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 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 341 bits (874), Expect = 4e-98 Identities = 195/498 (39%), Positives = 299/498 (60%), Gaps = 13/498 (2%) Query: 5 VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64 V+ + I K F AN I LD+R G I ALLGENGAGKSTLM++LAG L +G+I + Sbjct: 29 VVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV 88 Query: 65 NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124 +G SP + + GIGMV+QHFMLV++ TV EN++LG + +L + E+ A Sbjct: 89 DGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQS--PDMLLRPARMRDEVAA 146 Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184 L+E+YGLAVDP A++ +S+G +QRVEILK LYR + +LI DEPTAVLTP E +L M Sbjct: 147 LAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAM 206 Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQD-LAEMMVGRSVS 243 + +GK+++ I+HKL E+ +VAD + ++RRG+ ++ + +Q LA MVGR V Sbjct: 207 WRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDVV 266 Query: 244 FTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQA 303 ++ P +T+LS+ E+ + +SL+V+ GEI+ IAG+ GNGQ ELV+A Sbjct: 267 LQVDAKRLTPVDTVLSV------EHLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320 Query: 304 ITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYY 363 I GL + ++G + I G+ + + ++PEDR L + +N L T Sbjct: 321 ICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTT-- 378 Query: 364 KAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDL 423 + + L+ ++ + ++ E++V+ + PA+ SGGN QK +I RE R P++ Sbjct: 379 RNQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEV 438 Query: 424 LIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGI 483 ++ PT+GLD+ A E + RL+ R VLLV+ +L+E L L+DRIAV++ G+ + Sbjct: 439 IVAENPTQGLDISATEEVWGRLLEARST-SGVLLVTGDLNEALELADRIAVMYRGRFIDV 497 Query: 484 VTPETTNK-QELGILMAG 500 + T K Q +G++MAG Sbjct: 498 FDKDDTAKVQAIGLMMAG 515 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: 559 Number of extensions: 35 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 510 Length of database: 537 Length adjustment: 35 Effective length of query: 475 Effective length of database: 502 Effective search space: 238450 Effective search space used: 238450 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