Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 468 bits (1204), Expect = e-136 Identities = 242/493 (49%), Positives = 344/493 (69%), Gaps = 4/493 (0%) Query: 12 YLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIV 71 YLLE+ I+K FPGV AL +V L VRP ++ ALMGENGAGKSTL+K + GIYQ D+G I Sbjct: 22 YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81 Query: 72 FQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYQDT 130 +GK + F + A + GI+M+HQELNL+ S+ +N+W+GR + V+ +M++ T Sbjct: 82 LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141 Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 + L I++DP +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++TEKEV HLF+ Sbjct: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSL 250 II LK +G GIVYI+HKM E+F + DE+ + RDG +I Q + ++ D +I+MMVGR L Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 Query: 251 NQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310 +Q FP +E GD++L VR LT +DVSFDLH GEILGIAGL+G+ RT++ ET+F Sbjct: 262 SQLFPLRETPIGDLLLTVRDLT--LDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319 Query: 311 GIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370 GI SSG ITL GK + + AI GFAL+TE+R+ +G++ L + N ++ + +Y Sbjct: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379 Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430 G + +++ + + +RVKTP I +LSGGNQQK ++ RWL+T P +L+L Sbjct: 380 TGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLIL 438 Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490 DEPTRGIDVGAK EIY+LIA LA +G +I+ISSE+PE+LG++DR++VM G + G +D Sbjct: 439 DEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDR 498 Query: 491 KTTTQNEILRLAS 503 TQ ++++LAS Sbjct: 499 SEATQEKVMQLAS 511 Score = 76.3 bits (186), Expect = 3e-18 Identities = 56/246 (22%), Positives = 114/246 (46%), Gaps = 10/246 (4%) Query: 8 PSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67 P G+ LL +R + + GV +V+ ++ I + G G+G++ + + +FGI S Sbjct: 271 PIGDLLLTVRDL--TLDGV--FKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSS 326 Query: 68 GSIVFQGKEVDFHSAKEALENGISMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVD 122 G I GK V A+E G +++ ++ L SV++NM + P T F+ Sbjct: 327 GQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQ 386 Query: 123 QDKMYQDTKAIFDELDIDIDPRAR-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181 Q + + + +L + + + TLS Q +A+ N +++I+DEPT + Sbjct: 387 QKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGID 446 Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKI 241 ++ +I L G ++ IS ++ E+ + D + ++ +G+ + T +K+ Sbjct: 447 VGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKV 506 Query: 242 IAMMVG 247 + + G Sbjct: 507 MQLASG 512 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: 640 Number of extensions: 32 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 ( 7.4 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 Apr 09 2024. 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