Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= SwissProt::P23924 (506 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 275 bits (702), Expect = 4e-78 Identities = 163/479 (34%), Positives = 274/479 (57%), Gaps = 12/479 (2%) Query: 7 PPSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66 PP G L+ ++G+ K F V A D+++LN+ P + AL+GENGAGKSTL+ L G YQ D Sbjct: 18 PPQGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPD 77 Query: 67 SGSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKM 126 +G+I GK V F SA++A+E GI MV+Q LV +V +N+ LG+ F++ +M Sbjct: 78 AGTIALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQ--EGSFFLNPKEM 135 Query: 127 YQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186 + + +DIDP ARV LS+ + Q +EI K +++++I DEPT+ LT +E Sbjct: 136 RNRVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETF 195 Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIAT-QPLEGLDMDKIIAMM 245 HLF + K+ E+G IV+ISHK+EE+ + DEI ILR G+ E + M Sbjct: 196 HLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRM 255 Query: 246 VGRSLNQRFPDKENKP-GDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTD 304 VG+ + D+E P GD +L+VR+LT + + D++FDLH+GE++ + G+ G + Sbjct: 256 VGKEVLLEV-DREAMPHGDAVLQVRNLTGI---GLEDITFDLHQGEVVAVVGVAGNGQKA 311 Query: 305 IVETLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLI 364 +VE + G+R+ T+ + GK+ + A + + A + E+R L++ N L+ Sbjct: 312 LVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLL 371 Query: 365 SNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIG-SLSGGNQQKVIIGRWLLT 423 + + + + LD + DT +I ++ PG + LSGGN QK ++ R L Sbjct: 372 TTRQGFA-RGPWLDKKKAARDTTELIKKFDIR-PGRIAALAWQLSGGNLQKSVLARELYR 429 Query: 424 QPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNG 482 P +++ ++PT+G+D+ A +++ + A++ GI++++ ++ E L + DR+ V+ G Sbjct: 430 CPRLIVAEQPTQGLDIAATEQVWNHLL-AAREMAGILLVTGDLNEALQLADRVAVIYRG 487 Score = 78.2 bits (191), Expect = 7e-19 Identities = 50/206 (24%), Positives = 101/206 (49%), Gaps = 9/206 (4%) Query: 281 DVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINHGF 340 D+S +++ G + + G GA ++ ++ L G + +GTI L GK + +A +AI G Sbjct: 42 DISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGI 101 Query: 341 ALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGH 400 +V + + + + N L+ ++ + N + ++ +D P Sbjct: 102 GMVYQHFM---LVESMTVAENVLLGQEGSFFLNPKEMRNRVQELSVRYGLDI----DPAA 154 Query: 401 RTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGII 460 R + LS G +Q+V I + L +L+ DEPT + F +++ + ++A++GK I+ Sbjct: 155 R--VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIV 212 Query: 461 IISSEMPELLGITDRILVMSNGLVSG 486 IS ++ E+L + D I ++ G + G Sbjct: 213 FISHKLEEVLAVADEIAILRQGRIEG 238 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: 562 Number of extensions: 28 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: 514 Length adjustment: 34 Effective length of query: 472 Effective length of database: 480 Effective search space: 226560 Effective search space used: 226560 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 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