Align RnsD, 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 AZOBR_RS06635 AZOBR_RS06635 sugar ABC transporter permease
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__azobra:AZOBR_RS06635 Length = 324 Score = 199 bits (505), Expect = 1e-55 Identities = 114/326 (34%), Positives = 179/326 (54%), Gaps = 21/326 (6%) Query: 6 MLALLISSMLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFAHSFGK 65 ++ LL + + ATPL+ + ++SER+GVV++GLEG M+ GAF FA + Sbjct: 7 VVLLLADATIRVATPLVLAAFAALYSERAGVVDIGLEGKMLAGAF--------FAAAVAS 58 Query: 66 AT--PWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALYNKG 123 T PW+ + +L+H A I + + +VSG +N+L LA A + +G Sbjct: 59 YTGSPWLGLGAAVAASVALALVHGFACITHKGNQVVSGMAINILVAGLAPTLAYAWFRQG 118 Query: 124 QTDNISQSFGKFD------FPILSHIPFLGPIF---FQGTSLVAYLAVLFSVFAWFILTK 174 + + LS IP GP++ +++ +L VL V ++ T+ Sbjct: 119 GQTPLLPGEARLPQIHLPGVEALSGIPVFGPVYRELIDDANVLIWLTVLLVVATHWVFTR 178 Query: 175 TKFGLRLRSVGEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTIL 234 ++FGLRLR+VGE+P A DT G++V +RY V+I+G+L GI GA + + F Sbjct: 179 SRFGLRLRAVGENPSAVDTAGLSVTRLRYQAVIITGVLTGIAGAYLSTAHGAGFVRDMTA 238 Query: 235 GPGFIALAAMIFGKWNPIGAMLSSLFFGLSQSLAV--IGGQLPFLSKIPTVYLQIAPYAL 292 G G++ALAA+IFGKW P + + L F + ++ V G LP + IP ++Q+ PY L Sbjct: 239 GKGYLALAALIFGKWRPWPTLFACLLFAFTDAVQVRLQGVPLPVVGVIPVQFIQMLPYVL 298 Query: 293 TILVLAVFFGQAVAPKADGINYIKSK 318 T+L+LA F G+AVAPKA G+ Y+K + Sbjct: 299 TVLLLAGFVGRAVAPKASGVPYVKER 324 Lambda K H 0.328 0.143 0.422 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: 260 Number of extensions: 20 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: 318 Length of database: 324 Length adjustment: 28 Effective length of query: 290 Effective length of database: 296 Effective search space: 85840 Effective search space used: 85840 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: 48 (23.1 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