Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate AO356_00965 AO356_00965 sugar ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00965 Length = 517 Score = 338 bits (867), Expect = 3e-97 Identities = 185/493 (37%), Positives = 299/493 (60%), Gaps = 7/493 (1%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 +L +SGI K++ L ++NL + + AL GENGAGKSTL K + G+ +G + F Sbjct: 9 VLCVSGIGKTY-AQPVLTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67 Query: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132 QG++ S +A E G+ MV QELNL+ SV +N++L P+ G ++ + ++ + Sbjct: 68 QGQDYRPGSRTQAEELGVRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAIE 127 Query: 133 IFDELDID-IDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 ++ +D IDP VG L + QM+EIA+ + ++I+DEPT+ LT +EV LF Sbjct: 128 AMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQ 187 Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 I +L+ RG I+YISH++EE+ ++ + VLRDG + EP+A ++++ +MVGR L Sbjct: 188 ITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVGRELG 247 Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311 + + G L V+ LT R +RDVSF++ GEI GI+GL+GA RT+++ +FG Sbjct: 248 EHIDLGPRQIGAPALTVKGLT--RSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFG 305 Query: 312 IREKSAGTITLHG--KQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369 +GT+ L + ++ + ++A+ HG AL+TE+R+ G+ I N + N+ Sbjct: 306 ADPADSGTVALGSPARVVSIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALGNMPE 365 Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429 + GL++ S + Q +D+MR+++ + LSGGNQQKV+IGRWL +++ Sbjct: 366 ISS-AGLVNGSAELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVML 424 Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489 DEPTRGIDVGAKF+IY L+ EL ++GK ++++SS++ EL+ I DRI V+S G + + Sbjct: 425 FDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFE 484 Query: 490 TKTTTQNEILRLA 502 + TQ+++L A Sbjct: 485 RDSWTQDDLLAAA 497 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: 577 Number of extensions: 25 Number of successful extensions: 9 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: 517 Length adjustment: 35 Effective length of query: 471 Effective length of database: 482 Effective search space: 227022 Effective search space used: 227022 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