Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23205 Length = 517 Score = 461 bits (1186), Expect = e-134 Identities = 236/493 (47%), Positives = 341/493 (69%), Gaps = 4/493 (0%) Query: 12 YLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTIL 71 YLLE+ ++K FPGV AL +V L+VRP S+ ALMGENGAGKSTL+K + GIYQ D+G + Sbjct: 25 YLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELR 84 Query: 72 FQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRET 130 +GK + F + AL+ GI+M+HQELNL+ S+ +N+W+GR G+ VD +M+R T Sbjct: 85 LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCT 144 Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 + + L I +DP +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++TE EV HLF+ Sbjct: 145 ARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFS 204 Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250 II LK +G GI+YI+HKM E+F + DEV V RDG +I + + D +I+MMVGR L Sbjct: 205 IIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 264 Query: 251 NQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310 +Q FP +E GE++L VR+L+ + VSFDLH GEILGIAGL+G+ RT++ E +F Sbjct: 265 SQLFPVREQPIGELVLSVRDLS--LDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIF 322 Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370 G+ + G I L G+ + + + AI GFAL+TE+R+ +G++ L + N ++ + +Y Sbjct: 323 GVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 382 Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430 G + +++ + + +RVKTP I +LSGGNQQK ++ RWL+T P IL+L Sbjct: 383 VGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILIL 441 Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490 DEPTRGIDVGAK EIY+LI+ LA +G +I+ISSE+PE+LG++DR++VM G + G +D Sbjct: 442 DEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDR 501 Query: 491 KTTTQNEILRLAS 503 TQ +++LAS Sbjct: 502 SEATQERVMQLAS 514 Score = 68.6 bits (166), Expect = 5e-16 Identities = 53/246 (21%), Positives = 110/246 (44%), Gaps = 10/246 (4%) Query: 10 GEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69 GE +L + + S G+ V+ + I + G G+G++ + + +FG+ G Sbjct: 276 GELVLSVRDL--SLDGI--FKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGE 331 Query: 70 ILFQGKEIDFHSAKEALENGISMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVDQD 124 I G+ + A+E G +++ ++ L SV++NM + P F+ Q Sbjct: 332 IRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQK 391 Query: 125 KMYRETKAIFDELDIDIDPRAR-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEK 183 + + + +L + + + TLS Q +A+ N +I+I+DEPT + Sbjct: 392 ALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVG 451 Query: 184 EVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIA 243 ++ +I L G ++ IS ++ E+ + D V V+ +G + T + T ++++ Sbjct: 452 AKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQ 511 Query: 244 MMVGRS 249 + G S Sbjct: 512 LASGLS 517 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: 635 Number of extensions: 28 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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