Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 462 bits (1189), Expect = e-134 Identities = 236/498 (47%), Positives = 340/498 (68%), Gaps = 4/498 (0%) Query: 7 PPSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66 P YLLE+ ++K FPGV AL +V L VRP S+ ALMGENGAGKSTL+K + GIYQ D Sbjct: 21 PVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD 80 Query: 67 SGSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDK 125 +G + +GK V F + AL+ GI+M+HQELNL+ S+ +N+W+GR G +D + Sbjct: 81 AGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHRE 140 Query: 126 MYQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEV 185 M++ T + + L I++DP +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++T+KEV Sbjct: 141 MHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEV 200 Query: 186 NHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMM 245 HLF+II LK +G GI+YI+HKM E+F + DE+ + RDG +I Q + +D D +I+MM Sbjct: 201 AHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMM 260 Query: 246 VGRSLNQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDI 305 VGR L+Q FP +E GD+++ VR L + VSFDLH GEILGIAGL+G+ RT++ Sbjct: 261 VGRELSQLFPVREKPIGDLLMSVRDLR--LDGVFKGVSFDLHAGEILGIAGLMGSGRTNV 318 Query: 306 VETLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLIS 365 E +FGI G I L G+ + + AI GFAL+TE+R+ +G++ L + N ++ Sbjct: 319 AEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 378 Query: 366 NIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425 + +Y G + +++ + + +RVKTP I +LSGGNQQK ++ RWL+T P Sbjct: 379 VLPHYAGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNP 437 Query: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVS 485 IL+LDEPTRGIDVGAK EIY+LI+ LA +G +I+ISSE+PE+LG++DR++VM G + Sbjct: 438 RILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLM 497 Query: 486 GIVDTKTTTQNEILRLAS 503 G +D TQ +++LAS Sbjct: 498 GTLDRSEATQERVMQLAS 515 Score = 73.2 bits (178), Expect = 2e-17 Identities = 54/249 (21%), Positives = 112/249 (44%), Gaps = 10/249 (4%) Query: 8 PSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67 P G+ L+ +R + GV V+ ++ I + G G+G++ + + +FGI D Sbjct: 275 PIGDLLMSVRDLR--LDGV--FKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDG 330 Query: 68 GSIVFQGKEVDFHSAKEALENGISMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVD 122 G I G+ V A+E G +++ ++ L SV++NM + P F+ Sbjct: 331 GEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQ 390 Query: 123 QDKMYQDTKAIFDELDIDIDPRAR-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181 Q + + + +L + + + TLS Q +A+ N +I+I+DEPT + Sbjct: 391 QKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGID 450 Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKI 241 ++ +I L G ++ IS ++ E+ + D + ++ +G + T +++ Sbjct: 451 VGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERV 510 Query: 242 IAMMVGRSL 250 + + G S+ Sbjct: 511 MQLASGMSV 519 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: 638 Number of extensions: 26 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: 521 Length adjustment: 35 Effective length of query: 471 Effective length of database: 486 Effective search space: 228906 Effective search space used: 228906 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