Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 429 bits (1102), Expect = e-124 Identities = 219/492 (44%), Positives = 324/492 (65%), Gaps = 4/492 (0%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 +L++ G++K FPGV ALD ++L +R +HA+ GENGAGKSTL+K + G Y D G I + Sbjct: 22 ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICY 81 Query: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132 +GK + F S +A GI+++HQELNLV SV +N++L R P +G FVD + + Sbjct: 82 EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNANAQR 141 Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192 + +++ P VG LS++Q QM+EIAKA S +A+++IMDEPTSSLTE E LF II Sbjct: 142 CLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRII 201 Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQ 252 R+L+ G I+YISH+++E+ ++ D VTVLRDG+ IAT A T+++I+A MVGR+L+ Sbjct: 202 RELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGRALDD 261 Query: 253 RFPDKENKPGE-VILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311 +P +E+ P E V++ VR+L R + +SFDL KGEILG AGL+GA RT++ +FG Sbjct: 262 AYPPRESVPTEQVLMRVRDLQ--RTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIFG 319 Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371 +G+I L + + EAI HG A ++E+R+ G+ + + N +SN+R Sbjct: 320 AERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSNVRAIS 379 Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431 ++ G L S + + + + ++TP + +LSGGNQQK++I +WL IL D Sbjct: 380 SR-GFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFD 438 Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491 EPTRGIDVGAK+ IY+L+ LA G G+++ISSE+PELLG+TDRI V GL++ +++T+ Sbjct: 439 EPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETR 498 Query: 492 TTTQNEILRLAS 503 T+Q EIL AS Sbjct: 499 QTSQEEILHYAS 510 Score = 63.2 bits (152), Expect = 2e-14 Identities = 55/229 (24%), Positives = 101/229 (44%), Gaps = 16/229 (6%) Query: 32 VNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGIS 91 ++ +R I G GAG++ + + +FG + DSG+I + S +EA+ +GI+ Sbjct: 290 LSFDLRKGEILGFAGLMGAGRTEVARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIA 349 Query: 92 MVHQELN---LVLQRSVMDNMWLGRY---PTKGMFVDQDKMYRETKAIFD----ELDIDI 141 + ++ L L V N+ L ++G + E AI + EL I Sbjct: 350 YLSEDRKKDGLALSMPVAANITLSNVRAISSRGFL-----RFSEETAIAERYVRELAIRT 404 Query: 142 DPRARVG-TLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGC 200 ++ LS Q I I+K ++I+ DEPT + ++ ++ +L G Sbjct: 405 PTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGV 464 Query: 201 GIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249 G+V IS ++ E+ + D + V +G A + ++I+ GRS Sbjct: 465 GVVLISSELPELLGMTDRIAVFHEGLITAVLETRQTSQEEILHYASGRS 513 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: 587 Number of extensions: 20 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: 515 Length adjustment: 35 Effective length of query: 471 Effective length of database: 480 Effective search space: 226080 Effective search space used: 226080 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