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 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 348 bits (894), Expect = e-100 Identities = 194/502 (38%), Positives = 297/502 (59%), Gaps = 14/502 (2%) Query: 5 VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64 V+ + I K F AN I LD+ G I ALLGENGAGKSTLM++L+G L +G I + Sbjct: 34 VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93 Query: 65 NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124 +G AV SP + + GIGMV+QHFMLV++ TV EN++LG + + + E+ A Sbjct: 94 DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGAWLSPVHMSRVVAELAA 153 Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184 +YGL +DP A++ D+S+G +QRVEILK LYR + +LI DEPTAVLTP E ++L + Sbjct: 154 ---RYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEAL 210 Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQ-DLAEMMVGRSVS 243 + + GK+I+ I+HK+ E+ ++AD + ++RRG+ ++ S + +LA MVGR V Sbjct: 211 HRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVI 270 Query: 244 FTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQA 303 + P +P + +L + L + +KGLS EV+ GE+ IAG+ GNGQ ELV+ Sbjct: 271 LEVAAEPLEPGDRVLHVDGLAGD------GLKGLSFEVRKGEVFAIAGVAGNGQRELVEC 324 Query: 304 ITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYY 363 +TGLR+ G + + G + T+ + + ++PEDR L L + +N L Sbjct: 325 VTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTA-- 382 Query: 364 KAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDL 423 + + L+ + R ++ E++V+ PA+ SGGN QK ++ RE R P L Sbjct: 383 RGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSL 442 Query: 424 LIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGI 483 ++ PT+GLD+ A E + RL+ R VLLVS +L+E+L L+DR+AV++ G G+ Sbjct: 443 IVAENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAVMYRGCFIGL 501 Query: 484 VTPETTNKQE-LGILMAGGSIE 504 + TNK + +G++MAG S E Sbjct: 502 LDRSDTNKVDAIGLMMAGVSCE 523 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: 597 Number of extensions: 35 Number of successful extensions: 8 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: 524 Length adjustment: 35 Effective length of query: 475 Effective length of database: 489 Effective search space: 232275 Effective search space used: 232275 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 Apr 09 2024. 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