Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__HerbieS:HSERO_RS22465 Length = 518 Score = 395 bits (1015), Expect = e-114 Identities = 221/502 (44%), Positives = 322/502 (64%), Gaps = 11/502 (2%) Query: 11 EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--G 68 EYLLEM GI KSF GV+AL+ +++K+RP L GENGAGKSTL+K L G+Y + G Sbjct: 3 EYLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWEG 62 Query: 69 TILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPT-KGMFVDQDKMY 127 IL+ GK + HS ++ GI ++HQEL LV + SV +N+++G T G ++ MY Sbjct: 63 EILWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPAMY 122 Query: 128 RETKAIFDELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186 R + + EL++ DI+ V Q++EIAKA + +A+++I+DEP+SSLT E+ Sbjct: 123 RRAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASEIG 182 Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMV 246 L II+ LK RG VYISHK++E+ ++CD ++V+RDG+ IAT P+ + +DKII MV Sbjct: 183 VLLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKIITQMV 242 Query: 247 GRSLNQRFPDKENKPGEVILEVRNLT-----SLRQPSIRDVSFDLHKGEILGIAGLVGAK 301 GR + +P++ + GEV+LE RN+T + R+ + DVSF + +GEILGIAGLVGA Sbjct: 243 GREITAMYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGLVGAG 302 Query: 302 RTDIVETLFG-IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGF 360 RT++V +FG R + G + L GK + + ++I G +V E+R+ GI LD+G Sbjct: 303 RTELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIRRGLCMVPEDRKHHGIVPDLDVGQ 362 Query: 361 NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420 N ++ + N ++ +D S Q I MRVKT I SLSGGNQQK ++ + Sbjct: 363 NITLT-VLNRFSRGSRIDGSAELKTIQDEIGRMRVKTATPFLPITSLSGGNQQKAVLAKM 421 Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480 LL QP++L+LDEPTRG+DVGAK EIY+LI+ELAK G II++SSE+ E+LG++DR+LV+ Sbjct: 422 LLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAIIMVSSELAEVLGVSDRVLVIG 481 Query: 481 NGLVSGIVDTKTTTQNEILRLA 502 G + G +Q +L A Sbjct: 482 EGRLRGDFVNDNLSQETVLAAA 503 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: 622 Number of extensions: 28 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: 518 Length adjustment: 35 Effective length of query: 471 Effective length of database: 483 Effective search space: 227493 Effective search space used: 227493 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