Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 197 bits (501), Expect = 9e-55 Identities = 117/349 (33%), Positives = 191/349 (54%), Gaps = 26/349 (7%) Query: 3 NNIHSATSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDN 62 + +++ T+ + A +SA R++L L A L M+ FS S F + Sbjct: 561 DRMNAPTAPAAPAATPSSASVWRSQLGT-----YLGLLAVLAGMVALFSSLSEYFWSAET 615 Query: 63 LVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAA 122 ++I V+A+ T+V+I +GIDLSVG++M A + + WG +P A A Sbjct: 616 FITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAAILQWGWTVPAAAALA 675 Query: 123 IFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQD 182 + G + G I+G + ++P FI +LGM+ ++G + V++ +R Y Sbjct: 676 LATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQY------------- 722 Query: 183 SLIGDLIPSLPIPN------AVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGV 236 +GD I L P A L+ ++ + A ++L++TVFGR +G+NEEA+RL+GV Sbjct: 723 --VGDAISWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGV 780 Query: 237 KVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGT 296 +V V+ +G + G+AGL+ ++RL +A P G G EL IAAVVIGGTSL GG G+ Sbjct: 781 DPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGS 840 Query: 297 ILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRR 345 ++ T G I++VL GL + ++ + ++TG +I+ AV +D LR+RR Sbjct: 841 VVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTLRQRR 889 Lambda K H 0.326 0.139 0.398 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: 518 Number of extensions: 23 Number of successful extensions: 2 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: 347 Length of database: 892 Length adjustment: 36 Effective length of query: 311 Effective length of database: 856 Effective search space: 266216 Effective search space used: 266216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 53 (25.0 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