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 AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__azobra:AZOBR_RS06625 Length = 511 Score = 450 bits (1158), Expect = e-131 Identities = 234/506 (46%), Positives = 333/506 (65%), Gaps = 6/506 (1%) Query: 1 MAQH--VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPT 58 M QH +E R + K F AN ++L + KG IH ++GENGAGKST+M+++ G L Sbjct: 1 MPQHPPALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPAD 60 Query: 59 SGSIKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKA 118 G+I ++G V + SP + GIGMVHQHFMLV+ FTV EN++LG E + +A Sbjct: 61 GGTILVDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAEGGVTLAAGMARA 120 Query: 119 GQEIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQ 178 E+ L+ YGL VD + + ++ VGAQQRVEILK LYRGADILI DEPT VLTP E Sbjct: 121 RTELTRLARDYGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETD 180 Query: 179 ELMTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMV 238 L I+++L ++GK++++ITHKL EI + D VTV+RRG+ + V + T+ ++LAE+MV Sbjct: 181 HLFRILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMV 240 Query: 239 GRSVSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQS 298 GR V +EK P P +L + L V + G+ +KG+ L V+AGEI+GIAG+ GNGQS Sbjct: 241 GRKVLLRVEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQS 300 Query: 299 ELVQAITGLRKIKSGHLTIKGQDVT----KLSTRKITELSVGHVPEDRHRDGLILELTMA 354 EL++A+ G+R G + ++G+++T + + R + L VGHVPEDR R GL+ Sbjct: 301 ELLEALAGMRPPAEGSVRLRGEELTATPDRFTARGLRALGVGHVPEDRQRVGLVTGFEAQ 360 Query: 355 ENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIA 414 E L + +++ + + M +DVR + +PA FSGGNQQK ++A Sbjct: 361 ECAILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIVLA 420 Query: 415 REVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAV 474 RE++R+PDLL+V QPTRG+D+GAIE+IH+RL+A RD+GKA+LLVS ELDEI LSDRI V Sbjct: 421 REMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRILV 480 Query: 475 IHDGQIQGIVTPETTNKQELGILMAG 500 + DG++ G V P +++ LG++MAG Sbjct: 481 MFDGRLVGEVAPGEADERRLGLMMAG 506 Score = 82.8 bits (203), Expect = 3e-20 Identities = 61/232 (26%), Positives = 112/232 (48%), Gaps = 10/232 (4%) Query: 273 AIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRKITE 332 A + +SL V G I G+ G +G G+S ++ + G G + + G+ V S R Sbjct: 22 ANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTILVDGRPVAVRSPRDALA 81 Query: 333 LSVGHVPEDRHRDGLILE-LTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDV 391 +G V H+ ++++ T+ EN+ L L+ +++ R E D+ Sbjct: 82 AGIGMV----HQHFMLVDPFTVLENVLLGAEGGVTLAAGMARARTELTRLARDYGLEVDL 137 Query: 392 RGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDE 451 +P G QQ+ I + + R D+LI+ +PT L +++ + L A R++ Sbjct: 138 DRPVGELPV-----GAQQRVEILKALYRGADILILDEPTGVLTPQETDHLFRILRALREQ 192 Query: 452 GKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSI 503 GK V++++ +L EI+ L+D + V+ GQ+ V T+++EL LM G + Sbjct: 193 GKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVGRKV 244 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: 652 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 510 Length of database: 511 Length adjustment: 35 Effective length of query: 475 Effective length of database: 476 Effective search space: 226100 Effective search space used: 226100 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