Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate SM_b20855 SM_b20855 sugar uptake ABC transporter ATP-binding protein
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__Smeli:SM_b20855 Length = 504 Score = 376 bits (966), Expect = e-109 Identities = 196/493 (39%), Positives = 303/493 (61%), Gaps = 6/493 (1%) Query: 13 LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72 L ++ I+KSF G+ AL +VN +VRP +HAL+GENGAGKSTL++ L G G +V Sbjct: 5 LANLKSISKSFGGIHALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQGEVVI 64 Query: 73 QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKA 132 GK + ++A GI ++HQEL L SV +N++LG PT + + + + K Sbjct: 65 NGKRTELRDPRDARALGIVVIHQELALAPDLSVAENIFLGELPT---LISRFSLRRRAKQ 121 Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192 + D L DIDP VGTLSV+ Q++EIAKA S + KI++ DEPT+ L ++ L II Sbjct: 122 LIDRLGFDIDPGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLHQII 181 Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLNQ 252 R L++RG GIVYISH+++E+F + D +T+++DG+ + T + +D II MMVGR + Sbjct: 182 RGLRDRGVGIVYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKIDDIIRMMVGRPIAN 241 Query: 253 RFPDKENKP-GDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311 FP++ + G +L V+ L + R +RDVSF + GEI+G+ GL+G+ RT++ +FG Sbjct: 242 MFPERSQRTIGAELLNVKKLNAGRM--VRDVSFSVRAGEIVGLGGLIGSGRTEVARAIFG 299 Query: 312 IREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371 SGTI+L GK + + +A+ G LV E+R+ G+ I N+ ++ + + Sbjct: 300 ADPLDSGTISLKGKALKLKSPRDAVKAGIGLVPEDRKEHGVVIDKPIRVNATMARMSSVV 359 Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431 N +G L + ++D + S+R+K + SLSGGNQQKV++ +W ++++LD Sbjct: 360 NALGFLKPALERTDVTALGKSLRLKASSIDAPVSSLSGGNQQKVVLAKWFHAGGDVIILD 419 Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491 EPTRG+DVGAK EIY LI +LA+ GK +++ISSE EL G+ DR+L M G + G + Sbjct: 420 EPTRGVDVGAKAEIYALINKLAEDGKAVLVISSEHQELFGLCDRVLAMGQGQIRGELTPS 479 Query: 492 TTTQNEILRLASL 504 ++ +L L+ + Sbjct: 480 NYSEENLLGLSMM 492 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: 618 Number of extensions: 23 Number of successful extensions: 7 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: 504 Length adjustment: 34 Effective length of query: 472 Effective length of database: 470 Effective search space: 221840 Effective search space used: 221840 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 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