Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_106714515.1 CU102_RS28785 sugar ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >NCBI__GCF_003010955.1:WP_106714515.1 Length = 513 Score = 488 bits (1256), Expect = e-142 Identities = 252/494 (51%), Positives = 350/494 (70%), Gaps = 3/494 (0%) Query: 11 EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70 E+LL I K FPGV ALDNV +++ ++HALMGENGAGKSTL+K L GIY D G + Sbjct: 21 EFLLNAENIRKEFPGVLALDNVQFRLKRGTVHALMGENGAGKSTLMKILAGIYIPDQGEV 80 Query: 71 LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRE 129 +G I S +ALENGI+M+HQELNL+ +V +N+W+ R P G FVD KMY Sbjct: 81 YLKGLPIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNGFGFVDHGKMYDM 140 Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189 T +F L+I +DP ++V LSV+ QM+EIAKA SY + ++IMDEPTS+LTE+EV HLF Sbjct: 141 TADLFKRLNITLDPESQVRDLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVEHLF 200 Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249 IIR L+E+G GIVYI+HKM E+F++ DE +V RDG++I T +T D II MMVGR Sbjct: 201 QIIRDLREQGIGIVYITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDIIKMMVGRE 260 Query: 250 LNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309 + Q FP + G+V+L V++L SL+ DVSFD+ GEILG+AGLVG+ R+++ ET+ Sbjct: 261 ITQMFPKEIVPIGDVVLSVKDL-SLKNV-FHDVSFDVRAGEILGVAGLVGSGRSNVAETI 318 Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369 FG+ ++GTIT+ G+ I ++ +AI+HG A +TE+R+ TG LD+ N I+ +++ Sbjct: 319 FGVTPATSGTITIKGQPIKMNSPTQAISHGMAFITEDRKETGCLLILDVLENMQIAVLQD 378 Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429 K G ++ ++ + + D++RVKTP + +LSGGNQQKV+IGRWLLT P+IL+ Sbjct: 379 RFVKYGFVEEKQIAKACKAMSDTLRVKTPSLEETVENLSGGNQQKVLIGRWLLTNPKILI 438 Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489 LDEPTRGIDVGAK EI++LI++LAK G +I+ISSEMPE+LG++DRI+VM G V+G +D Sbjct: 439 LDEPTRGIDVGAKAEIHRLISQLAKTGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGFLD 498 Query: 490 TKTTTQNEILRLAS 503 TQ +++ LAS Sbjct: 499 RAEATQVKVMELAS 512 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: 615 Number of extensions: 23 Number of successful extensions: 6 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: 513 Length adjustment: 34 Effective length of query: 472 Effective length of database: 479 Effective search space: 226088 Effective search space used: 226088 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 24 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