE 482 Query: 482 GLVSGIVDTKTTTQNEILR 500 G G + TQ I+R Sbjct: 483 GQFVGHLPKAEATQENIMR 501 Lambda K H 0.319 0.137 0.388 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: 661 Number of extensions: 27 Number of successful extensions: 10 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 ( 7.4 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