Align RnsB, 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 PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 Length = 514 Score = 263 bits (673), Expect = 9e-75 Identities = 157/485 (32%), Positives = 266/485 (54%), Gaps = 7/485 (1%) Query: 11 ITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGSAVT 70 I K F A D+I+ G++HAL+GENGAGKSTL+ +L G P SG+++I + Sbjct: 21 IGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIGERTMD 80 Query: 71 IDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKALSEKYG 130 S + S G+ ++HQ LV TV EN+ LG+ G+++ Q+ A + Sbjct: 81 FKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALACLKGLA 140 Query: 131 LAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKE 190 +DP K+ +S+G +Q VEI K L RGA ++ FDEPT+ L+ EI LM I+ L E Sbjct: 141 DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRDE 200 Query: 191 GKSIILITHKLDEIRSVADRVTVIRRGKSIETV-EVSGTTSQDLAEMMVGRSVSFTIEKT 249 GK ++ ++H+++E+ + + VTV + G+ + T ++S T L MVGR + + Sbjct: 201 GKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDIQDIYDYR 260 Query: 250 PTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRK 309 P + L + L+ G + +S EV GEI+G+ G+ G G++EL++ ++GL + Sbjct: 261 PRQRGAVALKVDGLL-----GPGLREPVSFEVHKGEILGLFGLVGAGRTELLRLLSGLAR 315 Query: 310 IKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSH 369 +G L ++G ++ S R + PEDR ++G++ ++AEN+ + A + Sbjct: 316 HSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISA-RGAHSTF 374 Query: 370 NGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQP 429 +L ++ ++ V+ N SGGNQQKAI+ R + +L++ +P Sbjct: 375 GCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 Query: 430 TRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETT 489 TRG+D+GA I++ + EG AV++VS +L E++ +SDRI V+ +G ++G ++ E Sbjct: 435 TRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSREQA 494 Query: 490 NKQEL 494 N+ L Sbjct: 495 NESNL 499 Lambda K H 0.315 0.135 0.363 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: 583 Number of extensions: 43 Number of successful extensions: 6 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: 510 Length of database: 514 Length adjustment: 35 Effective length of query: 475 Effective length of database: 479 Effective search space: 227525 Effective search space used: 227525 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 52 (24.6 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