Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >NCBI__GCF_000469325.1:WP_022530418.1 Length = 508 Score = 316 bits (809), Expect = 1e-90 Identities = 178/492 (36%), Positives = 290/492 (58%), Gaps = 5/492 (1%) Query: 5 LLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSIL 64 ++L H+AK + GV AL D +L LRAG VHAL G NGAGKST + ++ G+ +R +G++ Sbjct: 12 VVLSMRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVT 71 Query: 65 LNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRT 124 L+G + P EA GI+ + QE+ P ++VAEN+++GR+P R G I D +N Sbjct: 72 LHGQDINPKTPQEAQDLGISTVYQEVNLCPNLSVAENVYIGRQPMRFGQI-DWHRMNADA 130 Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 +LL+SL+ VD T + SV+ Q++ IA+A V+I+DEPTS++ +E LF Sbjct: 131 VKLLESLDIHVDVTKTLDSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQLFA 190 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 IR L Q I++V+H + ++ I+D ++ R+G ++ D+ LV ++GQ+ Sbjct: 191 IIRHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIGQKF 250 Query: 245 TRID---HKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNC 301 + H+ ++ + ++++++S+ G HD S+ +R GE+LG+ GL+GSGR+E Sbjct: 251 VDANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEVAEL 310 Query: 302 IYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYK 361 ++G+T D G + + + P+ + + +EDRK SG+V SI NI LS Sbjct: 311 LFGVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSLQA 370 Query: 362 RLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLL 421 + I +K+ ++A+ + L IKT S+E + +SGGNQQKV+LA+ L+T+P L+ Sbjct: 371 K-KGLRRIPLKKQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDPKLLI 429 Query: 422 CDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIST 481 DEPTRGID K+EI +L+ + R G A I +SSE E++ DRI V + V T Sbjct: 430 LDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAVGELT 489 Query: 482 DTALSQEALLRL 493 D +SQ+ ++++ Sbjct: 490 DNQISQDNIMKV 501 Score = 74.3 bits (181), Expect = 9e-18 Identities = 54/224 (24%), Positives = 108/224 (48%), Gaps = 4/224 (1%) Query: 22 LRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAA 81 + D +++RAG V L G G+G++ +L G+T D G I + V+ P +ALA Sbjct: 281 VHDFSMAVRAGEVLGLAGLLGSGRTEVAELLFGVTHFDDGVIYVGNDEVKRMNPRKALAD 340 Query: 82 GIAMITQELEP---IPYMTVAENIWLGREPRRAGCIVDNKALNRRTRELLDSLEFDVDAT 138 + +++ + + +++ ENI L + ++ + K ++ +D L+ + Sbjct: 341 QLGYCSEDRKVSGIVGDLSIRENIMLSLQAKKGLRRIPLKKQQEVAQKYIDLLDIKTPSM 400 Query: 139 SP-MHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIV 197 + LS Q V +A+ + D +++I+DEPT I + + + I +L+ QG I+ Sbjct: 401 EKKIGDLSGGNQQKVLLARWLATDPKLLILDEPTRGIDINTKREIENLIVKLSRQGMAII 460 Query: 198 YVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241 ++S E+ + D + RD V I +D++++ I G Sbjct: 461 FISSEYEEMVRTCDRIIVLRDRHAVGELTDNQISQDNIMKVIAG 504 Lambda K H 0.319 0.135 0.381 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: 493 Number of extensions: 25 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: 495 Length of database: 508 Length adjustment: 34 Effective length of query: 461 Effective length of database: 474 Effective search space: 218514 Effective search space used: 218514 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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