Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate BWI76_RS04125 BWI76_RS04125 NupC/NupG family nucleoside CNT transporter
Query= uniprot:A0KU05 (419 letters) >FitnessBrowser__Koxy:BWI76_RS04125 Length = 425 Score = 555 bits (1430), Expect = e-163 Identities = 289/431 (67%), Positives = 353/431 (81%), Gaps = 18/431 (4%) Query: 1 MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60 M I+M L+G+VVLLAI LLS+N+KAINLRTV GA IQ G +LYVP G+ L ++S Sbjct: 1 MQIIMGLIGMVVLLAIAVLLSSNRKAINLRTVLGAWIIQVGIGALILYVPAGRTALLAMS 60 Query: 61 DAVSSVIGYAQNGIGFLFGDLANFKL-------GFIFAVNVLPVIVFFSSLIAVLYYLGI 113 + V++VI Y GIGF+FG L + K+ GF+FA+ VLPVIVFFSSLIAVLYYLGI Sbjct: 61 NGVANVIAYGNEGIGFIFGGLVSDKMFEVFGGGGFVFALRVLPVIVFFSSLIAVLYYLGI 120 Query: 114 MQWIIRIIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGG 173 MQ++IRI+GG L+ L TSRTES+SATANIFVGQTEAPLVVRP+I TMT+SELFA+M GG Sbjct: 121 MQFVIRILGGALRAVLKTSRTESLSATANIFVGQTEAPLVVRPYIATMTRSELFAVMCGG 180 Query: 174 LASIAGSVLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKND--MDELPEDP 231 LAS+AGSVLAGYAQMGVP+EYL+AASFMAAPGGLL AK++ PETE +++ M++ DP Sbjct: 181 LASVAGSVLAGYAQMGVPLEYLIAASFMAAPGGLLFAKIIVPETEQPRDNPAMEKNDADP 240 Query: 232 DKPANVLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELIL 291 PANVLDAAA+GA+SGM LALNVGAMLLAF+ LIA++NGI+ GVGGWF L+L++IL Sbjct: 241 QAPANVLDAAASGAASGMQLALNVGAMLLAFIALIALVNGILSGVGGWFNHPDLSLQMIL 300 Query: 292 GYIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLK---DIADGGMIVADT 348 G++F PLA++IGVPWNEA VAGSFIGQK+++NEFVAY+NF YLK ++A G+ V T Sbjct: 301 GWVFSPLAWVIGVPWNEATVAGSFIGQKLIINEFVAYMNFGEYLKADTEVAAAGLQVIST 360 Query: 349 GLAMTDRTKAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLM 408 TKAIISFALCGFANLSSIAIL+GGLG MAPNRR ++A+LG+RAV AG+L+NLM Sbjct: 361 ------HTKAIISFALCGFANLSSIAILIGGLGGMAPNRRQEIAQLGMRAVAAGTLSNLM 414 Query: 409 SATIAGLFLAI 419 SATIAG+FLA+ Sbjct: 415 SATIAGVFLAL 425 Lambda K H 0.325 0.142 0.407 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: 686 Number of extensions: 28 Number of successful extensions: 5 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: 419 Length of database: 425 Length adjustment: 32 Effective length of query: 387 Effective length of database: 393 Effective search space: 152091 Effective search space used: 152091 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: 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