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_RS26080 BPHYT_RS26080 ABC transporter ATPase
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__BFirm:BPHYT_RS26080 Length = 527 Score = 361 bits (927), Expect = e-104 Identities = 204/520 (39%), Positives = 308/520 (59%), Gaps = 29/520 (5%) Query: 5 VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64 V+ M I K+F F A ++L+L GE+H LLGENGAGKSTL N++ G+ +P +G++ + Sbjct: 10 VLRMDGIVKRFGAFQALTDVSLELFAGEVHCLLGENGAGKSTLCNVMFGVHQPDAGAMWL 69 Query: 65 NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124 +G+ SP + GI MVHQHF LVE +V +N++LG G LD K+ Q ++A Sbjct: 70 DGAPYQPHSPRDALTHGIAMVHQHFSLVEDVSVLDNLLLGQV---RGWLDRKREAQRVRA 126 Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184 L + GLA+DP+ ++AD+SVG +QRVEI+K L R +L+ DEPTAVL P+EI L+ Sbjct: 127 LVAELGLALDPDTRVADLSVGEKQRVEIVKCLIREPRLLVLDEPTAVLLPAEIDALLDTC 186 Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMV------ 238 +V G +++L+THKL EIR +A R TV++ G+ + L M+ Sbjct: 187 ARVVARGCAVVLVTHKLAEIRRIASRATVLQSGRVVARSSKPSADVDALVRAMIQRPDST 246 Query: 239 --GRSVSFTIEKTP----------TKP-KETILSIKDLVVNENRGIPAIKGLSLEVKAGE 285 G + + TP T+P + L I L V + G+ ++ +L V GE Sbjct: 247 DQGAAANSNASATPRSATRSTSPYTRPLADEALQIDGLTVRDADGVTRLEDCTLVVNRGE 306 Query: 286 IIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRD 345 I+GIAG++GNGQSEL + G++K +G ++G+D T+ + + +T VG VPEDRH Sbjct: 307 IVGIAGVEGNGQSELGAVLAGMQKASAGRFFVQGKDCTQAAPQTLTRAGVGVVPEDRHAV 366 Query: 346 GLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSG 405 G + ++++ ENL L + G + + R LMQ FDVR A+ + +G SG Sbjct: 367 GCVPDMSLTENLFLNRL--DDYARGGFMRRRAMRRDARALMQRFDVRAASPDVAFRGLSG 424 Query: 406 GNQQKAIIAREVDRDP-DLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDE 464 GNQQKA++ARE+ D +L+ +QPTRGLDVGA+ ++ + A RD G VLL+S ELDE Sbjct: 425 GNQQKAVLARELTLDGLAVLVAAQPTRGLDVGAVAAVYDHIRAARDAGVGVLLISSELDE 484 Query: 465 ILNLSDRIAVIHDGQIQGIVTPETT----NKQELGILMAG 500 ++ ++DR+ V++ G+I G PE + ++ +G MAG Sbjct: 485 LMAVADRVLVMYRGRIMGTCVPEASQFNLQRERIGAWMAG 524 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: 536 Number of extensions: 22 Number of successful extensions: 9 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: 527 Length adjustment: 35 Effective length of query: 475 Effective length of database: 492 Effective search space: 233700 Effective search space used: 233700 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