Align Nucleoside permease NupC; Nucleoside-transport system protein NupC (characterized)
to candidate BWI76_RS20540 BWI76_RS20540 NupC/NupG family nucleoside CNT transporter
Query= SwissProt::P0AFF2 (400 letters) >FitnessBrowser__Koxy:BWI76_RS20540 Length = 400 Score = 725 bits (1872), Expect = 0.0 Identities = 373/400 (93%), Positives = 395/400 (98%) Query: 1 MDRVLHFVLALAVVAILALLVSSDRKKIRIRYVIQLLVIEVLLAWFFLNSDVGLGFVKGF 60 MDRVLHF+LA+ VVAILALLVS +RK+IRIRYVIQLLVIEVLLAWFFLNSD+GLGFVKGF Sbjct: 1 MDRVLHFILAIVVVAILALLVSHNRKQIRIRYVIQLLVIEVLLAWFFLNSDIGLGFVKGF 60 Query: 61 SEMFEKLLGFANEGTNFVFGSMNDQGLAFFFLKVLCPIVFISALIGILQHIRVLPVIIRA 120 SEMFEKLLGFANEGTNFVFG+MND+GLAFFFLKVLCPIVFISALIGILQHIR+LP++IRA Sbjct: 61 SEMFEKLLGFANEGTNFVFGNMNDKGLAFFFLKVLCPIVFISALIGILQHIRILPIVIRA 120 Query: 121 IGFLLSKVNGMGKLESFNAVSSLILGQSENFIAYKDILGKISRNRMYTMAATAMSTVSMS 180 IG +LSK+NGMGKLESFNAVSSLILGQSENFIAYKDILGK+SRNRMYTMAATAMSTVSMS Sbjct: 121 IGTVLSKINGMGKLESFNAVSSLILGQSENFIAYKDILGKMSRNRMYTMAATAMSTVSMS 180 Query: 181 IVGAYMTMLEPKYVVAALVLNMFSTFIVLSLINPYRVDASEENIQMSNLHEGQSFFEMLG 240 IVGAYMTML+PKYVVAALVLNMFSTFIVLSLINPYRVD SEEN+QMSNLHEGQSFFEMLG Sbjct: 181 IVGAYMTMLQPKYVVAALVLNMFSTFIVLSLINPYRVDESEENLQMSNLHEGQSFFEMLG 240 Query: 241 EYILAGFKVAIIVAAMLIGFIALIAALNALFATVTGWFGYSISFQGILGYIFYPIAWVMG 300 EYILAGFKVAIIVAAMLIGFIALI+ALNALFATVTGWFGYSISFQGILGYIFYP+AWVMG Sbjct: 241 EYILAGFKVAIIVAAMLIGFIALISALNALFATVTGWFGYSISFQGILGYIFYPVAWVMG 300 Query: 301 VPSSEALQVGSIMATKLVSNEFVAMMDLQKIASTLSPRAEGIISVFLVSFANFSSIGIIA 360 VP+ EALQVGSIMATKLVSNEFVAMMDLQK+A+TLSPRAEGIIS+FLVSFANFSSIGIIA Sbjct: 301 VPAGEALQVGSIMATKLVSNEFVAMMDLQKVAATLSPRAEGIISIFLVSFANFSSIGIIA 360 Query: 361 GAVKGLNEEQGNVVSRFGLKLVYGSTLVSVLSASIAALVL 400 GA+KGLNEEQGNVVSRFGLKLVYGSTLVSVLSASIAALVL Sbjct: 361 GAIKGLNEEQGNVVSRFGLKLVYGSTLVSVLSASIAALVL 400 Lambda K H 0.328 0.141 0.393 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: 668 Number of extensions: 17 Number of successful extensions: 1 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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: 50 (23.9 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