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 BPHYT_RS21030 BPHYT_RS21030 ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__BFirm:BPHYT_RS21030 Length = 513 Score = 345 bits (885), Expect = 2e-99 Identities = 202/512 (39%), Positives = 295/512 (57%), Gaps = 18/512 (3%) Query: 6 IEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKIN 65 +E+ I K FD F+A D+R GE+HALLGENGAGKSTLMN+ AGL P +G+I + Sbjct: 5 LELVGIHKSFDGFIALSDAQFDVRWGELHALLGENGAGKSTLMNVAAGLYAPETGTISVG 64 Query: 66 GSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILD-----LKKAGQ 120 G V + P +A++GIGMVHQHF LV FTV ENI+LG + G L K + Sbjct: 65 GQPVRLSGPGDAARIGIGMVHQHFKLVSRFTVAENILLG--ISMGGAQPRYGKRLAKVRE 122 Query: 121 EIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180 I + G +DP+ +I+ +SV QQRVEILK L GA IL+ DEPTAVLT E L Sbjct: 123 AICSQCATLGFEIDPDRRISQLSVAEQQRVEILKVLLAGARILVLDEPTAVLTGQEAARL 182 Query: 181 MTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGR 240 + M+ L +G +++L+THK+ ++R ADRVTV+R G+++ T S + ++ + VG Sbjct: 183 LETMRLLASKGSAVVLVTHKMADVRRYADRVTVMRSGRTVNTFRPSEMSQAEVVRLAVGE 242 Query: 241 SVS------FTIEKTPTKPKETILSIKDLV--VNENRGIPAIKGLSLEVKAGEIIGIAGI 292 V+ + +P+ + ++ +G+PA+ G+ L V AGEI G+AG+ Sbjct: 243 VVAPEKPSIDAANRDRAEPRLLLRGVRSAASRTGTRQGLPALDGVDLTVHAGEIYGLAGV 302 Query: 293 DGNGQSELVQAITGLRKIKSGHLTIKGQ-DVTKLSTRKITELSVGHVPEDRHRDGLILEL 351 GNGQSEL+QAI GL + G + I+G D+ + S+ ++ + +P DR L L Sbjct: 303 GGNGQSELMQAIMGLLPLDEGTMVIEGAGDLRRASSVDRRDMGIACIPADRQTFALAGLL 362 Query: 352 TMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKG-FSGGNQQK 410 ++ EN A+ + + L+Y ++ ++ FDV G L + SGGN QK Sbjct: 363 SVVENFAIGQVHAGHYGNPLWLDYRRMEADAAKAVKHFDVLGVRSLRQSVSLLSGGNAQK 422 Query: 411 AIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSD 470 +IARE R P +++ P+RGLDV A +H RL A RDEG AVL++S +LDE+L L+D Sbjct: 423 LVIAREFSRRPRVVLAHSPSRGLDVRASAQVHARLRAARDEGAAVLIISEDLDEVLALAD 482 Query: 471 RIAVIHDGQIQGIVTPETTNKQELGILMAGGS 502 R V+ G+I G + ++Q +G M S Sbjct: 483 RAGVMVRGRIVGNFS-APVDRQAIGQAMVAHS 513 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: 577 Number of extensions: 21 Number of successful extensions: 7 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: 513 Length adjustment: 35 Effective length of query: 475 Effective length of database: 478 Effective search space: 227050 Effective search space used: 227050 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