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 Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034 Length = 517 Score = 312 bits (800), Expect = 2e-89 Identities = 193/493 (39%), Positives = 279/493 (56%), Gaps = 8/493 (1%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 +L + K YA P L L+L G V AL G NGAGKST I+ G+ G + Sbjct: 9 VLSVSGIGKTYAQ-PVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRF 67 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125 G + S+A GI M+ QEL +P ++VAEN++L P G I K L + Sbjct: 68 QGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHGGWI-SRKQLRKAAI 126 Query: 126 ELLDSLEFD-VDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 E + + D +D + + L + Q+VEIA+ DC V+I+DEPT+ + E + LF+ Sbjct: 127 EAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 I RL A+G I+Y+SHRL ELA++A ++ RDG V MA+ + + LV +VG+EL Sbjct: 187 QITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGREL 246 Query: 245 -TRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303 ID +G L V L+R+ + D+S ++R GEI GI GL+G+GR+E L I+ Sbjct: 247 GEHID--MGPRKIGAPALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIF 304 Query: 304 GLTVADSGSVTLQGKPMPIGL--PKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYK 361 G ADSG+V L + + P + G++L+TEDRK GL+LT SI +NIAL Sbjct: 305 GADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMP 364 Query: 362 RLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLL 421 +SS +N E LA+ + ++I+++S V+ +SGGNQQKVV+ + L + +L Sbjct: 365 VISSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVML 424 Query: 422 CDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIST 481 DEPTRGID GAK +IY LL + R G A +VVSS+ EL+ + DRI V GRL+ Sbjct: 425 FDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFE 484 Query: 482 DTALSQEALLRLA 494 + +Q+ LL A Sbjct: 485 RDSWTQDDLLAAA 497 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: 597 Number of extensions: 27 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: 495 Length of database: 517 Length adjustment: 34 Effective length of query: 461 Effective length of database: 483 Effective search space: 222663 Effective search space used: 222663 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 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