Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 291 bits (746), Expect = 3e-83 Identities = 166/492 (33%), Positives = 281/492 (57%), Gaps = 5/492 (1%) Query: 14 LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73 +++ I K + GV ALD+V+ V+P L GENG+GKSTL+K + G+ +GT+ Sbjct: 10 IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69 Query: 74 GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRE-TKA 132 G+E + + + G+ ++ Q+ +L SV +N+ + + + + R+ +A Sbjct: 70 GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129 Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192 D + + ID ARV TL V+Q Q++ I +A + A+++IMDEPT++LTEKEV L II Sbjct: 130 ALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGII 189 Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQ 252 R LKE G ++++SHK+ E+ ++ ++V VLR+G+ +A P + + M GR + + Sbjct: 190 RMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPE 249 Query: 253 RFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGI 312 P + +++V+ L + S D+SFDL GE+LGI GL+G RT + + LFG+ Sbjct: 250 VPPSDVAAGAQTLMQVQGLG--KAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGL 307 Query: 313 REKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKN 372 AG+I + G + + A V E+R + G++ I N + + + + Sbjct: 308 VTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTS 367 Query: 373 KVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDE 432 G LD + + + + ++VK P + SLSGGNQQ+V + RWL P +L+L+ Sbjct: 368 G-GFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNG 426 Query: 433 PTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKT 492 P+ G+DVG+K +I+ +I ELA++G G+I+IS ++PELL R+LVM G + ++ Sbjct: 427 PSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALEGTA 486 Query: 493 TTQNEIL-RLAS 503 T++++ RLAS Sbjct: 487 LTEDDLAHRLAS 498 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: 517 Number of extensions: 23 Number of successful extensions: 8 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: 498 Length adjustment: 34 Effective length of query: 472 Effective length of database: 464 Effective search space: 219008 Effective search space used: 219008 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