Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate H281DRAFT_01057 H281DRAFT_01057 monosaccharide ABC transporter ATP-binding protein, CUT2 family (TC 3.A.1.2.-)
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Burk376:H281DRAFT_01057 Length = 517 Score = 391 bits (1005), Expect = e-113 Identities = 213/499 (42%), Positives = 322/499 (64%), Gaps = 7/499 (1%) Query: 8 SSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67 S+G+ LLE+ I K FPGVK+LD V+L VR IHAL+GENGAGKSTL K + G+Y DS Sbjct: 8 SAGD-LLEVIRITKEFPGVKSLDQVSLGVRAGEIHALVGENGAGKSTLTKIMAGVYAPDS 66 Query: 68 GTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYP-TKGMFVDQDKM 126 G I F G+ + + SA +A +GI ++HQEL L Q +V +N++ G P T+ +D +M Sbjct: 67 GEIRFAGQPLQWKSAADAKRHGIHVIHQELVLFPQSTVAENIFAGAEPRTRIGVLDHGRM 126 Query: 127 YRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186 R+ +A+ EL + +D R RVG LSV+ QM+EIAKA + +++I+DEPT+ + KEV Sbjct: 127 NRDAQALLGELGVRLDSRERVGNLSVADQQMVEIAKAMAGETRVLILDEPTAVIAGKEVQ 186 Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMV 246 LF +R L+ +G IVYISH+++EIF+LCD VTV++DG+ +AT+ +A T D+++ +MV Sbjct: 187 LLFARVRALRAKGVAIVYISHRLDEIFELCDRVTVMKDGRKVATQSVANTTRDQLVRLMV 246 Query: 247 GRSLNQRFPDKE-NKPG-EVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTD 304 GR + +PDK PG +LEV L + + D S + GEI+GIAG+VG+ RT+ Sbjct: 247 GREMKDIYPDKPILAPGVPNVLEVNGLCVGNR--VVDASLTVRAGEIVGIAGMVGSGRTE 304 Query: 305 IVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLI 364 + +FG GT+ + G + AI G VTE+R+S G+ LD+ N Sbjct: 305 LAAGIFGALRAHRGTVDIGGTRRTRMTPRTAIRLGLGFVTEDRKSQGLLMLLDVAQNVTA 364 Query: 365 SNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQ 424 + + ++ GL+ + ++ Q I+ R+ + +LSGGNQQKV+I RW+ Sbjct: 365 TTLAQV-SRFGLMRPALERAAAQAAINEYRIAGAHPAGGVATLSGGNQQKVLISRWVRVC 423 Query: 425 PEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLV 484 +L+LDEPTRG+DVGAK EIY+++ EL +G GI++ISSE+ E++G++DR+LVM G + Sbjct: 424 KRVLILDEPTRGVDVGAKAEIYRVMRELTSRGLGILMISSELQEVIGMSDRVLVMREGRI 483 Query: 485 SGIVDTKTTTQNEILRLAS 503 +G V + T+++I+RLA+ Sbjct: 484 NGEVSGEQMTEHDIMRLAT 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: 590 Number of extensions: 29 Number of successful extensions: 9 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: 517 Length adjustment: 35 Effective length of query: 471 Effective length of database: 482 Effective search space: 227022 Effective search space used: 227022 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