Citrus Sinensis ID: 022911

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290
Protein Sequence
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccHHHHHHHcccccccccccccccccccccccccEEHHHHHHccccccHHHHHHHHHcccccccccHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccEEEEccccccccccccccccHHHccccccHHccccccccHcccccccHcccccccccccccccccccccccccccEEEEEHHHccccHHHHHHHHHHHccccccEEcHHHHHHcccccccccccEcccHHHHHHHHHccHHHcHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHcccccHEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccccccccccccccc
Coil and Loop (DISEMBL)
maveatssflscsskthflfnlrassspsswkKFTQSANFaaknrhvcrnerpnvscsAAAFAVQETLEKTRESVMASSAKemmpkidksGRLVVYAACLEGSDPIRLFEKRLnsrrepgyefdksslleynhmsfggppvttetVEEADELLRSDEEESAIEAEvlsappklVYSKLLLRFTRKLLVAVVDKWDAHVHiidkvvppiwkdqpagrILELSILHLAMSEITVVGTRHQIVINEAVDLAKrfcdgaapriiNGCLRTFVRNLEGtanieaskaskevpsev
Flexible Loop (DISEMBL)
maveatssflscssKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMAssakemmpkidksGRLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIeaevlsappklvYSKLLLRFTRKLLVAVVDKWDAHVHIIDkvvppiwkdqpAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGtanieaskaskevpsev
Low Complexity Region (SEG)
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
Disordered region (IsUnstruct)
***************THFLFNL************************VC********C*AAAFA***************************GRLVVYAACLEGSDPIRLFE********************************************************LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT****************
Disordered Region (DISOPRED)
*************SKTHFLFNLRASSSPS**********************************************************DKSGRLVVYAACLEGSDPIRLFEK*****REPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF***********************
Disordered Region (DISEMBL)
**********SCSSKTHFLFNLRAS*********TQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIE************
Disordered Region (DISPRO)
***********CSSKTHFLFNLRAS****S****TQSA**A****H***NERPNVS***************************MPKIDKSGRLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE******************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	290	2.2.26 [Sep-21-2011]
A7GWZ7	131	N utilization substance p	yes	no	0.220	0.488	0.393	6e-07
Q5N1J7	213	N utilization substance p	yes	no	0.231	0.314	0.420	1e-06
Q8GIR7	213	N utilization substance p	yes	no	0.231	0.314	0.420	1e-06
B1WXY6	209	N utilization substance p	yes	no	0.231	0.320	0.405	2e-06
Q18B61	169	N utilization substance p	yes	no	0.234	0.402	0.385	4e-06
B2J3F1	213	N utilization substance p	yes	no	0.275	0.375	0.348	5e-06
B8HYJ8	209	N utilization substance p	yes	no	0.275	0.382	0.365	6e-06
Q8RAD1	140	N utilization substance p	yes	no	0.275	0.571	0.376	8e-06
B7K4P4	211	N utilization substance p	yes	no	0.262	0.360	0.346	9e-06
B5YE05	144	N utilization substance p	yes	no	0.217	0.437	0.430	3e-05

>sp|A7GWZ7|NUSB_CAMC5 N utilization substance protein B homolog OS=Campylobacter curvus (strain 525.92) GN=nusB PE=3 SV=1

 Score = 55.1 bits (131), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 42/66 (63%), Gaps = 2/66 (3%)

Query: 201 IDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPR 258
           +D+++ P  K++   RI  +EL+IL L + E+   GT   ++INEA++LAK     +AP+
Sbjct: 59  LDEILKPYLKEKDIERIGIVELAILRLGVYEMKFTGTDKAVIINEAIELAKELGGDSAPK 118

Query: 259 IINGCL 264
            ING L
Sbjct: 119 FINGVL 124

Involved in the transcription termination process.
Campylobacter curvus (strain 525.92) (taxid: 360105)

>sp|Q5N1J7|NUSB_SYNP6 N utilization substance protein B homolog OS=Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) GN=nusB PE=3 SV=1

 Score = 53.9 bits (128), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 201 IDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPR 258
           ID+ +  +  D    R+  L+  IL LA +EI  +GT  Q+ INEAV+LA R+ D    R
Sbjct: 130 IDRTLNDVMVDWQLHRVPRLDQDILRLAAAEILFLGTPEQVAINEAVELANRYSDEEGRR 189

Query: 259 IINGCLRTF 267
            ING LR  
Sbjct: 190 FINGVLRRL 198

Involved in the transcription termination process.

Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (taxid: 269084)

>sp|Q8GIR7|NUSB_SYNE7 N utilization substance protein B homolog OS=Synechococcus elongatus (strain PCC 7942) GN=nusB PE=3 SV=1

 Score = 53.9 bits (128), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 201 IDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPR 258
           ID+ +  +  D    R+  L+  IL LA +EI  +GT  Q+ INEAV+LA R+ D    R
Sbjct: 130 IDRTLNDVMVDWQLHRVPRLDQDILRLAAAEILFLGTPEQVAINEAVELANRYSDEEGRR 189

Query: 259 IINGCLRTF 267
            ING LR  
Sbjct: 190 FINGVLRRL 198

Involved in the transcription termination process.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|B1WXY6|NUSB_CYAA5 N utilization substance protein B homolog OS=Cyanothece sp. (strain ATCC 51142) GN=nusB PE=3 SV=1

 Score = 53.1 bits (126), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 201 IDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPR 258
           ID+ +  + KD    R+  ++  IL LA++EI  +    ++ INEAV+LAKR+ D    R
Sbjct: 134 IDEQLEAVLKDWQLKRLAKIDQDILRLAVAEILFLDVPEKVSINEAVELAKRYSDDDGYR 193

Query: 259 IINGCLRTF 267
            ING LR F
Sbjct: 194 FINGVLRRF 202

Involved in the transcription termination process.

Cyanothece sp. (strain ATCC 51142) (taxid: 43989)

>sp|Q18B61|NUSB_CLOD6 N utilization substance protein B homolog OS=Clostridium difficile (strain 630) GN=nusB PE=3 SV=1

 Score = 52.4 bits (124), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 46/70 (65%), Gaps = 2/70 (2%)

Query: 201 IDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPR 258
           ID+++    K+    R+  +++SIL L++ EI  + T +++ INEAV+LAK +CD  +P+
Sbjct: 95  IDELINKHAKNWTVDRMPKVDVSILRLSVCEILYLDTPNKVSINEAVELAKIYCDDKSPK 154

Query: 259 IINGCLRTFV 268
            ING L + V
Sbjct: 155 FINGILGSVV 164

Involved in the transcription termination process.

Clostridium difficile (strain 630) (taxid: 272563)

>sp|B2J3F1|NUSB_NOSP7 N utilization substance protein B homolog OS=Nostoc punctiforme (strain ATCC 29133 / PCC 73102) GN=nusB PE=3 SV=1

 Score = 52.0 bits (123), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 49/86 (56%), Gaps = 6/86 (6%)

Query: 182 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS--ILHLAMSEITVVGTRHQI 239
           + ++L++ V    + + HIID+++     D    R+ +L   IL +A++E+  +G    I
Sbjct: 123 YAKELVITV----NENRHIIDELLSTALVDWQVTRLAQLDRDILQIAVAEMKFLGVPDSI 178

Query: 240 VINEAVDLAKRFCDGAAPRIINGCLR 265
            INEAV+LAKR+      R ING LR
Sbjct: 179 AINEAVELAKRYSGDDGHRFINGVLR 204

Involved in the transcription termination process.

Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (taxid: 63737)

>sp|B8HYJ8|NUSB_CYAP4 N utilization substance protein B homolog OS=Cyanothece sp. (strain PCC 7425 / ATCC 29141) GN=nusB PE=3 SV=1

 Score = 51.6 bits (122), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 197 HVHIIDKVVPPIWKDQPAGRILEL--SILHLAMSEITVVGTRHQIVINEAVDLAKRFCDG 254
           H   ID ++     D    R+ ++  +IL +A++EI  + T  Q+ INEAV+LAKR+ D 
Sbjct: 126 HRTAIDHLLETALVDWQFNRLAQIDRNILRIAVAEILYLKTPTQVTINEAVELAKRYSDE 185

Query: 255 AAPRIINGCLRTFVRNLEGTAN 276
              R +NG LR  + +LE  A 
Sbjct: 186 DGYRFVNGVLRRTIPHLEAQAQ 207

Involved in the transcription termination process.

Cyanothece sp. (strain PCC 7425 / ATCC 29141) (taxid: 395961)

>sp|Q8RAD1|NUSB_THETN N utilization substance protein B homolog OS=Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) GN=nusB PE=3 SV=1

 Score = 51.2 bits (121), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 46/85 (54%), Gaps = 5/85 (5%)

Query: 197 HVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDG 254
           H+  ID+ +    KD P  R+  ++L+IL  +M E+        I INEAV++AK++   
Sbjct: 54  HLEEIDREIEKYSKDWPLYRMPRIDLAILRCSMYEMLYGNIPVSISINEAVEIAKKYSTD 113

Query: 255 AAPRIINGCLRTFVRNL---EGTAN 276
            +P  ING L  FVR     EG AN
Sbjct: 114 DSPSFINGLLGAFVREKGLEEGEAN 138

Involved in the transcription termination process.

Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (taxid: 273068)

>sp|B7K4P4|NUSB_CYAP8 N utilization substance protein B homolog OS=Cyanothece sp. (strain PCC 8801) GN=nusB PE=3 SV=1

 Score = 51.2 bits (121), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 201 IDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPR 258
           ID+ +  +  D    R+  ++  IL +A++EI  +   +++ INEA+++AKR+ D    R
Sbjct: 134 IDQQLEAVLVDWQLNRLPKIDRDILRIAVAEILFLEIPNKVAINEAIEMAKRYSDDEGYR 193

Query: 259 IINGCLRTFVRNLEGTAN 276
            ING LR F   L  T N
Sbjct: 194 FINGVLRRFTERLRITNN 211

Involved in the transcription termination process.

Cyanothece sp. (strain PCC 8801) (taxid: 41431)

>sp|B5YE05|NUSB_DICT6 N utilization substance protein B homolog OS=Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12) GN=nusB PE=3 SV=1

 Score = 49.3 bits (116), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 209 WKDQPAGRILELSILHLAMSEI-TVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF 267
           WK +  G  LE +IL LA++E+ T       + +NEAV+LAK++    A R +NG LR  
Sbjct: 65  WKLERMG-ALERNILRLAIAEMFTFSDIPQAVTVNEAVELAKKYVSPEAGRFVNGILRNI 123

Query: 268 VRNLE 272
           VRN E
Sbjct: 124 VRNWE 128

Involved in the transcription termination process.

Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12) (taxid: 309799)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	290
225435806	288	PREDICTED: uncharacterized protein LOC10	0.889	0.895	0.649	1e-100
297746508	218	unnamed protein product [Vitis vinifera]	0.710	0.944	0.779	3e-96
224073118	218	predicted protein [Populus trichocarpa]	0.703	0.935	0.787	1e-95
449463840	378	PREDICTED: uncharacterized protein LOC10	0.682	0.523	0.733	2e-88
18416739	301	antitermination NusB domain-containing p	0.7	0.674	0.739	4e-83
2982469	286	putative protein [Arabidopsis thaliana]	0.7	0.709	0.739	5e-83
297799366	300	antitermination NusB domain-containing p	0.7	0.676	0.734	7e-83
388512429	288	unknown [Lotus japonicus]	0.855	0.861	0.570	8e-79
255564810	309	RNA binding protein, putative [Ricinus c	0.634	0.595	0.707	3e-76
363807164	289	uncharacterized protein LOC100809333 [Gl	0.893	0.896	0.567	2e-74

>gi|225435806|ref|XP_002285757.1| PREDICTED: uncharacterized protein LOC100265613 [Vitis vinifera]

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 189/291 (64%), Positives = 219/291 (75%), Gaps = 33/291 (11%)

Query: 15  KTHFLFNLRASSS-----PSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLE 69
           K HF+FN   SSS     P   K    S   ++          P  S   +A  V++ L+
Sbjct: 14  KPHFIFNFNHSSSCQFLTPLPTKLLINSKLLSS----------PRTSLRTSALTVEKPLD 63

Query: 70  KTRESVMASSAKEMMPKIDKSGR------------LVVYAACLEGSDPIRLFEKRLNSRR 117
           K       S  +EM+P+IDKSGR            L+ YAACLEGSDP+RLFE+R+N+RR
Sbjct: 64  K------PSEPREMLPRIDKSGRFCSPRAARELALLIAYAACLEGSDPVRLFERRMNARR 117

Query: 118 EPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSK 177
           EPGYEFDK SLLEYNHMSFGGPPVTTETVEEADELLR++E+ESAIEAEVLSAPPKLVY K
Sbjct: 118 EPGYEFDKDSLLEYNHMSFGGPPVTTETVEEADELLRNNEKESAIEAEVLSAPPKLVYGK 177

Query: 178 LLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRH 237
           L+LRFTRKLLVAVVDKW++HV +IDKV PP WK++PAGRILEL ILHLAMSEI V+GTRH
Sbjct: 178 LILRFTRKLLVAVVDKWNSHVLVIDKVAPPNWKNEPAGRILELCILHLAMSEIAVLGTRH 237

Query: 238 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPS 288
           QIVINEAVDLAKRFCDGAAPRIINGCLRTFV++LEGT    AS+ ++EV S
Sbjct: 238 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVKDLEGTGITRASETTQEVVS 288

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297746508|emb|CBI16564.3| unnamed protein product [Vitis vinifera]

 Score =  357 bits (916), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 170/218 (77%), Positives = 192/218 (88%), Gaps = 12/218 (5%)

Query: 83  MMPKIDKSGR------------LVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLE 130
           M+P+IDKSGR            L+ YAACLEGSDP+RLFE+R+N+RREPGYEFDK SLLE
Sbjct: 1   MLPRIDKSGRFCSPRAARELALLIAYAACLEGSDPVRLFERRMNARREPGYEFDKDSLLE 60

Query: 131 YNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAV 190
           YNHMSFGGPPVTTETVEEADELLR++E+ESAIEAEVLSAPPKLVY KL+LRFTRKLLVAV
Sbjct: 61  YNHMSFGGPPVTTETVEEADELLRNNEKESAIEAEVLSAPPKLVYGKLILRFTRKLLVAV 120

Query: 191 VDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKR 250
           VDKW++HV +IDKV PP WK++PAGRILEL ILHLAMSEI V+GTRHQIVINEAVDLAKR
Sbjct: 121 VDKWNSHVLVIDKVAPPNWKNEPAGRILELCILHLAMSEIAVLGTRHQIVINEAVDLAKR 180

Query: 251 FCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPS 288
           FCDGAAPRIINGCLRTFV++LEGT    AS+ ++EV S
Sbjct: 181 FCDGAAPRIINGCLRTFVKDLEGTGITRASETTQEVVS 218

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073118|ref|XP_002303980.1| predicted protein [Populus trichocarpa] gi|222841412|gb|EEE78959.1| predicted protein [Populus trichocarpa]

 Score =  355 bits (911), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 170/216 (78%), Positives = 190/216 (87%), Gaps = 12/216 (5%)

Query: 83  MMPKIDKSGR------------LVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLE 130
           MMPKIDKSGR            L++YAACLEGSDPIRLFEKR+N+RREPGYEFDK+SLLE
Sbjct: 1   MMPKIDKSGRFCSPRAARELALLIIYAACLEGSDPIRLFEKRMNARREPGYEFDKASLLE 60

Query: 131 YNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAV 190
           YNHMSFGGPPVTTETVEEADEL  SDE+ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAV
Sbjct: 61  YNHMSFGGPPVTTETVEEADELQLSDEKESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAV 120

Query: 191 VDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKR 250
           VDKWD+HV +IDKV PP WK++PAGRILE  ILH+AMSEITV+GTRHQIVINEAVDLAKR
Sbjct: 121 VDKWDSHVLVIDKVSPPNWKNEPAGRILEFCILHMAMSEITVLGTRHQIVINEAVDLAKR 180

Query: 251 FCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEV 286
           FCDGA PRIINGCLRTF+++L G +  + S A+++V
Sbjct: 181 FCDGAGPRIINGCLRTFLKDLSGASVAQTSDANEKV 216

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463840|ref|XP_004149639.1| PREDICTED: uncharacterized protein LOC101216754 [Cucumis sativus]

 Score =  331 bits (849), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 154/210 (73%), Positives = 180/210 (85%), Gaps = 12/210 (5%)

Query: 82  EMMPKIDKSGRL------------VVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLL 129
           EM+PK+DKSG+             +VYAACLEGSDP+RLFEKRLN+RRE GYEFDK+SL+
Sbjct: 166 EMIPKVDKSGKFCSPRAARELALSIVYAACLEGSDPVRLFEKRLNARRESGYEFDKTSLM 225

Query: 130 EYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVA 189
           EYNHMSFGGPPVT ET+EEADELLR DE +S IEAE+L+APPK+VYSKL+LRFTRKLLVA
Sbjct: 226 EYNHMSFGGPPVTVETIEEADELLRKDERDSTIEAEILAAPPKIVYSKLILRFTRKLLVA 285

Query: 190 VVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAK 249
           V D WD+    I+KV+PP WK++PAGRILEL ILHLAMSEITV+GTRHQIVINEAVDLAK
Sbjct: 286 VGDGWDSRALKIEKVIPPTWKNKPAGRILELCILHLAMSEITVIGTRHQIVINEAVDLAK 345

Query: 250 RFCDGAAPRIINGCLRTFVRNLEGTANIEA 279
           RFCDGAAPRIINGCLRTFV++++   ++ A
Sbjct: 346 RFCDGAAPRIINGCLRTFVKDIKEIDSMPA 375

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416739|ref|NP_567745.1| antitermination NusB domain-containing protein [Arabidopsis thaliana] gi|15450968|gb|AAK96755.1| putative protein [Arabidopsis thaliana] gi|30984514|gb|AAP42720.1| At4g26370 [Arabidopsis thaliana] gi|332659789|gb|AEE85189.1| antitermination NusB domain-containing protein [Arabidopsis thaliana]

 Score =  313 bits (803), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 159/215 (73%), Positives = 179/215 (83%), Gaps = 12/215 (5%)

Query: 84  MPKIDKSGRL------------VVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEY 131
           MPKIDKSGRL            ++YAACLEGSDPIRLFEKR+N+RREPGYEFDKSSLLEY
Sbjct: 85  MPKIDKSGRLSSPRAARELALVILYAACLEGSDPIRLFEKRINARREPGYEFDKSSLLEY 144

Query: 132 NHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVV 191
           NHMSFGGPPV TET EE DEL+R DE+ES IEAEVLSAPPKLVYSKL+LRF +KLL AVV
Sbjct: 145 NHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEVLSAPPKLVYSKLVLRFAKKLLAAVV 204

Query: 192 DKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRF 251
           DKWD+HV II+K+ PP WK  PAGRILE SILHLAMSE+ V+ TRH IVINEAVDLAKRF
Sbjct: 205 DKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLAMSEVAVLETRHPIVINEAVDLAKRF 264

Query: 252 CDGAAPRIINGCLRTFVRNLEGTANIEASKASKEV 286
           CDG+APRIINGCLRTFV++   T+  +A +  +EV
Sbjct: 265 CDGSAPRIINGCLRTFVKDRATTSTPQALELKQEV 299

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2982469|emb|CAA18233.1| putative protein [Arabidopsis thaliana] gi|7269489|emb|CAB79492.1| putative protein [Arabidopsis thaliana]

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 159/215 (73%), Positives = 179/215 (83%), Gaps = 12/215 (5%)

Query: 84  MPKIDKSGRL------------VVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEY 131
           MPKIDKSGRL            ++YAACLEGSDPIRLFEKR+N+RREPGYEFDKSSLLEY
Sbjct: 70  MPKIDKSGRLSSPRAARELALVILYAACLEGSDPIRLFEKRINARREPGYEFDKSSLLEY 129

Query: 132 NHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVV 191
           NHMSFGGPPV TET EE DEL+R DE+ES IEAEVLSAPPKLVYSKL+LRF +KLL AVV
Sbjct: 130 NHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEVLSAPPKLVYSKLVLRFAKKLLAAVV 189

Query: 192 DKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRF 251
           DKWD+HV II+K+ PP WK  PAGRILE SILHLAMSE+ V+ TRH IVINEAVDLAKRF
Sbjct: 190 DKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLAMSEVAVLETRHPIVINEAVDLAKRF 249

Query: 252 CDGAAPRIINGCLRTFVRNLEGTANIEASKASKEV 286
           CDG+APRIINGCLRTFV++   T+  +A +  +EV
Sbjct: 250 CDGSAPRIINGCLRTFVKDRATTSTPQALELKQEV 284

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799366|ref|XP_002867567.1| antitermination NusB domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297313403|gb|EFH43826.1| antitermination NusB domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  313 bits (801), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 158/215 (73%), Positives = 179/215 (83%), Gaps = 12/215 (5%)

Query: 84  MPKIDKSGRL------------VVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEY 131
           MPKIDKSGRL            ++YAACLEGSDPIRLFEKR+N+RREPGYEFDK+SLLEY
Sbjct: 84  MPKIDKSGRLSSPRAARELALVILYAACLEGSDPIRLFEKRINARREPGYEFDKTSLLEY 143

Query: 132 NHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVV 191
           NHMSFGGPPV TET EE DEL+R DE+ES IEAEVLSAPPKLVYSKL+LRF +KLL AVV
Sbjct: 144 NHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEVLSAPPKLVYSKLVLRFAKKLLAAVV 203

Query: 192 DKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRF 251
           DKWD+HV II+K+ PP WK  PAGRILE SILHLAMSE+ V+ TRH IVINEAVDLAKRF
Sbjct: 204 DKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLAMSEVAVLETRHPIVINEAVDLAKRF 263

Query: 252 CDGAAPRIINGCLRTFVRNLEGTANIEASKASKEV 286
           CDG+APRIINGCLRTFV++   T+  +A +  +EV
Sbjct: 264 CDGSAPRIINGCLRTFVKDRAATSTPQALELKQEV 298

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388512429|gb|AFK44276.1| unknown [Lotus japonicus]

 Score =  299 bits (766), Expect = 8e-79,   Method: Compositional matrix adjust.
 Identities = 154/270 (57%), Positives = 194/270 (71%), Gaps = 22/270 (8%)

Query: 27  SPSSW----KKFTQSANFAAKNRHVC----RNERPNVSCSAAAFAVQETLEKTRESVMAS 78
           SPSS+    K F   ++    NR       +N+     CS A+ AV   +++   S +  
Sbjct: 20  SPSSFATPSKCFPLPSSLVNHNRDFFLAKPQNKTLFTRCSVASSAV--AVDRDEASGLGK 77

Query: 79  SAKEMMPKIDKSGRL------------VVYAACLEGSDPIRLFEKRLNSRREPGYEFDKS 126
                +PK+DK+GR             ++YA+CLEG DP+RLFEKRLN RRE GY+FD+ 
Sbjct: 78  PDTVGLPKVDKTGRFCSPRAARELALSIIYASCLEGLDPVRLFEKRLNERREAGYQFDQR 137

Query: 127 SLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKL 186
            LLEYN MSF GPPVT ++ EEA+ELLR+ E+ES +EAE+LSAPPKLVY+KL+LRFTRKL
Sbjct: 138 KLLEYNPMSFAGPPVTVQSEEEANELLRNIEKESDLEAEILSAPPKLVYNKLILRFTRKL 197

Query: 187 LVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVD 246
           LVAV D WD+HV +I+KVVPP WKD+PAG+ILELSILHLAMSE+T + T HQIVINEAVD
Sbjct: 198 LVAVRDSWDSHVLVINKVVPPTWKDEPAGKILELSILHLAMSEMTKLETIHQIVINEAVD 257

Query: 247 LAKRFCDGAAPRIINGCLRTFVRNLEGTAN 276
           LAKR+CDGA+ RIINGCLRTF R+ E  ++
Sbjct: 258 LAKRYCDGASSRIINGCLRTFYRDTEKASD 287

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564810|ref|XP_002523399.1| RNA binding protein, putative [Ricinus communis] gi|223537349|gb|EEF38978.1| RNA binding protein, putative [Ricinus communis]

 Score =  291 bits (744), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 143/202 (70%), Positives = 164/202 (81%), Gaps = 18/202 (8%)

Query: 60  AAFAVQETLEKTRESVMASSAKEMMPKIDKSGR------------LVVYAACLEGSDPIR 107
           +AF V+++ E +      +  KEMMPKIDKSGR            +++YAACLEGSDP+R
Sbjct: 84  SAFVVEKSAENS------TKDKEMMPKIDKSGRFCSPRAARELALMMIYAACLEGSDPVR 137

Query: 108 LFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVL 167
           LFEKR+N+RRE GYEFDK+SLLEYNHMSFGGPPVTT+T+EEAD+LL SDE ESA+EAEVL
Sbjct: 138 LFEKRINARREAGYEFDKTSLLEYNHMSFGGPPVTTDTIEEADKLLSSDEIESALEAEVL 197

Query: 168 SAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAM 227
           SAPPKLVYSKLLLRFTRKLL AVV+KWD+HV IIDKV PP WK QP GRILE  ILHLAM
Sbjct: 198 SAPPKLVYSKLLLRFTRKLLAAVVEKWDSHVLIIDKVAPPNWKSQPGGRILEFCILHLAM 257

Query: 228 SEITVVGTRHQIVINEAVDLAK 249
           SEI VVGTRHQIVINE   ++K
Sbjct: 258 SEIAVVGTRHQIVINEFAFVSK 279

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807164|ref|NP_001242346.1| uncharacterized protein LOC100809333 [Glycine max] gi|255636077|gb|ACU18383.1| unknown [Glycine max]

 Score =  285 bits (729), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 164/289 (56%), Positives = 203/289 (70%), Gaps = 30/289 (10%)

Query: 1   MAVEATSSFLSCSSKTHFLFNLRASSSPSSW---KKFTQSANFAAKNRHVCRNERPNVSC 57
           + V  + S  S + K      LR SS PS     + F+Q+A F+ +N         ++  
Sbjct: 6   LPVCPSPSSCSATPKPRIPIPLR-SSFPSPLLHNRFFSQNAAFSLRN---------SLRT 55

Query: 58  SAAAFAVQE--TLEKTRESVMASSAKEMMPKIDKSGRL------------VVYAACLEGS 103
           S  A A  E   L K   +   +++   +PKIDK+GR             ++YAACLEG 
Sbjct: 56  STFALAQHEAPVLGKPDNN---NNSSPYLPKIDKTGRFCSPRAARELALSIIYAACLEGM 112

Query: 104 DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 163
           DP+RLFEKR+N+RRE GY+F++  LLEYNHMSFGGPPVT  + EEA+ELLR  EEESAIE
Sbjct: 113 DPVRLFEKRMNARREAGYKFNEERLLEYNHMSFGGPPVTVGSDEEANELLRHIEEESAIE 172

Query: 164 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL 223
           AEVL+APPKLVY+KL+LRFT+KLLVAV D WD+HV +I+K+ P  WK++PA +ILELSIL
Sbjct: 173 AEVLTAPPKLVYNKLILRFTKKLLVAVRDTWDSHVLVINKIAPQNWKNEPAAKILELSIL 232

Query: 224 HLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 272
           HLAMSE+ V+ TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF R LE
Sbjct: 233 HLAMSEMEVLETRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFFRELE 281

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	290
TAIR|locus:2131428	301	AT4G26370 [Arabidopsis thalian	0.975	0.940	0.59	1.5e-81
UNIPROTKB|P65582	140	nusB "N utilization substance	0.179	0.371	0.423	3.1e-05
UNIPROTKB|Q9KPU5	156	nusB "N utilization substance	0.406	0.756	0.309	7.1e-05
TIGR_CMR|VC_2267	156	VC_2267 "N utilization substan	0.406	0.756	0.309	7.1e-05
TIGR_CMR|CJE_0431	132	CJE_0431 "transcription antite	0.289	0.636	0.3	0.00018

TAIR|locus:2131428 AT4G26370 [Arabidopsis thaliana (taxid:3702)]

 Score = 818 (293.0 bits), Expect = 1.5e-81, P = 1.5e-81
 Identities = 177/300 (59%), Positives = 211/300 (70%)

Query:     3 VEATSSFLSCSSKTHFLFNLRASSSPSSWKK--FTQSANFAAKNRHVCRNERPNVSCSAA 60
             +E T S L   S ++  +   ++ SP S +   FT   +    N    R      S S+ 
Sbjct:     1 MEGTFSPLCLRSSSNLCY-FSSNVSPDSHRSIGFTLVDSLRPTNLVSLRTGNKRSSSSSL 59

Query:    61 AFAVQETLEKTRE-SVMASSAKEM-MPKIDKSGRL------------VVYAACLEGSDPI 106
                +  T    R  ++ A   K++ MPKIDKSGRL            ++YAACLEGSDPI
Sbjct:    60 RLFLSPTRSALRTPTISAEEVKDVPMPKIDKSGRLSSPRAARELALVILYAACLEGSDPI 119

Query:   107 RLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV 166
             RLFEKR+N+RREPGYEFDKSSLLEYNHMSFGGPPV TET EE DEL+R DE+ES IEAEV
Sbjct:   120 RLFEKRINARREPGYEFDKSSLLEYNHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEV 179

Query:   167 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLA 226
             LSAPPKLVYSKL+LRF +KLL AVVDKWD+HV II+K+ PP WK  PAGRILE SILHLA
Sbjct:   180 LSAPPKLVYSKLVLRFAKKLLAAVVDKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLA 239

Query:   227 MSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEV 286
             MSE+ V+ TRH IVINEAVDLAKRFCDG+APRIINGCLRTFV++   T+  +A +  +EV
Sbjct:   240 MSEVAVLETRHPIVINEAVDLAKRFCDGSAPRIINGCLRTFVKDRATTSTPQALELKQEV 299

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005739 "mitochondrion" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

UNIPROTKB|P65582 nusB "N utilization substance protein B homolog" [Streptococcus pneumoniae TIGR4 (taxid:170187)]

 Score = 104 (41.7 bits), Expect = 3.1e-05, P = 3.1e-05
 Identities = 22/52 (42%), Positives = 32/52 (61%)

Query:   217 ILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFV 268
             ++E ++L L + EIT   T   + +NEA++LAK F D  + R ING L  FV
Sbjct:    85 LVERNLLRLGVFEITSFDTPQLVAVNEAIELAKDFSDQKSARFINGLLSQFV 136

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q9KPU5 nusB "N utilization substance protein B homolog" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 109 (43.4 bits), Expect = 7.1e-05, P = 7.1e-05
 Identities = 39/126 (30%), Positives = 64/126 (50%)

Query:   141 VTTETVEEADE-LLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVH 199
             +T E V   +E  L S + +   E E  +A P L   +  + + R LL  VV     H  
Sbjct:    26 ITKENVATIEEQFLTSGKYD---EEEHRAAEPALAAPETDVSYFRDLLAGVVLN---HNE 79

Query:   200 IIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPR 258
             +  K+ P + +      ++EL++L LAM E+T      +++VINEA++LAK F    + +
Sbjct:    80 LDSKLRPFVSRPMQDLDMMELALLRLAMYEMTRREDVPYKVVINEAIELAKVFAAEDSHK 139

Query:   259 IINGCL 264
              +NG L
Sbjct:   140 FVNGVL 145

GO:0006353 "DNA-dependent transcription, termination" evidence=ISS

TIGR_CMR|VC_2267 VC_2267 "N utilization substance protein B" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 109 (43.4 bits), Expect = 7.1e-05, P = 7.1e-05
 Identities = 39/126 (30%), Positives = 64/126 (50%)

Query:   141 VTTETVEEADE-LLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVH 199
             +T E V   +E  L S + +   E E  +A P L   +  + + R LL  VV     H  
Sbjct:    26 ITKENVATIEEQFLTSGKYD---EEEHRAAEPALAAPETDVSYFRDLLAGVVLN---HNE 79

Query:   200 IIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPR 258
             +  K+ P + +      ++EL++L LAM E+T      +++VINEA++LAK F    + +
Sbjct:    80 LDSKLRPFVSRPMQDLDMMELALLRLAMYEMTRREDVPYKVVINEAIELAKVFAAEDSHK 139

Query:   259 IINGCL 264
              +NG L
Sbjct:   140 FVNGVL 145

GO:0006353 "DNA-dependent transcription, termination" evidence=ISS

TIGR_CMR|CJE_0431 CJE_0431 "transcription antitermination factor NusB" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 97 (39.2 bits), Expect = 0.00018, P = 0.00018
 Identities = 27/90 (30%), Positives = 45/90 (50%)

Query:   182 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQI 239
             FT  L   ++D    +++ ID+ +     D     +  +E +IL L   E+    T   I
Sbjct:    44 FTLNLYNGILD----NLNNIDETLNSFLNDNQITALGHVERAILRLGAYELLFTDTPSAI 99

Query:   240 VINEAVDLAKRFCDGAAPRIINGCLRTFVR 269
             VINEA++LAK   +  +P+ ING L   ++
Sbjct:   100 VINEAIELAKELANDNSPKFINGVLDALIK 129


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.129   0.369    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      290       290   0.00089  115 3  11 22  0.39    34
                                                     33  0.43    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  5
  No. of states in DFA:  618 (66 KB)
  Total size of DFA:  200 KB (2113 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  24.59u 0.10s 24.69t   Elapsed:  00:00:02
  Total cpu time:  24.59u 0.10s 24.69t   Elapsed:  00:00:02
  Start:  Sat May 11 02:03:38 2013   End:  Sat May 11 02:03:40 2013

GO:0006353 "DNA-dependent transcription, termination" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	290
cd00619	130	cd00619, Terminator_NusB, Transcription terminatio	2e-28
cd00447	129	cd00447, NusB_Sun, RNA binding domain of NusB (N p	5e-21
TIGR01951	129	TIGR01951, nusB, transcription antitermination fac	2e-10
pfam01029	126	pfam01029, NusB, NusB family	2e-09
PRK00202	137	PRK00202, nusB, transcription antitermination prot	9e-09
PRK09634	207	PRK09634, nusB, transcription antitermination prot	4e-08
COG0781	151	COG0781, NusB, Transcription termination factor [T	3e-06
PRK14902	444	PRK14902, PRK14902, 16S rRNA methyltransferase B;	5e-04

>gnl|CDD|238342 cd00619, Terminator_NusB, Transcription termination factor NusB (N protein-Utilization Substance B)

 Score =  105 bits (265), Expect = 2e-28
 Identities = 43/131 (32%), Positives = 68/131 (51%), Gaps = 4/131 (3%)

Query: 143 TETVEEADELLRSDEEESAIEAEVLSAPPKLVY-SKLLLRFTRKLLVAVVDKWDAHVHII 201
               E A + L + E    I AEV+S    L Y SK +L F  KL+  V++  +    +I
Sbjct: 2   RRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELI 61

Query: 202 DKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRII 260
           +K +     D+    I+E +IL LA+ E+  +    H +VINEA++LAKRF    + + +
Sbjct: 62  EKHLRNWSLDR--LAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFV 119

Query: 261 NGCLRTFVRNL 271
           NG L    ++L
Sbjct: 120 NGVLDKIAKDL 130

NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. Length = 130

>gnl|CDD|238253 cd00447, NusB_Sun, RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins

 Score = 85.9 bits (213), Expect = 5e-21
 Identities = 36/127 (28%), Positives = 56/127 (44%), Gaps = 5/127 (3%)

Query: 147 EEADELLRSDE-EESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVV 205
           E A + L   E         VLSA  KL  +K    F  +L+  V+        II  ++
Sbjct: 4   EIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLL 63

Query: 206 PPIWKDQPAGRILELSILHLAMSEI--TVVGTRHQIVINEAVDLAKRFCDGAAPRIINGC 263
                D+     ++ +IL L + E+   +      + INEAV+LAKRF D  + + +NG 
Sbjct: 64  KKWLLDR--LDKVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGV 121

Query: 264 LRTFVRN 270
           LR   + 
Sbjct: 122 LRRIAKE 128

This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the N-terminal non-catalytic RNA-binding domain with NusB. Length = 129

>gnl|CDD|233652 TIGR01951, nusB, transcription antitermination factor NusB

 Score = 57.1 bits (139), Expect = 2e-10
 Identities = 31/123 (25%), Positives = 58/123 (47%), Gaps = 10/123 (8%)

Query: 151 ELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWK 210
           +   S  +   I  E L         +    + R+L+  V++  +     ID+++ P  +
Sbjct: 14  QWELSGNDLEEIIEEFLEEEE---LDEEDREYFRELVRGVLENQEE----IDELISPHLE 66

Query: 211 DQPAGRI--LELSILHLAMSEIT-VVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF 267
           D    R+  ++ +IL LA  E+       +++VINEAV+LAK+F D  + + +NG L   
Sbjct: 67  DWTLERLDPVDRAILRLAAYELLYRPDVPYKVVINEAVELAKKFGDDDSHKFVNGVLDKI 126

Query: 268 VRN 270
            + 
Sbjct: 127 AKE 129

A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10 [Transcription, Transcription factors]. Length = 129

>gnl|CDD|216253 pfam01029, NusB, NusB family

 Score = 54.5 bits (132), Expect = 2e-09
 Identities = 32/126 (25%), Positives = 59/126 (46%), Gaps = 7/126 (5%)

Query: 147 EEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVP 206
           E A + L + EE  A   E+L    +    +    F  +L+  V+   +     +D ++ 
Sbjct: 5   ELALQALYAVEERGASLNELLDKLLEADLDERDRAFATELVYGVLRNLEE----LDALIE 60

Query: 207 PIWKDQPAGRI--LELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGC 263
            + ++ P  R+  ++ +IL L + E+  +      + INEAV+LAK+F    +   +NG 
Sbjct: 61  KLLENWPLERLDPVDRAILRLGLYELLYLDDIPPHVAINEAVELAKKFGGEKSAGFVNGV 120

Query: 264 LRTFVR 269
           LR   R
Sbjct: 121 LRKIAR 126

The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. Length = 126

>gnl|CDD|234686 PRK00202, nusB, transcription antitermination protein NusB; Reviewed

 Score = 52.5 bits (127), Expect = 9e-09
 Identities = 36/123 (29%), Positives = 62/123 (50%), Gaps = 11/123 (8%)

Query: 153 LRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQ 212
           L  ++    IEA++L       Y K    + R L+  VV+        +D+++ P  KD 
Sbjct: 19  LSGNDIAEIIEAQLLEEQ----YDKADPAYFRSLVRGVVENQAE----LDELISPYLKDW 70

Query: 213 PAGRI--LELSILHLAMSEIT-VVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 269
              R+  +E +IL LA+ E+       +++VINEA++LAK+F D  + + +NG L    +
Sbjct: 71  TLERLDPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAK 130

Query: 270 NLE 272
            L 
Sbjct: 131 ELR 133

Length = 137

>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB; Provisional

 Score = 52.2 bits (126), Expect = 4e-08
 Identities = 23/48 (47%), Positives = 28/48 (58%)

Query: 222 ILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 269
           IL LA+ EI  + T   + INEAV+LAKR+ D    R ING LR    
Sbjct: 153 ILRLAVVEILFLNTPAAVAINEAVELAKRYSDEQGRRFINGVLRRLQD 200

Length = 207

>gnl|CDD|223852 COG0781, NusB, Transcription termination factor [Transcription]

 Score = 45.8 bits (109), Expect = 3e-06
 Identities = 30/144 (20%), Positives = 61/144 (42%), Gaps = 22/144 (15%)

Query: 133 HMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVD 192
                G     + +E+ +E    +E +  +                   + R L+  V++
Sbjct: 23  QWELSGSVSAEDILEDIEEEFVENELDIELAD---------------SEYFRSLVKGVLE 67

Query: 193 KWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVG-TRHQIVINEAVDLAK 249
               +   +D+++ P  K     R+  +E +IL LA+ E+       +++VINEA++LAK
Sbjct: 68  ----NQEELDELISPHLKKWSLERLDLVERAILRLALYELLFRDDVPYKVVINEAIELAK 123

Query: 250 RFCDGAAPRIINGCLRTFVRNLEG 273
           +F    + + +NG L    + L  
Sbjct: 124 KFSGEDSHKFVNGVLDKIAKKLRP 147

Length = 151

>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional

 Score = 40.9 bits (97), Expect = 5e-04
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 240 VINEAVDLAKRFCDGAAPRIINGCLRTFVRN 270
            +NEAV++AK+       + +NG LR  +R 
Sbjct: 98  AVNEAVEIAKKRGHKGIAKFVNGVLRNILRE 128

Length = 444

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	290
PF01029	134	NusB: NusB family; InterPro: IPR006027 This domain	99.96
PRK00202	137	nusB transcription antitermination protein NusB; R	99.95
cd00619	130	Terminator_NusB Transcription termination factor N	99.95
TIGR01951	129	nusB transcription antitermination factor NusB. A	99.95
COG0781	151	NusB Transcription termination factor [Transcripti	99.95
cd00620	126	Methyltransferase_Sun N-terminal RNA binding domai	99.94
cd00447	129	NusB_Sun RNA binding domain of NusB (N protein-Uti	99.93
PRK09634	207	nusB transcription antitermination protein NusB; P	99.91
PRK10901	427	16S rRNA methyltransferase B; Provisional	99.89
PRK14904	445	16S rRNA methyltransferase B; Provisional	99.87
PRK14901	434	16S rRNA methyltransferase B; Provisional	99.87
PRK14902	444	16S rRNA methyltransferase B; Provisional	99.86
TIGR00563	426	rsmB ribosomal RNA small subunit methyltransferase	99.84
PRK14903	431	16S rRNA methyltransferase B; Provisional	99.83

>PF01029 NusB: NusB family; InterPro: IPR006027 This domain is found in a number of functionally different proteins: NusB a prokaryotic transcription factor involved in antitermination TIM44, the mitochondrial inner membrane translocase subunit RsmB, the 16S rRNA m5C967 methyltransferase NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site

Probab=99.96  E-value=2e-29  Score=209.46  Aligned_cols=124  Identities=27%  Similarity=0.352  Sum_probs=105.5

Q ss_pred             HHHHHHHHHHHhhh-------hcchhHHHHhc-CCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcC
Q 022911          144 ETVEEADELLRSDE-------EESAIEAEVLS-APPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAG  215 (290)
Q Consensus       144 ~aRe~AlqlL~~ve-------~~~~l~~~lL~-~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~  215 (290)
                      ++|+.|+|+|++++       ..+......+. ......+++.|++|+++|++|++++++.||++|++++ ++|+++|++
T Consensus         2 ~aR~~A~q~L~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~d~~~~~~lv~gv~~~~~~ld~~i~~~~-~~~~~~rl~   80 (134)
T PF01029_consen    2 KARELALQALYQVEFNDEEDEEEGQFLDEALEEELEESELSEEDRAFARELVYGVLRNKEELDALISKLL-KNWPLERLP   80 (134)
T ss_dssp             HHHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHHHHTHHHHHHHHHHTS-TSSTGGGSG
T ss_pred             hHHHHHHHHHHHHHccCCchhhhhhhHHHHHhhcccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCccccC
Confidence            58999999999993       32222222222 0001137899999999999999999999999999987 689999999


Q ss_pred             hHHHHHHHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHh
Q 022911          216 RILELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR  269 (290)
Q Consensus       216 ~vLdraILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r  269 (290)
                      ++ +++|||+|+|||+|+ ++|++++|||||++||+|+++++++|||||||+++|
T Consensus        81 ~~-~~~iLrla~~El~~~~~~p~~v~InEaVelak~~~~~~~~~fVNaVL~~~~R  134 (134)
T PF01029_consen   81 PV-DRAILRLAIYELLFLDDIPPHVAINEAVELAKKYGDEKSAGFVNAVLRRIAR  134 (134)
T ss_dssp             HH-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHH
T ss_pred             HH-HHHHHHHHHHHHHhcCCCCccchHHHHHHHHHHhCCCCcchhHHHHHHHhhC
Confidence            98 799999999999998 899999999999999999999999999999999986

Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. An N-terminal arginine-rich sequence is the probable RNA binding site, exhibiting aromatic residues as potential stacking partners for the RNA bases. The RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. In certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes [, ]. The antitermination proteins of E. coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle.; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1SQG_A 1SQF_A 3IMQ_A 3D3C_C 3D3B_A 1EY1_A 1EYV_A 1TZV_A 1TZT_B 1TZX_B ....

>PRK00202 nusB transcription antitermination protein NusB; Reviewed

Probab=99.95  E-value=3.8e-28  Score=203.64  Aligned_cols=130  Identities=27%  Similarity=0.344  Sum_probs=111.3

Q ss_pred             HHHHHHHHHHHHhhhhcchhHHHHhcCC-CCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHH
Q 022911          143 TETVEEADELLRSDEEESAIEAEVLSAP-PKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS  221 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~l~~~lL~~~-~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdra  221 (290)
                      ..+|+.|+++|++++.++.....++... ....+++.|++|+++|++||+++++.||++|++++ ++|++++++++ +++
T Consensus         4 ~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~~~~~~~d~~~~~~lv~gvlr~~~~lD~ii~~~l-~~~~~~~l~~~-~~~   81 (137)
T PRK00202          4 RKAREAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYL-KDWTLERLDPV-ERA   81 (137)
T ss_pred             HHHHHHHHHHHHHHHccCCCHHHHHHHHHHhcccchhhHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCHHHhhHH-HHH
Confidence            3589999999999987554332222221 11136788999999999999999999999999999 56999999998 699


Q ss_pred             HHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhcc
Q 022911          222 ILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT  274 (290)
Q Consensus       222 ILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~  274 (290)
                      |||+|+|||+|+ ++|++++|||||++||+|+++++++|||||||++.++....
T Consensus        82 iLr~a~~Ell~~~~~p~~~vinEaV~lak~~~~~~~~~fVNaVLr~i~r~~~~~  135 (137)
T PRK00202         82 ILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPA  135 (137)
T ss_pred             HHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCCcchhHHHHHHHHHHHhhcc
Confidence            999999999998 79999999999999999999999999999999999987543

>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B)

Probab=99.95  E-value=3.3e-28  Score=201.67  Aligned_cols=126  Identities=31%  Similarity=0.391  Sum_probs=109.1

Q ss_pred             HHHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHH
Q 022911          143 TETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS  221 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdra  221 (290)
                      ..+|+.|+++|++++.++.....++.... ...+++.|++|+++|++|++++++.+|++|++++ ++|++++++++ +++
T Consensus         2 ~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~~~~~~~d~~~~~~lv~gvlr~~~~ld~ii~~~l-~~~~~~~l~~~-~~~   79 (130)
T cd00619           2 RRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHL-RNWSLDRLAIV-ERA   79 (130)
T ss_pred             hHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCCHHHhhHH-HHH
Confidence            35799999999999876544333432211 1125678999999999999999999999999999 58989999998 699


Q ss_pred             HHHHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911          222 ILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN  270 (290)
Q Consensus       222 ILRlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~  270 (290)
                      |||+|+|||+|++ +|++++|||||++||+|+++++++|||||||++.++
T Consensus        80 iLria~~el~~~~~~p~~~vinEaV~lak~~~~~~~~~fVNaVLr~i~r~  129 (130)
T cd00619          80 ILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKD  129 (130)
T ss_pred             HHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCcchhHHHHHHHHHhhc
Confidence            9999999999987 999999999999999999999999999999999875

NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.

>TIGR01951 nusB transcription antitermination factor NusB

Probab=99.95  E-value=7.3e-28  Score=199.12  Aligned_cols=125  Identities=22%  Similarity=0.263  Sum_probs=107.8

Q ss_pred             HHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHH
Q 022911          144 ETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSI  222 (290)
Q Consensus       144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraI  222 (290)
                      .+|+.|+++|++++.++.....++.... ...+++.|++|+++|++|++++++.||++|+++++ +|++++++++ +++|
T Consensus         3 ~~R~~a~~~l~~~~~~~~~~~~~l~~~~~~~~l~~~d~~~~~~lv~~~lr~~~~ld~~i~~~~~-~~~~~~l~~~-~~~i   80 (129)
T TIGR01951         3 KARELALQALYQWELSGNDVEEIIEEFLEERELDEEDREYFLELVRGVLENQEEIDELISPHLK-DWSLERLDPV-DRAI   80 (129)
T ss_pred             HHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhHHHHHHHHHHHhc-CCCHHHhhHH-HHHH
Confidence            4799999999999865543332332211 11367889999999999999999999999999994 8999999998 6999


Q ss_pred             HHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911          223 LHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN  270 (290)
Q Consensus       223 LRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~  270 (290)
                      ||+|+|||+|+ ++|++++|||||++||+|+++++++|||||||++++.
T Consensus        81 Lr~a~~el~~~~~~p~~avineaV~lak~~~~~~~~~fVNaVLr~i~r~  129 (129)
T TIGR01951        81 LRLAAYELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAKE  129 (129)
T ss_pred             HHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCCchhhHHHHHHHHhhC
Confidence            99999999998 7999999999999999999999999999999999863

A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10.

>COG0781 NusB Transcription termination factor [Transcription]

Probab=99.95  E-value=1.2e-27  Score=206.03  Aligned_cols=131  Identities=23%  Similarity=0.298  Sum_probs=109.4

Q ss_pred             HHHHHHHHHHHHhhhhcch-----hHHHHhcCCC--CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcC
Q 022911          143 TETVEEADELLRSDEEESA-----IEAEVLSAPP--KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAG  215 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~-----l~~~lL~~~~--~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~  215 (290)
                      ..+|+.|+|+||+++.++.     ....+.....  .......+..|+..|+.||.+|...||.+|.+++ ++|+++|++
T Consensus        11 ~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~lv~gv~~~~~~iD~~I~~~L-~~w~~~rL~   89 (151)
T COG0781          11 RQARELAVQALYQWELSGSVSAEDILEDIEEEFVENELDIELADSEYFRSLVKGVLENQEELDELISPHL-KKWSLERLD   89 (151)
T ss_pred             HHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHhhcccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH-ccCCHHHhh
Confidence            4699999999999998544     1111221110  0012227899999999999999999999999999 569999999


Q ss_pred             hHHHHHHHHHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhccc
Q 022911          216 RILELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA  275 (290)
Q Consensus       216 ~vLdraILRlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~~  275 (290)
                      .+ ||+|||+|+|||+|.+ +|..|+|||||||||.|+++++++||||||+++++......
T Consensus        90 ~v-erAILRla~yEl~~~~dvP~~VvInEaielaK~f~~e~s~kFINgVLd~i~~~~~~~~  149 (151)
T COG0781          90 LV-ERAILRLALYELLFRDDVPYKVVINEAIELAKKFSGEDSHKFVNGVLDKIAKKLRPKE  149 (151)
T ss_pred             HH-HHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHhCCCCchHHHHHHHHHHHHHhhhhc
Confidence            98 9999999999999965 99999999999999999999999999999999998776543

>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun

Probab=99.94  E-value=4.6e-27  Score=194.53  Aligned_cols=123  Identities=22%  Similarity=0.182  Sum_probs=103.1

Q ss_pred             HHHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHHH
Q 022911          145 TVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILH  224 (290)
Q Consensus       145 aRe~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraILR  224 (290)
                      +|+.|+++|+++..++.....++........++.|++|+++|++|++++++.||++|+++++ +| ..+++++ +++|||
T Consensus         3 ~R~~A~~~L~~v~~~~~~~~~~l~~~~~~~~~~~d~~~~~~lv~g~~r~~~~ld~~i~~~l~-~~-~~~~~~~-~~~iLr   79 (126)
T cd00620           3 ARSTAAEVLRDVLQRGASLNAVLSALQKKDKSDRDRGLATELVYGTLRWLALLDWIINPLLK-KP-DVGKDPD-VRNLLR   79 (126)
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhC-CC-ccccCHH-HHHHHH
Confidence            69999999999977554333333221100125789999999999999999999999999994 34 4589998 699999


Q ss_pred             HHHHHhhccCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911          225 LAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN  270 (290)
Q Consensus       225 lAiyELlf~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~  270 (290)
                      +|+|||+|+++|++++|||||++||+|+++++++|||||||++.|+
T Consensus        80 ~a~~el~~~~~p~~avvneaVelak~~~~~~~~~fVNaVLr~i~r~  125 (126)
T cd00620          80 LGLYQLLYLDVPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRFERE  125 (126)
T ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHhCCCchhhHHHHHHHHHhcc
Confidence            9999999988999999999999999999999999999999999874

The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.

>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins

Probab=99.93  E-value=1.5e-25  Score=184.80  Aligned_cols=124  Identities=29%  Similarity=0.357  Sum_probs=105.4

Q ss_pred             HHHHHHHHHHhhhhc-chhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911          145 TVEEADELLRSDEEE-SAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL  223 (290)
Q Consensus       145 aRe~AlqlL~~ve~~-~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL  223 (290)
                      +|+.|+++|++++.. +.....++.......+++.|++|+++|++||+++++.||++|++++ ++|+++|++.+ ++.||
T Consensus         2 ~R~~a~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~gv~r~~~~ld~~i~~~~-~~~~~~r~~~~-~~~il   79 (129)
T cd00447           2 AREIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLL-KKWLLDRLDKV-DRAIL   79 (129)
T ss_pred             HHHHHHHHHHHHHhcCCCCHHHHHHHHHHcccchhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCChhhhhHH-HHHHH
Confidence            699999999999765 4333323222111136678999999999999999999999999999 68999999998 89999


Q ss_pred             HHHHHHhhcc--CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911          224 HLAMSEITVV--GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN  270 (290)
Q Consensus       224 RlAiyELlf~--diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~  270 (290)
                      +++.+|+.+.  ++|++++|||||++||+|+++++++|||||||++.++
T Consensus        80 ~l~~~el~~~~~~~p~~~vineaVelak~~~~~~~~~fVNaVLr~~~r~  128 (129)
T cd00447          80 RLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKE  128 (129)
T ss_pred             HHHHHHHHhCcCCCCchhHHHHHHHHHHHHCCCCcchhHHHHHHHHhhc
Confidence            9999998876  5999999999999999999999999999999999875

This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the

>PRK09634 nusB transcription antitermination protein NusB; Provisional

Probab=99.91  E-value=4.3e-24  Score=192.34  Aligned_cols=93  Identities=33%  Similarity=0.489  Sum_probs=90.3

Q ss_pred             HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHHHHHHHHhhccCCChhhHHHHHHHHHHhhCCCCC
Q 022911          177 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAA  256 (290)
Q Consensus       177 ~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraILRlAiyELlf~diP~~vaINEAVeLAK~y~~~~s  256 (290)
                      +++++|+++|++||+++++.||++|++++ ++|+++|++.+ |++|||+|+|||+|+++|++++|||||++||+|+++++
T Consensus       110 ~~~r~~a~~Lv~gvlr~~~~LD~iI~~~l-~~W~l~rL~~i-dr~ILRlavyELl~l~~P~~vaINEAVeLAK~~~~~~~  187 (207)
T PRK09634        110 EEVREYALERIGAVIRNRKEIDQLLDTVM-VGWQLKRLPRI-DRDILRLAVVEILFLNTPAAVAINEAVELAKRYSDEQG  187 (207)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHh-ccccccCCCHH-HHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHhCCCcc
Confidence            78999999999999999999999999999 79999999998 89999999999999999999999999999999999999


Q ss_pred             CCchHHHHhhHHhhh
Q 022911          257 PRIINGCLRTFVRNL  271 (290)
Q Consensus       257 ~~FVNaVLr~i~r~~  271 (290)
                      ++|||||||++.+..
T Consensus       188 ~~FVNaVLrri~r~~  202 (207)
T PRK09634        188 RRFINGVLRRLQDAL  202 (207)
T ss_pred             cchHHHHHHHHHHHh
Confidence            999999999999876

>PRK10901 16S rRNA methyltransferase B; Provisional

Probab=99.89  E-value=2.8e-23  Score=203.45  Aligned_cols=125  Identities=17%  Similarity=0.152  Sum_probs=108.9

Q ss_pred             HHHHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911          144 ETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL  223 (290)
Q Consensus       144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL  223 (290)
                      .+|+.|+++|++++.++.....++..... .+++.|++|+++|++||++++..||++|++++  +|++++++++ +++||
T Consensus         3 ~~R~~a~~~L~~~~~~~~~~~~~l~~~~~-~l~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~--~~~~~~l~~~-~r~iL   78 (427)
T PRK10901          3 NLRALAAAAILQVVDQGQSLSAALPALQQ-KVSDKDRALLQELCYGVLRRLPRLEWLIAQLL--AKPLKGKQRI-VHALL   78 (427)
T ss_pred             hHHHHHHHHHHHHHHcCCcHHHHHHHHHh-hCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHh--CCCccccCHH-HHHHH
Confidence            47999999999998766544334332111 36788999999999999999999999999998  3688999998 69999


Q ss_pred             HHHHHHhhccCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911          224 HLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE  272 (290)
Q Consensus       224 RlAiyELlf~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~  272 (290)
                      |||+|||+|+++|++++|||||++||+|+++++++|||||||++.++.+
T Consensus        79 rla~yell~~~iP~~a~vneaVelak~~~~~~~~~fVNaVLr~i~~~~~  127 (427)
T PRK10901         79 LVGLYQLLYTRIPAHAAVDETVEAAKALKRPWAKGLVNAVLRRFQREQE  127 (427)
T ss_pred             HHHHHHHhccCCCcchHHHHHHHHHHhcCCccchhhHHHHHHHhhhhhh
Confidence            9999999998899999999999999999999999999999999998643

>PRK14904 16S rRNA methyltransferase B; Provisional

Probab=99.87  E-value=2.6e-22  Score=197.62  Aligned_cols=126  Identities=17%  Similarity=0.180  Sum_probs=108.7

Q ss_pred             HHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHH
Q 022911          144 ETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSI  222 (290)
Q Consensus       144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraI  222 (290)
                      .+|+.|+++|++++.++.....++.... ...+++.|++|+++||+||++++..||++|++++  +|++++++++ +++|
T Consensus         3 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~~~l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~--~~~~~rl~~~-~r~i   79 (445)
T PRK14904          3 TARELALQVLQELETGERKSDTLLHRMLERSSLERNDRALATELVNGVLRYRLQLDFIISRFY--HHDLEKAAPV-LKNI   79 (445)
T ss_pred             hHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHc--CCChhhCCHH-HHHH
Confidence            5799999999999876554333332211 1137788999999999999999999999999998  3799999998 7999


Q ss_pred             HHHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911          223 LHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE  272 (290)
Q Consensus       223 LRlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~  272 (290)
                      ||+|+|||+|++ +|++++|||||++||+|+++++++|||||||+++++..
T Consensus        80 Lrla~~ell~~~~~p~~a~vneaVelak~~~~~~~~~fVNgVLr~i~~~~~  130 (445)
T PRK14904         80 LRLGVYQLLFLDRVPRWAAVNECVKLARKYKGEHMAKLVNGVLRNISPETI  130 (445)
T ss_pred             HHHHHHHHHhCCCCCCeeeHHHHHHHHHHhCCCccccchHHHHHHHHHhhc
Confidence            999999999974 99999999999999999999999999999999999753

>PRK14901 16S rRNA methyltransferase B; Provisional

Probab=99.87  E-value=4.7e-22  Score=195.21  Aligned_cols=124  Identities=20%  Similarity=0.191  Sum_probs=105.0

Q ss_pred             HHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911          145 TVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL  223 (290)
Q Consensus       145 aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL  223 (290)
                      +|+.|+++|++++.+ .....++.... ...+++.|++|+++||+||+++++.||++|++++ + |+..+++++ +|+||
T Consensus         3 ~R~~A~~~L~~i~~~-~~~~~~l~~~~~~~~l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~-~-~~~~~l~~~-~r~iL   78 (434)
T PRK14901          3 ARQLAWEILQAVARG-AYADVALERVLRKYPLSGADRALVTELVYGCIRRRRTLDAWIDQLG-K-KPAHKQPPD-LRWLL   78 (434)
T ss_pred             HHHHHHHHHHHHHcC-CchHHHHHHHHHhcCCChhHHHHHHHHHHHHHHhHHHHHHHHHHhc-C-CChhhcCHH-HHHHH
Confidence            799999999999875 32222222210 1136788999999999999999999999999997 3 666779998 69999


Q ss_pred             HHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911          224 HLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE  272 (290)
Q Consensus       224 RlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~  272 (290)
                      |+|+|||+|++ +|++++|||||++||+|+++++++|||||||++.++..
T Consensus        79 rla~yel~~~~~~p~~aavneaVelak~~~~~~~~~fVNgVLr~~~r~~~  128 (434)
T PRK14901         79 HLGLYQLRYMDRIPASAAVNTTVELAKQNGLGGLAGVVNGILRQYLRARE  128 (434)
T ss_pred             HHHHHHHHhCccCCcHHHHHHHHHHHHHcCchhhhhhcCHHHHHHHHhhh
Confidence            99999999975 99999999999999999999999999999999999744

>PRK14902 16S rRNA methyltransferase B; Provisional

Probab=99.86  E-value=1.2e-21  Score=192.65  Aligned_cols=124  Identities=18%  Similarity=0.179  Sum_probs=106.2

Q ss_pred             HHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHH
Q 022911          144 ETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSI  222 (290)
Q Consensus       144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraI  222 (290)
                      .+|+.|+++|++++.++.....++.... ...+++.|++|+++||+|++++++.||++|+++++ +  +++++++ +|+|
T Consensus         4 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~~~l~~~d~~~~~~lv~g~lr~~~~ld~~i~~~~~-~--~~~l~~~-~r~i   79 (444)
T PRK14902          4 NARELALEVLIKVENNGAYSNIALNKVLKKSELSDKDKALLTELVYGTIQRKLTLDYYLAPFIK-K--RKKLDPW-VRNL   79 (444)
T ss_pred             cHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHhHHHHHHHHHHHhh-h--hhhCCHH-HHHH
Confidence            5899999999999876543322322210 11378889999999999999999999999999994 3  7899998 6999


Q ss_pred             HHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhh
Q 022911          223 LHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNL  271 (290)
Q Consensus       223 LRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~  271 (290)
                      ||+|+|||+|. ++|++++|||||++||+|+++++++|||||||++.++.
T Consensus        80 Lrla~~el~~~~~~p~~~~ineav~lak~~~~~~~~~fVNaVL~~i~~~~  129 (444)
T PRK14902         80 LRMSLYQLLYLDKVPDHAAVNEAVEIAKKRGHKGIAKFVNGVLRNILREG  129 (444)
T ss_pred             HHHHHHHHHhccCCCCceeHHHHHHHHHHhCCCchhHHHHHHHHHHhhcc
Confidence            99999999996 59999999999999999999999999999999999864

>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB

Probab=99.84  E-value=9.3e-21  Score=185.54  Aligned_cols=121  Identities=18%  Similarity=0.126  Sum_probs=102.9

Q ss_pred             HHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHHHH
Q 022911          146 VEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHL  225 (290)
Q Consensus       146 Re~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraILRl  225 (290)
                      |+.|+++|++++.++.....++..  ...+++.|++|+++||+||++++..||++|+++++  |++++++++ .+ +||+
T Consensus         1 R~~A~~~L~~~~~~~~~~~~~~~~--~~~l~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~~--~~~~~l~~~-~~-~L~~   74 (426)
T TIGR00563         1 RSIAAQALEQLEQGQSLSNLLPPL--QQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMD--RPMKGKPRT-VH-YLIL   74 (426)
T ss_pred             CHHHHHHHHHHHcCCchHHHHHhh--hcCCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhC--CCccccCHH-HH-HHHH
Confidence            689999999998776654444332  22478899999999999999999999999999983  677888887 46 8888


Q ss_pred             HHHHhhc-cCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911          226 AMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE  272 (290)
Q Consensus       226 AiyELlf-~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~  272 (290)
                      ++||++| +++|++++|||||++||+|+++++++|||||||++.++.+
T Consensus        75 ~~~e~l~~~~~p~~aainEaVelaK~~~~~~~~~fVNgVLr~i~r~~~  122 (426)
T TIGR00563        75 VGLYQLLYTRIPAHAAVAETVEGAKAIKRKGLKGLVNGVLRRFQREQE  122 (426)
T ss_pred             HHHHHHhcCCCCCEehHHHHHHHHHhcCCccchhhHHHHHHHHhhcch
Confidence            8888765 6899999999999999999999999999999999999643

The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.

>PRK14903 16S rRNA methyltransferase B; Provisional

Probab=99.83  E-value=1.1e-20  Score=185.91  Aligned_cols=118  Identities=19%  Similarity=0.153  Sum_probs=100.5

Q ss_pred             HHHHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911          144 ETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL  223 (290)
Q Consensus       144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL  223 (290)
                      .+|+.|+++|.++..++......+..... .+++.|++|+++||+||+++++.||++|++++ ++|   +++++ +|+||
T Consensus         4 ~~R~~A~~~L~~v~~~~~~~~~~l~~~~~-~l~~~d~~~~~~lv~gvlr~~~~lD~~i~~~~-~~~---~l~~~-~r~iL   77 (431)
T PRK14903          4 NVRLLAYRLLRKYEKEKFIFREDVDSVLS-FLDDKDRRFFKELVWGVVRKEELLDWYINQLL-KKK---DIPPA-VRVAL   77 (431)
T ss_pred             CHHHHHHHHHHHHHhCCCchHHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCC---CCCHH-HHHHH
Confidence            57999999999998766433333332111 37899999999999999999999999999999 567   58888 59999


Q ss_pred             HHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911          224 HLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN  270 (290)
Q Consensus       224 RlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~  270 (290)
                      |+|+|||+|++ +|++++|||||++||++   ++++|||||||++.++
T Consensus        78 r~~~yel~~~~~~p~~aavneaV~lak~~---~~~~fVNaVLr~~~r~  122 (431)
T PRK14903         78 RMGAYQLLFMNSVPDYAAVSETVKLVKNE---NFKKLVNAVLRRLRTV  122 (431)
T ss_pred             HHHHHHHHhccCCCcceeHHHHHHHHhcc---chHHHHHHHHHHHHHh
Confidence            99999999987 79999999999999986   5679999999999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	290
3r2d_A	149	Protein NUSB, N utilization substance protein B; c	5e-11
3d3b_A	141	Protein NUSB, N utilization substance protein B; N	2e-10
1eyv_A	156	NUSB protein, N-utilizing substance protein B homo	2e-10
1tzv_A	142	NUSB protein, N utilization substance protein B ho	3e-10
1sqg_A	429	SUN protein, FMU protein; rossmann-fold, mixed bet	3e-04

>3r2d_A Protein NUSB, N utilization substance protein B; cross species NUSB-NUSE-RNA interaction; 2.20A {Aquifex aeolicus} PDB: 2jr0_A 3r2c_A* Length = 149

 Score = 58.9 bits (143), Expect = 5e-11
 Identities = 23/107 (21%), Positives = 46/107 (42%), Gaps = 7/107 (6%)

Query: 182 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRH-Q 238
           + +KL+   V   +     ID ++    K     R+  +E + L L ++E+  + ++   
Sbjct: 47  YAKKLVDTAVRHIEE----IDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPG 102

Query: 239 IVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKE 285
            V  + VDL K++ D  A + +NG L    +    ++  E      E
Sbjct: 103 RVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKEEKPSLKSE 149

>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT site, phage lambda, lambdan antitermina antitermination; HET: NHE; 1.30A {Escherichia coli} PDB: 3d3c_A 3imq_A 1ey1_A Length = 141

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 22/124 (17%), Positives = 52/124 (41%), Gaps = 11/124 (8%)

Query: 151 ELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWK 210
               S  + + +E + L+         + + + R+LL  V         ++   +     
Sbjct: 21  SWQLSQNDIADVEYQFLAEQD---VKDVDVLYFRELLAGVATNTAYLDGLMKPYL----- 72

Query: 211 DQPAGRI--LELSILHLAMSEIT-VVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF 267
            +    +  +E ++L +A+ E++      +++ INEA++LAK F    + + +NG L   
Sbjct: 73  SRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKA 132

Query: 268 VRNL 271
              +
Sbjct: 133 APVI 136

>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

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 20/121 (16%), Positives = 43/121 (35%), Gaps = 7/121 (5%)

Query: 155 SDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPA 214
                + +     +          L  +T  +   V +        ID ++    +    
Sbjct: 27  RGISAAEVVDTRAALAEAKPDIARLHPYTAAVARGVSEHAAH----IDDLITAHLRGWTL 82

Query: 215 GRI--LELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNL 271
            R+  ++ +IL +++ E+         +V++EAV LAK      +P  +NG L   +   
Sbjct: 83  DRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAKELSTDDSPGFVNGVLGQVMLVT 142

Query: 272 E 272
            
Sbjct: 143 P 143

>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

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 26/129 (20%), Positives = 52/129 (40%), Gaps = 11/129 (8%)

Query: 153 LRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQ 212
            R DE+   I  E+L       Y K      R+ +  + +        ID ++    +  
Sbjct: 21  FRRDEDLEQILEEILDET----YDKKAKEDARRYIRGIKENLSM----IDDLISRYLEKW 72

Query: 213 PAGRI--LELSILHLAMSEIT-VVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 269
              R+  ++ ++L LA  E+        ++ I+EA+++AKR+    + + +NG L    +
Sbjct: 73  SLNRLSVVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAKRYGTENSGKFVNGILDRIAK 132

Query: 270 NLEGTANIE 278
                   E
Sbjct: 133 EHAPKEKFE 141

>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

 Score = 41.0 bits (97), Expect = 3e-04
 Identities = 11/33 (33%), Positives = 14/33 (42%)

Query: 240 VINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 272
            + E V+ A          +ING LR F R  E
Sbjct: 98  ALAETVEGAIAIKRPQLKGLINGVLRQFQRQQE 130

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	290
1tzv_A	142	NUSB protein, N utilization substance protein B ho	99.97
3d3b_A	141	Protein NUSB, N utilization substance protein B; N	99.97
3r2d_A	149	Protein NUSB, N utilization substance protein B; c	99.96
1eyv_A	156	NUSB protein, N-utilizing substance protein B homo	99.95
1sqg_A	429	SUN protein, FMU protein; rossmann-fold, mixed bet	99.85
2yxl_A	450	PH0851 protein, 450AA long hypothetical FMU protei	99.81

>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*

Probab=99.97  E-value=3e-31  Score=223.08  Aligned_cols=131  Identities=16%  Similarity=0.222  Sum_probs=112.8

Q ss_pred             HHHHHHHHHHHHhhhhcch-hHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHH
Q 022911          143 TETVEEADELLRSDEEESA-IEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS  221 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~-l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdra  221 (290)
                      ..+|+.|+++|++++.++. ....++.......+++.|++|+++|++||+++++.||++|++++ ++|++++++++ +++
T Consensus         6 ~~aR~~A~~~L~~~~~~~~~~~~~~l~~~~~~~l~~~d~~~~~~Lv~gvl~~~~~lD~~I~~~l-~~w~l~rl~~~-~r~   83 (142)
T 1tzv_A            6 RRMRLAVFKALFQHEFRRDEDLEQILEEILDETYDKKAKEDARRYIRGIKENLSMIDDLISRYL-EKWSLNRLSVV-DRN   83 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCTTSCHHHHHHHHCCTTSCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC-SSSCGGGSCHH-HHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCChHHCCHH-HHH
Confidence            3689999999999987655 33333221100237889999999999999999999999999999 57999999998 799


Q ss_pred             HHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhccc
Q 022911          222 ILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA  275 (290)
Q Consensus       222 ILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~~  275 (290)
                      |||+|+|||+|. ++|++|+|||||++||+|+++++++|||||||++.++.+..+
T Consensus        84 iLrla~yEl~~~~~iP~~vaInEaVelaK~~~~~~~~~fVNgVL~~i~r~~~~~~  138 (142)
T 1tzv_A           84 VLRLATYELLFEKDIPIEVTIDEAIEIAKRYGTENSGKFVNGILDRIAKEHAPKE  138 (142)
T ss_dssp             HHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHCCGG
T ss_pred             HHHHHHHHHHhcCCCCchhHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHhcccc
Confidence            999999999996 699999999999999999999999999999999999876543

>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT site, phage lambda, lambdan antitermina antitermination; HET: NHE; 1.30A {Escherichia coli} PDB: 3d3c_A 3imq_A 1ey1_A

Probab=99.97  E-value=1.6e-30  Score=218.46  Aligned_cols=126  Identities=21%  Similarity=0.250  Sum_probs=109.2

Q ss_pred             HHHHHHHHHHHHhhhhcch-hHH---HHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHH
Q 022911          143 TETVEEADELLRSDEEESA-IEA---EVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRIL  218 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~-l~~---~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vL  218 (290)
                      ..+|+.|+++|++++.++. ...   .++...   .+++.|++|+++|++||+++++.||++|++++ + |++++++++ 
T Consensus         9 ~~aR~~A~~~L~~~~~~~~~~~~~~~~~~~~~---~l~~~d~~~~~~Lv~gvl~~~~~lD~~I~~~l-~-~~l~rl~~~-   82 (141)
T 3d3b_A            9 RRARECAVQALYSWQLSQNDIADVEYQFLAEQ---DVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-S-RLLEELGQV-   82 (141)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHS---CCTTSCHHHHHHHHHHHHHTHHHHHHHHGGGG-T-TCSSCCCHH-
T ss_pred             HHHHHHHHHHHHHHHccCCCHHHHHHHHHHhc---cCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHc-C-CCHHHcCHH-
Confidence            3689999999999976543 222   222211   25678999999999999999999999999999 4 999999998 


Q ss_pred             HHHHHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhcc
Q 022911          219 ELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT  274 (290)
Q Consensus       219 draILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~  274 (290)
                      +++|||+|+|||+|+ ++|++|+|||||++||+|+++++++|||||||+++++++..
T Consensus        83 ~r~iLrla~yEll~~~~iP~~vaInEaVelaK~~~~~~~~~fVNgVLr~i~r~~~~~  139 (141)
T 3d3b_A           83 EKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPN  139 (141)
T ss_dssp             HHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCTTHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHhCCCCCchhhHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhhc
Confidence            799999999999996 79999999999999999999999999999999999987654

>3r2d_A Protein NUSB, N utilization substance protein B; cross species NUSB-NUSE-RNA interaction; 2.20A {Aquifex aeolicus} PDB: 2jr0_A 3r2c_A* 4eya_A

Probab=99.96  E-value=8e-31  Score=223.03  Aligned_cols=133  Identities=20%  Similarity=0.253  Sum_probs=108.3

Q ss_pred             HHHHHHHHHHHHhhhhcchhHHHHhcCCC-CCC-CCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHH
Q 022911          143 TETVEEADELLRSDEEESAIEAEVLSAPP-KLV-YSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILEL  220 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~-l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdr  220 (290)
                      ..+|+.|+++|++++.++.....++.... ... +++.|++|+++|++||+++++.||++|++++ ++|+++|++++ ++
T Consensus         6 ~~aR~~A~q~L~~~~~~~~~~~~~l~~~~~~~~~~~~~dr~~~~~lv~gvl~~~~~lD~~i~~~l-~~w~~~rl~~~-~r   83 (149)
T 3r2d_A            6 KGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHL-KGWSIDRLGYV-ER   83 (149)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC----CGGGSCHH-HH
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCccccCHH-HH
Confidence            36999999999999876543332322110 012 6789999999999999999999999999999 68999999998 79


Q ss_pred             HHHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhccccc
Q 022911          221 SILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANI  277 (290)
Q Consensus       221 aILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~~~~  277 (290)
                      +|||+|+|||+|. ++|++|+|||||++||+|+++++++|||||||++.++....+.+
T Consensus        84 ~iLrla~yEl~~~~~iP~~vaInEaVelaK~~~~~~~~~fVNgVLr~i~r~~~~~~~~  141 (149)
T 3r2d_A           84 NALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKE  141 (149)
T ss_dssp             HHHHHHHHHHTTSCCSCHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHC------
T ss_pred             HHHHHHHHHHHHcCCCCCeehHHHHHHHHHHhCCCCccccchHHhhHHHHhhcccccc
Confidence            9999999999997 79999999999999999999999999999999999988776654

>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

Probab=99.95  E-value=3.3e-29  Score=214.56  Aligned_cols=129  Identities=20%  Similarity=0.228  Sum_probs=103.5

Q ss_pred             HHHHHHHHHHHHhhhhcchhHHHHhcCCCC----CCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHH
Q 022911          143 TETVEEADELLRSDEEESAIEAEVLSAPPK----LVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRIL  218 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~l~~~lL~~~~~----~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vL  218 (290)
                      ..+|+.|+++|++++.++.....++.....    ....+.+++|+++|++||+++++.||++|++++ ++|++++++++ 
T Consensus        11 ~~aR~~Alq~L~~~~~~~~~~~~~l~~~~~l~~~d~~~~~~~~~~~~lv~gvl~~~~~lD~~i~~~l-~~w~l~rl~~~-   88 (156)
T 1eyv_A           11 HQARKRAVALLFEAEVRGISAAEVVDTRAALAEAKPDIARLHPYTAAVARGVSEHAAHIDDLITAHL-RGWTLDRLPAV-   88 (156)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTSCCCCHHHHHHHHHHHHTHHHHHHHHHTTS-TTCCGGGSCHH-
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCChhhCCHH-
Confidence            469999999999998665322222111000    001123489999999999999999999999999 68999999998 


Q ss_pred             HHHHHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhc
Q 022911          219 ELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEG  273 (290)
Q Consensus       219 draILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~  273 (290)
                      +++|||+|+|||+|+ ++|++++|||||++||+|+++++++|||||||++.+....
T Consensus        89 ~r~iLrla~yel~~~~~iP~~v~InEaVelak~~~~~~~~~fVNgVLr~i~r~~~~  144 (156)
T 1eyv_A           89 DRAILRVSVWELLHAADVPEPVVVDEAVQLAKELSTDDSPGFVNGVLGQVMLVTPQ  144 (156)
T ss_dssp             HHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCTTHHHHHHHHHHHHC-----
T ss_pred             HHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHhCCCccccchHHHHHHHHHhHHh
Confidence            799999999999996 6999999999999999999999999999999999876533

>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

Probab=99.85  E-value=1.2e-21  Score=189.09  Aligned_cols=125  Identities=16%  Similarity=0.143  Sum_probs=107.2

Q ss_pred             HHHHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911          144 ETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL  223 (290)
Q Consensus       144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL  223 (290)
                      .+|+.|+++|++++.++.....++... ...+++.|++|+++||+||++++..||++|+++++ + ++++++++ +++||
T Consensus         6 ~aR~~A~~~L~~~~~~~~~~~~~l~~~-~~~~~~~dr~~~~~lv~gvlr~~~~ld~~i~~~~~-~-~~~~~~~~-~~~iL   81 (429)
T 1sqg_A            6 NLRSMAAQAVEQVVEQGQSLSNILPPL-QQKVSDKDKALLQELCFGVLRTLSQLDWLINKLMA-R-PMTGKQRT-VHYLI   81 (429)
T ss_dssp             CHHHHHHHHHHHHHHHCCCHHHHHHHH-HTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-S-CCCGGGHH-HHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHH-HhhCCHHHHHHHHHHHHHHHHhHHHHHHHHHHhcC-C-ChhhcCHH-HHHHH
Confidence            489999999999987653322222211 01378899999999999999999999999999984 4 78899998 79999


Q ss_pred             HHHHHHhhccCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911          224 HLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE  272 (290)
Q Consensus       224 RlAiyELlf~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~  272 (290)
                      |+|+|||+|.++|++++|||+|++||+|+++++++|||||||++.+...
T Consensus        82 rl~~yel~~~~~p~~~~ineaVelak~~~~~~~~~fvN~vL~~~~r~~~  130 (429)
T 1sqg_A           82 MVGLYQLLYTRIPPHAALAETVEGAIAIKRPQLKGLINGVLRQFQRQQE  130 (429)
T ss_dssp             HHHHHHHHHCCSCHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhCCCCchHhhHHHHHHHHHhccccchhhHHHHHHHHHHhhh
Confidence            9999999999999999999999999999988899999999999998653

>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii}

Probab=99.81  E-value=1e-20  Score=184.00  Aligned_cols=124  Identities=11%  Similarity=-0.061  Sum_probs=105.0

Q ss_pred             HHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCH-HHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHH
Q 022911          144 ETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSK-LLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS  221 (290)
Q Consensus       144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~-~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdra  221 (290)
                      .+|+.|+++|++++.++.....++.... ...+++ .|++|+++||+||++++..||++|+++++ + ++++++++ +++
T Consensus        12 ~~R~~A~~~L~~v~~~~~~~~~~l~~~~~~~~l~~~~dr~~~~~lv~gvlr~~~~ld~~i~~~~~-~-~~~~~~~~-~~~   88 (450)
T 2yxl_A           12 PKGIRAIIEAIRLGEIIKPSQYAKREAFKKHDVEEAWLNRVLTMIFYDIMKKQGLIDKVIKEIVG-V-TPLILDPW-LRA   88 (450)
T ss_dssp             HHHHHHHHHHHHHTTTSSSTHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S-CGGGSCHH-HHH
T ss_pred             hHHHHHHHHHHHHHhcCCcHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHhHHHHHHHHHHhcc-C-ChhhcCHH-HHH
Confidence            6899999999999866543222221100 012566 89999999999999999999999999984 3 78899998 799


Q ss_pred             HHHHHHHHhhccCCChhhHHH----HHHHHHHhhCCCCCCCchHHHHhhHHhhh
Q 022911          222 ILHLAMSEITVVGTRHQIVIN----EAVDLAKRFCDGAAPRIINGCLRTFVRNL  271 (290)
Q Consensus       222 ILRlAiyELlf~diP~~vaIN----EAVeLAK~y~~~~s~~FVNaVLr~i~r~~  271 (290)
                      |||+|+|||+| ++|++++||    |||++||+|+++++++|||||||++.+..
T Consensus        89 iLrla~yell~-~ip~~~ain~~~~eaVelak~~~~~~~~~fvNgvL~~~~r~~  141 (450)
T 2yxl_A           89 ALRVAVDIALF-HDPSSQTIKNLRWKASDFISSRTHPYVGMYFWDLLDKIFEYK  141 (450)
T ss_dssp             HHHHHHHHHHH-SCBCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHhc-CCCchHHhccccHHHHHHHHhccccccccchHHHHHHHhhcc
Confidence            99999999999 999999999    99999999998889999999999999863

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	290
d1sqga1	140	a.79.1.3 (A:5-144) Ribosomal RNA small subunit met	2e-09
d1tzva_	141	a.79.1.1 (A:) Antitermination factor NusB {Thermot	3e-09
d1ey1a_	139	a.79.1.1 (A:) Antitermination factor NusB {Escheri	4e-09
d1eyva_	131	a.79.1.1 (A:) Antitermination factor NusB {Mycobac	4e-09

>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

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: RmsB N-terminal domain-like
domain: Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 15/91 (16%), Positives = 32/91 (35%), Gaps = 3/91 (3%)

Query: 182 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVI 241
             ++L   V+        +I+K++      +         ++ + + ++          +
Sbjct: 39  LLQELCFGVLRTLSQLDWLINKLMARPMTGKQR---TVHYLIMVGLYQLLYTRIPPHAAL 95

Query: 242 NEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 272
            E V+ A          +ING LR F R  E
Sbjct: 96  AETVEGAIAIKRPQLKGLINGVLRQFQRQQE 126

>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]} Length = 141

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Thermotoga maritima [TaxId: 2336]

 Score = 52.1 bits (124), Expect = 3e-09
 Identities = 20/120 (16%), Positives = 42/120 (35%), Gaps = 5/120 (4%)

Query: 153 LRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQ 212
            R DE+   I  E+L       Y K      R+ +  + +       +I +     W   
Sbjct: 21  FRRDEDLEQILEEILDET----YDKKAKEDARRYIRGIKENLSMIDDLISRY-LEKWSLN 75

Query: 213 PAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 272
               +    +       +       ++ I+EA+++AKR+    + + +NG L    +   
Sbjct: 76  RLSVVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAKRYGTENSGKFVNGILDRIAKEHA 135

>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]} Length = 139

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Escherichia coli [TaxId: 562]

 Score = 52.0 bits (124), Expect = 4e-09
 Identities = 21/123 (17%), Positives = 51/123 (41%), Gaps = 7/123 (5%)

Query: 151 ELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWK 210
               S  + + +E + L+         + + + R+LL  V         ++   +  + +
Sbjct: 19  SWQLSQNDIADVEYQFLAEQD---VKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRLLE 75

Query: 211 DQPAGRILELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 269
           +         ++L +A+ E++      +++ INEA++LAK F    + + +NG L     
Sbjct: 76  ELGQVEK---AVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAP 132

Query: 270 NLE 272
            + 
Sbjct: 133 VIR 135

>d1eyva_ a.79.1.1 (A:) Antitermination factor NusB {Mycobacterium tuberculosis [TaxId: 1773]} Length = 131

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 52.1 bits (124), Expect = 4e-09
 Identities = 17/118 (14%), Positives = 35/118 (29%), Gaps = 1/118 (0%)

Query: 151 ELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWK 210
           E        + +     +          L  +T  +   V +       +I   +     
Sbjct: 15  EAEVRGISAAEVVDTRAALAEAKPDIARLHPYTAAVARGVSEHAAHIDDLITAHLRGWTL 74

Query: 211 DQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFV 268
           D+    +    +       +        +V++EAV LAK      +P  +NG L   +
Sbjct: 75  DRL-PAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAKELSTDDSPGFVNGVLGQVM 131

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	290
d1tzva_	141	Antitermination factor NusB {Thermotoga maritima [	99.96
d1ey1a_	139	Antitermination factor NusB {Escherichia coli [Tax	99.95
d1eyva_	131	Antitermination factor NusB {Mycobacterium tubercu	99.94
d1sqga1	140	Ribosomal RNA small subunit methyltransferase B, R	99.93

>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.96  E-value=3.4e-29  Score=206.78  Aligned_cols=131  Identities=16%  Similarity=0.223  Sum_probs=111.6

Q ss_pred             HHHHHHHHHHHHhhhhcch-hHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHH
Q 022911          143 TETVEEADELLRSDEEESA-IEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS  221 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~-l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdra  221 (290)
                      ..+|+.|+|+||+++.++. ....+........+++.|++|+++|++||+++++.||++|++++ ++|++++++++ +++
T Consensus         6 ~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~g~~~~~~~id~~I~~~~-~~~~~~rl~~~-~~~   83 (141)
T d1tzva_           6 RRMRLAVFKALFQHEFRRDEDLEQILEEILDETYDKKAKEDARRYIRGIKENLSMIDDLISRYL-EKWSLNRLSVV-DRN   83 (141)
T ss_dssp             HHHHHHHHHHHHHHTTCTTSCHHHHHHHHCCTTSCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC-SSSCGGGSCHH-HHH
T ss_pred             HHHHHHHHHHHHHHHhcCCccHHHHHHHHHHhccchhHHHHHHHHHHHHHHhHHHHHHHHHHhc-ccCChHHHHHH-HHH
Confidence            4689999999999986543 22222211111237899999999999999999999999999998 68999999998 799


Q ss_pred             HHHHHHHHhhc-cCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhccc
Q 022911          222 ILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA  275 (290)
Q Consensus       222 ILRlAiyELlf-~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~~  275 (290)
                      |||+|+|||+| .++|++|+|||||++||+|+++++++|||||||+++|+....+
T Consensus        84 iLr~a~~El~~~~~~p~~v~InEaVelak~~~~~~~~~fVNaVL~~i~r~~~~~e  138 (141)
T d1tzva_          84 VLRLATYELLFEKDIPIEVTIDEAIEIAKRYGTENSGKFVNGILDRIAKEHAPKE  138 (141)
T ss_dssp             HHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHCCGG
T ss_pred             HHHHHHHHHHhccccchhHHHHHHHHHHHHhCCCcccchHHHHHHHHHHHcCchh
Confidence            99999999998 5799999999999999999999999999999999999876543

>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=2.1e-28  Score=201.78  Aligned_cols=127  Identities=21%  Similarity=0.252  Sum_probs=109.9

Q ss_pred             HHHHHHHHHHHHhhhhcch-h---HHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHH
Q 022911          143 TETVEEADELLRSDEEESA-I---EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRIL  218 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~-l---~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vL  218 (290)
                      ..+|+.|+|+||+++.++. +   ...++...   .+++.|+.|++.|++||+++.+.||.+|++++ + |++++++++ 
T Consensus         7 ~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~~---~~~~~d~~~~~~l~~gv~~~~~~id~~I~~~l-~-~~~~r~~~~-   80 (139)
T d1ey1a_           7 RRARECAVQALYSWQLSQNDIADVEYQFLAEQ---DVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-S-RLLEELGQV-   80 (139)
T ss_dssp             CSHHHHHHHHHHHHHHHCCCSHHHHHHHHHTT---TSSSCCCHHHHHHHHHHHHHHHHHHHHHTTCC-C-SCTTTSCHH-
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhc---ccchhhHHHHHHHHHHHHHhHHHHHHHHHHHH-H-hhHHhcChH-
Confidence            3599999999999986543 2   22333332   36778999999999999999999999999998 3 669999998 


Q ss_pred             HHHHHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhccc
Q 022911          219 ELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA  275 (290)
Q Consensus       219 draILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~~  275 (290)
                      +++|||+|+|||+|. ++|++|+|||||++||.|+++++++|||||||+++++.++++
T Consensus        81 ~~~ILr~a~~El~~~~~~p~~viInE~Velak~~~~~~~~~fVNgVL~~i~k~~r~~e  138 (139)
T d1ey1a_          81 EKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNK  138 (139)
T ss_dssp             HHHHHHHHHHHHHSCSSCCSHHHHHHHHHHTTTTTCSSSSHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHHccCCCceehHHHHHHHHHHhCCCCccchHHHHHHHHHHHhCccC
Confidence            799999999999985 699999999999999999999999999999999999877653

>d1eyva_ a.79.1.1 (A:) Antitermination factor NusB {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.94  E-value=1.5e-27  Score=194.83  Aligned_cols=124  Identities=21%  Similarity=0.258  Sum_probs=104.1

Q ss_pred             HHHHHHHHHHHHhhhhcchhHHHHhcC----CCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHH
Q 022911          143 TETVEEADELLRSDEEESAIEAEVLSA----PPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRIL  218 (290)
Q Consensus       143 ~~aRe~AlqlL~~ve~~~~l~~~lL~~----~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vL  218 (290)
                      .++|+.|+|+||+++.++....+++..    .........+++|+++|++|++++.+.||.+|++++ ++|++++++++ 
T Consensus         3 ~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~gv~~~~~~id~~I~~~l-~~~~~~~l~~i-   80 (131)
T d1eyva_           3 HQARKRAVALLFEAEVRGISAAEVVDTRAALAEAKPDIARLHPYTAAVARGVSEHAAHIDDLITAHL-RGWTLDRLPAV-   80 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTSCCCCHHHHHHHHHHHHTHHHHHHHHHTTS-TTCCGGGSCHH-
T ss_pred             HHHHHHHHHHHHHHHhhCcCHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHhHHHHHHHHHHhh-hhhHHHHhhHH-
Confidence            469999999999998764422222110    000113455789999999999999999999999999 68999999998 


Q ss_pred             HHHHHHHHHHHhhc-cCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHH
Q 022911          219 ELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFV  268 (290)
Q Consensus       219 draILRlAiyELlf-~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~  268 (290)
                      +++|||+|+|||+| .++|.+++|||||++||+|+++++++|||||||+++
T Consensus        81 ~~~iLr~a~~El~~~~~~p~~viInE~V~lak~~~~~~~~kfiNaVL~kiv  131 (131)
T d1eyva_          81 DRAILRVSVWELLHAADVPEPVVVDEAVQLAKELSTDDSPGFVNGVLGQVM  131 (131)
T ss_dssp             HHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHSCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhcccCCchhHHHHHHHHHHHhCCCcccchhHHHHHhcC
Confidence            89999999999997 569999999999999999999999999999999973

>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]}

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: RmsB N-terminal domain-like
domain: Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=9.5e-27  Score=193.04  Aligned_cols=127  Identities=15%  Similarity=0.114  Sum_probs=107.8

Q ss_pred             HHHHHHHHHHHhhhh-cchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHH
Q 022911          144 ETVEEADELLRSDEE-ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSI  222 (290)
Q Consensus       144 ~aRe~AlqlL~~ve~-~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraI  222 (290)
                      .+|..|+|+|+++.. +..+...+ ... ...+++.|++|+++|++||+++++.||++|++++++ | +++++++ +++|
T Consensus         2 ~~R~~A~q~L~~v~~~g~~l~~~l-~~~-~~~l~~~dr~~~~~lv~gvlr~~~~ld~~i~~~l~~-~-~~~~~~~-~~~i   76 (140)
T d1sqga1           2 NLRSMAAQAVEQVVEQGQSLSNIL-PPL-QQKVSDKDKALLQELCFGVLRTLSQLDWLINKLMAR-P-MTGKQRT-VHYL   76 (140)
T ss_dssp             CHHHHHHHHHHHHHHHCCCHHHHH-HHH-HTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS-C-CCGGGHH-HHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCHHHHH-HHH-HHhCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhc-c-cchhhHH-HHHH
Confidence            379999999999965 44443322 211 123789999999999999999999999999999954 3 4788888 6999


Q ss_pred             HHHHHHHhhccCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhccc
Q 022911          223 LHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA  275 (290)
Q Consensus       223 LRlAiyELlf~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~~  275 (290)
                      ||+|+|||+|.++|++++|||||++||.|++++++||||||||++.|+.+...
T Consensus        77 Lr~a~~el~~~~~p~~avvneaV~lak~~~~~~~~~fVNaVLr~~~r~~~~~~  129 (140)
T d1sqga1          77 IMVGLYQLLYTRIPPHAALAETVEGAIAIKRPQLKGLINGVLRQFQRQQEELL  129 (140)
T ss_dssp             HHHHHHHHHHCCSCHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCccchHHHHHHHHHhCCCcccchhHHHHHHHHhCcHHHH
Confidence            99999999999999999999999999999999999999999999999776543