254780345

254780345

transcription antitermination protein NusB

GeneID in NCBI database:8209330Locus tag:CLIBASIA_01150
Protein GI in NCBI database:254780345Protein Accession:YP_003064758.1
Gene range:-(241187, 241699)Protein Length:170aa
Gene description:transcription antitermination protein NusB
COG prediction:[K] Transcription termination factor
KEGG prediction:nusB; transcription antitermination protein NusB; K03625 N utilization substance protein B
SEED prediction:Transcription termination protein NusB
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Transcription factors bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOP1 TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170
MTIQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSAITQ
cccccccccccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHccHHHHHHHHHHHHHHHHccccccEEHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccccc
ccccccccccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccccc
MTIQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCltekwsfsRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIahdffygdepkFINAVLDKvsrkeeikrsgcvsaitq
mtiqdnkkdlklshRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDkvsrkeeikrsgcvsaitq
MTIQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSAITQ
*********************AAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDK******************
MTIQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK**************
***********LSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKR*********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MTIQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSAITQ
MTIQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSAITQ
MTIQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSAITQ

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target170 transcription antitermination protein NusB [Candidatus
315122231170 transcription antitermination protein NusB [Candidatus 1 4e-67
222148209160 transcription antitermination protein NusB [Agrobacteri 1 6e-39
222085516160 transcription antitermination factor NusB [Agrobacteriu 1 2e-38
319408451156 N utilization substance protein B [Bartonella schoenbuc 1 2e-37
49475530158 transcription antitermination protein NusB [Bartonella 1 3e-37
319784157166 transcription antitermination factor NusB [Mesorhizobiu 1 2e-36
240850687156 transcription antitermination protein NusB [Bartonella 1 6e-36
260466838166 NusB antitermination factor [Mesorhizobium opportunistu 1 7e-36
163759209164 transcription antitermination protein NusB [Hoeflea pho 1 9e-36
227821538160 transcription antitermination protein NusB [Sinorhizobi 1 1e-35
>gi|315122231|ref|YP_004062720.1| transcription antitermination protein NusB [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 170 Back     alignment and organism information
 Score =  257 bits (656), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 121/170 (71%), Positives = 143/170 (84%)

Query: 1   MTIQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESV 60
           MTIQDNK  +KL+ RRGIAR++AVQALYQIDI+GCS  ++ISEYE +RFCAD ++D +++
Sbjct: 1   MTIQDNKTTVKLALRRGIARISAVQALYQIDIVGCSLVDVISEYEMHRFCADKDIDEDNI 60

Query: 61  YLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHS 120
           Y  VDLEWF  I+HGV+  K+ +D LISSCLTEKWSFSRLD+ILC+ILRAGV ELIECHS
Sbjct: 61  YSQVDLEWFHTIMHGVVKNKELVDSLISSCLTEKWSFSRLDLILCAILRAGVFELIECHS 120

Query: 121 VPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSAITQ 170
           VPV VIISEYVCIAHDF YGDEPKF+NAVLDKVSR  E++     SAI Q
Sbjct: 121 VPVRVIISEYVCIAHDFLYGDEPKFVNAVLDKVSRTPEVQSKRSDSAIIQ 170


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222148209|ref|YP_002549166.1| transcription antitermination protein NusB [Agrobacterium vitis S4] Length = 160 Back     alignment and organism information
>gi|222085516|ref|YP_002544046.1| transcription antitermination factor NusB [Agrobacterium radiobacter K84] Length = 160 Back     alignment and organism information
>gi|319408451|emb|CBI82106.1| N utilization substance protein B [Bartonella schoenbuchensis R1] Length = 156 Back     alignment and organism information
>gi|49475530|ref|YP_033571.1| transcription antitermination protein NusB [Bartonella henselae str. Houston-1] Length = 158 Back     alignment and organism information
>gi|319784157|ref|YP_004143633.1| transcription antitermination factor NusB [Mesorhizobium ciceri biovar biserrulae WSM1271] Length = 166 Back     alignment and organism information
>gi|240850687|ref|YP_002972087.1| transcription antitermination protein NusB [Bartonella grahamii as4aup] Length = 156 Back     alignment and organism information
>gi|260466838|ref|ZP_05813022.1| NusB antitermination factor [Mesorhizobium opportunistum WSM2075] Length = 166 Back     alignment and organism information
>gi|163759209|ref|ZP_02166295.1| transcription antitermination protein NusB [Hoeflea phototrophica DFL-43] Length = 164 Back     alignment and organism information
>gi|227821538|ref|YP_002825508.1| transcription antitermination protein NusB [Sinorhizobium fredii NGR234] Length = 160 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target170 transcription antitermination protein NusB [Candidatus
PRK00202137 PRK00202, nusB, transcription antitermination protein N 6e-33
TIGR01951129 TIGR01951, nusB, transcription antitermination factor N 1e-30
pfam01029126 pfam01029, NusB, NusB family 2e-22
cd00619130 cd00619, Terminator_NusB, Transcription termination fac 2e-19
cd00447129 cd00447, NusB_Sun, RNA binding domain of NusB (N protei 2e-15
cd00620126 cd00620, Methyltransferase_Sun, N-terminal RNA binding 4e-05
PRK14903 431 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provi 0.003
COG0781151 COG0781, NusB, Transcription termination factor [Transc 8e-28
PRK09634207 PRK09634, nusB, transcription antitermination protein N 2e-06
>gnl|CDD|178926 PRK00202, nusB, transcription antitermination protein NusB; Reviewed Back     alignment and domain information
>gnl|CDD|162621 TIGR01951, nusB, transcription antitermination factor NusB Back     alignment and domain information
>gnl|CDD|144570 pfam01029, NusB, NusB family Back     alignment and domain information
>gnl|CDD|29565 cd00619, Terminator_NusB, Transcription termination factor NusB (N protein-Utilization Substance B) Back     alignment and domain information
>gnl|CDD|29564 cd00447, NusB_Sun, RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins Back     alignment and domain information
>gnl|CDD|29566 cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of the methyltransferase Sun Back     alignment and domain information
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>gnl|CDD|31124 COG0781, NusB, Transcription termination factor [Transcription] Back     alignment and domain information
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 170 transcription antitermination protein NusB [Candidatus
TIGR01951140 nusB transcription antitermination factor NusB; InterPr 100.0
PRK00202132 nusB transcription antitermination protein NusB; Review 100.0
cd00619130 Terminator_NusB Transcription termination factor NusB ( 100.0
COG0781151 NusB Transcription termination factor [Transcription] 100.0
pfam01029126 NusB NusB family. The NusB protein is involved in the r 99.97
cd00447129 NusB_Sun RNA binding domain of NusB (N protein-Utilizat 99.97
cd00620126 Methyltransferase_Sun N-terminal RNA binding domain of 99.92
PRK10901 428 16S rRNA methyltransferase B; Provisional 99.89
TIGR00563 487 rsmB ribosomal RNA small subunit methyltransferase B; I 99.81
pfam09185140 DUF1948 Domain of unknown function (DUF1948). Members o 97.35
PRK09634206 nusB transcription antitermination protein NusB; Provis 99.93
>TIGR01951 nusB transcription antitermination factor NusB; InterPro: IPR011605 The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination Back     alignment and domain information
>PRK00202 nusB transcription antitermination protein NusB; Reviewed Back     alignment and domain information
>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B) Back     alignment and domain information
>COG0781 NusB Transcription termination factor [Transcription] Back     alignment and domain information
>pfam01029 NusB NusB family Back     alignment and domain information
>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins Back     alignment and domain information
>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun Back     alignment and domain information
>PRK10901 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase B; InterPro: IPR004573 This family consists of bacterial sequences related to Escherichia coli rsmB, an rRNA SAM-dependent methyltransferase Back     alignment and domain information
>pfam09185 DUF1948 Domain of unknown function (DUF1948) Back     alignment and domain information
>PRK09634 nusB transcription antitermination protein NusB; Provisional Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target170 transcription antitermination protein NusB [Candidatus
3d3b_A141 Structural And Functional Analysis Of The E. Coli N 6e-20
3imq_A141 Crystal Structure Of The Nusb101-S10(Delta Loop) Co 9e-20
1ey1_A139 Solution Structure Of Escherichia Coli Nusb Length 9e-20
1eyv_A156 The Crystal Structure Of Nusb From Mycobacterium Tu 3e-19
1tzt_A142 T. Maritima Nusb, P21 Length = 142 1e-18
2jr0_A148 Solution Structure Of Nusb From Aquifex Aeolicus Le 2e-12
1sqf_A 429 The Crystal Structure Of E. Coli Fmu Binary Complex 5e-10
>gi|220702382|pdb|3D3B|A Chain A, Structural And Functional Analysis Of The E. Coli Nusb-S10 Transcription Antitermination Complex. Length = 141 Back     alignment and structure
 Score =  100 bits (249), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 36/141 (25%), Positives = 61/141 (43%), Gaps = 13/141 (9%)

Query: 21  LAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRK 80
             AVQALY   +      ++  ++             E     VD+ +FR ++ GV    
Sbjct: 13  ECAVQALYSWQLSQNDIADVEYQFLA-----------EQDVKDVDVLYFRELLAGVATNT 61

Query: 81  QHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYG 140
            ++D L+   L+       L  +  ++LR  + EL +   VP +V I+E + +A  F   
Sbjct: 62  AYLDGLMKPYLSRL--LEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAE 119

Query: 141 DEPKFINAVLDKVSRKEEIKR 161
           D  KF+N VLDK +      +
Sbjct: 120 DSHKFVNGVLDKAAPVIRPNK 140


>gi|266618676|pdb|3IMQ|A Chain A, Crystal Structure Of The Nusb101-S10(Delta Loop) Complex Length = 141 Back     alignment and structure
gi|9257110|pdb|1EY1|A Chain A, Solution Structure Of Escherichia Coli Nusb Length = 139 Back     alignment and structure
gi|8569494|pdb|1EYV|A Chain A, The Crystal Structure Of Nusb From Mycobacterium Tuberculosis Length = 156 Back     alignment and structure
gi|52695948|pdb|1TZT|A Chain A, T. Maritima Nusb, P21 Length = 142 Back     alignment and structure
gi|168177029|pdb|2JR0|A Chain A, Solution Structure Of Nusb From Aquifex Aeolicus Length = 148 Back     alignment and structure
gi|49259108|pdb|1SQF|A Chain A, The Crystal Structure Of E. Coli Fmu Binary Complex With S- Adenosylmethionine At 2.1 A Resolution Length = 429 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target170 transcription antitermination protein NusB [Candidatus
1eyv_A156 NUSB protein, N-utilizing substance protein B homolog; 2e-25
3d3b_A141 Protein NUSB, N utilization substance protein B; NUSB, 1e-22
1q8c_A151 Hypothetical protein Mg027; structural genomics, NUSB, 1e-20
2jr0_A148 Protein NUSB, N utilization substance protein B homolog 2e-18
1tzv_A142 NUSB protein, N utilization substance protein B homolog 1e-17
1sqg_A 429 SUN protein, FMU protein; rossmann-fold, mixed beta she 1e-04
>1eyv_A NUSB protein, N-utilizing substance protein B homolog; helical bundle, structural genomics, PSI, protein structure initiative; 1.60A {Mycobacterium tuberculosis} SCOP: a.79.1.1 Length = 156 Back     alignment and structure
 Score =  110 bits (275), Expect = 2e-25
 Identities = 39/143 (27%), Positives = 63/143 (44%), Gaps = 9/143 (6%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           R  AR  AV  L++ ++ G S  E++          + + D+          +   +  G
Sbjct: 10  RHQARKRAVALLFEAEVRGISAAEVVDTRAALA---EAKPDIAR-----LHPYTAAVARG 61

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
           V +   HID LI++     W+  RL  +  +ILR  V EL+    VP  V++ E V +A 
Sbjct: 62  VSEHAAHIDDLITAH-LRGWTLDRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAK 120

Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
           +    D P F+N VL +V     
Sbjct: 121 ELSTDDSPGFVNGVLGQVMLVTP 143


>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT site, phage lambda, lambdan antitermination; HET: NHE; 1.30A {Escherichia coli K12} PDB: 3d3c_A 3imq_A 1ey1_A Length = 141 Back     alignment and structure
>1q8c_A Hypothetical protein Mg027; structural genomics, NUSB, GI 3844637, BSGC structure funded by NIH, protein structure initiative, PSI; 2.00A {Mycoplasma genitalium} SCOP: a.79.1.2 Length = 151 Back     alignment and structure
>2jr0_A Protein NUSB, N utilization substance protein B homolog; antiterminator, transcription; NMR {Aquifex aeolicus} Length = 148 Back     alignment and structure
>1tzv_A NUSB protein, N utilization substance protein B homolog; RNA-protein interaction, transcriptional antitermination, transcription regulation; 1.35A {Thermotoga maritima} SCOP: a.79.1.1 PDB: 1tzu_A 1tzt_A 1tzw_A 1tzx_A* Length = 142 Back     alignment and structure
>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet, methyltransferase-fold, RNA-binding domain; 1.65A {Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A Length = 429 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target170 transcription antitermination protein NusB [Candidatus
3d3b_A141 Protein NUSB, N utilization substance protein B; NUSB, 100.0
1eyv_A156 NUSB protein, N-utilizing substance protein B homolog; 100.0
2jr0_A148 Protein NUSB, N utilization substance protein B homolog 100.0
1tzv_A142 NUSB protein, N utilization substance protein B homolog 100.0
1q8c_A151 Hypothetical protein Mg027; structural genomics, NUSB, 99.96
1sqg_A 429 SUN protein, FMU protein; rossmann-fold, mixed beta she 99.85
2yxl_A 450 PH0851 protein, 450AA long hypothetical FMU protein; FM 99.66
>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT site, phage lambda, lambdan antitermination; HET: NHE; 1.30A {Escherichia coli K12} PDB: 3d3c_A 3imq_A 1ey1_A Back     alignment and structure
Probab=100.00  E-value=2.4e-34  Score=225.32  Aligned_cols=138  Identities=28%  Similarity=0.363  Sum_probs=125.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98132346999999999999995699989999999985310013221120144343999999999999989999999997
Q gi|254780345|r   10 LKLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISS   89 (170)
Q Consensus        10 ~~~~~~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~   89 (170)
                      |++ ..|+.||+.|+|+||++++++.+.++++.+|...           ......|..|+++++.|+.++...+|.+|.+
T Consensus         3 m~~-~~R~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~-----------~~~~~~d~~~~~~lv~gv~~~~~~ld~~I~~   70 (141)
T 3d3b_A            3 MEP-AARRRARECAVQALYSWQLSQNDIADVEYQFLAE-----------QDVKDVDVLYFRELLAGVATNTAYLDGLMKP   70 (141)
T ss_dssp             CCC-HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-----------SCCTTSCHHHHHHHHHHHHHTHHHHHHHHGG
T ss_pred             CCC-CHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-----------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998-4799999999999999984699999999999884-----------4444357999999999899739999999999


Q ss_pred             HHCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             410357633235348999999999986435578103398899999983387723149999999995233320
Q gi|254780345|r   90 CLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKR  161 (170)
Q Consensus        90 ~l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~  161 (170)
                      ++  +|+++|+++++++|||+|+||+++.+++|++|+|||||+|||.|++++++||||||||+++|+.+.++
T Consensus        71 ~l--~~~~~rl~~~~~~ILrla~~El~~~~~~p~~vvInE~VelAK~~~~~~~~~fVNaVL~~i~k~~r~~e  140 (141)
T 3d3b_A           71 YL--SRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNK  140 (141)
T ss_dssp             GG--TTCSSCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCTTHHHHHHHHHHHHHHHHCTTC
T ss_pred             HH--HHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             76--75598637989999999999998665899702199999999996899720338999999999847357



>1eyv_A NUSB protein, N-utilizing substance protein B homolog; helical bundle, structural genomics, PSI, protein structure initiative; 1.60A {Mycobacterium tuberculosis} SCOP: a.79.1.1 Back     alignment and structure
>2jr0_A Protein NUSB, N utilization substance protein B homolog; antiterminator, transcription; NMR {Aquifex aeolicus} Back     alignment and structure
>1tzv_A NUSB protein, N utilization substance protein B homolog; RNA-protein interaction, transcriptional antitermination, transcription regulation; 1.35A {Thermotoga maritima} SCOP: a.79.1.1 PDB: 1tzu_A 1tzt_A 1tzw_A 1tzx_A* Back     alignment and structure
>1q8c_A Hypothetical protein Mg027; structural genomics, NUSB, GI 3844637, BSGC structure funded by NIH, protein structure initiative, PSI; 2.00A {Mycoplasma genitalium} SCOP: a.79.1.2 Back     alignment and structure
>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet, methyltransferase-fold, RNA-binding domain; 1.65A {Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A Back     alignment and structure
>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii OT3} Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 170 transcription antitermination protein NusB [Candidatus
d1ey1a_139 a.79.1.1 (A:) Antitermination factor NusB {Escherichia 8e-20
d1eyva_131 a.79.1.1 (A:) Antitermination factor NusB {Mycobacteriu 3e-18
d1tzva_141 a.79.1.1 (A:) Antitermination factor NusB {Thermotoga m 2e-17
d1sqga1140 a.79.1.3 (A:5-144) Ribosomal RNA small subunit methyltr 8e-17
>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]} Length = 139 Back     information, alignment and structure

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Escherichia coli [TaxId: 562]
 Score = 90.2 bits (223), Expect = 8e-20
 Identities = 42/146 (28%), Positives = 68/146 (46%), Gaps = 14/146 (9%)

Query: 11  KLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFR 70
           K + RR  AR  AVQALY   +      ++  +     F A+ ++        VD+ +FR
Sbjct: 2   KPAARR-RARECAVQALYSWQLSQNDIADVEYQ-----FLAEQDVK------DVDVLYFR 49

Query: 71  VIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEY 130
            ++ GV     ++D L+   L        L  +  ++LR  + EL +   VP +V I+E 
Sbjct: 50  ELLAGVATNTAYLDGLMKPYL--SRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEA 107

Query: 131 VCIAHDFFYGDEPKFINAVLDKVSRK 156
           + +A  F   D  KF+N VLDK +  
Sbjct: 108 IELAKSFGAEDSHKFVNGVLDKAAPV 133


>d1eyva_ a.79.1.1 (A:) Antitermination factor NusB {Mycobacterium tuberculosis [TaxId: 1773]} Length = 131 Back     information, alignment and structure
>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]} Length = 141 Back     information, alignment and structure
>d1sqga1 a.79.1.3 (A:5-144) Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain {Escherichia coli [TaxId: 562]} Length = 140 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target170 transcription antitermination protein NusB [Candidatus
d1tzva_141 Antitermination factor NusB {Thermotoga maritima [TaxId 100.0
d1ey1a_139 Antitermination factor NusB {Escherichia coli [TaxId: 5 100.0
d1eyva_131 Antitermination factor NusB {Mycobacterium tuberculosis 99.97
d1sqga1140 Ribosomal RNA small subunit methyltransferase B, RsmB ( 99.94
d1q8ca_140 Hypothetical protein MG027 {Mycoplasma genitalium [TaxI 96.65
>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Thermotoga maritima [TaxId: 2336]
Probab=100.00  E-value=2.5e-33  Score=217.80  Aligned_cols=137  Identities=31%  Similarity=0.456  Sum_probs=120.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1323469999999999999956999-899999999853100132211201443439999999999999899999999974
Q gi|254780345|r   12 LSHRRGIARLAAVQALYQIDIIGCS-TTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSC   90 (170)
Q Consensus        12 ~~~~r~~aR~~aiq~Ly~~~~~~~~-~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~   90 (170)
                      |..+|+.||+.|+|+||++++++.. .+.+...+.            .......|+.|+++++.|+.++...+|.+|.++
T Consensus         1 Mk~pR~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~------------~~~~~~~d~~~~~~lv~g~~~~~~~id~~I~~~   68 (141)
T d1tzva_           1 MKTPRRRMRLAVFKALFQHEFRRDEDLEQILEEIL------------DETYDKKAKEDARRYIRGIKENLSMIDDLISRY   68 (141)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTTCTTSCHHHHHHHHC------------CTTSCHHHHHHHHHHHHHHHHTHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH------------HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99816999999999999998449962999999998------------841366679999999999998099999999985


Q ss_pred             HCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             10357633235348999999999986435578103398899999983387723149999999995233320
Q gi|254780345|r   91 LTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKR  161 (170)
Q Consensus        91 l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~  161 (170)
                      + ++|+++|+++++++|||+|+||+++++++|++|+|||||+|||.|++++++||||||||+++|+.+..+
T Consensus        69 ~-~~~~~~rl~~~~~~iLr~a~~El~~~~~~p~~v~InEaVelak~~~~~~~~~fVNaVL~~i~r~~~~~e  138 (141)
T d1tzva_          69 L-EKWSLNRLSVVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAKRYGTENSGKFVNGILDRIAKEHAPKE  138 (141)
T ss_dssp             C-SSSCGGGSCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHCCGG
T ss_pred             C-CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCHH
T ss_conf             2-158738888899999999999998533330358999999999985888632118999999998757511



>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1eyva_ a.79.1.1 (A:) Antitermination factor NusB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1sqga1 a.79.1.3 (A:5-144) Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1q8ca_ a.79.1.2 (A:) Hypothetical protein MG027 {Mycoplasma genitalium [TaxId: 2097]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 170 transcription antitermination protein NusB [Candid
1eyv_A_156 (A:) NUSB protein, N-utilizing substance protein B 4e-25
2jr0_A_148 (A:) Protein NUSB, N utilization substance protein 1e-24
1tzv_A_142 (A:) NUSB protein, N utilization substance protein 2e-24
3d3b_A_141 (A:) Protein NUSB, N utilization substance protein 1e-23
1sqg_A_1-142142 (A:1-142) SUN protein, FMU protein; rossmann-fold, 3e-20
>1eyv_A (A:) NUSB protein, N-utilizing substance protein B homolog; helical bundle, structural genomics, PSI, protein structure initiative; 1.60A {Mycobacterium tuberculosis}Length = 156 Back     alignment and structure
 Score =  108 bits (272), Expect = 4e-25
 Identities = 39/143 (27%), Positives = 60/143 (41%), Gaps = 9/143 (6%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           R  AR  AV  L++ ++ G S  E++                          +   +  G
Sbjct: 10  RHQARKRAVALLFEAEVRGISAAEVVDTRAALA--EAKPDIAR------LHPYTAAVARG 61

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
           V +   HID LI++ L   W+  RL  +  +ILR  V EL+    VP  V++ E V +A 
Sbjct: 62  VSEHAAHIDDLITAHLR-GWTLDRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAK 120

Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
           +    D P F+N VL +V     
Sbjct: 121 ELSTDDSPGFVNGVLGQVMLVTP 143


>2jr0_A (A:) Protein NUSB, N utilization substance protein B homolog; antiterminator, transcription; NMR {Aquifex aeolicus}Length = 148 Back     alignment and structure
>1tzv_A (A:) NUSB protein, N utilization substance protein B homolog; RNA-protein interaction, transcriptional antitermination, transcription regulation; 1.35A {Thermotoga maritima}Length = 142 Back     alignment and structure
>3d3b_A (A:) Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT site, phage lambda, lambdan antitermination; HET: NHE; 1.30A {Escherichia coli K12} PDB: 3d3c_A 3imq_A 1ey1_ALength = 141 Back     alignment and structure
>1sqg_A (A:1-142) SUN protein, FMU protein; rossmann-fold, mixed beta sheet, methyltransferase-fold, RNA-binding domain; 1.65A {Escherichia coli}Length = 142 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target170 transcription antitermination protein NusB [Candidatus
2jr0_A_148 Protein NUSB, N utilization substance protein B ho 99.98
1tzv_A_142 NUSB protein, N utilization substance protein B ho 99.98
1eyv_A_156 NUSB protein, N-utilizing substance protein B homo 99.98
3d3b_A_141 Protein NUSB, N utilization substance protein B; N 99.97
1sqg_A_1-142142 SUN protein, FMU protein; rossmann-fold, mixed bet 99.97
1q8c_A_151 Hypothetical protein Mg027; structural genomics, N 96.68
2yxl_A_1-143143 PH0851 protein, 450AA long hypothetical FMU protei 91.83
>2jr0_A (A:) Protein NUSB, N utilization substance protein B homolog; antiterminator, transcription; NMR {Aquifex aeolicus} Back     alignment and structure
Probab=99.98  E-value=9.7e-32  Score=210.55  Aligned_cols=141  Identities=23%  Similarity=0.295  Sum_probs=128.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             32346999999999999995699989999999985310013221120144343999999999999989999999997410
Q gi|254780345|r   13 SHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLT   92 (170)
Q Consensus        13 ~~~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~   92 (170)
                      +..|+.+|+.|+|+||+++.++.++.+++..+..+.          ......|+.|++++++|++++...||.+|++++ 
T Consensus         1 M~~r~~aR~~a~q~L~~~~~~~~~~~~~l~~~~~~~----------~~~~~~d~~~~~~l~~gv~~~~~~ld~~i~~~l-   69 (148)
T 2jr0_A            1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEK----------NIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHL-   69 (148)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHT----------TCCCHHHHHHHHHHHHHHHTSHHHHHHHHHTTT-
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_conf             961899999999999998740979999999999886----------314524999999998789984999999999853-


Q ss_pred             CCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             357633235348999999999986435578103398899999983387723149999999995233320378
Q gi|254780345|r   93 EKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGC  164 (170)
Q Consensus        93 ~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~~~~  164 (170)
                      ++|+++|+++++++|||+|+||++|++++|++++|||||+|||.|++++++||||||||+++++.+......
T Consensus        70 ~~~~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvIneaVelak~~~~~~~~~fVNaVL~~i~r~~~~~~~~~  141 (148)
T 2jr0_A           70 KGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKEE  141 (148)
T ss_dssp             TTCCTTSSCHHHHHHHHHHHHHHTTTCCSSHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCHHHHHC
T ss_conf             058778888999999999999997635799741699999999996888643008999999999622023321



>1tzv_A (A:) NUSB protein, N utilization substance protein B homolog; RNA-protein interaction, transcriptional antitermination, transcription regulation; 1.35A {Thermotoga maritima} Back     alignment and structure
>1eyv_A (A:) NUSB protein, N-utilizing substance protein B homolog; helical bundle, structural genomics, PSI, protein structure initiative; 1.60A {Mycobacterium tuberculosis} Back     alignment and structure
>3d3b_A (A:) Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT site, phage lambda, lambdan antitermination; HET: NHE; 1.30A {Escherichia coli K12} PDB: 3d3c_A 3imq_A 1ey1_A Back     alignment and structure
>1sqg_A (A:1-142) SUN protein, FMU protein; rossmann-fold, mixed beta sheet, methyltransferase-fold, RNA-binding domain; 1.65A {Escherichia coli} Back     alignment and structure
>1q8c_A (A:) Hypothetical protein Mg027; structural genomics, NUSB, GI 3844637, BSGC structure funded by NIH, protein structure initiative, PSI; 2.00A {Mycoplasma genitalium} Back     alignment and structure
>2yxl_A (A:1-143) PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii OT3} Back     alignment and structure