Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 334 bits (857), Expect = 4e-96 Identities = 179/491 (36%), Positives = 288/491 (58%), Gaps = 4/491 (0%) Query: 12 YLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTIL 71 Y++EM I K FPG+ A DNV L+V+ IHAL+GENGAGKSTL+ LFG+YQ + G IL Sbjct: 3 YVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEIL 62 Query: 72 FQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETK 131 +GK + A GI MVHQ LV + +V +N+ LG+ PT G ++ K + + Sbjct: 63 VKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVE 122 Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 I + + +DP A++ +SV Q +EI K A+I+I DEPT++LT +E+ L I Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182 Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 ++KL G I+ I+HK++EI ++CD TV+R G+ I T ++ T D + AMMVGR +N Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242 Query: 252 QRFPDKENKPGEVILEVRNLT---SLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVET 308 +P + +L++++L S ++ D+ ++H GEILG+AG+ G +T+++E Sbjct: 243 FSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEA 302 Query: 309 LFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISN-I 367 + G+R+ + G I L+G+ I + G + ++R G+ +G N ++ Sbjct: 303 ITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYY 362 Query: 368 RNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEI 427 + + G+L+ + + +I+ V+TP T +LSGGNQQK II R + P++ Sbjct: 363 QKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDL 422 Query: 428 LMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGI 487 L+ +PTRG+DVGA I+ + + KGK +++IS E+ E+L ++DRI V+ G + I Sbjct: 423 LIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAI 482 Query: 488 VDTKTTTQNEI 498 VD T +NE+ Sbjct: 483 VDADKTNENEL 493 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: 596 Number of extensions: 26 Number of successful extensions: 5 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: 509 Length adjustment: 34 Effective length of query: 472 Effective length of database: 475 Effective search space: 224200 Effective search space used: 224200 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 Apr 09 2024. 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