Align Nucleoside permease NupC; Nucleoside-transport system protein NupC (characterized)
to candidate BWI76_RS10810 BWI76_RS10810 NupC family nucleoside transporter
Query= SwissProt::P0AFF2 (400 letters) >FitnessBrowser__Koxy:BWI76_RS10810 Length = 394 Score = 565 bits (1457), Expect = e-166 Identities = 293/400 (73%), Positives = 348/400 (87%), Gaps = 6/400 (1%) Query: 1 MDRVLHFVLALAVVAILALLVSSDRKKIRIRYVIQLLVIEVLLAWFFLNSDVGLGFVKGF 60 M + LHF+LAL V+ LA L S DRKKIRIRY+IQL+VIEV LA+FFL+++ GL VK Sbjct: 1 MTQFLHFLLALVVILALAWLASYDRKKIRIRYIIQLIVIEVALAFFFLHAESGLWLVKNI 60 Query: 61 SEMFEKLLGFANEGTNFVFGSMNDQGLAFFFLKVLCPIVFISALIGILQHIRVLPVIIRA 120 + FE LLGFA EGTNFVFG M+++GLAF FL VLCPIVFISALIGILQH R+LP+ IR Sbjct: 61 ASFFESLLGFAAEGTNFVFGGMSEKGLAFIFLGVLCPIVFISALIGILQHWRILPIFIRL 120 Query: 121 IGFLLSKVNGMGKLESFNAVSSLILGQSENFIAYKDILGKISRNRMYTMAATAMSTVSMS 180 IG LLSKVNGMGKLESFNAVSSLILGQSENFIAYK +LG +S R++TM+ATAMSTVS+S Sbjct: 121 IGTLLSKVNGMGKLESFNAVSSLILGQSENFIAYKGVLGDLSSRRLFTMSATAMSTVSLS 180 Query: 181 IVGAYMTMLEPKYVVAALVLNMFSTFIVLSLINPYRVDASEENIQMSNLHEGQSFFEMLG 240 IVGAYM+ML+ KYVVAAL+LNMFSTFIVLS+INP R+ SEE I++ LHE QSFFEMLG Sbjct: 181 IVGAYMSMLDAKYVVAALILNMFSTFIVLSIINPTRL-GSEEEIKLEKLHESQSFFEMLG 239 Query: 241 EYILAGFKVAIIVAAMLIGFIALIAALNALFATVTGWFGYSISFQGILGYIFYPIAWVMG 300 EYILAGFKVA+I+ AMLIGFIALI+A+NALFAT+ G +SFQ ILGY+FYP+AW++G Sbjct: 240 EYILAGFKVAMIILAMLIGFIALISAINALFATIFG-----LSFQQILGYVFYPLAWLIG 294 Query: 301 VPSSEALQVGSIMATKLVSNEFVAMMDLQKIASTLSPRAEGIISVFLVSFANFSSIGIIA 360 +P S+AL GSIMATKLV+NEFVAM++LQKIA++++PR GI+SVFLVSFANF+SIGIIA Sbjct: 295 IPLSDALNAGSIMATKLVANEFVAMIELQKIAASMTPRGLGILSVFLVSFANFASIGIIA 354 Query: 361 GAVKGLNEEQGNVVSRFGLKLVYGSTLVSVLSASIAALVL 400 GA+KGLNE+QGN+VSRFGL+LVYG+TLVS+LSAS A LVL Sbjct: 355 GAIKGLNEQQGNIVSRFGLRLVYGATLVSLLSASFAGLVL 394 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: 555 Number of extensions: 19 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 369 Effective length of database: 363 Effective search space: 133947 Effective search space used: 133947 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