Citrus Sinensis ID: 018197

---

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-------300-------310-------320-------330-------340-------350-------36
Protein Sequence
MKFEPDVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTPSKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLGI
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHHcccEEEcccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccHHHHHHHHccccccccEEHHHHHHHHHHHccccccHHccccEEEEEEEEcEEEEEccccccccHHHHHHHHHccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccHHHHHHHccccHHHHccccHHccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHHHHHHcccEEEEcccccccccccccccccccccccEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHccccccccEEHHHHHHHHHHHccccHHEEEccEEEEEEEEccEEEEEccccccHHHHHHHHHHHcccEEEEEcccccEccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccEEEcccccccccccccccccccccccccccccccccccHHHcccccccccccEEEEcccccHHHcHHcccHHHHHHcHHccHcccccccc
Coil and Loop (DISEMBL)
mkfepdvspiESARARFLQIIVDHFINDHvievtdsgaeysqqpgqdklskrknrdvqyegdprfalPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAkkfpkkgsctykrRELATSLETRTRFPELVIQEEKRVRFVVVNGldivekpnnmpiedaEWFKRLtgrnevaisaqdykfysprhkyrrvasnsvsnipvlpgfpgtdnsstmvtaqgfhtisepqnqqqtpskhhmqplshqpqfhhihnnhhqqihqgqqhpahfsqnhrcgppphlpdiahahqsptisqhmaclqpltgghvgerlhvmpaspakfcdecgapylretskfcsecgvkrlgi
Flexible Loop (DISEMBL)
mkfepdvsPIESARARFLQIIVDHFINDHVIEVTdsgaeysqqpgqdklskrknrdvqyeGDPRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSlakkfpkkgsctykrrelatsletrtrfpelviqeekrvrfVVVNgldivekpnnmpiedAEWFKRLTGRNEVAisaqdykfysprHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTPSKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLREtskfcsecgvkrlgi
Low Complexity Region (SEG)
MKFEPDVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTPSKHHMQPLShqpqfhhihnnhhqqihqgqqhpahFSQNHRCGPPPHLPDIAHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLGI
Disordered region (IsUnstruct)
*************RARFLQIIVDHFINDHVIEVT***************************DPRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQDYKFYSPRHKYRRVASNSVSNIPVL********************************************************************************************HMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGV*****
Disordered Region (DISOPRED)
****PDVSPIESARARFLQIIVDHFINDHVIE*******************************RFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQDYKFYSPRHKY*************************************************************************************************************CLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRL**
Disordered Region (DISEMBL)
*********IESARARFLQIIVDHFINDHVIEVTDSG*********************YEGDPRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTI********************QPQFHHIH********************HRCGPPPHLPDIAHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLGI
Disordered Region (DISPRO)
**F*PDVSPIESARARFLQIIVDHFINDHVIEVTDS******************RDVQYEGDPRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGF**************************************************QQIH*GQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGV*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKFEPDVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTPSKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLGI
Positional Conservation
no confident homologs detected

---

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	359	2.2.26 [Sep-21-2011]
Q56XX3	432	Uncharacterized protein A	yes	no	0.913	0.759	0.662	1e-127
Q5PPV5	323	Zinc finger C2HC domain-c	N/A	no	0.128	0.142	0.456	9e-05
Q96GY0	325	Zinc finger C2HC domain-c	yes	no	0.133	0.147	0.416	0.0005
Q5REC0	324	Zinc finger C2HC domain-c	yes	no	0.122	0.135	0.431	0.0008

>sp|Q56XX3|Y2215_ARATH Uncharacterized protein At2g02148 OS=Arabidopsis thaliana GN=At2g02148 PE=2 SV=1

 Score =  456 bits (1173), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 241/364 (66%), Positives = 278/364 (76%), Gaps = 36/364 (9%)

Query: 6   DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYS-QQPGQDKLSK--RKNRDVQYEGD 62
           DVSPIE+AR RFLQII+D+FI+ HVIEV +S  ++     G+D  SK  RK+ D +YEGD
Sbjct: 95  DVSPIEAARGRFLQIILDYFISQHVIEVCESKRDHDVDSGGRDSNSKVKRKSDDTRYEGD 154

Query: 63  PRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSC 122
           P FALPLMY+AN+YETLV + N+RLAS NGIR+KTIGVALEAAGGLYR L KKFPKKG+C
Sbjct: 155 PSFALPLMYIANLYETLVGEANVRLASLNGIRDKTIGVALEAAGGLYRKLTKKFPKKGTC 214

Query: 123 TYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRN 182
            Y+RRELATS+ETRTRFPELVI EEKRVRFVVVNGLDIVEKP+++PIE+AEWFKRLTGRN
Sbjct: 215 MYRRRELATSVETRTRFPELVIHEEKRVRFVVVNGLDIVEKPSDLPIEEAEWFKRLTGRN 274

Query: 183 EVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQ 242
           EVAISA+DYKFY PR K+RR+  NSVS+I  LP FPG D SST+   QGF    E Q+QQ
Sbjct: 275 EVAISARDYKFYCPRRKHRRL-QNSVSSINGLPTFPGID-SSTLANTQGFR---EDQSQQ 329

Query: 243 Q---TPSKHHMQPLSHQPQFH---HIHNNHHQQIHQGQQHPAHF-SQNHRCGPPPHLPDI 295
           Q   +PSKHHM  LSH  QFH   H  + HHQ I+Q Q    H+ SQNH+C      P++
Sbjct: 330 QHTPSPSKHHMSSLSH--QFHQSIHQSHQHHQSIYQSQHAATHYPSQNHQCD-----PEL 382

Query: 296 AHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVK 355
           +H          MACLQPLTGG      HVMP SPAKFCD+CGA YLRETSKFCSECG K
Sbjct: 383 SHT--------QMACLQPLTGG------HVMPNSPAKFCDQCGAQYLRETSKFCSECGSK 428

Query: 356 RLGI 359
           RLGI
Sbjct: 429 RLGI 432

Arabidopsis thaliana (taxid: 3702)

>sp|Q5PPV5|ZC21A_XENLA Zinc finger C2HC domain-containing protein 1A OS=Xenopus laevis GN=zc2hc1a PE=2 SV=1

 Score = 48.1 bits (113), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 27/46 (58%)

Query: 312 QPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRL 357
           +PL  GH+    + M     KFC ECG  Y  E +KFC ECGV+R+
Sbjct: 276 KPLNDGHIRAADNNMSGQLTKFCHECGTKYPVEWAKFCCECGVRRM 321

Xenopus laevis (taxid: 8355)

>sp|Q96GY0|ZC21A_HUMAN Zinc finger C2HC domain-containing protein 1A OS=Homo sapiens GN=ZC2HC1A PE=1 SV=2

 Score = 45.8 bits (107), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 27/48 (56%)

Query: 310 CLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRL 357
           C   L GG++       P +  KFC ECG  Y  E +KFC ECG++R+
Sbjct: 276 CASSLNGGNIKGIEGHSPGNLPKFCHECGTKYPVEWAKFCCECGIRRM 323

Homo sapiens (taxid: 9606)

>sp|Q5REC0|ZC21A_PONAB Zinc finger C2HC domain-containing protein 1A OS=Pongo abelii GN=ZC2HC1A PE=2 SV=1

 Score = 45.1 bits (105), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 314 LTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRL 357
           L GG++       P + +KFC ECG  Y  E +KFC ECG++R+
Sbjct: 279 LNGGNIKGIEGNSPGNLSKFCHECGTKYPVEWAKFCCECGIRRM 322

Pongo abelii (taxid: 9601)

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	359
297738286	456	unnamed protein product [Vitis vinifera]	0.972	0.765	0.815	1e-170
359473523	452	PREDICTED: uncharacterized protein At2g0	0.963	0.765	0.813	1e-167
255555531	448	cgi-62, putative [Ricinus communis] gi|2	0.961	0.770	0.764	1e-157
449463503	455	PREDICTED: uncharacterized protein At2g0	0.955	0.753	0.725	1e-153
356512247	440	PREDICTED: uncharacterized protein At2g0	0.961	0.784	0.75	1e-151
224101991	424	predicted protein [Populus trichocarpa]	0.871	0.738	0.791	1e-146
356528164	423	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.905	0.768	0.713	1e-140
229914885	1023	putative PPR repeat protein [Eutrema hal	0.949	0.333	0.686	1e-135
297817834	1010	hypothetical protein ARALYDRAFT_484139 [	0.949	0.337	0.674	1e-131
312190399	1128	unknown [Eutrema parvulum]	0.944	0.300	0.682	1e-131

>gi|297738286|emb|CBI27487.3| unnamed protein product [Vitis vinifera]

 Score =  604 bits (1557), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 288/353 (81%), Positives = 316/353 (89%), Gaps = 4/353 (1%)

Query: 6   DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRF 65
           D+SPIE+ARARF+QIIVDHFI+DHVIEV DS A+Y+ Q GQDKL+KRK+R+VQYEGDPRF
Sbjct: 107 DISPIEAARARFMQIIVDHFIDDHVIEVADSEADYNGQSGQDKLNKRKSREVQYEGDPRF 166

Query: 66  ALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYK 125
            LPLMYVANMYETLVN+VN+RLAS NGIREKTIGVALEAAGGLYR LAKKFPKKG CT+K
Sbjct: 167 VLPLMYVANMYETLVNEVNIRLASLNGIREKTIGVALEAAGGLYRRLAKKFPKKGPCTFK 226

Query: 126 RRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVA 185
           RRELATS+ETRTRFPELVIQEEKRVRFVVVNGL IV+KPN++PI+DAEWFKRLTGR+EVA
Sbjct: 227 RRELATSIETRTRFPELVIQEEKRVRFVVVNGLVIVDKPNSVPIDDAEWFKRLTGRDEVA 286

Query: 186 ISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTP 245
           +SA+DYKFYSPRHKYRRVASN VSNIP LP FPGTD S TM +AQGF T++EPQNQQ TP
Sbjct: 287 VSARDYKFYSPRHKYRRVASNPVSNIPGLPTFPGTDTSPTMASAQGFRTVNEPQNQQATP 346

Query: 246 SKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTIS 305
           SKHHMQ LS   QFH IH NHHQ IHQ  QH AHFS +H+CGPP HLP+I H HQSPTI 
Sbjct: 347 SKHHMQSLS---QFHPIHQNHHQPIHQ-TQHSAHFSHSHQCGPPSHLPEIPHGHQSPTIP 402

Query: 306 QHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLG 358
           QHMACLQP+TGGHV  RLHV+P SPAKFCDECGAPYLRETSKFCSECG KR G
Sbjct: 403 QHMACLQPITGGHVSGRLHVLPTSPAKFCDECGAPYLRETSKFCSECGGKRFG 455

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473523|ref|XP_003631314.1| PREDICTED: uncharacterized protein At2g02148-like [Vitis vinifera]

 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 287/353 (81%), Positives = 313/353 (88%), Gaps = 7/353 (1%)

Query: 6   DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRF 65
           D+SPIE+ARARF+QIIVDHFI+DHVIEV DS A+Y+ Q GQDKL+KRK+R+VQYEGDPRF
Sbjct: 106 DISPIEAARARFMQIIVDHFIDDHVIEVADSEADYNGQSGQDKLNKRKSREVQYEGDPRF 165

Query: 66  ALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYK 125
            LPLMYVANMYETLVN+VN+RLAS NGIREKTIGVALEAAGGLYR LAKKFPKKG CT+K
Sbjct: 166 VLPLMYVANMYETLVNEVNIRLASLNGIREKTIGVALEAAGGLYRRLAKKFPKKGPCTFK 225

Query: 126 RRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVA 185
           RRELATS+ETRTRFPELVIQEEKRVRFVVVNGL IV+KPN++PI+DAEWFKRLTGR+EVA
Sbjct: 226 RRELATSIETRTRFPELVIQEEKRVRFVVVNGLVIVDKPNSVPIDDAEWFKRLTGRDEVA 285

Query: 186 ISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTP 245
           +SA+DYKFYSPRHKYRRVASN VSNIP LP FPGTD S TM +AQGF T   PQNQQ TP
Sbjct: 286 VSARDYKFYSPRHKYRRVASNPVSNIPGLPTFPGTDTSPTMASAQGFRT---PQNQQATP 342

Query: 246 SKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTIS 305
           SKHHMQ LS   QFH IH NHHQ IHQ  QH AHFS +H+CGPP HLP+I H HQSPTI 
Sbjct: 343 SKHHMQSLS---QFHPIHQNHHQPIHQ-TQHSAHFSHSHQCGPPSHLPEIPHGHQSPTIP 398

Query: 306 QHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLG 358
           QHMACLQP+TGGHV  RLHV+P SPAKFCDECGAPYLRETSKFCSECG KR G
Sbjct: 399 QHMACLQPITGGHVSGRLHVLPTSPAKFCDECGAPYLRETSKFCSECGGKRFG 451

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555531|ref|XP_002518802.1| cgi-62, putative [Ricinus communis] gi|223542183|gb|EEF43727.1| cgi-62, putative [Ricinus communis]

 Score =  559 bits (1440), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 273/357 (76%), Positives = 305/357 (85%), Gaps = 12/357 (3%)

Query: 6   DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQD-KLSKRKNRDVQYEGDPR 64
           DVSPIESAR+RFLQ+IVDHFI DHVI+V D+ A+Y     QD KL+KRK+ DVQYEGDP 
Sbjct: 101 DVSPIESARSRFLQLIVDHFIIDHVIQVPDNEADYLSHSAQDNKLNKRKSGDVQYEGDPT 160

Query: 65  FALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTY 124
           +ALPLMYVANMYE+LVNDVN+RLAS NGIR+KTIG+ALEAAGGLYR +AKKFPKKGSC +
Sbjct: 161 YALPLMYVANMYESLVNDVNVRLASLNGIRDKTIGLALEAAGGLYRRIAKKFPKKGSCVF 220

Query: 125 KRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEV 184
           KRRELATSLETRTRFPELVIQE KRVRFVVVNGLD+VEKPNNM IEDAEWFKRLTGRNEV
Sbjct: 221 KRRELATSLETRTRFPELVIQEVKRVRFVVVNGLDVVEKPNNMSIEDAEWFKRLTGRNEV 280

Query: 185 AISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQT 244
           A+S++DYKFYSPRHKYRRVA    SN+P LP  P TD+  +M +AQGF +   PQ +QQ 
Sbjct: 281 AVSSRDYKFYSPRHKYRRVA----SNVPGLPTLPATDSPPSMASAQGFRS---PQTEQQP 333

Query: 245 PSKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTI 304
           P+KHH+  +SHQPQFH IH NHH Q+HQ  QH   FSQNH+CG   HLP+IAHA+QSP I
Sbjct: 334 PAKHHVDSMSHQPQFHPIHQNHH-QVHQS-QHSTQFSQNHQCGTTSHLPEIAHANQSPNI 391

Query: 305 SQHMAC--LQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLGI 359
           SQHMA   LQPLTGGHVG RLH+MPASPAKFCDECGAPYLRETSKFCSECG KRLGI
Sbjct: 392 SQHMAYLQLQPLTGGHVGGRLHLMPASPAKFCDECGAPYLRETSKFCSECGTKRLGI 448

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463503|ref|XP_004149473.1| PREDICTED: uncharacterized protein At2g02148-like [Cucumis sativus]

 Score =  546 bits (1408), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 264/364 (72%), Positives = 298/364 (81%), Gaps = 21/364 (5%)

Query: 6   DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRF 65
           D+SPIE+ARARFLQIIVDHFI+DH++EVT++  +Y  Q GQDKL+KRK ++VQYE DP+F
Sbjct: 103 DISPIEAARARFLQIIVDHFIHDHILEVTETDNDYISQSGQDKLTKRKTKEVQYEADPKF 162

Query: 66  ALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYK 125
            LPLMYVANMYETLVND N+RLAS +GIR+K IGVALEAAGGLYR LA+KFPKKG CTYK
Sbjct: 163 VLPLMYVANMYETLVNDANIRLASLSGIRDKNIGVALEAAGGLYRKLAQKFPKKGPCTYK 222

Query: 126 RRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVA 185
           RRELATSLETRTRFPELV+QEEKRVRFVVVNGLDIVEKPN M  EDAEWF+RLTGR+EVA
Sbjct: 223 RRELATSLETRTRFPELVVQEEKRVRFVVVNGLDIVEKPNRMSTEDAEWFRRLTGRSEVA 282

Query: 186 ISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQ------ 239
           +SAQDYKFYSPRHKYRRVA+NSVS+I  L       N S +V    F +I +P       
Sbjct: 283 VSAQDYKFYSPRHKYRRVAANSVSSISSL-------NVSGIVI---FSSICDPSLYGNIF 332

Query: 240 ----NQQQTPSKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDI 295
                QQQTP KHH+Q L HQPQF  IH NHHQ +HQ  QH +HF+ NH CG P  L DI
Sbjct: 333 CKCILQQQTPCKHHIQQLPHQPQFQSIHQNHHQSMHQS-QHTSHFAHNHHCGQPSQLQDI 391

Query: 296 AHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVK 355
           +H H SPT+SQHMA LQPL+GGHVG RLH+ P+SPAKFCDECGAPYLRETSKFCSECGVK
Sbjct: 392 SHTHHSPTLSQHMASLQPLSGGHVGGRLHLQPSSPAKFCDECGAPYLRETSKFCSECGVK 451

Query: 356 RLGI 359
           RLGI
Sbjct: 452 RLGI 455

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512247|ref|XP_003524832.1| PREDICTED: uncharacterized protein At2g02148-like [Glycine max]

 Score =  540 bits (1391), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 267/356 (75%), Positives = 300/356 (84%), Gaps = 11/356 (3%)

Query: 6   DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRF 65
           D+SPIESARARFLQIIVDHFI+D VIEV DS A+Y+   GQDK+SKR+ R++QYEGDP F
Sbjct: 92  DISPIESARARFLQIIVDHFIDDRVIEVPDSEADYT---GQDKMSKRRTREIQYEGDPNF 148

Query: 66  ALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYK 125
            LPLMYVANMYE+LV+DVN RLAS NGIREKTIGVALEAAGGLYR LAKKFPKKG CT+K
Sbjct: 149 TLPLMYVANMYESLVSDVNNRLASLNGIREKTIGVALEAAGGLYRRLAKKFPKKGPCTFK 208

Query: 126 RRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVA 185
           RRELATS+ETRTRFPELVIQEEKRVRFVVVNGL IVEKPNNMPI+DAEWFKRLTGR+EVA
Sbjct: 209 RRELATSMETRTRFPELVIQEEKRVRFVVVNGLRIVEKPNNMPIDDAEWFKRLTGRSEVA 268

Query: 186 ISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTP 245
           ISA DYKFYSPRHKYRR AS S+SNI  +P +PG +NS+ + T QGFH+   PQNQQQTP
Sbjct: 269 ISASDYKFYSPRHKYRRGASISLSNIQDIPSYPGAENSTALATPQGFHS---PQNQQQTP 325

Query: 246 SKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTIS 305
            KH +Q L HQPQFH +  N +Q +HQ  QH   +S N + GPP HLP+I+HAHQ  +IS
Sbjct: 326 CKHQLQSLPHQPQFHPVLQN-NQTMHQS-QHAGPYSHNPQSGPPSHLPEISHAHQPISIS 383

Query: 306 QHMACLQPLT---GGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLG 358
           QHMACLQPLT    G  G RLH++P +PAKFCDECGAPYLRETSKFCSECG KRLG
Sbjct: 384 QHMACLQPLTGGHVGGHGGRLHMLPTTPAKFCDECGAPYLRETSKFCSECGSKRLG 439

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101991|ref|XP_002312503.1| predicted protein [Populus trichocarpa] gi|222852323|gb|EEE89870.1| predicted protein [Populus trichocarpa]

 Score =  524 bits (1350), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 254/321 (79%), Positives = 281/321 (87%), Gaps = 8/321 (2%)

Query: 6   DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRF 65
           DVSPIESARARFLQIIVDHFI+DHVIEV D+ +EY+  PGQDKL+KRK+ DVQYEGDPRF
Sbjct: 99  DVSPIESARARFLQIIVDHFISDHVIEVADNESEYAAHPGQDKLTKRKSGDVQYEGDPRF 158

Query: 66  ALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYK 125
           ALPLMYVANMYETLVNDVN+RLAS NG+R+KTIGVALEAAGGLYR +AKKFPKKGSC +K
Sbjct: 159 ALPLMYVANMYETLVNDVNMRLASLNGVRDKTIGVALEAAGGLYRRMAKKFPKKGSCIFK 218

Query: 126 RRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVA 185
           RRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKP++MPI DAEWF+RLTGR+EVA
Sbjct: 219 RRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPSSMPIVDAEWFRRLTGRSEVA 278

Query: 186 ISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTP 245
           +SAQDYKFYSPRHK+RRV    +SNIP L   P  DNSSTM TAQGF +   PQN+QQTP
Sbjct: 279 VSAQDYKFYSPRHKFRRV----LSNIPGLATLPTEDNSSTMTTAQGFRS---PQNEQQTP 331

Query: 246 SKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTIS 305
           SKHH+Q LSHQPQFH I+ NHHQ++HQ  QH   FSQNH+CGPP H+P+IAHA  SPTI 
Sbjct: 332 SKHHVQLLSHQPQFHPINQNHHQEVHQS-QHATQFSQNHQCGPPSHMPEIAHATHSPTIP 390

Query: 306 QHMACLQPLTGGHVGERLHVM 326
           QHM  LQPLTGGHVG RLH M
Sbjct: 391 QHMVYLQPLTGGHVGGRLHSM 411

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528164|ref|XP_003532675.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein At2g02148-like [Glycine max]

 Score =  504 bits (1298), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 252/353 (71%), Positives = 284/353 (80%), Gaps = 28/353 (7%)

Query: 6   DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRF 65
           DVSPIE ARARFLQI+VDHF+ D VIE+ DS A+ +   GQDK+SKR+  ++QYEGDP F
Sbjct: 98  DVSPIEPARARFLQIVVDHFVEDRVIEMPDSEADCA---GQDKMSKRRTSEIQYEGDPNF 154

Query: 66  ALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYK 125
           ALPLMY+ANMYE+LV+DVN RLAS NGIREKTIGVALEAAGGLYR LAKKFPKKG CT+K
Sbjct: 155 ALPLMYMANMYESLVSDVNNRLASLNGIREKTIGVALEAAGGLYRKLAKKFPKKGPCTFK 214

Query: 126 RRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVA 185
           RRELATS+ETRTRFPELVIQEEKRVRFVVVNGL IVEKPNN+PI+DAEWFKRLTGR+EVA
Sbjct: 215 RRELATSMETRTRFPELVIQEEKRVRFVVVNGLRIVEKPNNVPIDDAEWFKRLTGRSEVA 274

Query: 186 ISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQQTP 245
           ISA DYKFYSPRHKYRR AS S+SNI  +P                      PQNQQQTP
Sbjct: 275 ISANDYKFYSPRHKYRRGASISLSNIQDIP----------------------PQNQQQTP 312

Query: 246 SKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHLPDIAHAHQSPTIS 305
            KHH+Q L HQPQ H +  N +Q +HQ  QH   +S N + G P HLP+I+HAHQ  +IS
Sbjct: 313 CKHHLQSLPHQPQLHPVLQN-NQTMHQS-QHAGPYSHNPQSG-PSHLPEISHAHQPISIS 369

Query: 306 QHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRLG 358
           QHM CLQPLTGG+VG RLH++P +PAKFCDECGAPYLRETSKFCSECG KRLG
Sbjct: 370 QHMTCLQPLTGGNVGGRLHMLPTTPAKFCDECGAPYLRETSKFCSECGSKRLG 422

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|229914885|gb|ACQ90610.1| putative PPR repeat protein [Eutrema halophilum]

 Score =  487 bits (1254), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 254/370 (68%), Positives = 290/370 (78%), Gaps = 29/370 (7%)

Query: 6    DVSPIESARARFLQIIVDHFINDHVIEVTDSGA--EYSQQPGQDKLS---KRKNRDVQYE 60
            DVSPIESAR RFLQII+D+FI+ HVIEV ++    E     GQD  +   KRK+ D +YE
Sbjct: 667  DVSPIESARGRFLQIILDYFISQHVIEVCENKRDHETGSGGGQDNNNTKVKRKSDDTKYE 726

Query: 61   GDPRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKG 120
            GDP FALPLMY+AN+YETLV + N+RLAS  GIREKTIGVALEAAGGLYR L KKFPKKG
Sbjct: 727  GDPSFALPLMYIANLYETLVGEANVRLASLTGIREKTIGVALEAAGGLYRKLTKKFPKKG 786

Query: 121  SCTYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTG 180
            +C Y+RRELATS+ETRTRFPELVI EEKRVRFVVVNGLDIVEKP+N+PIEDAEWFKRLTG
Sbjct: 787  ACMYRRRELATSVETRTRFPELVIHEEKRVRFVVVNGLDIVEKPDNLPIEDAEWFKRLTG 846

Query: 181  RNEVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQN 240
            RNEVA+SA+DYKFY PRHK+RRV  NSVS+I  LP FPG D SST+   QGF ++SE Q+
Sbjct: 847  RNEVAVSARDYKFYCPRHKHRRV-QNSVSSIHGLPTFPGMD-SSTLANTQGFRSVSEDQS 904

Query: 241  QQQ------TPSKHHMQPLSHQP-QFH---HIHNNHHQQIHQGQQHPAHF-SQNHRCGPP 289
            QQQ      +PSKHHM  LSH P QFH   H  ++HHQ I+Q Q   AHF  QNH+C   
Sbjct: 905  QQQQQQHTPSPSKHHMSSLSHHPHQFHQPIHQSHHHHQPIYQSQHAAAHFPGQNHQCD-- 962

Query: 290  PHLPDIAHAHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFC 349
               P+++H HQSP+ISQHMACLQPLTGG      HVMP SPAKFCD+CGA YLR+TSKFC
Sbjct: 963  ---PELSHTHQSPSISQHMACLQPLTGG------HVMPTSPAKFCDQCGAQYLRDTSKFC 1013

Query: 350  SECGVKRLGI 359
            SECG KR GI
Sbjct: 1014 SECGCKRFGI 1023

Source: Eutrema halophilum

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297817834|ref|XP_002876800.1| hypothetical protein ARALYDRAFT_484139 [Arabidopsis lyrata subsp. lyrata] gi|297322638|gb|EFH53059.1| hypothetical protein ARALYDRAFT_484139 [Arabidopsis lyrata subsp. lyrata]

 Score =  475 bits (1222), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 244/362 (67%), Positives = 285/362 (78%), Gaps = 21/362 (5%)

Query: 6    DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLS---KRKNRDVQYEGD 62
            DVSPIE+AR RFLQII+D+FI+ HVIEV ++  ++    G    S   KRK+ D +YEGD
Sbjct: 662  DVSPIEAARGRFLQIILDYFISQHVIEVAENKRDHETDSGGRDNSNKVKRKSDDTRYEGD 721

Query: 63   PRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSC 122
            P FALPLMY+AN+YETLV + N+RLAS NGIR+KTIGVALEAAGGLYR L KKFPKKG+C
Sbjct: 722  PSFALPLMYIANLYETLVGEANVRLASLNGIRDKTIGVALEAAGGLYRKLTKKFPKKGTC 781

Query: 123  TYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRN 182
             Y+RRELATS+ETRTRFPELVI EEKRVRFVVVNGLDIVEKP+++PIEDAEWFKRLTGRN
Sbjct: 782  MYRRRELATSVETRTRFPELVIHEEKRVRFVVVNGLDIVEKPDDLPIEDAEWFKRLTGRN 841

Query: 183  EVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQ 242
            +VAISA+DYKFY PR K+RR+  NSVS+I  LP FPG D SST+ + QGF +++E Q+QQ
Sbjct: 842  DVAISARDYKFYCPRRKHRRL-QNSVSSISGLPTFPGID-SSTLASTQGFRSVNEDQSQQ 899

Query: 243  Q---TPSKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPA-HF-SQNHRCGPPPHLPDIAH 297
            Q   +PSKHHM  LSHQ       ++HH Q     QH A HF  QNH+C      P+++H
Sbjct: 900  QHTPSPSKHHMSSLSHQFHQSIHQSHHHHQSIYQNQHAATHFPGQNHQCD-----PELSH 954

Query: 298  AHQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRL 357
             HQSP+ISQHMACLQPLTGG      HVMP SPAKFCD+CGA YLRETSKFCSECG KRL
Sbjct: 955  THQSPSISQHMACLQPLTGG------HVMPNSPAKFCDQCGAQYLRETSKFCSECGSKRL 1008

Query: 358  GI 359
            GI
Sbjct: 1009 GI 1010

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312190399|gb|ADQ43199.1| unknown [Eutrema parvulum]

 Score =  474 bits (1219), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 249/365 (68%), Positives = 287/365 (78%), Gaps = 26/365 (7%)

Query: 6    DVSPIESARARFLQIIVDHFINDHVIEVTDSGAEYSQQPGQDKLS---KRKNRDVQYEGD 62
            +VSPIESAR RFLQII+D+FI+ HVIEV ++  ++    G    S   KRK+ D +YEGD
Sbjct: 779  EVSPIESARGRFLQIILDYFISQHVIEVCENKRDHEADSGGKDNSNKVKRKSDDTRYEGD 838

Query: 63   PRFALPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSC 122
            P FALPLMY+AN+YETLV + N+R+AS NGIREKT+GVALEAAGGLYR L KKFPKK +C
Sbjct: 839  PSFALPLMYIANLYETLVGEANVRVASLNGIREKTLGVALEAAGGLYRKLTKKFPKK-TC 897

Query: 123  TYKRRELATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRN 182
             Y+RRELATS+ETRTRFPELVI EEKRVRFVVVNGLDIVEKP+N+PIEDAE F+RLTGRN
Sbjct: 898  MYRRRELATSVETRTRFPELVIHEEKRVRFVVVNGLDIVEKPDNIPIEDAE-FQRLTGRN 956

Query: 183  EVAISAQDYKFYSPRHKYRRVASNSVSNIPVLPGFPGTDNSSTMVTAQGFHTISEPQNQQ 242
            EVA+SA+DYKFY PRHK+RRV  NSVS I  LP FPG D SST+   QGF ++SE Q+QQ
Sbjct: 957  EVAVSARDYKFYCPRHKHRRV-QNSVSTIHGLPTFPGID-SSTLADTQGFPSVSEDQSQQ 1014

Query: 243  QTP--SKHHMQPLSHQP-QFH---HIHNNHHQQIHQGQQHPAHF-SQNHRCGPPPHLPDI 295
             TP  SKHHM  LSH P QFH   H   +HHQ I+QGQ   AHF S NH+C      P++
Sbjct: 1015 HTPSSSKHHMSSLSHHPHQFHQSIHQSQHHHQSIYQGQHAAAHFPSPNHQCD-----PEL 1069

Query: 296  AHA-HQSPTISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLRETSKFCSECGV 354
            +HA HQSP+ISQHM CLQPLTGG      HVMP SPAKFCD+CG+ YLRETSKFCSECG 
Sbjct: 1070 SHAQHQSPSISQHMTCLQPLTGG------HVMPTSPAKFCDQCGSQYLRETSKFCSECGS 1123

Query: 355  KRLGI 359
            KRLGI
Sbjct: 1124 KRLGI 1128

Source: Eutrema parvulum

Species: Eutrema parvulum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

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	359
UNIPROTKB|Q96GY0	325	ZC2HC1A "Zinc finger C2HC doma	0.130	0.144	0.448	0.00072

UNIPROTKB|Q96GY0 ZC2HC1A "Zinc finger C2HC domain-containing protein 1A" [Homo sapiens (taxid:9606)]

 Score = 113 (44.8 bits), Expect = 0.00072, P = 0.00072
 Identities = 22/49 (44%), Positives = 29/49 (59%)

Query:   310 CLQPLTGGHV-GERLHVMPASPAKFCDECGAPYLRETSKFCSECGVKRL 357
             C   L GG++ G   H  P +  KFC ECG  Y  E +KFC ECG++R+
Sbjct:   276 CASSLNGGNIKGIEGH-SPGNLPKFCHECGTKYPVEWAKFCCECGIRRM 323


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        0.318   0.134   0.402    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      359       334   0.00091  116 3  11 22  0.40    34
                                                     33  0.45    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:  1
  No. of states in DFA:  605 (64 KB)
  Total size of DFA:  232 KB (2127 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:  27.82u 0.11s 27.93t   Elapsed:  00:00:01
  Total cpu time:  27.82u 0.11s 27.93t   Elapsed:  00:00:01
  Start:  Sat May 11 00:04:36 2013   End:  Sat May 11 00:04:37 2013

GO:0046872 "metal ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q56XX3	Y2215_ARATH	No assigned EC number	0.6620	0.9136	0.7592	yes	no

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

Your Input: GSVIVG00021282001 SubName- Full=Chromosome chr1 scaffold_22, whole genome shotgun sequence; (455 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	359
pfam13248	26	pfam13248, zf-ribbon_3, zinc-ribbon domain	0.001
pfam13240	23	pfam13240, zinc_ribbon_2, zinc-ribbon domain	0.003
PHA03420	137	PHA03420, PHA03420, E4 protein; Provisional	0.004

>gnl|CDD|205428 pfam13248, zf-ribbon_3, zinc-ribbon domain

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 1/25 (4%)

Query: 331 AKFCDECGAPYLRETSKFCSECGVK 355
            KFC  CGA  L   +KFC  CG K
Sbjct: 2   TKFCPNCGAE-LEPDAKFCPNCGAK 25

This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773. Length = 26

>gnl|CDD|205420 pfam13240, zinc_ribbon_2, zinc-ribbon domain

 Score = 34.4 bits (80), Expect = 0.003
 Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 1/21 (4%)

Query: 333 FCDECGAPYLRETSKFCSECG 353
           FC  CGA  L + +KFC  CG
Sbjct: 1   FCPNCGAE-LPDGAKFCPNCG 20

This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773. Length = 23

>gnl|CDD|177648 PHA03420, PHA03420, E4 protein; Provisional

 Score = 36.9 bits (85), Expect = 0.004
 Identities = 15/59 (25%), Positives = 20/59 (33%)

Query: 234 TISEPQNQQQTPSKHHMQPLSHQPQFHHIHNNHHQQIHQGQQHPAHFSQNHRCGPPPHL 292
             +E Q+ Q+    H     +      H H + HQQ     Q   H  Q H   P   L
Sbjct: 26  GRAENQHIQREGGNHRTWDPADYLDRPHHHPHRHQQDDHHLQDRQHLPQQHLQRPHHPL 84

Length = 137

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	359
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	98.31
PF13248	26	zf-ribbon_3: zinc-ribbon domain	98.24
COG4260	345	Membrane protease subunit, stomatin/prohibitin fam	97.67
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	97.16
PF12773	50	DZR: Double zinc ribbon	96.84
PF12773	50	DZR: Double zinc ribbon	96.52
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	96.01
KOG3940	351	consensus Uncharacterized conserved protein [Funct	95.76
smart00661	52	RPOL9 RNA polymerase subunit 9.	95.41
PRK00420	112	hypothetical protein; Validated	95.37
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	94.91
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	93.81
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	93.29
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	93.14
PRK07418	616	acetolactate synthase 3 catalytic subunit; Reviewe	92.62
PRK14714	1337	DNA polymerase II large subunit; Provisional	92.41
COG2816	279	NPY1 NTP pyrophosphohydrolases containing a Zn-fin	92.03
PRK00241	256	nudC NADH pyrophosphatase; Reviewed	91.72
PRK04023	1121	DNA polymerase II large subunit; Validated	91.47
PRK04023	1121	DNA polymerase II large subunit; Validated	90.94
PRK12496	164	hypothetical protein; Provisional	90.81
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	90.79
PRK12495	226	hypothetical protein; Provisional	90.59
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	90.55
PF13248	26	zf-ribbon_3: zinc-ribbon domain	90.39
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	90.08
PRK14714	1337	DNA polymerase II large subunit; Provisional	89.85
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	89.35
PRK00432	50	30S ribosomal protein S27ae; Validated	89.13
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	88.76
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	87.78
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	87.78
PF09889	59	DUF2116: Uncharacterized protein containing a Zn-r	87.58
COG1545	140	Predicted nucleic-acid-binding protein containing	87.53
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	87.21
COG0675	364	Transposase and inactivated derivatives [DNA repli	87.15
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	87.01
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	86.67
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	86.29
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	85.82
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	85.81
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	85.31
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	84.43
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	84.02
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	83.87
PF10083	158	DUF2321: Uncharacterized protein conserved in bact	83.29
PF14319	111	Zn_Tnp_IS91: Transposase zinc-binding domain	81.96
PF11781	36	RRN7: RNA polymerase I-specific transcription init	81.89
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	81.6
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	81.41
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	80.8

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=98.31  E-value=2.7e-07  Score=59.04  Aligned_cols=23  Identities=39%  Similarity=1.091  Sum_probs=20.7

Q ss_pred             CCCcCCCCCCCCCCCCCcccCCcC
Q 018197          333 FCDECGAPYLRETSKFCSECGVKR  356 (359)
Q Consensus       333 FCpeCGt~l~~~~AKFCpECGtKr  356 (359)
                      ||++||+++. ++++||++||+++
T Consensus         1 ~Cp~CG~~~~-~~~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEIE-DDAKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCCC-CcCcchhhhCCcC
Confidence            7999999997 4699999999975

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=98.24  E-value=5.2e-07  Score=58.42  Aligned_cols=25  Identities=44%  Similarity=1.054  Sum_probs=21.4

Q ss_pred             CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197          331 AKFCDECGAPYLRETSKFCSECGVKR  356 (359)
Q Consensus       331 sKFCpeCGt~l~~~~AKFCpECGtKr  356 (359)
                      .++|++||+.+ ..+++||+.||+++
T Consensus         2 ~~~Cp~Cg~~~-~~~~~fC~~CG~~L   26 (26)
T PF13248_consen    2 EMFCPNCGAEI-DPDAKFCPNCGAKL   26 (26)
T ss_pred             cCCCcccCCcC-CcccccChhhCCCC
Confidence            47899999965 46799999999985

>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]

Probab=97.67  E-value=2.1e-05  Score=76.94  Aligned_cols=54  Identities=19%  Similarity=0.156  Sum_probs=43.3

Q ss_pred             hhhhhhhccchhhhHhhheeEeEEEeecceeeccCCCCChhhHHHHHHHhcccccccccc
Q 018197          130 ATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQ  189 (359)
Q Consensus       130 Ats~etrt~fpelv~~EekrvrfvVVnGl~IVE~p~Nlp~eDqewfkRLtgr~EVai~g~  189 (359)
                      |.++|--..+.|+++..-+++|+.|+++-  |- ++|+|+|-|.-|++   |+--++.||
T Consensus       188 an~~elsk~m~e~Ld~q~~q~Gm~v~sfq--va-Sisypde~Q~lin~---r~s~~M~gD  241 (345)
T COG4260         188 ANQMELSKYMAEVLDEQWTQYGMAVDSFQ--VA-SISYPDESQALINM---RNSGAMLGD  241 (345)
T ss_pred             hhHHHHHHHHHHHHhHHHHhhCceEeeEE--EE-EecCcHHHHHHHHh---hcccccccC
Confidence            34555556778999999999999999988  77 89999999988776   444677776

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=97.16  E-value=0.0002  Score=47.28  Aligned_cols=24  Identities=46%  Similarity=0.996  Sum_probs=20.6

Q ss_pred             CCCCcCCCCCCCCCCCCCcccCCcC
Q 018197          332 KFCDECGAPYLRETSKFCSECGVKR  356 (359)
Q Consensus       332 KFCpeCGt~l~~~~AKFCpECGtKr  356 (359)
                      |-||+||+.++. .+|+||.||...
T Consensus         1 K~CP~C~~~V~~-~~~~Cp~CG~~F   24 (26)
T PF10571_consen    1 KTCPECGAEVPE-SAKFCPHCGYDF   24 (26)
T ss_pred             CcCCCCcCCchh-hcCcCCCCCCCC
Confidence            679999999875 599999999754

Several members are annotated as putative helicases.

>PF12773 DZR: Double zinc ribbon

Probab=96.84  E-value=0.0007  Score=47.99  Aligned_cols=25  Identities=44%  Similarity=1.161  Sum_probs=11.3

Q ss_pred             CCCCCcCCCCCC--CCCCCCCcccCCc
Q 018197          331 AKFCDECGAPYL--RETSKFCSECGVK  355 (359)
Q Consensus       331 sKFCpeCGt~l~--~~~AKFCpECGtK  355 (359)
                      ++||+.||+++.  ....++|+.||+.
T Consensus        12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~   38 (50)
T PF12773_consen   12 AKFCPHCGTPLPPPDQSKKICPNCGAE   38 (50)
T ss_pred             ccCChhhcCChhhccCCCCCCcCCcCC
Confidence            445555555544  3333444444443

>PF12773 DZR: Double zinc ribbon

Probab=96.52  E-value=0.0018  Score=45.86  Aligned_cols=25  Identities=40%  Similarity=0.990  Sum_probs=21.1

Q ss_pred             CCCCCCCCcCCCCCCCCCCCCCcccC
Q 018197          328 ASPAKFCDECGAPYLRETSKFCSECG  353 (359)
Q Consensus       328 ~~~sKFCpeCGt~l~~~~AKFCpECG  353 (359)
                      ....++|+.||+.+. .+++||++||
T Consensus        26 ~~~~~~C~~Cg~~~~-~~~~fC~~CG   50 (50)
T PF12773_consen   26 DQSKKICPNCGAENP-PNAKFCPNCG   50 (50)
T ss_pred             cCCCCCCcCCcCCCc-CCcCccCccc
Confidence            455789999999965 5699999998

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=96.01  E-value=0.0023  Score=42.80  Aligned_cols=26  Identities=35%  Similarity=0.879  Sum_probs=17.6

Q ss_pred             CCCCCCcCCCCC---CCCCCCCCcccCCc
Q 018197          330 PAKFCDECGAPY---LRETSKFCSECGVK  355 (359)
Q Consensus       330 ~sKFCpeCGt~l---~~~~AKFCpECGtK  355 (359)
                      +.+||+.||.++   ..+|++-|+.||..
T Consensus         2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred             CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence            468999999997   45689999999963

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>KOG3940 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.76  E-value=0.0044  Score=61.46  Aligned_cols=28  Identities=18%  Similarity=0.364  Sum_probs=24.8

Q ss_pred             CCCCCcCCCCCC-CCCCCCCcccCCcCcC
Q 018197          331 AKFCDECGAPYL-RETSKFCSECGVKRLG  358 (359)
Q Consensus       331 sKFCpeCGt~l~-~~~AKFCpECGtKr~~  358 (359)
                      .+|||+||..+. ..|+|||++|+..++.
T Consensus       322 ~~~Cp~cg~r~~~~~~ak~~~~c~~r~~i  350 (351)
T KOG3940|consen  322 YVQCPHCGRRFNEQAAAKHIPKCVNRVHI  350 (351)
T ss_pred             cccCccccccchHHHHHhhcccccccccc
Confidence            599999999997 6799999999988653

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=95.41  E-value=0.011  Score=41.94  Aligned_cols=24  Identities=33%  Similarity=0.928  Sum_probs=18.2

Q ss_pred             CCCCcCCCCCCCC-C----CCCCcccCCc
Q 018197          332 KFCDECGAPYLRE-T----SKFCSECGVK  355 (359)
Q Consensus       332 KFCpeCGt~l~~~-~----AKFCpECGtK  355 (359)
                      +|||+||..+... +    -..|+.||..
T Consensus         1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~   29 (52)
T smart00661        1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYE   29 (52)
T ss_pred             CCCCCCCCccccccCCCCCEEECCcCCCe
Confidence            6999999988433 2    3569999975

>PRK00420 hypothetical protein; Validated

Probab=95.37  E-value=0.0084  Score=51.32  Aligned_cols=26  Identities=27%  Similarity=0.675  Sum_probs=22.7

Q ss_pred             CCCCCcCCCCCC--CCCCCCCcccCCcC
Q 018197          331 AKFCDECGAPYL--RETSKFCSECGVKR  356 (359)
Q Consensus       331 sKFCpeCGt~l~--~~~AKFCpECGtKr  356 (359)
                      +.-||.||+++.  ..+..|||.||...
T Consensus        23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~   50 (112)
T PRK00420         23 SKHCPVCGLPLFELKDGEVVCPVHGKVY   50 (112)
T ss_pred             cCCCCCCCCcceecCCCceECCCCCCee
Confidence            588999999996  57899999999864

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=94.91  E-value=0.0069  Score=42.27  Aligned_cols=23  Identities=43%  Similarity=1.190  Sum_probs=12.4

Q ss_pred             CCCCcCCCCC---CCC----CCCCCcccCC
Q 018197          332 KFCDECGAPY---LRE----TSKFCSECGV  354 (359)
Q Consensus       332 KFCpeCGt~l---~~~----~AKFCpECGt  354 (359)
                      |||+.||.++   +++    .-.+|+.||.
T Consensus         1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~   30 (34)
T PF14803_consen    1 KFCPQCGGPLERRIPEGDDRERLVCPACGF   30 (34)
T ss_dssp             -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred             CccccccChhhhhcCCCCCccceECCCCCC
Confidence            7999999998   221    2568999985

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=93.81  E-value=0.046  Score=46.24  Aligned_cols=27  Identities=33%  Similarity=0.840  Sum_probs=20.2

Q ss_pred             CCCC-CCcCCCCC--CCCCCCCCcccCCcC
Q 018197          330 PAKF-CDECGAPY--LRETSKFCSECGVKR  356 (359)
Q Consensus       330 ~sKF-CpeCGt~l--~~~~AKFCpECGtKr  356 (359)
                      +.|. |++||+++  +...-.-||.||+-.
T Consensus         7 GtKR~Cp~CG~kFYDLnk~PivCP~CG~~~   36 (108)
T PF09538_consen    7 GTKRTCPSCGAKFYDLNKDPIVCPKCGTEF   36 (108)
T ss_pred             CCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence            4454 99999997  333567799999864

The function of members of this family is unknown.

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=93.29  E-value=0.031  Score=49.27  Aligned_cols=25  Identities=44%  Similarity=1.162  Sum_probs=20.9

Q ss_pred             CCCCCcCCCCCCC-CCCCCCcccCCc
Q 018197          331 AKFCDECGAPYLR-ETSKFCSECGVK  355 (359)
Q Consensus       331 sKFCpeCGt~l~~-~~AKFCpECGtK  355 (359)
                      ++-||.||+++.. .|--|||-||.+
T Consensus        28 ~~hCp~Cg~PLF~KdG~v~CPvC~~~   53 (131)
T COG1645          28 AKHCPKCGTPLFRKDGEVFCPVCGYR   53 (131)
T ss_pred             HhhCcccCCcceeeCCeEECCCCCce
Confidence            6789999999964 467799999965

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=93.14  E-value=0.04  Score=39.21  Aligned_cols=24  Identities=33%  Similarity=0.703  Sum_probs=18.4

Q ss_pred             CCcCCCCCC---CCCCCCCcccCCcCc
Q 018197          334 CDECGAPYL---RETSKFCSECGVKRL  357 (359)
Q Consensus       334 CpeCGt~l~---~~~AKFCpECGtKr~  357 (359)
                      |++||+.+.   ......||.||.++.
T Consensus         6 C~~CG~~~~~~~~~~~~~Cp~CG~~~~   32 (46)
T PRK00398          6 CARCGREVELDEYGTGVRCPYCGYRIL   32 (46)
T ss_pred             CCCCCCEEEECCCCCceECCCCCCeEE
Confidence            999999872   222689999999853

>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed

Probab=92.62  E-value=0.065  Score=54.66  Aligned_cols=27  Identities=41%  Similarity=0.966  Sum_probs=22.1

Q ss_pred             CCCCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197          329 SPAKFCDECGAPYLRETSKFCSECGVKR  356 (359)
Q Consensus       329 ~~sKFCpeCGt~l~~~~AKFCpECGtKr  356 (359)
                      ...++|++||+.+. ..+|||++||.++
T Consensus       590 ~~~~~~~~~~~~~~-~~~~f~~~~g~~~  616 (616)
T PRK07418        590 AELIYCSNCGAKNP-STHRFCPECGTKL  616 (616)
T ss_pred             cCcccCCCCCCcCc-cccccchhhCCCC
Confidence            35678999999854 5699999999875

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=92.41  E-value=0.088  Score=59.77  Aligned_cols=25  Identities=28%  Similarity=0.668  Sum_probs=15.8

Q ss_pred             CCCcCCCCCCCC--CCCCCcccCCcCc
Q 018197          333 FCDECGAPYLRE--TSKFCSECGVKRL  357 (359)
Q Consensus       333 FCpeCGt~l~~~--~AKFCpECGtKr~  357 (359)
                      +|+.||+.+...  ++.|||.||+++.
T Consensus       694 ~CPsCGaev~~des~a~~CP~CGtplv  720 (1337)
T PRK14714        694 VCPDCGAEVPPDESGRVECPRCDVELT  720 (1337)
T ss_pred             eCccCCCccCCCccccccCCCCCCccc
Confidence            355555554322  3779999998864

>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]

Probab=92.03  E-value=0.075  Score=51.70  Aligned_cols=27  Identities=26%  Similarity=0.784  Sum_probs=23.5

Q ss_pred             CCCCCCCcCCCCC---CCCCCCCCcccCCc
Q 018197          329 SPAKFCDECGAPY---LRETSKFCSECGVK  355 (359)
Q Consensus       329 ~~sKFCpeCGt~l---~~~~AKFCpECGtK  355 (359)
                      ...+||+.||+++   ..++++-|+.||..
T Consensus       109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~  138 (279)
T COG2816         109 RSHRFCGRCGTKTYPREGGWARVCPKCGHE  138 (279)
T ss_pred             hhCcCCCCCCCcCccccCceeeeCCCCCCc
Confidence            6689999999998   35689999999986

>PRK00241 nudC NADH pyrophosphatase; Reviewed

Probab=91.72  E-value=0.088  Score=49.32  Aligned_cols=27  Identities=30%  Similarity=0.815  Sum_probs=22.6

Q ss_pred             CCCCCCCcCCCCCC---CCCCCCCcccCCc
Q 018197          329 SPAKFCDECGAPYL---RETSKFCSECGVK  355 (359)
Q Consensus       329 ~~sKFCpeCGt~l~---~~~AKFCpECGtK  355 (359)
                      ...+||+.||+++.   ....+.|+.||..
T Consensus        97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~  126 (256)
T PRK00241         97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRER  126 (256)
T ss_pred             hcCccccccCCCCeecCCceeEECCCCCCE
Confidence            66899999999973   4568999999965

>PRK04023 DNA polymerase II large subunit; Validated

Probab=91.47  E-value=0.11  Score=58.10  Aligned_cols=39  Identities=13%  Similarity=0.158  Sum_probs=17.2

Q ss_pred             hhHHHHHHHHHHHHHHHHhhhhhccccchhhhhHHHHhh
Q 018197           67 LPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAA  105 (359)
Q Consensus        67 LPLmyvANlyetlv~~vn~rlasl~g~~ekt~gvaleaa  105 (359)
                      +|--|+---|+..+...+.......++-+-|.--||+.|
T Consensus       420 ~Ps~y~~EWW~qe~~~~~~~~~~~~~l~~p~~~eA~~~s  458 (1121)
T PRK04023        420 LPSSYCEEWWIQELEAAGAEYEPEFDLENPSQEEALKIS  458 (1121)
T ss_pred             CCccccHHHHHHHHHhcccccCccccccCCCHHHHHHHH
Confidence            444455444444443333333223333344555666543

>PRK04023 DNA polymerase II large subunit; Validated

Probab=90.94  E-value=0.12  Score=57.66  Aligned_cols=23  Identities=26%  Similarity=0.652  Sum_probs=11.2

Q ss_pred             CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197          331 AKFCDECGAPYLRETSKFCSECGVKR  356 (359)
Q Consensus       331 sKFCpeCGt~l~~~~AKFCpECGtKr  356 (359)
                      .+||+.||+...   ...||+||.+.
T Consensus       651 i~fCP~CG~~~~---~y~CPKCG~El  673 (1121)
T PRK04023        651 VYRCPRCGIEVE---EDECEKCGREP  673 (1121)
T ss_pred             ceeCccccCcCC---CCcCCCCCCCC
Confidence            445555555432   24455555553

>PRK12496 hypothetical protein; Provisional

Probab=90.81  E-value=0.15  Score=45.33  Aligned_cols=25  Identities=28%  Similarity=0.691  Sum_probs=19.9

Q ss_pred             CCCCcCCCCCCC-CCCCCCcccCCcC
Q 018197          332 KFCDECGAPYLR-ETSKFCSECGVKR  356 (359)
Q Consensus       332 KFCpeCGt~l~~-~~AKFCpECGtKr  356 (359)
                      +.|+.||..+.. ....|||.||.++
T Consensus       128 ~~C~gC~~~~~~~~~~~~C~~CG~~~  153 (164)
T PRK12496        128 KVCKGCKKKYPEDYPDDVCEICGSPV  153 (164)
T ss_pred             EECCCCCccccCCCCCCcCCCCCChh
Confidence            349999999964 2468999999985

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=90.79  E-value=0.1  Score=33.53  Aligned_cols=13  Identities=54%  Similarity=1.290  Sum_probs=11.3

Q ss_pred             CCCCCCCcCCCCC
Q 018197          329 SPAKFCDECGAPY  341 (359)
Q Consensus       329 ~~sKFCpeCGt~l  341 (359)
                      .+++||+.||+++
T Consensus        11 ~~~~fC~~CG~~l   23 (23)
T PF13240_consen   11 DDAKFCPNCGTPL   23 (23)
T ss_pred             CcCcchhhhCCcC
Confidence            5689999999975

>PRK12495 hypothetical protein; Provisional

Probab=90.59  E-value=0.12  Score=49.14  Aligned_cols=27  Identities=37%  Similarity=0.971  Sum_probs=22.5

Q ss_pred             CCCCCCcCCCCCCC-CCCCCCcccCCcC
Q 018197          330 PAKFCDECGAPYLR-ETSKFCSECGVKR  356 (359)
Q Consensus       330 ~sKFCpeCGt~l~~-~~AKFCpECGtKr  356 (359)
                      ..++|+.||.+++. +|..||+.|+...
T Consensus        41 sa~hC~~CG~PIpa~pG~~~Cp~CQ~~~   68 (226)
T PRK12495         41 TNAHCDECGDPIFRHDGQEFCPTCQQPV   68 (226)
T ss_pred             chhhcccccCcccCCCCeeECCCCCCcc
Confidence            37889999999963 4789999999763

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=90.55  E-value=0.14  Score=37.17  Aligned_cols=23  Identities=30%  Similarity=1.152  Sum_probs=19.5

Q ss_pred             CCCCCcCCCCCC--CCCCCCCcccC
Q 018197          331 AKFCDECGAPYL--RETSKFCSECG  353 (359)
Q Consensus       331 sKFCpeCGt~l~--~~~AKFCpECG  353 (359)
                      +..||.||.++.  ..+..||+.|+
T Consensus        17 ~~~Cp~C~~PL~~~k~g~~~Cv~C~   41 (41)
T PF06677_consen   17 DEHCPDCGTPLMRDKDGKIYCVSCG   41 (41)
T ss_pred             cCccCCCCCeeEEecCCCEECCCCC
Confidence            678999999984  45788999997

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=90.39  E-value=0.11  Score=33.61  Aligned_cols=13  Identities=54%  Similarity=1.124  Sum_probs=11.4

Q ss_pred             CCCCCCCcCCCCC
Q 018197          329 SPAKFCDECGAPY  341 (359)
Q Consensus       329 ~~sKFCpeCGt~l  341 (359)
                      .+.+||+.||++|
T Consensus        14 ~~~~fC~~CG~~L   26 (26)
T PF13248_consen   14 PDAKFCPNCGAKL   26 (26)
T ss_pred             cccccChhhCCCC
Confidence            5689999999985

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=90.08  E-value=0.086  Score=36.61  Aligned_cols=24  Identities=33%  Similarity=0.905  Sum_probs=15.8

Q ss_pred             CCCCcCCCCCCCC----CCCCCcccCCc
Q 018197          332 KFCDECGAPYLRE----TSKFCSECGVK  355 (359)
Q Consensus       332 KFCpeCGt~l~~~----~AKFCpECGtK  355 (359)
                      +|||+||.-|.+.    ....|..||..
T Consensus         2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~   29 (35)
T PF02150_consen    2 RFCPECGNLLYPKEDKEKRVACRTCGYE   29 (35)
T ss_dssp             -BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred             eeCCCCCccceEcCCCccCcCCCCCCCc
Confidence            7999999998322    12259999864

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=89.85  E-value=0.16  Score=57.72  Aligned_cols=22  Identities=27%  Similarity=0.819  Sum_probs=10.7

Q ss_pred             CCCCcCCCCCCCCCCCCCcccCCc
Q 018197          332 KFCDECGAPYLRETSKFCSECGVK  355 (359)
Q Consensus       332 KFCpeCGt~l~~~~AKFCpECGtK  355 (359)
                      +||++||++...  .-+||.||.+
T Consensus       680 ~fCP~CGs~te~--vy~CPsCGae  701 (1337)
T PRK14714        680 NRCPDCGTHTEP--VYVCPDCGAE  701 (1337)
T ss_pred             ccCcccCCcCCC--ceeCccCCCc
Confidence            355555555422  1255555554

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=89.35  E-value=0.18  Score=36.78  Aligned_cols=24  Identities=38%  Similarity=0.823  Sum_probs=19.1

Q ss_pred             CCcCCCCCC--CCCCCCCcccCCcCc
Q 018197          334 CDECGAPYL--RETSKFCSECGVKRL  357 (359)
Q Consensus       334 CpeCGt~l~--~~~AKFCpECGtKr~  357 (359)
                      |.+||+.+.  ..+.--||+||.+++
T Consensus         5 C~~Cg~~~~~~~~~~irC~~CG~rIl   30 (44)
T smart00659        5 CGECGRENEIKSKDVVRCRECGYRIL   30 (44)
T ss_pred             CCCCCCEeecCCCCceECCCCCceEE
Confidence            999999873  235788999998864

present in RNA polymerase I, II and III

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=89.13  E-value=0.21  Score=37.24  Aligned_cols=26  Identities=31%  Similarity=0.732  Sum_probs=19.4

Q ss_pred             CCCCCCcCCC-CC-CCCCCCCCcccCCc
Q 018197          330 PAKFCDECGA-PY-LRETSKFCSECGVK  355 (359)
Q Consensus       330 ~sKFCpeCGt-~l-~~~~AKFCpECGtK  355 (359)
                      ..+|||.||. -+ ...+..-|..||..
T Consensus        19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt   46 (50)
T PRK00432         19 KNKFCPRCGSGFMAEHLDRWHCGKCGYT   46 (50)
T ss_pred             ccCcCcCCCcchheccCCcEECCCcCCE
Confidence            3679999999 44 33457789999964

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=88.76  E-value=0.16  Score=34.40  Aligned_cols=24  Identities=21%  Similarity=0.614  Sum_probs=17.2

Q ss_pred             CCcCCCCCC------C--CCCCCCcccCCcCc
Q 018197          334 CDECGAPYL------R--ETSKFCSECGVKRL  357 (359)
Q Consensus       334 CpeCGt~l~------~--~~AKFCpECGtKr~  357 (359)
                      ||+||+.+-      .  ...-.||.||+.+.
T Consensus         5 CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         5 CPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             CCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence            999999761      1  11248999998764

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=87.78  E-value=0.33  Score=38.12  Aligned_cols=25  Identities=32%  Similarity=0.937  Sum_probs=16.0

Q ss_pred             CCCC-CCcCCCCCC--------CCCCCCCcccCC
Q 018197          330 PAKF-CDECGAPYL--------RETSKFCSECGV  354 (359)
Q Consensus       330 ~sKF-CpeCGt~l~--------~~~AKFCpECGt  354 (359)
                      .++| ||+||+.++        ....--||+||.
T Consensus        23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF   56 (59)
T PRK14890         23 AVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF   56 (59)
T ss_pred             cCEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence            4666 888888732        233556888875

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=87.78  E-value=0.23  Score=41.70  Aligned_cols=27  Identities=15%  Similarity=0.423  Sum_probs=19.6

Q ss_pred             CCCCCCCcCCCCCCCC-CCCCCcccCCc
Q 018197          329 SPAKFCDECGAPYLRE-TSKFCSECGVK  355 (359)
Q Consensus       329 ~~sKFCpeCGt~l~~~-~AKFCpECGtK  355 (359)
                      +..-+|..||...... .-..||.||..
T Consensus        68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~   95 (113)
T PRK12380         68 PAQAWCWDCSQVVEIHQHDAQCPHCHGE   95 (113)
T ss_pred             CcEEEcccCCCEEecCCcCccCcCCCCC
Confidence            4456799999887554 33349999975

>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown

Probab=87.58  E-value=0.16  Score=39.42  Aligned_cols=25  Identities=40%  Similarity=0.962  Sum_probs=20.4

Q ss_pred             CCCCCCcCCCCCCCCCCCCCc-ccCCc
Q 018197          330 PAKFCDECGAPYLRETSKFCS-ECGVK  355 (359)
Q Consensus       330 ~sKFCpeCGt~l~~~~AKFCp-ECGtK  355 (359)
                      +-|-|+.||++++. +-.||+ +|+..
T Consensus         2 ~HkHC~~CG~~Ip~-~~~fCS~~C~~~   27 (59)
T PF09889_consen    2 PHKHCPVCGKPIPP-DESFCSPKCREE   27 (59)
T ss_pred             CCCcCCcCCCcCCc-chhhhCHHHHHH
Confidence            35779999999985 499995 99865

They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.

>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]

Probab=87.53  E-value=0.26  Score=42.76  Aligned_cols=24  Identities=29%  Similarity=0.978  Sum_probs=20.8

Q ss_pred             CCCCCcCCCCCCCCCCCCCcccCCc
Q 018197          331 AKFCDECGAPYLRETSKFCSECGVK  355 (359)
Q Consensus       331 sKFCpeCGt~l~~~~AKFCpECGtK  355 (359)
                      +.-|.+||.-+.++ ..+||.||.+
T Consensus        29 g~kC~~CG~v~~PP-r~~Cp~C~~~   52 (140)
T COG1545          29 GTKCKKCGRVYFPP-RAYCPKCGSE   52 (140)
T ss_pred             EEEcCCCCeEEcCC-cccCCCCCCC
Confidence            45699999999766 8999999988

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=87.21  E-value=0.27  Score=41.50  Aligned_cols=32  Identities=16%  Similarity=0.425  Sum_probs=22.2

Q ss_pred             cCCCCCCCCCCcCCCCCCCC-CCCC-CcccCCcC
Q 018197          325 VMPASPAKFCDECGAPYLRE-TSKF-CSECGVKR  356 (359)
Q Consensus       325 i~p~~~sKFCpeCGt~l~~~-~AKF-CpECGtKr  356 (359)
                      +---+..-+|..||...... ...+ ||.||...
T Consensus        65 Ie~vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~   98 (117)
T PRK00564         65 IVDEKVELECKDCSHVFKPNALDYGVCEKCHSKN   98 (117)
T ss_pred             EEecCCEEEhhhCCCccccCCccCCcCcCCCCCc
Confidence            33334556799999887554 3455 99999863

>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=87.15  E-value=0.34  Score=42.94  Aligned_cols=28  Identities=32%  Similarity=0.611  Sum_probs=22.4

Q ss_pred             CCCCCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197          326 MPASPAKFCDECGAPYLRETSKFCSECGVK  355 (359)
Q Consensus       326 ~p~~~sKFCpeCGt~l~~~~AKFCpECGtK  355 (359)
                      .|..+++-|+.||.  .....-+||.||..
T Consensus       304 ~~~~tS~~C~~cg~--~~~r~~~C~~cg~~  331 (364)
T COG0675         304 PPYYTSKTCPCCGH--LSGRLFKCPRCGFV  331 (364)
T ss_pred             CCCCCcccccccCC--ccceeEECCCCCCe
Confidence            35788999999999  33345689999986

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=87.01  E-value=0.23  Score=34.77  Aligned_cols=10  Identities=50%  Similarity=1.192  Sum_probs=4.8

Q ss_pred             CCCcccCCcC
Q 018197          347 KFCSECGVKR  356 (359)
Q Consensus       347 KFCpECGtKr  356 (359)
                      ||||+||.++
T Consensus         1 kfC~~CG~~l   10 (34)
T PF14803_consen    1 KFCPQCGGPL   10 (34)
T ss_dssp             -B-TTT--B-
T ss_pred             CccccccChh
Confidence            8999999986

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=86.67  E-value=0.31  Score=37.52  Aligned_cols=25  Identities=28%  Similarity=0.731  Sum_probs=20.1

Q ss_pred             CCCCCcCCCCCC-CCCCCCCcccCCc
Q 018197          331 AKFCDECGAPYL-RETSKFCSECGVK  355 (359)
Q Consensus       331 sKFCpeCGt~l~-~~~AKFCpECGtK  355 (359)
                      ..-|+.||.++. .+..-.||+||++
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~Cgap   30 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAP   30 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCc
Confidence            456999999984 5668899999987

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=86.29  E-value=0.32  Score=40.84  Aligned_cols=28  Identities=18%  Similarity=0.332  Sum_probs=20.4

Q ss_pred             CCCCCCCcCCCCCCCCC-CCCCcccCCcC
Q 018197          329 SPAKFCDECGAPYLRET-SKFCSECGVKR  356 (359)
Q Consensus       329 ~~sKFCpeCGt~l~~~~-AKFCpECGtKr  356 (359)
                      +..-+|..||..+.... ..-||.||...
T Consensus        68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~   96 (115)
T TIGR00100        68 PVECECEDCSEEVSPEIDLYRCPKCHGIM   96 (115)
T ss_pred             CcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence            44567999998886543 44499999864

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=85.82  E-value=0.4  Score=33.21  Aligned_cols=24  Identities=42%  Similarity=0.841  Sum_probs=17.6

Q ss_pred             CCcCCCCCC--CCCCCCCcccCCcCc
Q 018197          334 CDECGAPYL--RETSKFCSECGVKRL  357 (359)
Q Consensus       334 CpeCGt~l~--~~~AKFCpECGtKr~  357 (359)
                      |.+||+...  ...+--|++||.+++
T Consensus         3 C~~Cg~~~~~~~~~~irC~~CG~RIl   28 (32)
T PF03604_consen    3 CGECGAEVELKPGDPIRCPECGHRIL   28 (32)
T ss_dssp             ESSSSSSE-BSTSSTSSBSSSS-SEE
T ss_pred             CCcCCCeeEcCCCCcEECCcCCCeEE
Confidence            889999872  334678999998865

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=85.81  E-value=0.54  Score=31.71  Aligned_cols=24  Identities=29%  Similarity=0.833  Sum_probs=17.1

Q ss_pred             CCCcCCCCCC------CCCCCCCcccCCcC
Q 018197          333 FCDECGAPYL------RETSKFCSECGVKR  356 (359)
Q Consensus       333 FCpeCGt~l~------~~~AKFCpECGtKr  356 (359)
                      .|++||..+-      .....-||+||...
T Consensus         7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~   36 (41)
T smart00834        7 RCEDCGHTFEVLQKISDDPLATCPECGGDV   36 (41)
T ss_pred             EcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence            3999999761      13356799999853

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=85.31  E-value=0.38  Score=40.44  Aligned_cols=28  Identities=14%  Similarity=0.402  Sum_probs=20.1

Q ss_pred             CCCCCCCcCCCCCCCC-CC-CCCcccCCcC
Q 018197          329 SPAKFCDECGAPYLRE-TS-KFCSECGVKR  356 (359)
Q Consensus       329 ~~sKFCpeCGt~l~~~-~A-KFCpECGtKr  356 (359)
                      +..-+|..||..+... .. ..||.||...
T Consensus        68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~   97 (114)
T PRK03681         68 EAECWCETCQQYVTLLTQRVRRCPQCHGDM   97 (114)
T ss_pred             CcEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence            4556799999887643 33 3399999763

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.43  E-value=0.31  Score=34.34  Aligned_cols=24  Identities=25%  Similarity=0.747  Sum_probs=16.5

Q ss_pred             CCCcCCCCCC----CCCCCCCcccCCcC
Q 018197          333 FCDECGAPYL----RETSKFCSECGVKR  356 (359)
Q Consensus       333 FCpeCGt~l~----~~~AKFCpECGtKr  356 (359)
                      .||.||...+    ..+--.|++||.-+
T Consensus         2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl   29 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPERGELVCPNCGLVL   29 (43)
T ss_dssp             SBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred             CCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence            4999999862    23455899999764

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=84.02  E-value=0.63  Score=36.92  Aligned_cols=27  Identities=30%  Similarity=0.806  Sum_probs=17.2

Q ss_pred             CCCCC-CCcCCCCCC--------CCCCCCCcccCCc
Q 018197          329 SPAKF-CDECGAPYL--------RETSKFCSECGVK  355 (359)
Q Consensus       329 ~~sKF-CpeCGt~l~--------~~~AKFCpECGtK  355 (359)
                      ..++| ||+||..++        ..+---||+||..
T Consensus        24 ~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~   59 (61)
T COG2888          24 TAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE   59 (61)
T ss_pred             ceeEeeCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence            34667 888886653        2334568888853

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=83.87  E-value=0.7  Score=34.52  Aligned_cols=34  Identities=24%  Similarity=0.519  Sum_probs=25.6

Q ss_pred             cccCCCCCCCCCCcCCCCCCC---CCCCCCcccCCcC
Q 018197          323 LHVMPASPAKFCDECGAPYLR---ETSKFCSECGVKR  356 (359)
Q Consensus       323 ~~i~p~~~sKFCpeCGt~l~~---~~AKFCpECGtKr  356 (359)
                      ..+.|.-+++-|+.||.....   ...-.|++||...
T Consensus        20 ~~v~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~   56 (69)
T PF07282_consen   20 VEVDEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEM   56 (69)
T ss_pred             EEECCCCCccCccCcccccccccccceEEcCCCCCEE
Confidence            345677789999999999854   2355799999874

More information about these proteins can be found at Protein of the Month: Transposase [].

>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454

Probab=83.29  E-value=0.54  Score=42.92  Aligned_cols=11  Identities=27%  Similarity=0.963  Sum_probs=6.8

Q ss_pred             CCCCcccCCcC
Q 018197          346 SKFCSECGVKR  356 (359)
Q Consensus       346 AKFCpECGtKr  356 (359)
                      ..||.+||++.
T Consensus        68 PsYC~~CGkpy   78 (158)
T PF10083_consen   68 PSYCHNCGKPY   78 (158)
T ss_pred             ChhHHhCCCCC
Confidence            45666666654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.

>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain

Probab=81.96  E-value=0.66  Score=38.94  Aligned_cols=25  Identities=24%  Similarity=0.711  Sum_probs=18.6

Q ss_pred             CCCCcCCCCCCCC---CCCCCcccCCcC
Q 018197          332 KFCDECGAPYLRE---TSKFCSECGVKR  356 (359)
Q Consensus       332 KFCpeCGt~l~~~---~AKFCpECGtKr  356 (359)
                      -.|++||......   ..+|||.||.+.
T Consensus        43 ~~C~~Cg~~~~~~~SCk~R~CP~C~~~~   70 (111)
T PF14319_consen   43 YRCEDCGHEKIVYNSCKNRHCPSCQAKA   70 (111)
T ss_pred             eecCCCCceEEecCcccCcCCCCCCChH
Confidence            3488898876432   488999999874

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=81.89  E-value=0.49  Score=33.26  Aligned_cols=23  Identities=26%  Similarity=0.876  Sum_probs=19.7

Q ss_pred             CCcCCCCC--CCCCCCCCcccCCcC
Q 018197          334 CDECGAPY--LRETSKFCSECGVKR  356 (359)
Q Consensus       334 CpeCGt~l--~~~~AKFCpECGtKr  356 (359)
                      |+.||+..  ..+|-.||-+||+..
T Consensus        11 C~~C~~~~~~~~dG~~yC~~cG~~~   35 (36)
T PF11781_consen   11 CPVCGSRWFYSDDGFYYCDRCGHQS   35 (36)
T ss_pred             CCCCCCeEeEccCCEEEhhhCceEc
Confidence            99999986  567899999999864

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=81.60  E-value=0.64  Score=40.15  Aligned_cols=15  Identities=20%  Similarity=0.543  Sum_probs=10.9

Q ss_pred             CCCCCCCcCCCCCCC
Q 018197          329 SPAKFCDECGAPYLR  343 (359)
Q Consensus       329 ~~sKFCpeCGt~l~~  343 (359)
                      +...+|..||.....
T Consensus        68 p~~~~C~~CG~~~~~   82 (135)
T PRK03824         68 EAVLKCRNCGNEWSL   82 (135)
T ss_pred             ceEEECCCCCCEEec
Confidence            345669999977644

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=81.41  E-value=0.44  Score=33.47  Aligned_cols=25  Identities=28%  Similarity=0.818  Sum_probs=18.5

Q ss_pred             CCCcCCCCC-----CCCCCCCCcccCCcCc
Q 018197          333 FCDECGAPY-----LRETSKFCSECGVKRL  357 (359)
Q Consensus       333 FCpeCGt~l-----~~~~AKFCpECGtKr~  357 (359)
                      .|+.||+.|     ++.....|..||.++.
T Consensus         3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~   32 (36)
T PF05191_consen    3 ICPKCGRIYHIEFNPPKVEGVCDNCGGELV   32 (36)
T ss_dssp             EETTTTEEEETTTB--SSTTBCTTTTEBEB
T ss_pred             CcCCCCCccccccCCCCCCCccCCCCCeeE
Confidence            599999987     3445789999998753

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed

Probab=80.80  E-value=0.86  Score=35.17  Aligned_cols=23  Identities=35%  Similarity=0.839  Sum_probs=17.3

Q ss_pred             CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197          331 AKFCDECGAPYLRETSKFCSECGVKR  356 (359)
Q Consensus       331 sKFCpeCGt~l~~~~AKFCpECGtKr  356 (359)
                      .+.|+.||.--+   .+.||+||.+.
T Consensus         5 mr~C~~CgvYTL---k~~CP~CG~~t   27 (56)
T PRK13130          5 IRKCPKCGVYTL---KEICPVCGGKT   27 (56)
T ss_pred             ceECCCCCCEEc---cccCcCCCCCC
Confidence            466888887765   67888888774

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	359
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	96.03
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	93.18
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	93.13
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	92.95
1vk6_A	269	NADH pyrophosphatase; 1790429, structural genomics	91.89
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	91.39
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	91.1
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	90.5
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	86.11
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	85.56
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	84.8
3irb_A	145	Uncharacterized protein from DUF35 family; 1381535	80.75

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=96.03  E-value=0.0034  Score=48.47  Aligned_cols=29  Identities=31%  Similarity=0.792  Sum_probs=22.6

Q ss_pred             CCCCC-CCcCCCC--CCCCCCCCCcccCCcCc
Q 018197          329 SPAKF-CDECGAP--YLRETSKFCSECGVKRL  357 (359)
Q Consensus       329 ~~sKF-CpeCGt~--l~~~~AKFCpECGtKr~  357 (359)
                      ....+ |++||..  +....+-+|++||.+++
T Consensus        25 ~~v~Y~C~~CG~~~e~~~~d~irCp~CG~RIL   56 (70)
T 1twf_L           25 ATLKYICAECSSKLSLSRTDAVRCKDCGHRIL   56 (70)
T ss_dssp             CCCCEECSSSCCEECCCTTSTTCCSSSCCCCC
T ss_pred             ceEEEECCCCCCcceeCCCCCccCCCCCceEe
Confidence            34455 9999999  45566889999999765

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=93.18  E-value=0.02  Score=41.48  Aligned_cols=26  Identities=31%  Similarity=0.721  Sum_probs=19.7

Q ss_pred             CCCCCCcCCCCC---CCCCCCCCcccCCc
Q 018197          330 PAKFCDECGAPY---LRETSKFCSECGVK  355 (359)
Q Consensus       330 ~sKFCpeCGt~l---~~~~AKFCpECGtK  355 (359)
                      .-+|||+||+.+   .......|+.||..
T Consensus        18 ~~k~CP~CG~~~fm~~~~~R~~C~kCG~t   46 (50)
T 3j20_Y           18 KNKFCPRCGPGVFMADHGDRWACGKCGYT   46 (50)
T ss_dssp             SSEECSSSCSSCEEEECSSEEECSSSCCE
T ss_pred             ecccCCCCCCceEEecCCCeEECCCCCCE
Confidence            378999999965   23357789999953

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=93.13  E-value=0.013  Score=46.79  Aligned_cols=22  Identities=23%  Similarity=0.623  Sum_probs=11.9

Q ss_pred             CCCcCCCCCCC-----CCCCCCcccCC
Q 018197          333 FCDECGAPYLR-----ETSKFCSECGV  354 (359)
Q Consensus       333 FCpeCGt~l~~-----~~AKFCpECGt  354 (359)
                      |||+||.++-.     ...+||++||.
T Consensus        33 fCPeCgq~Le~lkACGA~~yFC~~C~~   59 (81)
T 2jrp_A           33 LCPDCRQPLQVLKACGAVDYFCQNGHG   59 (81)
T ss_dssp             ECSSSCSCCCEEEETTEEEECCTTTTC
T ss_pred             cCcchhhHHHHHHhcCCcCeeeccCCC
Confidence            66666666610     12566666664

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=92.95  E-value=0.023  Score=47.55  Aligned_cols=25  Identities=28%  Similarity=0.723  Sum_probs=18.8

Q ss_pred             CCCCcCCCCCCCCC-CCCCcccCCcC
Q 018197          332 KFCDECGAPYLRET-SKFCSECGVKR  356 (359)
Q Consensus       332 KFCpeCGt~l~~~~-AKFCpECGtKr  356 (359)
                      .-|..||..+.... ..|||+||.++
T Consensus       133 y~C~~Cg~~~~~~~~~~~Cp~CG~~~  158 (165)
T 2lcq_A          133 YVCIGCGRKFSTLPPGGVCPDCGSKV  158 (165)
T ss_dssp             EEESSSCCEESSCCGGGBCTTTCCBE
T ss_pred             EECCCCCCcccCCCCCCcCCCCCCcc
Confidence            34999999885332 45999999874

>1vk6_A NADH pyrophosphatase; 1790429, structural genomics, JCSG, PS protein structure initiative, joint center for structural G hydrolase; HET: MSE; 2.20A {Escherichia coli} SCOP: d.113.1.4 d.113.1.4 g.41.14.1 PDB: 2gb5_A

Probab=91.89  E-value=0.047  Score=49.55  Aligned_cols=27  Identities=30%  Similarity=0.717  Sum_probs=22.4

Q ss_pred             CCCCCCCcCCCCC---CCCCCCCCcccCCc
Q 018197          329 SPAKFCDECGAPY---LRETSKFCSECGVK  355 (359)
Q Consensus       329 ~~sKFCpeCGt~l---~~~~AKFCpECGtK  355 (359)
                      ...+||+.||+++   ...+.+.|+.||..
T Consensus       105 ~~~~fC~~CG~~~~~~~~~~~~~C~~C~~~  134 (269)
T 1vk6_A          105 RSHKYCGYCGHEMYPSKTEWAMLCSHCRER  134 (269)
T ss_dssp             HTTSBCTTTCCBEEECSSSSCEEESSSSCE
T ss_pred             hcCCccccCCCcCccCCCceeeeCCCCCCE
Confidence            4679999999998   34578999999974

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=91.39  E-value=0.042  Score=43.88  Aligned_cols=24  Identities=17%  Similarity=0.685  Sum_probs=19.5

Q ss_pred             CCCCcCCCCCCCCCCCCCcccCCcCc
Q 018197          332 KFCDECGAPYLRETSKFCSECGVKRL  357 (359)
Q Consensus       332 KFCpeCGt~l~~~~AKFCpECGtKr~  357 (359)
                      ..|..||..+... | |||+||+++.
T Consensus        19 ~~C~~C~~~~~~~-a-fCPeCgq~Le   42 (81)
T 2jrp_A           19 AHCETCAKDFSLQ-A-LCPDCRQPLQ   42 (81)
T ss_dssp             EECTTTCCEEEEE-E-ECSSSCSCCC
T ss_pred             eECccccccCCCc-c-cCcchhhHHH
Confidence            3499999988754 6 9999999873

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=91.10  E-value=0.16  Score=38.78  Aligned_cols=28  Identities=29%  Similarity=0.716  Sum_probs=21.8

Q ss_pred             CCCC-CCcCCCCCCC--CCCCCCcccCCcCc
Q 018197          330 PAKF-CDECGAPYLR--ETSKFCSECGVKRL  357 (359)
Q Consensus       330 ~sKF-CpeCGt~l~~--~~AKFCpECGtKr~  357 (359)
                      ...+ |.+||+....  ...--|++||.+++
T Consensus        19 ~v~Y~C~~Cg~~~~l~~~~~iRC~~CG~RIL   49 (63)
T 3h0g_L           19 TMIYLCADCGARNTIQAKEVIRCRECGHRVM   49 (63)
T ss_dssp             CCCCBCSSSCCBCCCCSSSCCCCSSSCCCCC
T ss_pred             CeEEECCCCCCeeecCCCCceECCCCCcEEE
Confidence            4566 9999999732  24788999999875

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=90.50  E-value=0.13  Score=43.44  Aligned_cols=28  Identities=18%  Similarity=0.511  Sum_probs=21.4

Q ss_pred             CCCCCCCcCCCCCCCCC-------CCCCcccCCcC
Q 018197          329 SPAKFCDECGAPYLRET-------SKFCSECGVKR  356 (359)
Q Consensus       329 ~~sKFCpeCGt~l~~~~-------AKFCpECGtKr  356 (359)
                      .+.+|||+||.-|.+..       .-.|+.||...
T Consensus        22 ~~~~FCPeCgNmL~pked~~~~~l~~~CrtCgY~~   56 (133)
T 3qt1_I           22 TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVE   56 (133)
T ss_dssp             CCCCBCTTTCCBCBCCBCTTTCCBCCBCSSSCCBC
T ss_pred             cCCeeCCCCCCEeeECccCCCceeEEECCCCCCcE
Confidence            34799999999985442       36899999753

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=86.11  E-value=0.35  Score=35.59  Aligned_cols=25  Identities=40%  Similarity=0.739  Sum_probs=20.9

Q ss_pred             CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197          331 AKFCDECGAPYLRETSKFCSECGVKR  356 (359)
Q Consensus       331 sKFCpeCGt~l~~~~AKFCpECGtKr  356 (359)
                      .+.|+.||+.++ .++..|..||.+.
T Consensus        14 k~iCpkC~a~~~-~gaw~CrKCG~~~   38 (51)
T 3j21_g           14 KYVCLRCGATNP-WGAKKCRKCGYKR   38 (51)
T ss_dssp             EEECTTTCCEEC-TTCSSCSSSSSCC
T ss_pred             CccCCCCCCcCC-CCceecCCCCCcc
Confidence            456999999955 5799999999884

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=85.56  E-value=0.25  Score=39.87  Aligned_cols=28  Identities=18%  Similarity=0.493  Sum_probs=20.4

Q ss_pred             CCCCCCCcCCCCCCCCCC-C-CCcccCCcC
Q 018197          329 SPAKFCDECGAPYLRETS-K-FCSECGVKR  356 (359)
Q Consensus       329 ~~sKFCpeCGt~l~~~~A-K-FCpECGtKr  356 (359)
                      +....|.+||..+..... . -||.||...
T Consensus        71 p~~~~C~~CG~~~e~~~~~~~~CP~Cgs~~  100 (119)
T 2kdx_A           71 KVELECKDCSHVFKPNALDYGVCEKCHSKN  100 (119)
T ss_dssp             CCEEECSSSSCEECSCCSTTCCCSSSSSCC
T ss_pred             cceEEcCCCCCEEeCCCCCCCcCccccCCC
Confidence            445669999998744333 4 599999884

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=84.80  E-value=0.28  Score=36.05  Aligned_cols=26  Identities=27%  Similarity=0.796  Sum_probs=19.1

Q ss_pred             CCCCCCcCCCCCC---CCCCCCCcccCCc
Q 018197          330 PAKFCDECGAPYL---RETSKFCSECGVK  355 (359)
Q Consensus       330 ~sKFCpeCGt~l~---~~~AKFCpECGtK  355 (359)
                      ..+|||.||.-+.   ..+.-.|..||..
T Consensus        17 ~~~fCPkCG~~~~ma~~~dr~~C~kCgyt   45 (55)
T 2k4x_A           17 KHRFCPRCGPGVFLAEHADRYSCGRCGYT   45 (55)
T ss_dssp             SSCCCTTTTTTCCCEECSSEEECTTTCCC
T ss_pred             ccccCcCCCCceeEeccCCEEECCCCCCE
Confidence            3799999999653   1235589999964

>3irb_A Uncharacterized protein from DUF35 family; 13815350, protein with unknown function from DUF35 family, S genomics; 1.80A {Sulfolobus solfataricus}

Probab=80.75  E-value=0.38  Score=40.40  Aligned_cols=23  Identities=30%  Similarity=0.882  Sum_probs=19.4

Q ss_pred             CCCCcCCCCCCCCCCCCCcccCCc
Q 018197          332 KFCDECGAPYLRETSKFCSECGVK  355 (359)
Q Consensus       332 KFCpeCGt~l~~~~AKFCpECGtK  355 (359)
                      .-|..||+.+.++ ..+||.||..
T Consensus        48 ~rC~~CG~~~~PP-r~~Cp~C~s~   70 (145)
T 3irb_A           48 SKCSKCGRIFVPA-RSYCEHCFVK   70 (145)
T ss_dssp             EECTTTCCEEESC-CSEETTTTEE
T ss_pred             EEeCCCCcEEcCc-hhhCcCCCCC
Confidence            3599999998766 7899999975

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	359
d2cona1	66	RNA-binding protein NOB1 (Nin one binding) {Mouse	82.91
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	81.36

>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: NOB1 zinc finger-like
family: NOB1 zinc finger-like
domain: RNA-binding protein NOB1 (Nin one binding)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.91  E-value=0.26  Score=36.06  Aligned_cols=23  Identities=30%  Similarity=0.647  Sum_probs=15.4

Q ss_pred             CCCcCCCCCCCCCCCCCcccCCc
Q 018197          333 FCDECGAPYLRETSKFCSECGVK  355 (359)
Q Consensus       333 FCpeCGt~l~~~~AKFCpECGtK  355 (359)
                      .|..|=+....-+-.|||.||.+
T Consensus        10 rC~aCf~~t~~~~k~FCpkCGn~   32 (66)
T d2cona1          10 RCHGCFKTTSDMNRVFCGHCGNK   32 (66)
T ss_dssp             ECSSSCCEESCSSCCSCSSSCCS
T ss_pred             EeeecCcCcCCcccccCcccCCC
Confidence            37777665555556788888875

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=81.36  E-value=0.21  Score=33.61  Aligned_cols=24  Identities=25%  Similarity=0.663  Sum_probs=18.1

Q ss_pred             CCCCcCCCCC--CCCCCCCCcccCCc
Q 018197          332 KFCDECGAPY--LRETSKFCSECGVK  355 (359)
Q Consensus       332 KFCpeCGt~l--~~~~AKFCpECGtK  355 (359)
                      -.||+|+..+  .....--|||||.-
T Consensus         4 P~CP~C~seytYedg~l~vCPeC~hE   29 (38)
T d2akla2           4 PPCPQCNSEYTYEDGALLVCPECAHE   29 (38)
T ss_dssp             CCCTTTCCCCCEECSSSEEETTTTEE
T ss_pred             CcCCCCCCcceEcCCCEEECCcccCc
Confidence            3599999998  34456679999953