Align RnsC, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate GFF384 PGA1_c03950 putative permease protein
Query= TCDB::Q8DU38 (358 letters) >FitnessBrowser__Phaeo:GFF384 Length = 364 Score = 155 bits (391), Expect = 2e-42 Identities = 109/345 (31%), Positives = 168/345 (48%), Gaps = 10/345 (2%) Query: 1 MSKKTQKLVVPLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSP 60 M K +++PLIS+IL IL A++++ G DPI A + A GS G + Sbjct: 4 MPKWADVVLIPLISLILAAILSALVILGIGEDPIAAVNLMVSGALGSTYGWGYTLYYATN 63 Query: 61 LILIALGFAVASRAGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAASGG 120 + L +VA A FNIG GQA G + L P L ++ L A G Sbjct: 64 FLFTGLAVSVAFHARLFNIGGEGQAMLGGLGVALVCLYIPWPHWSLALIFASLGAALFGA 123 Query: 121 VVGAIPGFLRAYLGTSEVIVTIMMNYIVLYIGNAII-----QDGFAKNIMRNSDSSIYVG 175 AIP +L+A G+ VI TIM N+I + N ++ +G ++++ Sbjct: 124 AWAAIPAYLQAKRGSHIVITTIMFNFIAAAVLNYVLVNLLRPEGSMDPATARFPEAVHLP 183 Query: 176 HNASYQTEWLRALTNNSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAG 235 + + N+ F +A+ A + VW L+ +T LG+EIR+ G + + + YAG Sbjct: 184 SLHELLAPIGIEFSKAAPANVSFLVAVAACIAVWLLIWRTKLGYEIRAYGNSEYGALYAG 243 Query: 236 MSAKRTIVLSMIISGALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGI 295 +S + +++M+ISG LAG+ +G + V S+ GF G+AV+L+ + P G+ Sbjct: 244 ISPVKITMVAMLISGGLAGMMATNNVMGEAERL-VLNSTEGAGFIGIAVALMGRSHPFGV 302 Query: 296 FLSAFLFGALSVGAPGMSISDATHVGTPPELIKVVTALIIFFVGA 340 FL+A LFG L G + A P ELI V+ AL+I F GA Sbjct: 303 FLAAILFGFLYQGGAEL----ALWTSIPRELIVVIQALVILFTGA 343 Lambda K H 0.325 0.141 0.416 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: 314 Number of extensions: 15 Number of successful extensions: 4 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: 358 Length of database: 364 Length adjustment: 29 Effective length of query: 329 Effective length of database: 335 Effective search space: 110215 Effective search space used: 110215 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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