Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 342 bits (878), Expect = 2e-98 Identities = 200/506 (39%), Positives = 305/506 (60%), Gaps = 19/506 (3%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD-SGTIL 71 LL + I K+FPGV+AL V L +HALMGENGAGKSTL+K L G Y D G Sbjct: 10 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 69 Query: 72 FQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETK 131 G+ + + A + G+++++QEL+L SV +N++LGR + V + M R Sbjct: 70 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 129 Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 L D P A V +LS++Q Q++EIA+A + A+I++MDEPT+ L+ E + LF + Sbjct: 130 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 189 Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 IR+L+ G I+YISH+M EI +L D VTVLRDG ++ T A L+ ++ MMVGR L+ Sbjct: 190 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 249 Query: 252 QRFPDKENK--PGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309 + + EV+L VR++ R+ ++ SFDL GE+LG+AGLVGA RT++ + Sbjct: 250 GFYTKTHGQAVEREVMLSVRDVADGRR--VKGCSFDLRAGEVLGLAGLVGAGRTELARLV 307 Query: 310 FGIREKSAGTITLHGK-------QINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNS 362 FG ++ G + + + +AI+ G A +TE+R+ G+ +LD + Sbjct: 308 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGL--FLDQSVHE 365 Query: 363 LISNIRNYKNKVGL--LDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420 I+ I ++ +GL L+ + + T ID++ ++ + +G+LSGGNQQKV++ R Sbjct: 366 NINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRL 425 Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480 L QP +L+LDEPTRG+D+GAK EIY+LI LA+ G I++ISSE+PE++G+ DR+LVM Sbjct: 426 LEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMR 485 Query: 481 NGLVSGIV---DTKTTTQNEILRLAS 503 G ++G V + TQ I+ LA+ Sbjct: 486 EGTLAGEVRPAGSAAETQERIIALAT 511 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: 588 Number of extensions: 35 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: 537 Length adjustment: 35 Effective length of query: 471 Effective length of database: 502 Effective search space: 236442 Effective search space used: 236442 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