Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034 Length = 517 Score = 330 bits (847), Expect = 6e-95 Identities = 200/514 (38%), Positives = 293/514 (57%), Gaps = 9/514 (1%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 +L + GI K++ A L+ + LT+ GE+ AL GENGAGKSTL K++ G+ AP G++ Sbjct: 9 VLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRF 67 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 GR + GI ++ QEL + P +SVA N+F+ + L + G I +R Sbjct: 68 QGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDN-LPSHGGWISRKQLRKAAI 126 Query: 126 AVLRQLGA-GFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184 + Q+G L G L I QQ VEIAR L+ ++I+DEPTA L+ RE E LF Sbjct: 127 EAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186 Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244 + RL+ G++IIYISHR+ E+ +A R+ VLRDG+ V +SE++V +MVGR L Sbjct: 187 QITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGREL 246 Query: 245 SEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304 E H + P P + K+R SF+VRAGE+ G +GL+GAGRTEL RL Sbjct: 247 GE---HIDMGPRKIGA-PALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRL 302 Query: 305 LFGADPRSGGDILL--EGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV 362 +FGAD G + L + V I P A+ GIA + EDRKG+GL L +++AN + Sbjct: 303 IFGADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGN 362 Query: 363 ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422 + G V + +A+ I + ++ + P V +LSGGNQQKV++ RWLE V Sbjct: 363 MPVISSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTV 422 Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482 ++ DEPTRG+D+ AK +IY L+ L QG A+VV+SS+L E++ ICDR+ V+ G + Sbjct: 423 MLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDT 482 Query: 483 LAGAAITQENIMRLATDTNVPRTAPASHSSPTPL 516 + TQ++++ A R A + ++P L Sbjct: 483 FERDSWTQDDLLAAAFAGYQKRDALFNEAAPRDL 516 Lambda K H 0.320 0.135 0.378 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: 693 Number of extensions: 39 Number of successful extensions: 8 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: 521 Length of database: 517 Length adjustment: 35 Effective length of query: 486 Effective length of database: 482 Effective search space: 234252 Effective search space used: 234252 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