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 WP_002878337.1 B506_RS03300 ABC transporter permease
Query= TCDB::Q8DU38 (358 letters) >NCBI__GCF_000387565.1:WP_002878337.1 Length = 379 Score = 342 bits (878), Expect = 7e-99 Identities = 171/352 (48%), Positives = 243/352 (69%), Gaps = 4/352 (1%) Query: 1 MSKKTQKLVVPLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSP 60 +S KT++L+VP++SVI G ++GAIIM+++ YDP AY +F+ A GS IGE R +P Sbjct: 4 VSPKTKRLLVPIVSVIAGFLVGAIIMLVWSYDPFQAYSSMFESALGSANGIGETIRNATP 63 Query: 61 LILIALGFAVASRAGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAASGG 120 LI IA+GF ++S AGFFNIGL GQA AGW+ A W LA LP +++ ++ G+ +G Sbjct: 64 LIFIAIGFQISSAAGFFNIGLPGQAQAGWLTAIWIGLAFKGLPVYILLPFEIIAGSLAGA 123 Query: 121 VVGAIPGFLRAYLGTSEVIVTIMMNYIVLYIGNAIIQDGFAKNIMRNSDSSIYVGHNASY 180 +V I G+LRAY GT+EVI TIM+NYIVLY+ + QD K++ ++D++ +G + S Sbjct: 124 LVAGIAGWLRAYFGTNEVISTIMLNYIVLYLCQYLHQDVMNKSLRVDTDTTKTIGASGSL 183 Query: 181 QTEWLRALTNNSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAKR 240 + WL + SR++ G FLAIIA+V+ W+L+ KTT+GFEI++VGLNP AS YAGMS K+ Sbjct: 184 RIPWLSEMFGGSRISGGIFLAIIALVIFWFLMKKTTVGFEIKAVGLNPFASRYAGMSDKK 243 Query: 241 TIVLSMIISGALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSAF 300 I++SM++SGA GLGGVV+GLGT+ N + QT++L IG+DGM+V+LL S IGI L++ Sbjct: 244 NIIISMLLSGAFCGLGGVVQGLGTYQNYFTQTTTLDIGWDGMSVALLGGMSAIGILLASL 303 Query: 301 LFGALSVGAPGMSISDATHVGTPPELIKVVTALIIFFVGAHYIIEHYIKPRK 352 LF L +G GM T G P E++ +V A IIFFV + + K +K Sbjct: 304 LFSILKIGGLGMQ----TAAGIPFEIVSIVIAAIIFFVAISWAVGLLFKEKK 351 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: 400 Number of extensions: 19 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: 358 Length of database: 379 Length adjustment: 30 Effective length of query: 328 Effective length of database: 349 Effective search space: 114472 Effective search space used: 114472 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 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