Citrus Sinensis ID: 020809

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-
Protein Sequence
MAASKLVIFSLFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHcHHcccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHcccccccccccccccccHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHcccEEcc
Coil and Loop (DISEMBL)
MAASKLVIFSLFFALILTAadvsiqgedvppltasdavdssplkIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIEthwnahgkpAMDVAIQKALEKKAqagkwvqphVETIkakwipavKEQWVVFTTnvephvqtLKTKTIEACEatktavtphIIRVQEVVDPYFQVY
Flexible Loop (DISEMBL)
MAASKLVIFSLFFALILTAADVSIQGEDVPPltasdavdssplKIELDQLKSKIRSLEshidektqelkgkdevvAQKEkaiqdkserIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLeklqkindeqkskirkteraLKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEAtktavtphiirvQEVVDPYFQVY
Low Complexity Region (SEG)
MAASKLVIFSLFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNlkkesekqqkekealeaRAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY
Disordered region (IsUnstruct)
****KLVIFSLFFALILTAADVSIQ*********************************************************************************************************************************************************************************TEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQ**
Disordered Region (DISOPRED)
*****LV*FSLFFALILTAAD*******************************************************************************************************************************************************************************************WLPPWLAVHLL*********************************************KWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY
Disordered Region (DISEMBL)
MAASKLVIFSLFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLK************LEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA*************VHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY
Disordered Region (DISPRO)
**ASKLVIFSLFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAASKLVIFSLFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIExxxxxxxxxxxxxxxxxxxxxLKGKDEVxxxxxxxxxxxxxxxxxxxxxxxxxxxxExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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	321
255574131	440	conserved hypothetical protein [Ricinus	0.965	0.704	0.666	1e-115
224121216	446	predicted protein [Populus trichocarpa]	0.993	0.715	0.675	1e-112
224115694	447	predicted protein [Populus trichocarpa]	0.993	0.713	0.660	1e-110
225429824	449	PREDICTED: uncharacterized protein LOC10	0.996	0.712	0.628	1e-109
363806748	446	uncharacterized protein LOC100781922 pre	0.971	0.699	0.603	1e-104
217074086	404	unknown [Medicago truncatula]	0.959	0.762	0.594	1e-101
357466595	439	hypothetical protein MTR_3g109330 [Medic	0.959	0.701	0.594	1e-101
388521969	435	unknown [Lotus japonicus]	0.953	0.703	0.576	1e-97
449509133	448	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.990	0.709	0.565	2e-92
449437044	448	PREDICTED: uncharacterized protein LOC10	0.990	0.709	0.562	5e-92

>gi|255574131|ref|XP_002527981.1| conserved hypothetical protein [Ricinus communis] gi|223532607|gb|EEF34393.1| conserved hypothetical protein [Ricinus communis]

 Score =  422 bits (1084), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 212/318 (66%), Positives = 263/318 (82%), Gaps = 8/318 (2%)

Query: 4   SKLVIFSLFFALILTA--ADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLESHI 61
           + L IFS F ALI +A  AD+S++ +D   L +S AV SS  KI+LDQL SKI +LES I
Sbjct: 3   ANLAIFSFFLALIFSAVRADISLESDD--QLISSHAVHSSAFKIQLDQLNSKIHALESQI 60

Query: 62  DEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADEL 121
           DE+T+ELK KD +++Q +K I+D S+ I+SLQ E+SSLQKKE ++AAEQV KAHARA EL
Sbjct: 61  DERTRELKNKDAIISQNDKIIKDNSDSILSLQTEISSLQKKEKIDAAEQVGKAHARAGEL 120

Query: 122 EKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERAL 181
           EKQ++N+KKE E Q +EKEALEARA EAEKKI++L  KLE LQKINDEQKSK+RKTERAL
Sbjct: 121 EKQVENIKKEVETQNREKEALEARANEAEKKIAELHLKLENLQKINDEQKSKLRKTERAL 180

Query: 182 KVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAI 241
           KVAEEE+M+AKFEATS++KEL EVH AWLPPWLAV L++    I+THWN HG+PAM++ I
Sbjct: 181 KVAEEELMKAKFEATSKTKELMEVHGAWLPPWLAVELVR----IQTHWNEHGRPAMELVI 236

Query: 242 QKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKT 301
           QKAL+KKA A KW +PH++T+K KW+PAVKEQW++  T+VEPHVQ+L TKTIEA EA+KT
Sbjct: 237 QKALDKKAHAEKWAKPHLDTVKTKWVPAVKEQWLLIVTHVEPHVQSLTTKTIEAYEASKT 296

Query: 302 AVTPHIIRVQEVVDPYFQ 319
           A+TPH+ RVQEVV PYFQ
Sbjct: 297 AITPHVSRVQEVVGPYFQ 314

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224121216|ref|XP_002330772.1| predicted protein [Populus trichocarpa] gi|118485922|gb|ABK94806.1| unknown [Populus trichocarpa] gi|222872574|gb|EEF09705.1| predicted protein [Populus trichocarpa]

 Score =  410 bits (1055), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 216/320 (67%), Positives = 250/320 (78%), Gaps = 1/320 (0%)

Query: 1   MAASKLVIFSLFFALILTAADVSIQGEDVPPLTAS-DAVDSSPLKIELDQLKSKIRSLES 59
           MAASKL   S+ F   LT   V     D   +T S  AVDSS  KIELDQLKSKI +LES
Sbjct: 1   MAASKLASLSILFIFALTLTAVVSVRADYDDITGSVAAVDSSAFKIELDQLKSKIHALES 60

Query: 60  HIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARAD 119
           HIDEKT+ELKGKD+++A KEK IQ+K + I SLQ ELSSLQ     +A EQV KAHARA 
Sbjct: 61  HIDEKTKELKGKDDMIALKEKIIQEKVDSIGSLQSELSSLQNNGKTDAQEQVRKAHARAG 120

Query: 120 ELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTER 179
           ELEKQ+D L KE E QQK+KEALEARA EAEKKIS+L+ KL  L KIN+EQKSKIRKTER
Sbjct: 121 ELEKQVDKLAKELETQQKKKEALEARASEAEKKISELNLKLADLAKINEEQKSKIRKTER 180

Query: 180 ALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDV 239
           ALK+AEEE+++ K EATS++KEL EVH AWLPPWLAV L+  QSL +THWN HGKP M++
Sbjct: 181 ALKIAEEELLKTKSEATSKAKELMEVHGAWLPPWLAVQLVHWQSLAQTHWNEHGKPVMEL 240

Query: 240 AIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEAT 299
           AIQ+ALEKKAQA KW +PHVETIK KW+PA+KEQWVV  T VEPHVQ+L  KT+E  EA+
Sbjct: 241 AIQRALEKKAQAEKWAKPHVETIKTKWVPAIKEQWVVIATQVEPHVQSLTVKTVEIYEAS 300

Query: 300 KTAVTPHIIRVQEVVDPYFQ 319
           KT +T HIIRVQE+VDP FQ
Sbjct: 301 KTTITAHIIRVQEIVDPCFQ 320

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115694|ref|XP_002332119.1| predicted protein [Populus trichocarpa] gi|118488228|gb|ABK95933.1| unknown [Populus trichocarpa] gi|222874939|gb|EEF12070.1| predicted protein [Populus trichocarpa]

 Score =  405 bits (1042), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 212/321 (66%), Positives = 253/321 (78%), Gaps = 2/321 (0%)

Query: 1   MAASKLVIFSLFF--ALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLE 58
           MAASKL   S+ F  ALI TA  V    +D     ++ AVD S LKIELDQLKSKI + E
Sbjct: 1   MAASKLAFLSILFVFALIFTAVGVRADVDDDNTAESAAAVDLSALKIELDQLKSKIHAHE 60

Query: 59  SHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARA 118
           SHIDEKT+EL GKD ++AQKE  IQ+K + I SLQ E+SSL+KK  ++A E V KAHARA
Sbjct: 61  SHIDEKTKELNGKDVMIAQKETIIQEKVDSIASLQSEISSLKKKGKIDAQELVGKAHARA 120

Query: 119 DELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTE 178
            ELEKQ++ L KE E QQ+E EALEARA EAEKKIS+L+ KL  L+KIN EQKSKIRKTE
Sbjct: 121 GELEKQMEKLSKELETQQQENEALEARASEAEKKISELNFKLADLEKINVEQKSKIRKTE 180

Query: 179 RALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMD 238
           RALK+AEEE+++ K EA S++KEL EVH AWLPPWLAV L++ QSL +THW+ HGKP M+
Sbjct: 181 RALKIAEEELIKTKSEAISKAKELMEVHGAWLPPWLAVQLIRWQSLAQTHWSEHGKPTME 240

Query: 239 VAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEA 298
           +AIQKALEKKAQA KW +PHVETIK KW+PA+KEQWVV TT V+PHVQ+L  KT++  EA
Sbjct: 241 LAIQKALEKKAQAEKWAEPHVETIKTKWVPAIKEQWVVITTQVKPHVQSLTAKTVQIYEA 300

Query: 299 TKTAVTPHIIRVQEVVDPYFQ 319
           +KT VTPHIIRVQE+ DPYFQ
Sbjct: 301 SKTTVTPHIIRVQEIADPYFQ 321

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429824|ref|XP_002280828.1| PREDICTED: uncharacterized protein LOC100254151 [Vitis vinifera] gi|296081785|emb|CBI20790.3| unnamed protein product [Vitis vinifera]

 Score =  402 bits (1033), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 203/323 (62%), Positives = 251/323 (77%), Gaps = 3/323 (0%)

Query: 1   MAASKLVIFSLFFALILTA--ADVSIQGEDVP-PLTASDAVDSSPLKIELDQLKSKIRSL 57
           M ASKL    +FFALI     AD SI   D P  +  S++ +S  LKIEL  L+ KI++L
Sbjct: 1   MGASKLATLFIFFALIFCKIRADASIDEVDQPQGVVLSESSESEALKIELALLQEKIQTL 60

Query: 58  ESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHAR 117
           E+HIDE+++ELK KDE++AQKEK +Q+KS  I  LQ E+ SLQKK T +A EQ+ KA+AR
Sbjct: 61  ETHIDERSKELKSKDEIIAQKEKIVQEKSNSITQLQNEIVSLQKKGTSDAEEQLGKAYAR 120

Query: 118 ADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKT 177
           A ELEKQ+D LKKE E QQKEK ALE+RA EAE+K  +L++K+E L+KI DEQK++IRKT
Sbjct: 121 ASELEKQVDKLKKEIETQQKEKAALESRANEAERKTRELNSKVESLKKITDEQKTRIRKT 180

Query: 178 ERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAM 237
           ERAL+VAEEEMM+AKF+A S++KEL EVH AWLPPW A HL+ CQS +E HWN HGKPA+
Sbjct: 181 ERALQVAEEEMMKAKFDANSKTKELMEVHGAWLPPWFANHLISCQSFMEVHWNKHGKPAL 240

Query: 238 DVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACE 297
           D   QKALEKKAQA KW +PHVET K KWIPA+K+QW+  TT +EPHVQ L TKT+EA E
Sbjct: 241 DTLTQKALEKKAQAQKWSEPHVETFKTKWIPAIKDQWLEITTYLEPHVQLLCTKTVEAYE 300

Query: 298 ATKTAVTPHIIRVQEVVDPYFQV 320
           A+K A+TPH+I+VQE  DPYFQV
Sbjct: 301 ASKNAITPHVIKVQEFGDPYFQV 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363806748|ref|NP_001242275.1| uncharacterized protein LOC100781922 precursor [Glycine max] gi|255642485|gb|ACU21506.1| unknown [Glycine max]

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 195/323 (60%), Positives = 245/323 (75%), Gaps = 11/323 (3%)

Query: 1   MAASKLVIF----SLFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRS 56
           MA  KL +F    +L FA++   AD+SI+G    P       D+S ++I+LDQL SKI+ 
Sbjct: 1   MAPPKLFVFALSVTLIFAIVGAEADISIEGSTPEP-------DTSAIRIQLDQLNSKIQI 53

Query: 57  LESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHA 116
           LES I EK +E+K KDE++A+KEK+I+DKS  I SLQ E++SLQKK +L+A EQV KAHA
Sbjct: 54  LESQISEKLEEVKKKDEIIAEKEKSIEDKSITIQSLQNEIASLQKKGSLDAEEQVGKAHA 113

Query: 117 RADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK 176
           RA EL+KQ+D LK+E E Q KEK   E R  E EKKI DL++KLE LQKIN+EQK KI+K
Sbjct: 114 RAGELQKQVDKLKRELETQNKEKVNWETRVPELEKKIHDLNSKLEDLQKINEEQKKKIQK 173

Query: 177 TERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPA 236
           TERALKVAEEEM++AKFEAT+  KEL E H AWLPPWLAVH +  +S +++HWN HGKPA
Sbjct: 174 TERALKVAEEEMVKAKFEATAIEKELRETHGAWLPPWLAVHYIHSKSFVDSHWNKHGKPA 233

Query: 237 MDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEAC 296
           +++  QKALEKKAQAGKW +PHVETIK KW+PAVKEQW V  TN EPHVQ L TKT+   
Sbjct: 234 LEMVTQKALEKKAQAGKWAEPHVETIKTKWVPAVKEQWSVVKTNAEPHVQLLTTKTVGVY 293

Query: 297 EATKTAVTPHIIRVQEVVDPYFQ 319
           EA+K A++PH+ + +E VDPY+Q
Sbjct: 294 EASKNAISPHLSKAKEFVDPYYQ 316

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074086|gb|ACJ85403.1| unknown [Medicago truncatula]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 192/323 (59%), Positives = 242/323 (74%), Gaps = 15/323 (4%)

Query: 1   MAASKLVIFS----LFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRS 56
           MA  KL +F+    L F+ + + ADVSI+  D           SS LKI+LDQL SKI+S
Sbjct: 1   MAPPKLFVFAISVALIFSFVTSEADVSIEDSD-----------SSALKIQLDQLNSKIQS 49

Query: 57  LESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHA 116
           LES I EKTQELK KD+V+A+KEK  QDK   I SLQ E++SLQKK +L+A EQV KA+A
Sbjct: 50  LESQISEKTQELKKKDQVIAEKEKLFQDKLSSIQSLQNEVASLQKKGSLDAEEQVGKAYA 109

Query: 117 RADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK 176
           RA EL+KQ+D LK E E Q  EK   E+R  + EKKI DL++KLE +QKIN+EQK +IRK
Sbjct: 110 RAGELQKQVDKLKSELEAQNSEKVNWESRVAKLEKKIHDLNSKLEDVQKINEEQKKQIRK 169

Query: 177 TERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPA 236
           TERALKVAEEEM++AK EAT+++KEL+E H AWLPPWLAVH ++ +S+ E+HWN HGKP 
Sbjct: 170 TERALKVAEEEMLKAKLEATTKAKELSETHGAWLPPWLAVHYIRSKSVAESHWNEHGKPL 229

Query: 237 MDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEAC 296
           ++V  QKALEKKAQAGKW +PHVETIK KW+PAVKEQW V  T  EPHVQ L +KT+E  
Sbjct: 230 LEVISQKALEKKAQAGKWAEPHVETIKTKWVPAVKEQWSVVKTKAEPHVQALTSKTVEVY 289

Query: 297 EATKTAVTPHIIRVQEVVDPYFQ 319
           +++K A+ PH+ + +E VDPY+Q
Sbjct: 290 KSSKDALAPHLNKAKECVDPYYQ 312

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357466595|ref|XP_003603582.1| hypothetical protein MTR_3g109330 [Medicago truncatula] gi|355492630|gb|AES73833.1| hypothetical protein MTR_3g109330 [Medicago truncatula] gi|388509130|gb|AFK42631.1| unknown [Medicago truncatula]

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 192/323 (59%), Positives = 242/323 (74%), Gaps = 15/323 (4%)

Query: 1   MAASKLVIFS----LFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRS 56
           MA  KL +F+    L F+ + + ADVSI+  D           SS LKI+LDQL SKI+S
Sbjct: 1   MAPPKLFVFAISVALIFSFVTSEADVSIEDSD-----------SSALKIQLDQLNSKIQS 49

Query: 57  LESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHA 116
           LES I EKTQELK KD+V+A+KEK  QDK   I SLQ E++SLQKK +L+A EQV KA+A
Sbjct: 50  LESQISEKTQELKKKDQVIAEKEKLFQDKLSSIQSLQNEVASLQKKGSLDAEEQVGKAYA 109

Query: 117 RADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK 176
           RA EL+KQ+D LK E E Q  EK   E+R  + EKKI DL++KLE +QKIN+EQK +IRK
Sbjct: 110 RAGELQKQVDKLKSELEAQNSEKVNWESRVAKLEKKIHDLNSKLEDVQKINEEQKKQIRK 169

Query: 177 TERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPA 236
           TERALKVAEEEM++AK EAT+++KEL+E H AWLPPWLAVH ++ +S+ E+HWN HGKP 
Sbjct: 170 TERALKVAEEEMLKAKLEATTKAKELSETHGAWLPPWLAVHYIRSKSVAESHWNEHGKPL 229

Query: 237 MDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEAC 296
           ++V  QKALEKKAQAGKW +PHVETIK KW+PAVKEQW V  T  EPHVQ L +KT+E  
Sbjct: 230 LEVISQKALEKKAQAGKWAEPHVETIKTKWVPAVKEQWSVVKTKAEPHVQALTSKTVEVY 289

Query: 297 EATKTAVTPHIIRVQEVVDPYFQ 319
           +++K A+ PH+ + +E VDPY+Q
Sbjct: 290 KSSKDALAPHLNKAKECVDPYYQ 312

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388521969|gb|AFK49046.1| unknown [Lotus japonicus]

 Score =  362 bits (929), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 185/321 (57%), Positives = 236/321 (73%), Gaps = 15/321 (4%)

Query: 1   MAASKLVIFSLFFALI--LTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLE 58
           MA  KL +F+L  ALI  ++AAD  +  +D              +KI+LDQL S+I +LE
Sbjct: 1   MAPPKLFLFTLSLALIFSISAADAGVSHDD-------------SVKIQLDQLNSRILTLE 47

Query: 59  SHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARA 118
           S I +K+QELK KDEV+A+KEK IQDKS  + SLQ E++SLQKK +L+A E+V KAHARA
Sbjct: 48  SQIKDKSQELKKKDEVIAEKEKFIQDKSSTVESLQNEVASLQKKGSLDAQEEVGKAHARA 107

Query: 119 DELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTE 178
            EL+KQ++NLK+E EKQ KEK   E R  E EKKI DL++KLE +QK+N+EQK+KIRKTE
Sbjct: 108 GELQKQVENLKRELEKQNKEKVNWETRVAELEKKIHDLNSKLEDIQKVNEEQKTKIRKTE 167

Query: 179 RALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMD 238
           RALKVAEEEM++AK EA S+++EL E H  WLPPWLAVH ++ +SL+E HWN HGKP ++
Sbjct: 168 RALKVAEEEMVKAKLEANSKARELIEAHGNWLPPWLAVHYIRSKSLVEAHWNKHGKPVLE 227

Query: 239 VAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEA 298
           V  QKALEKKAQA KW +PH+ET+K KWIPAVK+QW    T  EP VQ L+TK+ E  E 
Sbjct: 228 VVTQKALEKKAQAEKWAEPHLETVKTKWIPAVKQQWSEVKTQAEPRVQLLRTKSFEVYET 287

Query: 299 TKTAVTPHIIRVQEVVDPYFQ 319
           +K A+ PH    +E VDPY+Q
Sbjct: 288 SKKAIDPHFSNAKEFVDPYYQ 308

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449509133|ref|XP_004163503.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein LOC101229984 [Cucumis sativus]

 Score =  345 bits (884), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 182/322 (56%), Positives = 239/322 (74%), Gaps = 4/322 (1%)

Query: 1   MAASKLVIFSLFFALILT--AAD--VSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRS 56
           MA SKL I SLF AL+LT   AD  + ++ + +  +  SD  + S LK+ELDQLK KI+ 
Sbjct: 1   MAISKLAILSLFLALVLTQLRADESLDVEAQHIVEVVRSDDSEFSDLKLELDQLKFKIQK 60

Query: 57  LESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHA 116
           LES +D KT ELK +DEV+AQKEK I  K + I  L+ E++SLQKK  L+A EQV KA++
Sbjct: 61  LESDLDVKTXELKRRDEVIAQKEKVISAKLDSISLLESEIASLQKKGKLDAEEQVGKAYS 120

Query: 117 RADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK 176
           RA ELE+Q+D+LK++ E    EKE+ E  A EAEKK  + S +LE LQKI++EQKSKIR 
Sbjct: 121 RAHELERQVDDLKRQLEILNGEKESWETLANEAEKKTLEASLRLESLQKIHEEQKSKIRV 180

Query: 177 TERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPA 236
           TERAL+V++EEM +AKFEA +R KELTEVH AWLPPWLA H  Q QSLI+THWN H KPA
Sbjct: 181 TERALEVSKEEMRKAKFEAATRIKELTEVHGAWLPPWLASHYDQFQSLIKTHWNKHAKPA 240

Query: 237 MDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEAC 296
           +DV IQKA +K AQA KW +PHV+T+K K+IP VKE+W+V  TNV+PHV+TL  KT+E  
Sbjct: 241 IDVVIQKASDKTAQAAKWAEPHVKTVKIKYIPIVKERWLVVKTNVKPHVETLTAKTVEFY 300

Query: 297 EATKTAVTPHIIRVQEVVDPYF 318
           + +K+ +TP+ ++ +E + PY+
Sbjct: 301 QTSKSVITPYAVKSKEAISPYY 322

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437044|ref|XP_004136302.1| PREDICTED: uncharacterized protein LOC101216465 [Cucumis sativus]

 Score =  343 bits (880), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 181/322 (56%), Positives = 238/322 (73%), Gaps = 4/322 (1%)

Query: 1   MAASKLVIFSLFFALILT--AAD--VSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRS 56
           MA SKL I SLF AL+ T   AD  + ++ + +  +  SD  + S LK+ELDQLK KI+ 
Sbjct: 1   MAISKLAILSLFLALVFTQLRADESLDVEAQHIVEVVRSDDSEFSDLKLELDQLKFKIQK 60

Query: 57  LESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHA 116
           LES +D K QELK +DEV+AQKEK I  K + I  L+ E++SLQKK  L+A EQV KA++
Sbjct: 61  LESDLDVKNQELKRRDEVIAQKEKVITAKLDSISLLESEIASLQKKGKLDAEEQVGKAYS 120

Query: 117 RADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK 176
           RA ELE+Q+D+LK++ E    EKE+ E  A EAEKK  + S +LE LQKI++EQKSKIR 
Sbjct: 121 RAHELERQVDDLKRQLEILNGEKESWETLANEAEKKTLEASLRLESLQKIHEEQKSKIRV 180

Query: 177 TERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPA 236
           TERAL+V++EEM +AKFEA +R KELTEVH AWLPPWLA H  Q QSLI+THWN H KPA
Sbjct: 181 TERALEVSKEEMRKAKFEAATRIKELTEVHGAWLPPWLASHYDQFQSLIKTHWNKHAKPA 240

Query: 237 MDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEAC 296
           +DV IQKA +K AQA KW +PHV+T+K K+IP VKE+W+V  TNV+PHV+TL  KT+E  
Sbjct: 241 IDVVIQKASDKTAQAAKWAEPHVKTVKIKYIPIVKERWLVVKTNVKPHVETLTAKTVEFY 300

Query: 297 EATKTAVTPHIIRVQEVVDPYF 318
           + +K+ +TP+ ++ +E + PY+
Sbjct: 301 QTSKSVITPYAVKSKEAISPYY 322

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	321
TAIR|locus:2128166	437	AT4G31340 "AT4G31340" [Arabido	0.971	0.713	0.526	8.2e-83
TAIR|locus:2061067	440	AT2G24420 [Arabidopsis thalian	0.965	0.704	0.506	2.6e-79
TAIR|locus:2126470	388	AT4G30090 "AT4G30090" [Arabido	0.520	0.430	0.305	1.9e-16
UNIPROTKB|F1PCW0	2240	GOLGA4 "Uncharacterized protei	0.763	0.109	0.235	2e-07
SGD|S000002764	944	SPC110 "Inner plaque spindle p	0.517	0.175	0.248	3.6e-06
TAIR|locus:2099114	318	PMD1 "peroxisomal and mitochon	0.647	0.654	0.235	1.1e-05
DICTYBASE|DDB_G0286985	1024	zipA "zipper-like domain-conta	0.576	0.180	0.228	1.4e-05
WB|WBGene00002978	284	lev-11 [Caenorhabditis elegans	0.535	0.605	0.186	1.9e-05
UNIPROTKB|Q22866	284	lev-11 "Tropomyosin isoforms a	0.535	0.605	0.186	1.9e-05
ZFIN|ZDB-GENE-040625-114	284	tpm2 "tropomyosin 2 (beta)" [D	0.479	0.542	0.254	3.3e-05

TAIR|locus:2128166 AT4G31340 "AT4G31340" [Arabidopsis thaliana (taxid:3702)]

 Score = 830 (297.2 bits), Expect = 8.2e-83, P = 8.2e-83
 Identities = 168/319 (52%), Positives = 225/319 (70%)

Query:     1 MAASKLVIFSLFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLESH 60
             MAA+KLV   L  AL+ T +  +    D P ++ +   D S  KI LDQL +KIR+LES 
Sbjct:     1 MAAAKLVAL-LLLALLFTTSVFA--DADEPEVSEAAGSDGSS-KIHLDQLNAKIRALESQ 56

Query:    61 IDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE 120
             IDEKT+E++GKDEVVA+KEK ++++ ++I SLQ E+SSLQKK + ++A+Q+ KA ARADE
Sbjct:    57 IDEKTREVQGKDEVVAEKEKLLKEREDKIASLQTEVSSLQKKGSSDSAKQLGKAQARADE 116

Query:   121 LEKQIDNXXXXXXXXXXXXXXXXXRAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERA 180
             LEKQ++                  R  EAEKK+ +L++ L+KLQK N+EQK+KI K ERA
Sbjct:   117 LEKQVEVLKNFLEQKNKEKDSTEARTNEAEKKLRELNSSLDKLQKTNEEQKNKIGKLERA 176

Query:   181 LKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVA 240
             +K+AEEEM+R K EAT+++KEL E H +WLPPWLAVH  + Q+  ETHW AHGKPA++  
Sbjct:   177 IKIAEEEMLRTKLEATTKAKELLEAHGSWLPPWLAVHWFKFQTYTETHWEAHGKPAVETV 236

Query:   241 IQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATK 300
             I K  E KAQA KW +PHVE +K K+IPA+KE     T +VEPH +TL  K  EA  ++K
Sbjct:   237 ILKVTEAKAQAEKWAEPHVENVKTKYIPAIKE---TVTIHVEPHFRTLSIKAKEAYHSSK 293

Query:   301 TAVTPHIIRVQEVVDPYFQ 319
             +AV+PHI+ VQE VDPY+Q
Sbjct:   294 SAVSPHIVTVQEFVDPYYQ 312

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0006007 "glucose catabolic process" evidence=RCA

GO:0042732 "D-xylose metabolic process" evidence=RCA

TAIR|locus:2061067 AT2G24420 [Arabidopsis thaliana (taxid:3702)]

 Score = 797 (285.6 bits), Expect = 2.6e-79, P = 2.6e-79
 Identities = 164/324 (50%), Positives = 220/324 (67%)

Query:     1 MAASKLVIFSLFFALILTA-----ADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIR 55
             MAA+KLV   L  AL+        AD  I G D P L  SD  D     IELDQL +KIR
Sbjct:     1 MAAAKLVALLLLLALVFNFTTCIFADAGIDGGDEPKLR-SDGGD-----IELDQLNAKIR 54

Query:    56 SLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAH 115
             +LES ID+KT+ELKG++E+V +KEK +Q++ +++ SL+ E+SSL+KK + ++ E + KA 
Sbjct:    55 ALESQIDDKTKELKGREELVTEKEKLLQERQDKVASLETEVSSLRKKGSSDSVELLSKAQ 114

Query:   116 ARADELEKQIDNXXXXXXXXXXXXXXXXXRAIEAEKKISDLSAKLEKLQKINDEQKSKIR 175
             ARA ELEKQ++                  +  E EKK+++L++++EKL K N+EQK+KIR
Sbjct:   115 ARATELEKQVEVLKKFLEQKNKEKELIEAQTSETEKKLNELNSRVEKLHKTNEEQKNKIR 174

Query:   176 KTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKP 235
             K ERALK++EEEM+R K EAT+++KEL EVH AWLPPW AVH    Q++  THW+AHGKP
Sbjct:   175 KLERALKISEEEMLRTKHEATTKAKELMEVHGAWLPPWFAVHWSSFQTVAGTHWDAHGKP 234

Query:   236 AMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEA 295
              M+   QK    K QA KW +PH+  +K K+IPA+KE      T+VEPHVQTL TK  EA
Sbjct:   235 VMEKVTQKVTLAKNQAEKWAKPHMANVKTKYIPAIKE---TVKTHVEPHVQTLSTKAKEA 291

Query:   296 CEATKTAVTPHIIRVQEVVDPYFQ 319
               A+K+AVTPHI++ QE VDPY+Q
Sbjct:   292 YHASKSAVTPHIVKFQEHVDPYYQ 315

GO:0005576 "extracellular region" evidence=ISM

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

TAIR|locus:2126470 AT4G30090 "AT4G30090" [Arabidopsis thaliana (taxid:3702)]

 Score = 217 (81.4 bits), Expect = 1.9e-16, P = 1.9e-16
 Identities = 52/170 (30%), Positives = 89/170 (52%)

Query:   151 KKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWL 210
             K  S++  K+ +LQK     K ++ +T+R  ++  E  +  K  A   SK L  +   W 
Sbjct:   100 KHASEVEEKVYELQKQVFGLKREV-ETQRKRRLEVEAELADKKVAQLSSK-LENI-DGWF 156

Query:   211 PPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAV 270
                L ++  + Q+ + T W+ H  P +   +Q    K  Q  KW +PH+ET+ ++WIP++
Sbjct:   157 LSKLGLNPTESQAYLMTLWHQHLSPTLHTTLQMVSMKIEQVQKWSEPHIETLNSQWIPSI 216

Query:   271 KEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQV 320
             K+  V  T  +EP VQ +  K+IE    +K A+TPH+I+  +    Y +V
Sbjct:   217 KDACVTITIYLEPKVQYITDKSIELLYTSKQALTPHLIQGFDASYYYLEV 266

GO:0003674 "molecular_function" evidence=ND

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0005783 "endoplasmic reticulum" evidence=IDA

UNIPROTKB|F1PCW0 GOLGA4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 154 (59.3 bits), Expect = 2.0e-07, P = 2.0e-07
 Identities = 65/276 (23%), Positives = 128/276 (46%)

Query:    49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL----SSLQKKET 104
             Q +S I+ L+  ++ KT+E   KDE +   ++ +  ++ER+V L+ E+    S L+KKE 
Sbjct:  1473 QYQSTIKELQMQLELKTKEASEKDEQIQLLKEDLDQQNERLVCLKGEMEDKKSKLEKKEC 1532

Query:   105 LNAAEQVDKAHARADELEKQIDNXXXXXXXXXXXXXXXXXRAIEAEKKISDLSAKLEKLQ 164
              N   ++    AR  ELE+ +                   +  + E+K  ++  KL+ +Q
Sbjct:  1533 -NLETELKTQTARIAELEEHLTQKTTEIKSLSEVLNSYNQQK-DTEQK--EMRQKLQHIQ 1588

Query:   165 KINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSL 224
             ++ DE+  ++++ E  +   E+++   K E  ++ KEL   +S+          L+ +  
Sbjct:  1589 ELGDEKDCRVKEAEEKVSRLEKQVSSMKSELETKKKELDHANSSMKGKEEEFKALEDRLE 1648

Query:   225 IETHWN-AHGKPAMD---VAIQKAL-----EKKAQAGKWVQPHVETIKAKWIPAVKEQWV 275
             +E+    A  K   +   VAI+K L     EK+ Q  K  + H+  +  K    ++E+  
Sbjct:  1649 LESAAKLAELKKKAEQKIVAIKKQLLSQMEEKEQQYKKDTEGHLGELNTK----LQEK-- 1702

Query:   276 VFTTNVEPHVQTL--KTKTIEACEATKTAVTPHIIR 309
                   E  +Q L  K K++E    ++ +V P  ++
Sbjct:  1703 ------EREIQVLEEKLKSVEGLPQSEASVVPTSVK 1732

GO:0000042 "protein targeting to Golgi" evidence=IEA

SGD|S000002764 SPC110 "Inner plaque spindle pole body (SPB) component" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 139 (54.0 bits), Expect = 3.6e-06, P = 3.6e-06
 Identities = 43/173 (24%), Positives = 83/173 (47%)

Query:    39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS 98
             +S  LK EL++L++K     S    K  ELK     +A+ E+ I  K+ ++++ + +L+S
Sbjct:   326 ESKRLKDELNELETKFSENGSQSSAKENELKMLKNKIAELEEEISTKNSQLIAKEGKLAS 385

Query:    99 LQKKETL--NAAEQVD-KAHARADELEKQIDNXXXXXXXXXXXXXXXXXRAIEAEKKISD 155
             L  + T   +   Q D +  +R +EL+K  D                  R I+ +KK+  
Sbjct:   386 LMAQLTQLESKLNQRDSQLGSREEELKKTNDKLQKDIRIAREETVSKDERIIDLQKKVKQ 445

Query:   156 LSAKLEKLQKINDEQKS----KIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
             L   L  ++K + E K+    ++   ++ +K+ E ++  A+ + +   KEL E
Sbjct:   446 LENDLFVIKKTHSESKTITDNELESKDKLIKILENDLKVAQEKYSKMEKELKE 498

GO:0005816 "spindle pole body" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000742 "karyogamy involved in conjugation with cellular fusion" evidence=IGI;IMP

GO:0005200 "structural constituent of cytoskeleton" evidence=IPI

GO:0005823 "central plaque of spindle pole body" evidence=IDA

GO:0005822 "inner plaque of spindle pole body" evidence=IDA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0007020 "microtubule nucleation" evidence=IPI

GO:0005737 "cytoplasm" evidence=IEA

TAIR|locus:2099114 PMD1 "peroxisomal and mitochondrial division factor 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 128 (50.1 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 52/221 (23%), Positives = 102/221 (46%)

Query:    39 DSSPLKIELDQLKSKI---RSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKE 95
             ++  LK  L++L  +I   + +E+ ++++  E++ + E   +++KA++  S R V L+ E
Sbjct:    42 ENRELKERLERLTGEIEEMKDVEAEMNQRFGEMEKEIEEYEEEKKALEAISTRAVELETE 101

Query:    96 LSSLQKKETLNAAEQVDKAHARADELEKQIDNXXXXXXXXXXXXXXXXXRAIEAEKKISD 155
             +S+L   + + +   VDK      EL+K +                      E EK++ D
Sbjct:   102 VSNLHD-DLITSLNGVDKTAEEVAELKKALAEIVEKLEGCEKEAEGLRKDRAEVEKRVRD 160

Query:   156 LSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA--KFEATSRSKELTEVHSAW-LPP 212
             L  K+  L+    E+KSK  ++E  ++  ++E  R   + + T     L  V +   L  
Sbjct:   161 LERKIGVLEVREMEEKSKKLRSEEEMREIDDEKKREIEELQKTVIVLNLELVKNVEELKK 220

Query:   213 WLAVHLLQCQSLIETHWNAHGKPAMDVAIQK-ALEKKAQAG 252
             W +   L  ++L ET      K   ++ ++K  L KK + G
Sbjct:   221 WKSKKKLTEEALSETQ-----KREKELELKKDELLKKVEEG 256

GO:0005737 "cytoplasm" evidence=ISM

GO:0005739 "mitochondrion" evidence=IDA

GO:0009536 "plastid" evidence=IDA

GO:0005777 "peroxisome" evidence=IDA

GO:0005778 "peroxisomal membrane" evidence=IDA

GO:0007005 "mitochondrion organization" evidence=IMP

GO:0007031 "peroxisome organization" evidence=IMP

GO:0031966 "mitochondrial membrane" evidence=IDA

DICTYBASE|DDB_G0286985 zipA "zipper-like domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 134 (52.2 bits), Expect = 1.4e-05, P = 1.4e-05
 Identities = 45/197 (22%), Positives = 87/197 (44%)

Query:    17 LTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLESHIDE---KTQELKGKDE 73
             L++ D  +  +D    T   +++S    ++ DQL SK + L+S  D+   K QEL+   +
Sbjct:   699 LSSKDEQLSNKD----TQIKSIESDLQSVK-DQLSSKDQELQSTKDQLSSKDQELQSTKD 753

Query:    74 VVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNXXXXXX 133
              ++ K++ +Q   +++         L  K+T       D+  ++  EL+   D       
Sbjct:   754 QLSTKDQELQSAKDQLSCQSSTTDQLSAKDT-ELQSTKDQLSSKDSELQSIKDQLSTKDS 812

Query:   134 XXXXXXXXXXXRAIEAEKKISDLSAKLEKLQKINDEQKSK---IRKTERALKVAEEEMMR 190
                        +  E +     LS+K   LQ + D+  SK   ++ T+  L   ++E+  
Sbjct:   813 ELQSSKDQLSSKDSELQSIKDQLSSKDSDLQSVKDQLSSKDSDLQSTKDQLSSKDQELQS 872

Query:   191 AKFEATSRSKELTEVHS 207
              K E TS+ +EL ++ S
Sbjct:   873 VKDELTSKDQELQQITS 889

GO:0005615 "extracellular space" evidence=IDA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0044351 "macropinocytosis" evidence=RCA

WB|WBGene00002978 lev-11 [Caenorhabditis elegans (taxid:6239)]

 Score = 125 (49.1 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 33/177 (18%), Positives = 90/177 (50%)

Query:    32 LTASDAVDSSPLKI--ELDQLKSKIRSLESHIDEKTQEL-KGKDEVVAQKEKAIQDKSER 88
             L  +DA +    +I  +L++++ ++R  +  + +   +L K ++++ A   K +++K + 
Sbjct:    19 LDRADAAEEKVRQITEKLERVEEELRDTQKKMTQTGDDLDKAQEDLSAATSK-LEEKEKT 77

Query:    89 IVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNXXXXXXXXXXXXXXXXXRAIE 148
             +   + E++SL ++ TL   E++++A  R     ++++                  R+++
Sbjct:    78 VQEAEAEVASLNRRMTL-LEEELERAEERLKIATEKLEEATHNVDESERVRKVMENRSLQ 136

Query:   149 AEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEV 205
              E++ + + A+L++ Q + +E   K  +  R L + E ++ RA+  A +   ++ E+
Sbjct:   137 DEERANTVEAQLKEAQLLAEEADRKYDEVARKLAMVEADLERAEERAEAGENKIVEL 193

GO:0040015 "negative regulation of multicellular organism growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0010171 "body morphogenesis" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0060465 "pharynx development" evidence=IMP

GO:0018991 "oviposition" evidence=IMP

GO:0040017 "positive regulation of locomotion" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0030728 "ovulation" evidence=IMP

GO:0000910 "cytokinesis" evidence=IMP

GO:0030833 "regulation of actin filament polymerization" evidence=IDA

GO:0043393 "regulation of protein binding" evidence=IDA

GO:0005865 "striated muscle thin filament" evidence=IDA

GO:0051015 "actin filament binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0030835 "negative regulation of actin filament depolymerization" evidence=IDA

UNIPROTKB|Q22866 lev-11 "Tropomyosin isoforms a/b/d/f" [Caenorhabditis elegans (taxid:6239)]

 Score = 125 (49.1 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 33/177 (18%), Positives = 90/177 (50%)

Query:    32 LTASDAVDSSPLKI--ELDQLKSKIRSLESHIDEKTQEL-KGKDEVVAQKEKAIQDKSER 88
             L  +DA +    +I  +L++++ ++R  +  + +   +L K ++++ A   K +++K + 
Sbjct:    19 LDRADAAEEKVRQITEKLERVEEELRDTQKKMTQTGDDLDKAQEDLSAATSK-LEEKEKT 77

Query:    89 IVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNXXXXXXXXXXXXXXXXXRAIE 148
             +   + E++SL ++ TL   E++++A  R     ++++                  R+++
Sbjct:    78 VQEAEAEVASLNRRMTL-LEEELERAEERLKIATEKLEEATHNVDESERVRKVMENRSLQ 136

Query:   149 AEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEV 205
              E++ + + A+L++ Q + +E   K  +  R L + E ++ RA+  A +   ++ E+
Sbjct:   137 DEERANTVEAQLKEAQLLAEEADRKYDEVARKLAMVEADLERAEERAEAGENKIVEL 193

GO:0009790 "embryo development" evidence=IMP

GO:0034609 "spicule insertion" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0040011 "locomotion" evidence=IMP

GO:0007015 "actin filament organization" evidence=IMP

GO:0051015 "actin filament binding" evidence=IDA

ZFIN|ZDB-GENE-040625-114 tpm2 "tropomyosin 2 (beta)" [Danio rerio (taxid:7955)]

 Score = 123 (48.4 bits), Expect = 3.3e-05, P = 3.3e-05
 Identities = 42/165 (25%), Positives = 77/165 (46%)

Query:    43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
             L+ EL  L+ K++ +E  +D+ ++ LK   E + Q EK   D    + SL + +  L ++
Sbjct:    39 LEEELLALQKKLKGVEDELDKYSESLKDAQEKLEQAEKKAADAEAEVASLNRRIQ-LVEE 97

Query:   103 ETLNAAEQVDKAHARADELEKQIDNXXXXXXXXXXXXXXXXXRAIEAEKKISDLSAKLEK 162
             E   A E++  A  + +E EK  D                  RA + E+K+     +L++
Sbjct:    98 ELDRAQERLATALQKLEEAEKAADESERGMKVIEN-------RATKDEEKMEIQEMQLKE 150

Query:   163 LQKINDEQKSKIRKTERALKVAEEEMMRAKFEAT---SRSKELTE 204
              + I +E   K  +  R L + E E+ R++  A    ++S +L E
Sbjct:   151 AKHIAEEADRKYEEVARKLVILEGELERSEERAEVAEAKSGDLEE 195

GO:0005865 "striated muscle thin filament" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	321
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-13
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-11
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	8e-11
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-09
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-09
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-09
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	5e-09
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	5e-09
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-08
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	1e-08
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-08
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	5e-08
COG1579	239	COG1579, COG1579, Zn-ribbon protein, possibly nucl	6e-08
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	7e-08
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	8e-08
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	2e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-07
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	6e-07
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	7e-07
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	7e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-06
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-06
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-06
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	7e-06
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	8e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-06
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	1e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	1e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	2e-05
PRK00106	535	PRK00106, PRK00106, hypothetical protein; Provisio	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	3e-05
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	3e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	4e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	6e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	7e-05
COG1579	239	COG1579, COG1579, Zn-ribbon protein, possibly nucl	1e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	1e-04
PRK09039	343	PRK09039, PRK09039, hypothetical protein; Validate	1e-04
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	1e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	2e-04
PRK11637	428	PRK11637, PRK11637, AmiB activator; Provisional	2e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	3e-04
pfam13166	713	pfam13166, AAA_13, AAA domain	3e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	4e-04
COG5185	622	COG5185, HEC1, Protein involved in chromosome segr	4e-04
PRK10636	638	PRK10636, PRK10636, putative ABC transporter ATP-b	5e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	6e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	6e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	7e-04
pfam12329	74	pfam12329, TMF_DNA_bd, TATA element modulatory fac	7e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	8e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	8e-04
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	9e-04
pfam08614	194	pfam08614, ATG16, Autophagy protein 16 (ATG16)	9e-04
COG1283	533	COG1283, NptA, Na+/phosphate symporter [Inorganic	9e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.001
COG4372	499	COG4372, COG4372, Uncharacterized protein conserve	0.001
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	0.001
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
PRK11448	1123	PRK11448, hsdR, type I restriction enzyme EcoKI su	0.002
pfam08317	321	pfam08317, Spc7, Spc7 kinetochore protein	0.002
COG3096	1480	COG3096, MukB, Uncharacterized protein involved in	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.003
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.003
pfam03962	188	pfam03962, Mnd1, Mnd1 family	0.003
smart00787	312	smart00787, Spc7, Spc7 kinetochore protein	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.004
PRK05771	646	PRK05771, PRK05771, V-type ATP synthase subunit I;	0.004
PTZ00262	639	PTZ00262, PTZ00262, subtilisin-like protease; Prov	0.004

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 69.7 bits (171), Expect = 4e-13
 Identities = 46/166 (27%), Positives = 91/166 (54%), Gaps = 1/166 (0%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           LK E+++L+ K ++L+  ++E  +EL+  +  +   E+ ++   +R   L++E+  L++ 
Sbjct: 777 LKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEE- 835

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
           E     E++D+     +ELEK+++ LK+E E+ + EKE LE    E E++  +L  +L +
Sbjct: 836 EIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRE 895

Query: 163 LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
           L+    E K +I K    L+  E ++ R + E     +EL E +  
Sbjct: 896 LESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYED 941

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 64.4 bits (157), Expect = 3e-11
 Identities = 48/175 (27%), Positives = 100/175 (57%), Gaps = 6/175 (3%)

Query: 39  DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS 98
           + + L+ EL+QL+S++  LE  ++E  +EL+   E + + E+ ++   E +  L++E+  
Sbjct: 724 ELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEE 783

Query: 99  L------QKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKK 152
           L       ++E     E++++A  R D LE+++++L++  E+ ++E E LE    E E+K
Sbjct: 784 LEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEK 843

Query: 153 ISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHS 207
           + +L  +LE+L+K  +E K ++ + E   +  E+E+   + E     +EL E+ S
Sbjct: 844 LDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELES 898

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 62.8 bits (153), Expect = 8e-11
 Identities = 40/168 (23%), Positives = 89/168 (52%), Gaps = 6/168 (3%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL-QK 101
           L+ EL++L+ +++  E  ++E T EL+  +E + +    + +  E I  LQKEL +L  +
Sbjct: 237 LREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANE 296

Query: 102 KETLN-----AAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
              L        E++     + +ELE Q++ L+ + ++  +E   LE +  E ++++  L
Sbjct: 297 ISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESL 356

Query: 157 SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
            A+LE+L+   +E +S++ + E  L+    ++ + + +  S + E+  
Sbjct: 357 EAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIER 404

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 58.6 bits (142), Expect = 2e-09
 Identities = 40/161 (24%), Positives = 82/161 (50%), Gaps = 1/161 (0%)

Query: 44  KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE 103
           ++EL  L +K++ L   ++E  +EL   +E + + ++ +++  + I  L+ EL  L+++ 
Sbjct: 224 ELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREEL 283

Query: 104 TLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKL 163
                E ++       ELE +I  L++  E+ + E E LE R  E ++KI  L  +LE+ 
Sbjct: 284 EELQEELLELKEEIE-ELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEER 342

Query: 164 QKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
           + + +E +  + + E A +  EE++     E     + L E
Sbjct: 343 ETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALRE 383

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 58.5 bits (142), Expect = 2e-09
 Identities = 42/185 (22%), Positives = 86/185 (46%), Gaps = 10/185 (5%)

Query: 34  ASDAVDSSPL--KIELDQLKSKIRSLESHIDEKTQELKGK-------DEVVAQKEKAIQD 84
            S   +SS L  + E+++L+ KI  LE  I E  + L          +E + Q  K +++
Sbjct: 664 GSAKTNSSILERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEE 723

Query: 85  KSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEA 144
            S +I +L+K+L+ L+ +      E++ +      ELE +I+ L++  E+ ++E    EA
Sbjct: 724 LSRQISALRKDLARLEAEVE-QLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEA 782

Query: 145 RAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
              E E +I  L  +L+ L++  DE ++++           E +   +    +  + L +
Sbjct: 783 EIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLED 842

Query: 205 VHSAW 209
           +    
Sbjct: 843 LEEQI 847

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 57.0 bits (138), Expect = 5e-09
 Identities = 38/169 (22%), Positives = 82/169 (48%), Gaps = 3/169 (1%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKS---ERIVSLQKELSSL 99
           LK E+++L+ +I  L   ++E   EL+  +E + + ++ I+      E   +L +EL  L
Sbjct: 293 LKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQL 352

Query: 100 QKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAK 159
             +      E  +K  A  +ELE+  + L++E  + + E   +     E +++I  L  +
Sbjct: 353 LAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEER 412

Query: 160 LEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
           LE+L +  ++ K ++++ E  L+  + E+     E     ++L E+   
Sbjct: 413 LERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDR 461

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 57.4 bits (139), Expect = 5e-09
 Identities = 37/172 (21%), Positives = 84/172 (48%), Gaps = 6/172 (3%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+ EL++L+ ++  L   ++E ++++    + +A+ E  ++   ERI  L KEL+ L+ +
Sbjct: 703 LRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAE 762

Query: 103 ETLNAAE------QVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
                        ++ +A A  +ELE QI+ LK+E +  ++  + L A      ++ ++L
Sbjct: 763 IEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANL 822

Query: 157 SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
             +LE L++     + ++   E  ++   E++     E     + + E+ S 
Sbjct: 823 RERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESE 874

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 57.0 bits (138), Expect = 5e-09
 Identities = 41/177 (23%), Positives = 87/177 (49%), Gaps = 14/177 (7%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSE--------RIVSLQKELS 97
           +L  L+ ++  L   I E  + L+  ++++ +  K I+D  E        +I  L+ E++
Sbjct: 245 QLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEIA 304

Query: 98  SLQKKETLN------AAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEK 151
           SL++           A E++ K  A  D+L  +I+ L++E E+++K ++ L     E ++
Sbjct: 305 SLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKE 364

Query: 152 KISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
           ++ DL A+LE++ K   E + +++     L+  + E+   K E     +EL  +   
Sbjct: 365 ELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEE 421

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 55.9 bits (135), Expect = 1e-08
 Identities = 35/159 (22%), Positives = 82/159 (51%), Gaps = 1/159 (0%)

Query: 44  KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE 103
           K EL +L+ ++  LE+ +++  +ELK     +   E  +++   ++  L+++L  L+++ 
Sbjct: 666 KRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKREL 725

Query: 104 TLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKL 163
                E      +R +ELE++++ L++E E+ Q+  E LE      E+ ++ L  ++E+L
Sbjct: 726 AALEEELEQLQ-SRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEEL 784

Query: 164 QKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKEL 202
           ++     + ++ + E  L+ AE  +   + E  S  +  
Sbjct: 785 EEKRQALQEELEELEEELEEAERRLDALERELESLEQRR 823

Length = 1163

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 55.8 bits (135), Expect = 1e-08
 Identities = 42/170 (24%), Positives = 84/170 (49%), Gaps = 6/170 (3%)

Query: 41  SPLKIELDQLKSKIRSLESH-----IDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKE 95
             L+ +L +L+  +  LE+      I E   EL   +E V++ E  +++  +++  L  E
Sbjct: 768 EELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLE 827

Query: 96  LSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISD 155
              L+K E     EQ      +   +EK+I+NL  + E+ ++E E LEA   + E ++ D
Sbjct: 828 KEYLEK-EIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGD 886

Query: 156 LSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEV 205
           L  + ++L+    E + KI + E  ++   + +   K +  +  +EL+E+
Sbjct: 887 LKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEI 936

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 55.9 bits (136), Expect = 1e-08
 Identities = 43/144 (29%), Positives = 78/144 (54%), Gaps = 11/144 (7%)

Query: 64  KTQELKGKDEVVAQKEKAIQDKSERIVSLQK-ELSSLQKKETLN-AAEQVDKAHARADEL 121
           K   L+ K+E+   + +  ++  ER   LQK E   LQK+E L+   E ++K     ++ 
Sbjct: 56  KEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKK 115

Query: 122 EKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLS---AKLEKLQKINDEQKSKIRKTE 178
           EK+++  ++E EK+++E E L    ++  ++IS L+   AK   L+K+ +E + +     
Sbjct: 116 EKELEQKQQELEKKEEELEELIEEQLQELERISGLTAEEAKEILLEKVEEEARHEAAVL- 174

Query: 179 RALKVAEEEMMRAKFEATSRSKEL 202
             +K  EEE   AK EA  ++KE+
Sbjct: 175 --IKEIEEE---AKEEADKKAKEI 193

Length = 520

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 54.3 bits (131), Expect = 5e-08
 Identities = 44/167 (26%), Positives = 83/167 (49%), Gaps = 20/167 (11%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           LK EL  L+S++R +E+ +DE +QEL               D S +I  ++KE+  L+++
Sbjct: 686 LKRELSSLQSELRRIENRLDELSQEL--------------SDASRKIGEIEKEIEQLEQE 731

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKL-- 160
           E        +        LE++I+N+K E ++ +   E LE    + E+ ++DL A+L  
Sbjct: 732 EEKLKERLEELE-EDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSH 790

Query: 161 EKLQKINDE---QKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
            ++ +I  E    + ++ + E  L+  E+++ R   E     KE+ E
Sbjct: 791 SRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQE 837

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

 Score = 52.4 bits (126), Expect = 6e-08
 Identities = 40/157 (25%), Positives = 81/157 (51%), Gaps = 1/157 (0%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL 105
            L + K+++ +L   ++    EL+  +  V+Q E  IQ+  ERI   +++LS+++ +  L
Sbjct: 32  ALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDEREL 91

Query: 106 NAAEQ-VDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQ 164
            A    +  A  R + LE ++  L +E EK +KE E L+ R    EK +++  A+LE+  
Sbjct: 92  RALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLEKNLAEAEARLEEEV 151

Query: 165 KINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKE 201
               E+  ++      LK   +  + +++E   ++K+
Sbjct: 152 AEIREEGQELSSKREELKEKLDPELLSEYERIRKNKK 188

Length = 239

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 53.5 bits (129), Expect = 7e-08
 Identities = 42/154 (27%), Positives = 80/154 (51%), Gaps = 19/154 (12%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL 105
           EL++++  I  L+  IDEK Q+L+       ++E+   +K+ER  +L KE    +  E L
Sbjct: 178 ELEEVEENIERLDLIIDEKRQQLER-----LRRER---EKAERYQALLKEKREYEGYELL 229

Query: 106 NAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKL-- 163
              E +++       +E+Q+ +L++E EK  +E   LE R  E E+ + +L+ K++ L  
Sbjct: 230 KEKEALERQKEA---IERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGE 286

Query: 164 ------QKINDEQKSKIRKTERALKVAEEEMMRA 191
                 ++   E +++I   ER++   E E+  A
Sbjct: 287 EEQLRVKEKIGELEAEIASLERSIAEKERELEDA 320

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 53.5 bits (129), Expect = 8e-08
 Identities = 40/171 (23%), Positives = 83/171 (48%), Gaps = 4/171 (2%)

Query: 39  DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS 98
           +   LK  L++L+  + SLE  I+    ELK  +  + + E+ +    E +  L+  LS 
Sbjct: 731 EEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSH 790

Query: 99  LQKKETLNAAEQVDKAH----ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKIS 154
            +  E      ++++      AR  E+E++++ L  E E  +KE + L+ + I+ +++I 
Sbjct: 791 SRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIK 850

Query: 155 DLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEV 205
            +  ++E L    +E + ++ + E AL+  E  +   K E      +L E+
Sbjct: 851 SIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLREL 901

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 51.5 bits (124), Expect = 2e-07
 Identities = 40/147 (27%), Positives = 75/147 (51%), Gaps = 5/147 (3%)

Query: 58  ESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL--NAAEQVDKAH 115
           E+   +K   L+ K+EV   + +  ++  ER   LQ+    L ++E       E +DK  
Sbjct: 44  EAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERRLLQREETLDRKMESLDKKE 103

Query: 116 ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIR 175
              ++ EK++ N +K  +++++E E L A   E  ++IS L+ + E  + + +E + + R
Sbjct: 104 ENLEKKEKELSNKEKNLDEKEEELEELIAEQREELERISGLTQE-EAKEILLEEVEEEAR 162

Query: 176 KTERALKVAEEEMMRAKFEATSRSKEL 202
             E A  + E E   AK EA  ++KE+
Sbjct: 163 -HEAAKLIKEIE-EEAKEEADKKAKEI 187

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 51.5 bits (123), Expect = 4e-07
 Identities = 36/165 (21%), Positives = 73/165 (44%), Gaps = 1/165 (0%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL 105
            +D L+  +R  +  I+   QEL+ ++E++AQ       + E+   LQ+E   L  KE  
Sbjct: 239 RIDLLQELLRDEQEEIESSKQELEKEEEILAQ-VLKENKEEEKEKKLQEEELKLLAKEEE 297

Query: 106 NAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQK 165
               ++ K   R  + E+++   +KE +K +KE +  +    E EK++ +L  K E  ++
Sbjct: 298 ELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEE 357

Query: 166 INDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWL 210
             ++ +    K E+  +    +        +S +K   E      
Sbjct: 358 EEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKN 402

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 51.3 bits (123), Expect = 5e-07
 Identities = 44/170 (25%), Positives = 99/170 (58%), Gaps = 10/170 (5%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL--Q 100
           L+  L++LK KI +L+  ++E+   L+  ++++A+ E+A ++  E++ +L +EL  L   
Sbjct: 321 LEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEA 380

Query: 101 KKETLNAAE-QVDKAHARADELEKQIDNLKKE-------SEKQQKEKEALEARAIEAEKK 152
            +E L   E ++ +     +EL+++I++L++         E  ++E + LEA   E + +
Sbjct: 381 LREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTE 440

Query: 153 ISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKEL 202
           + +L+ +LE+L++  +E + ++++ ER L   +EE+ R + E +S    L
Sbjct: 441 LEELNEELEELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEARL 490

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 50.5 bits (121), Expect = 6e-07
 Identities = 34/162 (20%), Positives = 81/162 (50%), Gaps = 1/162 (0%)

Query: 41  SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ 100
           S  K      K +++ LE  + E   +L+  +E +   +  ++   + +  L+++L  L+
Sbjct: 656 SRNKRSSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELE 715

Query: 101 KKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKL 160
           ++       ++       ++L+ +++ L++E E+ ++E E L+ R  E E+++  L   L
Sbjct: 716 RQLEE-LKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEAL 774

Query: 161 EKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKEL 202
            KL++  +E + K +  +  L+  EEE+  A+    +  +EL
Sbjct: 775 AKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALEREL 816

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 50.8 bits (122), Expect = 6e-07
 Identities = 32/162 (19%), Positives = 83/162 (51%), Gaps = 1/162 (0%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L  E+ +L+ + + L   +    ++L+  +  + + E  + + +E +  L+++L  L++ 
Sbjct: 293 LANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKE- 351

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
           E  +   ++++  A  +ELE +++ L+++ E  + +   LE +      +I  L A+LE+
Sbjct: 352 ELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLER 411

Query: 163 LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
           L+   +  + +I +  + L+ AE + ++A+ E      E  +
Sbjct: 412 LEDRRERLQQEIEELLKKLEEAELKELQAELEELEEELEELQ 453

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 50.5 bits (121), Expect = 7e-07
 Identities = 41/166 (24%), Positives = 78/166 (46%), Gaps = 15/166 (9%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           +K ++ +L+++I SLE  I EK +EL+  +E +A+ E  I      I  L++E+   +K 
Sbjct: 292 VKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERK- 350

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
                         R D+L ++   LK+E E  + E E ++    E   ++ D   KLEK
Sbjct: 351 --------------RRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEK 396

Query: 163 LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
           L++  +E K ++ + +  L+   EE+            ++ E+   
Sbjct: 397 LKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEE 442

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 50.4 bits (121), Expect = 7e-07
 Identities = 37/157 (23%), Positives = 81/157 (51%), Gaps = 14/157 (8%)

Query: 43  LKIELDQLKSKI------RSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL 96
           L+ E+++++ ++         E  I+   +  +  +E++A++ + I++K ER   L++  
Sbjct: 487 LEEEVEEVEERLERAEDLVEAEDRIERLEERREDLEELIAERRETIEEKRERAEELRERA 546

Query: 97  SSL------QKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAE 150
           + L      +++    A E+ ++A     EL  ++  LK+  E  ++ +  L A A +AE
Sbjct: 547 AELEAEAEEKREAAAEAEEEAEEAREEVAELNSKLAELKERIESLERIRTLLAAIA-DAE 605

Query: 151 KKISDLSAKLEKLQKINDEQKSKIR-KTERALKVAEE 186
            +I  L  K E L ++NDE++ ++  K ER  ++  E
Sbjct: 606 DEIERLREKREALAELNDERRERLAEKRERKRELEAE 642

Length = 880

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 49.7 bits (119), Expect = 1e-06
 Identities = 39/170 (22%), Positives = 89/170 (52%), Gaps = 15/170 (8%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+ EL+ L+  +  L+  I+E  ++ +   E + + E+ +++   R+ +L++EL SL+  
Sbjct: 763 LEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLE-- 820

Query: 103 ETLNAAEQVDKAHARADELEKQI-------DNLKKESEKQQKEKEALEARAIEAEKKISD 155
                 ++ ++     +ELE++I       D L++E E+ +KE E L+    E E +  +
Sbjct: 821 ------QRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEE 874

Query: 156 LSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEV 205
           L  +L++L++  +E + ++R+ E  L   +EE+ + +        +L  +
Sbjct: 875 LEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERL 924

Length = 1163

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 48.9 bits (117), Expect = 2e-06
 Identities = 31/159 (19%), Positives = 68/159 (42%), Gaps = 8/159 (5%)

Query: 37  AVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL 96
                 L  E  +LK ++  L + ++E  +E     + +    + ++     I  L++EL
Sbjct: 349 RKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKREL 408

Query: 97  SSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
             LQ        E++ +      +L   I  ++ +  + ++EKE       + E K+  L
Sbjct: 409 DRLQ--------EELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQL 460

Query: 157 SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEA 195
           +A L K ++   + K +  + E+ L   + E+  A+ +A
Sbjct: 461 AADLSKYEQELYDLKEEYDRVEKELSKLQRELAEAEAQA 499

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 48.9 bits (117), Expect = 2e-06
 Identities = 33/139 (23%), Positives = 75/139 (53%), Gaps = 12/139 (8%)

Query: 40  SSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL 99
            S L+ E+ ++++++R +E  ++  T E +  ++ + + ++   D  E+I S++KE+ +L
Sbjct: 800 LSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENL 859

Query: 100 QK---------KETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAE 150
                      +E   A   ++       +L+K+ D L+ +  + +++ E LEA+  +  
Sbjct: 860 NGKKEELEEELEELEAALRDLESRLG---DLKKERDELEAQLRELERKIEELEAQIEKKR 916

Query: 151 KKISDLSAKLEKLQKINDE 169
           K++S+L AKLE L++   E
Sbjct: 917 KRLSELKAKLEALEEELSE 935

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 49.0 bits (116), Expect = 2e-06
 Identities = 43/164 (26%), Positives = 79/164 (48%), Gaps = 15/164 (9%)

Query: 48   DQLKSKIRSLESHIDE---KTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKET 104
            D+ K K    +   D    K +E K   E    + +A  D++E      +E +   +K+ 
Sbjct: 1318 DEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEA----AEEKAEAAEKKK 1373

Query: 105  LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQ 164
              A ++ D A  +A+E +K  D  KK++E+ +K+ + L+  A  A+KK  +   K E+ +
Sbjct: 1374 EEAKKKADAAKKKAEEKKKA-DEAKKKAEEDKKKADELKKAA-AAKKKADEAKKKAEEKK 1431

Query: 165  KINDEQK--SKIRKTERALKVAEE----EMMRAKFEATSRSKEL 202
            K ++ +K   + +K + A K AEE    E  + K E   ++ E 
Sbjct: 1432 KADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEA 1475

Length = 2084

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.2 bits (115), Expect = 3e-06
 Identities = 35/133 (26%), Positives = 76/133 (57%), Gaps = 1/133 (0%)

Query: 76  AQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQ 135
            + E+ + +   ++  L++EL SL K E  +  + +++   + +ELE+Q++ LK+E    
Sbjct: 670 KELEEELAELEAQLEKLEEELKSL-KNELRSLEDLLEELRRQLEELERQLEELKRELAAL 728

Query: 136 QKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEA 195
           ++E E L++R  E E+++ +L  +LE+LQ+  +E + ++   E AL   +EE+   + + 
Sbjct: 729 EEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKR 788

Query: 196 TSRSKELTEVHSA 208
            +  +EL E+   
Sbjct: 789 QALQEELEELEEE 801

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.8 bits (114), Expect = 5e-06
 Identities = 34/168 (20%), Positives = 78/168 (46%), Gaps = 3/168 (1%)

Query: 42   PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK 101
             L+ +LD+L+ ++  LE  ++E  +EL+  +    + E  +++  E    L++EL  L+ 
Sbjct: 839  ELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELES 898

Query: 102  KETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALE--ARAIEAEKKISDLSAK 159
            +      E+++K   R +ELE +++ L+ E  + ++E E         E E++I  L  +
Sbjct: 899  ELA-ELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETELEREIERLEEE 957

Query: 160  LEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHS 207
            +E L  +N     +  + E   +  + +    +       + + E+  
Sbjct: 958  IEALGPVNLRAIEEYEEVEERYEELKSQREDLEEAKEKLLEVIEELDK 1005

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.8 bits (114), Expect = 5e-06
 Identities = 37/150 (24%), Positives = 81/150 (54%), Gaps = 3/150 (2%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+ EL+ L+ +   LE  I+E  +E++  +E + + E+ +++  + +  L++EL  L+  
Sbjct: 812 LERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEA- 870

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
           E     +++ +     +ELE+++  L+ E  + ++E E L  R  E E K+  L  +L +
Sbjct: 871 EKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPE 930

Query: 163 LQ-KINDEQKSKIRKT-ERALKVAEEEMMR 190
           L+ ++ +E +  +    ER ++  EEE+  
Sbjct: 931 LEEELEEEYEDTLETELEREIERLEEEIEA 960

Length = 1163

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.8 bits (113), Expect = 6e-06
 Identities = 45/166 (27%), Positives = 80/166 (48%), Gaps = 11/166 (6%)

Query: 44   KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE 103
            K E  +++  ++  E     K +E K  +E    K KA + K       + E    ++ E
Sbjct: 1588 KAEEARIEEVMKLYEEEKKMKAEEAKKAEE---AKIKAEELKKAEEEKKKVEQLKKKEAE 1644

Query: 104  TLNAAEQVDKAH----ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAK 159
                AE++ KA      +A E  K+ +  KK++E+ +K +E  E +A EA KK ++ + K
Sbjct: 1645 EKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEED-EKKAAEALKKEAEEAKK 1703

Query: 160  LEKLQKINDEQKSK---IRKTERALKVAEEEMMRAKFEATSRSKEL 202
             E+L+K   E+K K   ++K E   K+  EE  +   E   +++E 
Sbjct: 1704 AEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEA 1749

Length = 2084

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 47.4 bits (113), Expect = 7e-06
 Identities = 45/172 (26%), Positives = 88/172 (51%), Gaps = 8/172 (4%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+  L  L+ ++  LE+ ++E   +L    E +A+ E+ +++  E + SL+ EL  L+ +
Sbjct: 307 LRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAE 366

Query: 103 ----ETLNAA--EQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
               E+      EQ++   ++  +LE QI +L  E E+ +   E LE R    +++I +L
Sbjct: 367 LEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEEL 426

Query: 157 SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
             KLE+ +    E ++++ + E  L+  +EE+ R +       +EL E   A
Sbjct: 427 LKKLEEAEL--KELQAELEELEEELEELQEELERLEEALEELREELEEAEQA 476

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 47.4 bits (113), Expect = 8e-06
 Identities = 47/166 (28%), Positives = 86/166 (51%), Gaps = 12/166 (7%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL--- 99
           LK +L +LK +I+SL+  + EK +ELK K   +   EK + +  E +  L KEL  L   
Sbjct: 530 LKEKLIKLKGEIKSLKKEL-EKLEELKKKLAEL---EKKLDELEEELAELLKELEELGFE 585

Query: 100 ---QKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
              + +E L   E     +    + EK+++  +KE +K ++E +       E EK++ +L
Sbjct: 586 SVEELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEEL 645

Query: 157 SAKLEKLQKINDEQKSKIRKTERALKVAEE-EMMRAKFEATSRSKE 201
             +LE+L+K   E++ +    E  L+++ E   +RA+ E   + +E
Sbjct: 646 RKELEELEKKYSEEEYE-ELREEYLELSRELAGLRAELEELEKRRE 690

Length = 880

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.0 bits (112), Expect = 9e-06
 Identities = 38/171 (22%), Positives = 90/171 (52%), Gaps = 12/171 (7%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSER-----------IVSLQK 94
           +L++ +  +  LE  ++E  ++L+  +    + E+  + K+E            +  L+K
Sbjct: 180 KLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRK 239

Query: 95  ELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKIS 154
           EL  L+++ +    E++++     +E EK+I+ LK E E+ ++E E L+   +E +++I 
Sbjct: 240 ELEELEEELS-RLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIE 298

Query: 155 DLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEV 205
           +L  ++  L++  +E ++++ + E  L+  +E++   K E   R   L E+
Sbjct: 299 ELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEEL 349

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 37/165 (22%), Positives = 81/165 (49%), Gaps = 1/165 (0%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+ +++QLK ++++L   +DE   EL   +E  A   + ++    RI + ++ L  L++ 
Sbjct: 787 LEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEE- 845

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
           +    +E ++   A  +ELE+ I+ L+ E E    E+ +LE        ++ +LS +L +
Sbjct: 846 QIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRE 905

Query: 163 LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHS 207
           L+    E + ++ +    L   E  +   +    +  + L+E +S
Sbjct: 906 LESKRSELRRELEELREKLAQLELRLEGLEVRIDNLQERLSEEYS 950

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 37/160 (23%), Positives = 71/160 (44%), Gaps = 16/160 (10%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQ---KELSSLQKK 102
           EL++LK +I  LE  ++      +  +E + + E+ I++  + I  L+   KEL  L++K
Sbjct: 232 ELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEK 291

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
                            +L +  +    E  + +K    LE      E++I +L  K E+
Sbjct: 292 AE------------EYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEER 339

Query: 163 LQKINDEQKSKIRKTERALKVAEE-EMMRAKFEATSRSKE 201
           L+++  + K   ++ E   +  E  E  +AK E   R K+
Sbjct: 340 LEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKK 379

Length = 880

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 46.7 bits (111), Expect = 1e-05
 Identities = 38/164 (23%), Positives = 88/164 (53%), Gaps = 1/164 (0%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
               L++L+ +I  LE  ++     L+  +E++ +K K+++++ E++    ++L S  ++
Sbjct: 289 KIERLEELEREIEELEEELEGLRALLEELEELL-EKLKSLEERLEKLEEKLEKLESELEE 347

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
                 E       R  ELE++++ L+KE EK  +  + LE    E ++++++LSA LE+
Sbjct: 348 LAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEE 407

Query: 163 LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVH 206
           +Q+  +E + ++ + ER L+  EEE+ + + +      +   + 
Sbjct: 408 IQEELEELEKELEELERELEELEEEIKKLEEQINQLESKELMIA 451

Length = 908

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.9 bits (109), Expect = 2e-05
 Identities = 35/176 (19%), Positives = 88/176 (50%), Gaps = 10/176 (5%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL--- 99
           L+ E+  L+ ++  LE+ ++E  + L+   E +   ++ ++++   +  L++ L+ L   
Sbjct: 300 LEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEA 359

Query: 100 --QKKETLNAAEQVDKAH-----ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKK 152
             + +E L+A  +  +           ELE ++  ++ E E+ ++E E+LE R     ++
Sbjct: 360 KEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSER 419

Query: 153 ISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
           + DL  +L++L+   +E ++++ +    L+  EE++   +       +EL E+   
Sbjct: 420 LEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELAELQEE 475

Length = 1163

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 47/169 (27%), Positives = 90/169 (53%), Gaps = 15/169 (8%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL 105
           EL +++ K R L   + E  + LK + E++  KE A     E++  L+++L     +E  
Sbjct: 467 ELKEIEEKERKLRKELRELEKVLKKESELIKLKELA-----EQLKELEEKLKKYNLEELE 521

Query: 106 NAAEQVDKAHARADELEKQIDNLKKESEKQQ---KEKEALEARAIEAEKKISDLSAKLEK 162
             AE+ +K   +  +L+ +I +LKKE EK +   K+   LE +  E E+++++L  +LE+
Sbjct: 522 KKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKKKLAELEKKLDELEEELAELLKELEE 581

Query: 163 LQ-KINDEQKSKIRKTERA------LKVAEEEMMRAKFEATSRSKELTE 204
           L  +  +E + ++++ E        LK AE+E+ R + E     +EL +
Sbjct: 582 LGFESVEELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDK 630

Length = 880

>gnl|CDD|178867 PRK00106, PRK00106, hypothetical protein; Provisional

 Score = 46.0 bits (109), Expect = 2e-05
 Identities = 33/119 (27%), Positives = 60/119 (50%), Gaps = 12/119 (10%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL--QKKE 103
           EL Q++S++    + +D K + L  K++ +  KE+++ DKS+ I   ++++  L  QKK 
Sbjct: 98  ELKQIESRLTERATSLDRKDENLSSKEKTLESKEQSLTDKSKHIDEREEQVEKLEEQKKA 157

Query: 104 TLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
            L     + +A AR   L +  + L  E          +  R  EAE+++ D S K+ K
Sbjct: 158 ELERVAALSQAEAREIILAETENKLTHE----------IATRIREAEREVKDRSDKMAK 206

Length = 535

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.1 bits (107), Expect = 3e-05
 Identities = 33/153 (21%), Positives = 66/153 (43%), Gaps = 15/153 (9%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
            LK EL++L+++   LE  + E  +E +  +E + + E  + +  E I  L++ L  L+ K
Sbjct: 861  LKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAK 920

Query: 103  ET---------------LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAI 147
                                     +     + LE++I+ L   + +  +E E +E R  
Sbjct: 921  LERLEVELPELEEELEEEYEDTLETELEREIERLEEEIEALGPVNLRAIEEYEEVEERYE 980

Query: 148  EAEKKISDLSAKLEKLQKINDEQKSKIRKTERA 180
            E + +  DL    EKL ++ +E   + R+  + 
Sbjct: 981  ELKSQREDLEEAKEKLLEVIEELDKEKRERFKE 1013

Length = 1163

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 45.4 bits (108), Expect = 3e-05
 Identities = 35/142 (24%), Positives = 74/142 (52%), Gaps = 8/142 (5%)

Query: 48  DQLKSKIRSLESHIDEKTQELKGKDEV---VAQKEKAIQDKSERIVSLQKELSSLQKKET 104
             L   I+ ++  I+   + +K  + +   + +KEK +++    I  +  EL  L+++  
Sbjct: 165 KNLGEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREE-- 222

Query: 105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQ 164
               E+++K     +EL+++I+ L+KE E  +  K  LE +  E E++I +L  ++E+L+
Sbjct: 223 ---LEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELE 279

Query: 165 KINDEQKSKIRKTERALKVAEE 186
           +   E K    K E  +K++E 
Sbjct: 280 EKVKELKELKEKAEEYIKLSEF 301

Length = 880

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 45.0 bits (106), Expect = 3e-05
 Identities = 26/109 (23%), Positives = 51/109 (46%), Gaps = 2/109 (1%)

Query: 84  DKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALE 143
           +    +  L++  S    K      E++DK    AD+ +++ D  +  ++KQ+ E    +
Sbjct: 195 NFRRDMTDLKERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQ 254

Query: 144 ARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAK 192
             A    K     S K +K  ++ + QK +I K +  +K  +EE ++AK
Sbjct: 255 QEAKNLPKPADTSSPKEDK--QVAENQKREIEKAQIEIKKNDEEALKAK 301

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 45.1 bits (107), Expect = 4e-05
 Identities = 37/141 (26%), Positives = 76/141 (53%), Gaps = 7/141 (4%)

Query: 45  IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKET 104
           I+L +   +       I+++   L+ +   + ++ K +++K ER+  L+K+L  L+K+  
Sbjct: 296 IKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKR-- 353

Query: 105 LNAAEQVDKAHARADELEKQIDNLKKES-----EKQQKEKEALEARAIEAEKKISDLSAK 159
           L   E+  + +  A   +++++ LKK       EK +KE E LE    E E++IS ++A+
Sbjct: 354 LEELEERHELYEEAKAKKEELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITAR 413

Query: 160 LEKLQKINDEQKSKIRKTERA 180
           + +L+K   E K  I + ++A
Sbjct: 414 IGELKKEIKELKKAIEELKKA 434

Length = 880

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.7 bits (105), Expect = 5e-05
 Identities = 36/144 (25%), Positives = 70/144 (48%), Gaps = 4/144 (2%)

Query: 63   EKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKA-HARADEL 121
            +K +E +  +E+   +E  +   + R  +++ E    +K + L  AE+  KA  A+  E 
Sbjct: 1243 KKAEEERNNEEIRKFEEARMAHFARRQAAIKAE--EARKADELKKAEEKKKADEAKKAEE 1300

Query: 122  EKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERAL 181
            +K+ D  KK++E+ +K  EA + +A EA+KK      K E+ +K  +  K++        
Sbjct: 1301 KKKADEAKKKAEEAKKADEA-KKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEA 1359

Query: 182  KVAEEEMMRAKFEATSRSKELTEV 205
            + AEE+   A+ +     K+    
Sbjct: 1360 EAAEEKAEAAEKKKEEAKKKADAA 1383

Length = 2084

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 44.7 bits (106), Expect = 6e-05
 Identities = 39/149 (26%), Positives = 73/149 (48%), Gaps = 7/149 (4%)

Query: 68  LKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKET-----LNAAEQ-VDKAHARADEL 121
            +G       +   +Q   ER+  L++ELSSLQ +       L+   Q +  A  +  E+
Sbjct: 662 PRGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEI 721

Query: 122 EKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERAL 181
           EK+I+ L++E EK ++  E LE      E++I ++ ++L++L+   +E +  + K E AL
Sbjct: 722 EKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEAL 781

Query: 182 KVAEEEMMRAKF-EATSRSKELTEVHSAW 209
              E  +  ++  E  +   +L E  S  
Sbjct: 782 NDLEARLSHSRIPEIQAELSKLEEEVSRI 810

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 44.3 bits (105), Expect = 7e-05
 Identities = 41/170 (24%), Positives = 91/170 (53%), Gaps = 5/170 (2%)

Query: 43  LKIELDQLKSKIRSLESHID--EKTQELKGKDEVV--AQKEKAIQDKSERIVSLQKELSS 98
           L+  L++L+ ++  LE   +  E+ QELK +   +  A     +++  + +  L++ELS 
Sbjct: 191 LEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSR 250

Query: 99  LQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSA 158
           L++ E     E++++A    +EL+ +++ L++E E+ Q+E   L+    E E +IS L  
Sbjct: 251 LEE-ELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRE 309

Query: 159 KLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
           +LE+L+   +E + ++ + +  ++  +EE+   +       + L E+  A
Sbjct: 310 RLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEA 359

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 44.3 bits (105), Expect = 7e-05
 Identities = 28/134 (20%), Positives = 61/134 (45%), Gaps = 12/134 (8%)

Query: 76  AQKEKAI--QDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESE 133
            Q EKA   ++    +  L+  L  L+ +E               +EL++++   ++E E
Sbjct: 207 RQAEKAERYKELKAELRELELALLVLRLEE----------LREELEELQEELKEAEEELE 256

Query: 134 KQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKF 193
           +   E + LE +  E   ++S+L  ++E+LQK      ++I + E+  ++  E +   + 
Sbjct: 257 ELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLER 316

Query: 194 EATSRSKELTEVHS 207
           +      +L E+ S
Sbjct: 317 QLEELEAQLEELES 330

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 30/145 (20%), Positives = 65/145 (44%), Gaps = 10/145 (6%)

Query: 45  IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKET 104
           + + +L  +   LE  I E  + LK     +    KA++     +  L+ ++S L+    
Sbjct: 10  LAIQKLDLEKDRLEPRIKEIRKALKKAKAELEALNKALEALEIELEDLENQVSQLE---- 65

Query: 105 LNAAEQVDKAHARADELEKQIDNLKKESE--KQQKEKEALEARAIEAEKKISDLSAKLEK 162
                ++ +   R    E+++  +K E E      E +  + R    E ++++L  ++EK
Sbjct: 66  ----SEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEK 121

Query: 163 LQKINDEQKSKIRKTERALKVAEEE 187
           L+K  ++ K ++ + E+ L  AE  
Sbjct: 122 LEKEIEDLKERLERLEKNLAEAEAR 146

Length = 239

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 43.0 bits (102), Expect = 1e-04
 Identities = 32/113 (28%), Positives = 61/113 (53%), Gaps = 4/113 (3%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL--QKKE 103
           EL +L+ ++   E  +D K + L  K+E + +KEK + +K + +   ++EL  L  +++E
Sbjct: 77  ELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQRE 136

Query: 104 TLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
            L     + +  A+   LE+  +  + E+ K  KE E  EA+  EA+KK  ++
Sbjct: 137 ELERISGLTQEEAKEILLEEVEEEARHEAAKLIKEIEE-EAKE-EADKKAKEI 187

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 43.2 bits (101), Expect = 1e-04
 Identities = 39/135 (28%), Positives = 65/135 (48%), Gaps = 7/135 (5%)

Query: 64   KTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDK----AHARAD 119
            K +E +  DE+   +EK   D++++    +K   + +K E    A++  K    A  +AD
Sbjct: 1273 KAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKAD 1332

Query: 120  ELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSK---IRK 176
              +K+ +  KK +E  + E EA    A  AE+K      K E+ +K  D  K K    +K
Sbjct: 1333 AAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKK 1392

Query: 177  TERALKVAEEEMMRA 191
             + A K AEE+  +A
Sbjct: 1393 ADEAKKKAEEDKKKA 1407

Length = 2084

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 27/97 (27%), Positives = 55/97 (56%), Gaps = 4/97 (4%)

Query: 86  SERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALE-- 143
            ER+  LQ+EL+ LQ+ E     EQ+ +      EL++++  L+ E E+ QKE   ++  
Sbjct: 65  RERLPELQQELAELQE-ELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQL 123

Query: 144 -ARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTER 179
            A AIE +++  +L  +L +L++ N+  +++  + + 
Sbjct: 124 SANAIELDEENRELREELAELKQENEALEAENERLQE 160

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated

 Score = 43.0 bits (102), Expect = 1e-04
 Identities = 31/140 (22%), Positives = 62/140 (44%), Gaps = 20/140 (14%)

Query: 65  TQELKGKDEVVAQ--------------KEKAIQDKSERIVSLQKELSSLQ------KKET 104
           ++E+ GKD  + +              + +  QD  + + +L+  LS+ +      +   
Sbjct: 45  SREISGKDSALDRLNSQIAELADLLSLERQGNQDLQDSVANLRASLSAAEAERSRLQALL 104

Query: 105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQ 164
              A     A  RA EL +++D+ K+ S +   + E L  +     ++++ L A L+  +
Sbjct: 105 AELAGAGAAAEGRAGELAQELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASE 164

Query: 165 KINDEQKSKIRKTERALKVA 184
           K + E ++KI    R L VA
Sbjct: 165 KRDRESQAKIADLGRRLNVA 184

Length = 343

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 43.3 bits (103), Expect = 1e-04
 Identities = 35/143 (24%), Positives = 73/143 (51%), Gaps = 15/143 (10%)

Query: 44  KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE 103
           K +L++L + +  LE  +++K +E +   +   + ++ +++K E++   + +L    +KE
Sbjct: 515 KEKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKE 574

Query: 104 TLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKL 163
              A + + +A   ADE+ K++  L+K      K  E +EAR     K+++      EK 
Sbjct: 575 ---AQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEAR-----KRLNK---ANEKK 623

Query: 164 QKINDEQKSKIRKTERALKVAEE 186
           +K     K K ++ +  LKV +E
Sbjct: 624 EKK----KKKQKEKQEELKVGDE 642

Length = 782

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 41/162 (25%), Positives = 78/162 (48%), Gaps = 12/162 (7%)

Query: 49  QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK-ETLNA 107
           +LK+++R LE  +      L+   E + + ++ +++  E +  L  EL  L++K E L  
Sbjct: 217 ELKAELRELELAL--LVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRL 274

Query: 108 AEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKIN 167
                       ELE++I+ L+KE      E   LE +     +++++L  +LE+L+   
Sbjct: 275 EVS---------ELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQL 325

Query: 168 DEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAW 209
           +E +SK+ +    L   EE++   K E  S   EL E+ +  
Sbjct: 326 EELESKLDELAEELAELEEKLEELKEELESLEAELEELEAEL 367

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 25/104 (24%), Positives = 54/104 (51%), Gaps = 5/104 (4%)

Query: 50  LKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAE 109
            + ++  L+  + E  +EL    E +A+ ++  Q+  + + +L+ EL  LQK+       
Sbjct: 64  ARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKE-----LA 118

Query: 110 QVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKI 153
           ++ +  A A EL+++   L++E  + ++E EALEA     ++  
Sbjct: 119 RIKQLSANAIELDEENRELREELAELKQENEALEAENERLQENE 162

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 25/97 (25%), Positives = 51/97 (52%), Gaps = 4/97 (4%)

Query: 56  SLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAH 115
           +  +H  +   +LK   + +A KEK+++ + ++  SL  +L   Q++    A+ ++ +  
Sbjct: 37  AFSAHASDNRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKK-QEEAISQASRKLRETQ 95

Query: 116 ARADELEKQIDNLK---KESEKQQKEKEALEARAIEA 149
              ++L KQID L     + E+QQ  +E L A  ++A
Sbjct: 96  NTLNQLNKQIDELNASIAKLEQQQAAQERLLAAQLDA 132

Length = 428

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 38/146 (26%), Positives = 65/146 (44%), Gaps = 11/146 (7%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK- 101
            L+ EL++L  ++R LES   E  +EL+   E +AQ E  ++    RI +LQ+ LS     
Sbjct: 892  LRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRIDNLQERLSEEYSL 951

Query: 102  ------KETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISD 155
                         +  ++A  R   LE +I  L   +    +E E L+ R      +  D
Sbjct: 952  TLEEAEALENKIEDDEEEARRRLKRLENKIKELGPVNLAAIEEYEELKERYDFLTAQKED 1011

Query: 156  LSAKLEKLQ----KINDEQKSKIRKT 177
            L+   E L+    +I+ E + + + T
Sbjct: 1012 LTEAKETLEEAIEEIDREARERFKDT 1037

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 42.3 bits (99), Expect = 3e-04
 Identities = 32/145 (22%), Positives = 65/145 (44%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L  E ++LKS++  LE    +  ++LK  ++ + + EK ++ + E I  L+KEL  L+ K
Sbjct: 292 LAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIK 351

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
                 E+      +    + + + L K+  + ++   A + +  E E K  +       
Sbjct: 352 REAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLL 411

Query: 163 LQKINDEQKSKIRKTERALKVAEEE 187
           L+    E+     + +  LK+ EE 
Sbjct: 412 LELSEQEEDLLKEEKKEELKIVEEL 436

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.1 bits (98), Expect = 3e-04
 Identities = 43/163 (26%), Positives = 78/163 (47%), Gaps = 13/163 (7%)

Query: 34   ASDAVDSSPLKIELDQLK-SKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSL 92
            A+D  +++  K E  + K  + +       +K +E K  DE    K+KA +DK +     
Sbjct: 1355 AADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEA---KKKAEEDKKKADELK 1411

Query: 93   QKELSSLQKKETLNAAEQVDKAH--ARADELEKQIDNLKKESEKQQK----EKEALEARA 146
            +   +  +  E    AE+  KA    +  E  K+ D  KK++E+ +K    +K+A EA+ 
Sbjct: 1412 KAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKK 1471

Query: 147  IEAEKKISDLSAKLEKLQKINDEQKSK---IRKTERALKVAEE 186
             +  KK ++ + K ++ +K  +E K K    +K   A K A+E
Sbjct: 1472 ADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADE 1514

Length = 2084

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 40.8 bits (96), Expect = 3e-04
 Identities = 18/105 (17%), Positives = 51/105 (48%), Gaps = 2/105 (1%)

Query: 38  VDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS 97
            D+   +  L +L+ ++  L+  + E  ++L    +   + ++ +      +  LQKEL+
Sbjct: 59  SDTPSARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELA 118

Query: 98  SLQK--KETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKE 140
            +++     +   E+  +      EL+++ + L+ E+E+ Q+ ++
Sbjct: 119 RIKQLSANAIELDEENRELREELAELKQENEALEAENERLQENEQ 163

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 42.3 bits (100), Expect = 3e-04
 Identities = 34/135 (25%), Positives = 62/135 (45%), Gaps = 19/135 (14%)

Query: 39  DSSPLKIELDQLKSKIRSLESHIDEKTQEL--------------KGKDEVVAQKEKAIQD 84
           D   LK  L+ L+  +      ++EK ++                  D + A  E  I++
Sbjct: 321 DVEELKALLEALEEILEKNLQKLEEKLKDPSTSIELESITDLIESINDIIDAINEL-IRE 379

Query: 85  KSERIVSLQKELSSLQKK----ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKE 140
            +E+I +L+KE +  +KK          E +D        LEK I++L+KE ++ + E +
Sbjct: 380 HNEKIDNLKKEKNKAKKKLWLHLVAELKEDIDAYQKEKKGLEKAINSLEKEIKQLEAEIK 439

Query: 141 ALEARAIEAEKKISD 155
           ALE    E EK++++
Sbjct: 440 ALEKEIKELEKQLTN 454

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 41.6 bits (98), Expect = 4e-04
 Identities = 37/147 (25%), Positives = 75/147 (51%), Gaps = 9/147 (6%)

Query: 45  IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKET 104
           +EL   + ++   E  + +  +EL    E +A+ EK +++  + +  L+K+ S  + +E 
Sbjct: 605 LELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEEL 664

Query: 105 LNAAEQVDKAHARAD----ELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKL 160
                ++ +  A       ELEK+ + +KK  EK ++E E  E    +A+K++  L   L
Sbjct: 665 REEYLELSRELAGLRAELEELEKRREEIKKTLEKLKEELEERE----KAKKELEKLEKAL 720

Query: 161 EKLQKINDE-QKSKIRKTERALKVAEE 186
           E+++++ ++ +K K    ERAL    E
Sbjct: 721 ERVEELREKVKKYKALLKERALSKVGE 747

Length = 880

>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]

 Score = 41.5 bits (97), Expect = 4e-04
 Identities = 30/167 (17%), Positives = 69/167 (41%), Gaps = 10/167 (5%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL 105
           ++  LK++  +L   I E   ++  K + + +K +A++  S +  +    +   + +E  
Sbjct: 272 DIANLKTQNDNLYEKIQE-AMKISQKIKTLREKWRALKSDSNKYENYVNAMKQ-KSQEWP 329

Query: 106 NAAEQ----VDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLE 161
              E+    ++        L+  ID L K+  KQ    E  E    E EK    L+ +L+
Sbjct: 330 GKLEKLKSEIELKEEEIKALQSNIDELHKQLRKQGISTEQFELMNQEREK----LTRELD 385

Query: 162 KLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
           K+   +D+    ++  +   +   + + +   +  S  + +T   S 
Sbjct: 386 KINIQSDKLTKSVKSRKLEAQGIFKSLEKTLRQYDSLIQNITRSRSQ 432

Length = 622

>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein; Provisional

 Score = 41.3 bits (97), Expect = 5e-04
 Identities = 35/122 (28%), Positives = 54/122 (44%), Gaps = 19/122 (15%)

Query: 93  QKELSSLQKKETLNAAEQVDK----AHARAD------ELEKQIDNLKKESEKQQKEKEAL 142
           Q+ LS +QK+E        +     A AR D      EL  Q   L+KE  + +KE E L
Sbjct: 516 QQWLSDVQKQENQTDEAPKENNANSAQARKDQKRREAELRTQTQPLRKEIARLEKEMEKL 575

Query: 143 EARAIEAEKKISDLS-------AKLEKLQKINDEQKSKIRKTERALKVAEE--EMMRAKF 193
            A+  +AE+K+ D         A+L    +     KS + + E A   A+E  E M  + 
Sbjct: 576 NAQLAQAEEKLGDSELYDQSRKAELTACLQQQASAKSGLEECEMAWLEAQEQLEQMLLEG 635

Query: 194 EA 195
           ++
Sbjct: 636 QS 637

Length = 638

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 41.2 bits (97), Expect = 6e-04
 Identities = 29/140 (20%), Positives = 62/140 (44%), Gaps = 15/140 (10%)

Query: 54  IRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDK 113
             ++E+  +E     +   + + +   A Q  +E   SL+++   L+        E+ ++
Sbjct: 309 AEAVEARREELEDRDEELRDRLEECRVAAQAHNEEAESLREDADDLE--------ERAEE 360

Query: 114 AHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISD-------LSAKLEKLQKI 166
               A ELE +++  ++  E +++E E LE    E  ++  D           LE+L++ 
Sbjct: 361 LREEAAELESELEEAREAVEDRREEIEELEEEIEELRERFGDAPVDLGNAEDFLEELREE 420

Query: 167 NDEQKSKIRKTERALKVAEE 186
            DE + +  + E  L+ A E
Sbjct: 421 RDELREREAELEATLRTARE 440

Length = 880

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 40.8 bits (96), Expect = 6e-04
 Identities = 31/161 (19%), Positives = 65/161 (40%), Gaps = 19/161 (11%)

Query: 47  LDQLKSKIRSLESHIDE---KTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE 103
               K K+  +E  + E        + K  V+                L + LS ++++E
Sbjct: 354 YLAYKPKLEKVERKLPELGIWKDVERIKALVIRGY------------PLAEALSKVKEEE 401

Query: 104 TLNAAEQVDKAHARADE--LEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLE 161
                ++  +   R +    EK+I  L++  E+ ++E   L+    E +++I  L ++LE
Sbjct: 402 -RPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELE 460

Query: 162 KLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKEL 202
           + ++     K +  +  RA     E + +   E   R +EL
Sbjct: 461 RFRR-EVRDKVRKDREIRARDRRIERLEKELEEKKKRVEEL 500

Length = 652

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 41.2 bits (97), Expect = 7e-04
 Identities = 31/149 (20%), Positives = 60/149 (40%), Gaps = 19/149 (12%)

Query: 40  SSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL 99
               + +L++LK +I  L+  +D   +EL+   E +A    AI     +I  L++E    
Sbjct: 387 LKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDK 446

Query: 100 QKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAK 159
             +  +   E          +LE+   +L K     ++E   L+      EK++S L  +
Sbjct: 447 ALE--IKKQEW---------KLEQLAADLSKY----EQELYDLKEEYDRVEKELSKLQRE 491

Query: 160 LEKLQKINDEQKSKIRKTERALKVAEEEM 188
           L + +     Q     +  R  +  EE +
Sbjct: 492 LAEAEA----QARASEERVRGGRAVEEVL 516

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|221533 pfam12329, TMF_DNA_bd, TATA element modulatory factor 1 DNA binding

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 32/72 (44%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 79  EKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKE 138
           EK + +K E+I  L +E   L KKE L     + K  A+  ELEK+I  LKK+ EK +KE
Sbjct: 4   EKKLAEKDEQIAQLMEEGEKLSKKE-LKHNNTIKKLRAKNKELEKEIAELKKKLEKLEKE 62

Query: 139 KEALEARAIEAE 150
            E LE R   AE
Sbjct: 63  LENLEERLKRAE 74

This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. Length = 74

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 40.8 bits (96), Expect = 8e-04
 Identities = 37/149 (24%), Positives = 71/149 (47%), Gaps = 9/149 (6%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+ +   LK +I+S+E  I+    + +  +E + + E A++D   R+  L+KE   L+ +
Sbjct: 838 LQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQ 897

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
             L   E+      + +ELE QI+  +K   + + + EALE    E E    +     E+
Sbjct: 898 --LRELER------KIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKGEDEEIPEE 949

Query: 163 LQKINDEQKSKIRKTERALKVAEEEMMRA 191
              + D Q  ++++ E  ++  E   M A
Sbjct: 950 ELSLEDVQA-ELQRVEEEIRALEPVNMLA 977

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 40.9 bits (96), Expect = 8e-04
 Identities = 35/176 (19%), Positives = 75/176 (42%), Gaps = 14/176 (7%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEV-VAQKEKAIQDKSERIVSLQKELSSLQK 101
           L   L+ ++  + +LE  + E  +  + ++E    + E+ I+   ER+  L++E   L++
Sbjct: 194 LSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEE 253

Query: 102 KET---------LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKK 152
            +          L A +  ++     + L ++++   +  E+ ++E E LE         
Sbjct: 254 LKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRAL 313

Query: 153 ISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
           + +L   LEKL+      + ++ K E  L+  E E+     E    +K L E    
Sbjct: 314 LEELEELLEKLK----SLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKE 365

Length = 908

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 40.6 bits (96), Expect = 9e-04
 Identities = 29/112 (25%), Positives = 57/112 (50%), Gaps = 14/112 (12%)

Query: 111 VDKAHARADELEKQIDNLKKESEKQQK--EKEALEARAI--EAEKKISDLSAKLEKLQKI 166
           +++A     E +++++ L    E+ ++  E++A EA A+  EAEK   +L  K EKLQ+ 
Sbjct: 504 IEEAKKLIGEDKEKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEE 563

Query: 167 NDEQKSKIRKT-ERALKVAEEE---------MMRAKFEATSRSKELTEVHSA 208
            D+   +  K  ++A+K A++E          ++    A+ ++ EL E    
Sbjct: 564 EDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKR 615

Length = 782

>gnl|CDD|219934 pfam08614, ATG16, Autophagy protein 16 (ATG16)

 Score = 39.4 bits (92), Expect = 9e-04
 Identities = 19/60 (31%), Positives = 34/60 (56%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+ E+ QL+  I  L S I     E++   E + +KEK  +   + ++SL  EL++L++K
Sbjct: 107 LRREIQQLEKTIAELRSEITSLETEIRDLREELQEKEKDNETLQDELISLNIELNALEEK 166

Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. Length = 194

>gnl|CDD|224202 COG1283, NptA, Na+/phosphate symporter [Inorganic ion transport and metabolism]

 Score = 40.3 bits (95), Expect = 9e-04
 Identities = 38/220 (17%), Positives = 81/220 (36%), Gaps = 44/220 (20%)

Query: 2   AASKLVIFSLFFALILT------------AADVSIQGEDVPPLTA----SDAVDS----- 40
            A+ +    L F ++L                  I G++   +        A+DS     
Sbjct: 274 PAALIAHAHLLFNIVLALAALPFTGLLARFVTRLIPGDEDDEIEPKHLDETALDSPVVAL 333

Query: 41  SPLKIEL-------DQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQ 93
           +    E+       +Q+  ++        +K +E++  ++ V +  + I+    R+    
Sbjct: 334 ANAAREVLRLGDSIEQMLERLYEYIEGDAKKVKEIRKLEDAVDRLYEEIKLYLARLSKE- 392

Query: 94  KELSSLQKKETLNAAEQVDKA--------HAR--ADELEKQIDNLKKESEKQQKEKEALE 143
                L ++E+   AE +D A              +  +K+I N +  SE   +E +AL 
Sbjct: 393 ----GLSEEESRRWAEIIDAAINLEHIGDIIERLLELADKKIANGRAFSEDGLEELDALF 448

Query: 144 ARAIEAEKKISDLSAKLEK-LQKINDEQKSKIRKTERALK 182
           A  +E  +    +    +  L +   E+K ++R+ ER   
Sbjct: 449 ALTLENLRLAISVLVTGDLELARRLVERKKRVRRLERRSS 488

Length = 533

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 30/120 (25%), Positives = 62/120 (51%), Gaps = 10/120 (8%)

Query: 100 QKKETLNAAEQVDKAHARAD----ELEKQIDNLKKESEKQQKEKEALEARAIEAEKKIS- 154
           ++KET    E+  +   R +    ELE+Q+ +L++++EK ++ KE L+A   E E  +  
Sbjct: 173 RRKETERKLERTRENLDRLEDILNELERQLKSLERQAEKAERYKE-LKAELRELELALLV 231

Query: 155 ----DLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWL 210
               +L  +LE+LQ+   E + ++ +    L+  EE++   + E +   +E+ E+     
Sbjct: 232 LRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELY 291

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 29/131 (22%), Positives = 54/131 (41%), Gaps = 2/131 (1%)

Query: 100 QKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAK 159
           +++E     E++++   +  ELEK +  L+KE E+ ++E E L     E  ++IS L   
Sbjct: 675 RRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

Query: 160 LEKLQKI--NDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVH 217
           L +L+      E++      E     AE E +  + E         E     L   +   
Sbjct: 735 LARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQL 794

Query: 218 LLQCQSLIETH 228
             + ++L E  
Sbjct: 795 KEELKALREAL 805

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 13/93 (13%), Positives = 45/93 (48%), Gaps = 2/93 (2%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL 105
           EL +L+ ++  L+  + E  QE +   + ++  E  ++   + +  +++  ++  + +  
Sbjct: 74  ELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEE 133

Query: 106 NA--AEQVDKAHARADELEKQIDNLKKESEKQQ 136
           N    E++ +     + LE + + L++  +++ 
Sbjct: 134 NRELREELAELKQENEALEAENERLQENEQRRW 166

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

 Score = 40.0 bits (93), Expect = 0.001
 Identities = 22/149 (14%), Positives = 62/149 (41%), Gaps = 11/149 (7%)

Query: 20  ADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLE---SHIDEKTQELKGKDEVVA 76
           A ++ Q +D+     + A     L+ +   L++  + L+   + +  +  +LK +   + 
Sbjct: 140 ARLTKQAQDLQTRLKTLAEQRRQLEAQAQSLQASQKQLQASATQLKSQVLDLKLRSAQIE 199

Query: 77  QKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQ 136
           Q+ + +  ++    +  +EL+         AA+Q  +A     + + QI    ++   + 
Sbjct: 200 QEAQNLATRANAAQARTEELARRAA-----AAQQTAQA---IQQRDAQISQKAQQIAARA 251

Query: 137 KEKEALEARAIEAEKKISDLSAKLEKLQK 165
           ++    E +    E   + L  ++ +L+ 
Sbjct: 252 EQIRERERQLQRLETAQARLEQEVAQLEA 280

Length = 499

>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional

 Score = 40.3 bits (95), Expect = 0.001
 Identities = 28/102 (27%), Positives = 54/102 (52%), Gaps = 9/102 (8%)

Query: 91  SLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAE 150
            +Q +L +L K++ L A +++ +       LE+ +  L K  ++Q++E E L+ +  +A 
Sbjct: 40  DVQAQLDALNKQKLLEAEDKLVQQD-----LEQTLALLDK-IDRQKEETEQLKQQLAQAP 93

Query: 151 KKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAK 192
            K+    A+LE L+  NDE+    R+T   L + + E   A+
Sbjct: 94  AKLRQAQAELEALKDDNDEET---RETLSTLSLRQLESRLAQ 132

Length = 1113

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 39.4 bits (93), Expect = 0.002
 Identities = 26/118 (22%), Positives = 64/118 (54%), Gaps = 15/118 (12%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL 105
           EL + +++++ LE  + +K + L  K E++ ++E+ ++ K + +   Q+EL   +++   
Sbjct: 76  ELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEE 135

Query: 106 NAAEQVDK----AHARADELEKQI-DNLKKESEKQ------QKEKEALEARAIEAEKK 152
              EQ+ +    +   A+E ++ + + +++E+  +      + E+EA E    EA+KK
Sbjct: 136 LIEEQLQELERISGLTAEEAKEILLEKVEEEARHEAAVLIKEIEEEAKE----EADKK 189

Length = 520

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 40/191 (20%), Positives = 88/191 (46%), Gaps = 25/191 (13%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQ---KEKAIQDKSERIVSLQKELSSL 99
           L    ++   ++R +E  +    +E+ G +E + +   KE+ +++  +++  L+K L  L
Sbjct: 298 LSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEEL 357

Query: 100 QK--------KETLNAAEQVDKAHA--RADELEKQIDNLKKESEKQQKEKEALEARAIEA 149
           ++        K      E++ K       ++LEK+++ L+K  E+ ++E   + AR  E 
Sbjct: 358 EERHELYEEAKAKKEELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGEL 417

Query: 150 EKKISDLSAKLEKLQKI------------NDEQKSKIRKTERALKVAEEEMMRAKFEATS 197
           +K+I +L   +E+L+K              + +K  + +    LK  E+E+   + +   
Sbjct: 418 KKEIKELKKAIEELKKAKGKCPVCGRELTEEHRKELLEEYTAELKRIEKELKEIEEKERK 477

Query: 198 RSKELTEVHSA 208
             KEL E+   
Sbjct: 478 LRKELRELEKV 488

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 43/169 (25%), Positives = 84/169 (49%), Gaps = 12/169 (7%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+ +LD+L+ ++  L   ++E   E   + E   ++ +   ++   +   +KEL   +K+
Sbjct: 561 LEKKLDELEEELAELLKELEELGFESVEELEERLKELEPFYNEYLELKDAEKELEREEKE 620

Query: 103 ------ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
                 E   A E++ +   R +EL K+++ L+K+    ++E E L    +E  ++++ L
Sbjct: 621 LKKLEEELDKAFEELAETEKRLEELRKELEELEKKYS--EEEYEELREEYLELSRELAGL 678

Query: 157 SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEV 205
            A+LE+L+K  +E K  + K +  L    EE  +AK E     K L  V
Sbjct: 679 RAELEELEKRREEIKKTLEKLKEEL----EEREKAKKELEKLEKALERV 723

Length = 880

>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R; Provisional

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 27/105 (25%), Positives = 47/105 (44%), Gaps = 11/105 (10%)

Query: 100 QKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAK 159
            +       ++V     + +   ++    +  +E QQ+E  ALE  A E E+K  +L A+
Sbjct: 140 PENLLHALQQEVLTLKQQLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQELEAQ 199

Query: 160 LEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
           LE+LQ+    + S+ RK +R              +A  R  EL+E
Sbjct: 200 LEQLQE-KAAETSQERKQKR---------KEITDQAAKRL-ELSE 233

Length = 1123

>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 19/84 (22%), Positives = 44/84 (52%), Gaps = 3/84 (3%)

Query: 44  KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE 103
            +EL++ + ++RSL   I EK ++L+   + + +   AI+  + +   L +E++  +K  
Sbjct: 206 PLELEKARQELRSLSVKISEKRKQLEELQQELQELTIAIEALTNKKSELLEEIAEAEKIR 265

Query: 104 TLN---AAEQVDKAHARADELEKQ 124
                 +A+++ K  A+   L+K 
Sbjct: 266 EECRGWSAKEISKLKAKVSLLQKL 289

This domain is found in cell division proteins which are required for kinetochore-spindle association. Length = 321

>gnl|CDD|225638 COG3096, MukB, Uncharacterized protein involved in chromosome partitioning [Cell division and chromosome partitioning]

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 35/166 (21%), Positives = 72/166 (43%), Gaps = 32/166 (19%)

Query: 35   SDAVDSSPLKIEL-DQLKSKIRSLESHIDEKTQELKGK-------DEVVAQKEKAIQDKS 86
            SD+ +      +L ++L+ ++   E+      ++L+         ++V+A  + +   K 
Sbjct: 973  SDSAEMLSENSDLNEKLRQRLEQAEAERTRAREQLRQHQAQLSQYNQVLASLKSSYDTKK 1032

Query: 87   ERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARA 146
            E +  LQ+EL  +  +    A E   +A  R DEL  Q+   +              +R 
Sbjct: 1033 ELLNELQQELQDIGVRADSGAEE---RARIRRDELHAQLSTNR--------------SRR 1075

Query: 147  IEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAK 192
             + EK+++   A+++ L +       K+RK ER      E+++ AK
Sbjct: 1076 NQLEKQLTFCEAEMDNLTR-------KLRKLERDYFEMREQVVTAK 1114

Length = 1480

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.4 bits (91), Expect = 0.003
 Identities = 33/151 (21%), Positives = 72/151 (47%), Gaps = 8/151 (5%)

Query: 58   ESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAH-- 115
            E + +E  +  + +    A+++ AI+ +  R     K+    +K +    AE+  KA   
Sbjct: 1248 ERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEA 1307

Query: 116  ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKI----SDLSAKLEKLQKINDEQK 171
             +  E  K+ D  KK++E+ +K+ +A + +A EA+K      ++  A  ++ +   ++ +
Sbjct: 1308 KKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAE 1367

Query: 172  SKIRKTERALKVAEEEMMRAKFEATSRSKEL 202
            +  +K E A K A+    + K E   ++ E 
Sbjct: 1368 AAEKKKEEAKKKADA--AKKKAEEKKKADEA 1396

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.4 bits (91), Expect = 0.003
 Identities = 42/170 (24%), Positives = 74/170 (43%), Gaps = 6/170 (3%)

Query: 44   KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE 103
            K + D+ K    + +   + K  E   K +   + E+A +    +    +K+   L+K E
Sbjct: 1496 KKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAE 1555

Query: 104  TLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEA--RAIEAEKKISDLSAKLE 161
             L  AE+  KA       E +   L+K  E ++ E+  +E   +  E EKK+    AK  
Sbjct: 1556 ELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKA 1615

Query: 162  KLQKINDEQKSK---IRKTERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
            +  KI  E+  K    +K    LK  E E  + K E   +++E  ++ +A
Sbjct: 1616 EEAKIKAEELKKAEEEKKKVEQLKKKEAEEKK-KAEELKKAEEENKIKAA 1664

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.0 bits (90), Expect = 0.003
 Identities = 27/139 (19%), Positives = 62/139 (44%)

Query: 63   EKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELE 122
            +K  E K  +E     E   + +  +     K+ +   KK+   A ++ ++A   A+  +
Sbjct: 1290 KKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAK 1349

Query: 123  KQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALK 182
             + +    E+E  +++ EA E +  EA+KK      K E+ +K ++ +K      ++A +
Sbjct: 1350 AEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADE 1409

Query: 183  VAEEEMMRAKFEATSRSKE 201
            + +    + K +   +  E
Sbjct: 1410 LKKAAAAKKKADEAKKKAE 1428

Length = 2084

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.0 bits (91), Expect = 0.003
 Identities = 36/154 (23%), Positives = 78/154 (50%), Gaps = 8/154 (5%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEK------AIQDKSERIVSLQKEL 96
           L+ EL++L+ +I+ LE  I++   +     E+    EK       + ++ E+ +    EL
Sbjct: 422 LERELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYEL 481

Query: 97  SSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
              + +E L+  ++  +     +ELEK++  L++E  +  + +EAL+    E  +K+ +L
Sbjct: 482 ELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENL 541

Query: 157 SAKLE--KLQKINDEQKSKIRKTERALKVAEEEM 188
             +LE  K +    + K ++R+ E  L+  +E +
Sbjct: 542 LEELEELKEKLQLQQLKEELRQLEDRLQELKELL 575

Length = 908

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 16/96 (16%), Positives = 46/96 (47%), Gaps = 10/96 (10%)

Query: 107 AAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKI 166
           A E++ +      EL++++  L+++  + Q+E + L+      E ++  L  +L +++++
Sbjct: 64  ARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQL 123

Query: 167 ----------NDEQKSKIRKTERALKVAEEEMMRAK 192
                     N E + ++ + ++  +  E E  R +
Sbjct: 124 SANAIELDEENRELREELAELKQENEALEAENERLQ 159

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 28/116 (24%), Positives = 52/116 (44%), Gaps = 8/116 (6%)

Query: 82  IQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEA 141
           +++  E +  L KEL  L + E L  AE   +  A  D L+++ID L  E ++ ++  + 
Sbjct: 1   LKELREALAELAKELRKLTEDEKLAEAE---EEKAEYDALKEEIDKLDAEIDRLEELLDE 57

Query: 142 LEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATS 197
           LEA+   A  +      + E+ +    E ++ +R  +     A  E  +A    T 
Sbjct: 58  LEAKP-AASGEGGGGEEEEEEAKAEAAEFRAYLRGGDD----ALAEERKALSTGTD 108

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 29/100 (29%), Positives = 53/100 (53%), Gaps = 9/100 (9%)

Query: 85  KSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEA 144
            S+ +  L+  L  L+K        ++++   R  EL+ QI+ LKK  E+ ++  E LE 
Sbjct: 60  PSQALNKLKTRLEKLKK--------ELEELKQRIAELQAQIEKLKKGREETEERTELLEE 111

Query: 145 RAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVA 184
              + EK++  L A+LEK +K + E+  K+++  +  K A
Sbjct: 112 LK-QLEKELKKLKAELEKYEKNDPERIEKLKEETKVAKEA 150

This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Length = 188

>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           ELD+ K K++ L   I  K ++L+  +E + + E  I+D + +   L  E++  +KK
Sbjct: 205 ELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEAEKK 261

This domain is found in cell division proteins which are required for kinetochore-spindle association. Length = 312

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 28/129 (21%), Positives = 63/129 (48%), Gaps = 1/129 (0%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
           L+ EL ++++++  L+  I+   + L+   E +   ++ +++    +  LQ EL  L ++
Sbjct: 388 LEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEE 447

Query: 103 ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
                 EQ+++   R  ELE+++  L++E ++ +KE  +LEAR    E +          
Sbjct: 448 LE-ELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEARLDRLEAEQRASQGVRAV 506

Query: 163 LQKINDEQK 171
           L+ +     
Sbjct: 507 LEALESGLP 515

Length = 1163

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 19/100 (19%), Positives = 45/100 (45%), Gaps = 4/100 (4%)

Query: 80  KAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEK 139
           + + D    +++L K    ++    L+  ++ +       E  K++ +  K+  + + E 
Sbjct: 337 RNLDDNDLTLLALTKLYEEVKSNTDLSGDKRQE----LLKEYNKKLQDYTKKLGEVKDET 392

Query: 140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTER 179
           +A E    +A+++        +K ++  DE K K +K ER
Sbjct: 393 DASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDER 432

Length = 434

>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated

 Score = 38.8 bits (91), Expect = 0.004
 Identities = 44/233 (18%), Positives = 90/233 (38%), Gaps = 59/233 (25%)

Query: 34  ASDAVDSSPLKIELDQLKSKIRSLESHIDEKTQEL-KGKDEVVAQKEKAIQDKSERIVSL 92
            S+A+D   L+  L +L       +    +  +EL K  +E + + EK I++  E I  L
Sbjct: 55  LSEALDK--LRSYLPKLNPLREEKKKVSVKSLEELIKDVEEELEKIEKEIKELEEEISEL 112

Query: 93  QKELSSLQKKETLNAAE-----------------------QVDKAHARADELEKQIDN-- 127
           + E+  L+++  +   E                        V +      +LE  ++N  
Sbjct: 113 ENEIKELEQE--IERLEPWGNFDLDLSLLLGFKYVSVFVGTVPEDKLEELKLESDVENVE 170

Query: 128 ---------------LKKESEKQQKEKEALEARAIEAEKK------ISDLSAKLEKLQKI 166
                          LK+ S++ ++E + L    +E E++      I ++  +LE+++K 
Sbjct: 171 YISTDKGYVYVVVVVLKELSDEVEEELKKLGFERLELEEEGTPSELIREIKEELEEIEKE 230

Query: 167 NDEQKSKIR----KTERALKVAEE--EMMRAKFEATSRSK--ELTEVHSAWLP 211
            +    +++    K    L    E  E+   + EA S+    + T     W+P
Sbjct: 231 RESLLEELKELAKKYLEELLALYEYLEIELERAEALSKFLKTDKTFAIEGWVP 283

Length = 646

>gnl|CDD|240338 PTZ00262, PTZ00262, subtilisin-like protease; Provisional

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 25/107 (23%), Positives = 51/107 (47%), Gaps = 11/107 (10%)

Query: 81  AIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKE 140
           A  D  E+I S   EL  L K E        + ++ R + +E  +++   +S   ++E +
Sbjct: 37  ARNDDGEKIGS---ELRFLGKVERG-----AETSNLRGEGVEADVNSSNPDSASPKEELQ 88

Query: 141 ALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEE 187
            ++ +   +  ++S L   L+      DE K+K+RK ++ L++   E
Sbjct: 89  KIQGQQESSPPQVSHL---LQDDSHNMDEMKTKLRKKKKILRLIVSE 132

Length = 639

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	321
PRK11637	428	AmiB activator; Provisional	99.29
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	98.94
PRK11637	428	AmiB activator; Provisional	98.6
COG4942	420	Membrane-bound metallopeptidase [Cell division and	98.56
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	98.42
PRK09039	343	hypothetical protein; Validated	98.31
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	98.29
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	98.11
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	98.06
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	98.02
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	98.0
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	97.99
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	97.96
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	97.96
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	97.95
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	97.84
PRK03918	880	chromosome segregation protein; Provisional	97.75
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	97.74
PHA02562	562	46 endonuclease subunit; Provisional	97.66
COG4942	420	Membrane-bound metallopeptidase [Cell division and	97.66
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	97.65
PRK02224	880	chromosome segregation protein; Provisional	97.59
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	97.59
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	97.57
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	97.56
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	97.53
PRK09039	343	hypothetical protein; Validated	97.49
PRK04778	569	septation ring formation regulator EzrA; Provision	97.48
PHA02562	562	46 endonuclease subunit; Provisional	97.44
PRK03918	880	chromosome segregation protein; Provisional	97.39
KOG0996	1293	consensus Structural maintenance of chromosome pro	97.39
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	97.35
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	97.34
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	97.27
PRK04863	1486	mukB cell division protein MukB; Provisional	97.26
COG4372	499	Uncharacterized protein conserved in bacteria with	97.25
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	97.13
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	97.07
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	97.02
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	96.99
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	96.94
KOG0996	1293	consensus Structural maintenance of chromosome pro	96.92
PRK01156	895	chromosome segregation protein; Provisional	96.92
PF00038	312	Filament: Intermediate filament protein; InterPro:	96.89
PRK04863	1486	mukB cell division protein MukB; Provisional	96.88
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	96.83
KOG0933	1174	consensus Structural maintenance of chromosome pro	96.81
PRK04778	569	septation ring formation regulator EzrA; Provision	96.76
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	96.75
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	96.72
KOG0964	1200	consensus Structural maintenance of chromosome pro	96.67
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	96.61
PF00038	312	Filament: Intermediate filament protein; InterPro:	96.6
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	96.58
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	96.48
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	96.47
PRK11281	1113	hypothetical protein; Provisional	96.44
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	96.42
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	96.4
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	96.38
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	96.34
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	96.33
PRK01156	895	chromosome segregation protein; Provisional	96.31
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	96.31
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	96.28
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	96.27
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	96.25
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	96.24
KOG4674	1822	consensus Uncharacterized conserved coiled-coil pr	96.19
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	96.14
PF14662	193	CCDC155: Coiled-coil region of CCDC155	96.12
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	96.12
PF12795	240	MscS_porin: Mechanosensitive ion channel porin dom	96.08
KOG0933	1174	consensus Structural maintenance of chromosome pro	96.07
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	96.07
COG4372	499	Uncharacterized protein conserved in bacteria with	96.05
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	96.03
KOG0976	1265	consensus Rho/Rac1-interacting serine/threonine ki	95.97
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	95.97
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	95.96
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	95.92
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	95.91
KOG0963	629	consensus Transcription factor/CCAAT displacement	95.91
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	95.89
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	95.79
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	95.77
KOG0964	1200	consensus Structural maintenance of chromosome pro	95.76
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	95.71
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	95.6
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	95.59
PF06160	560	EzrA: Septation ring formation regulator, EzrA ; I	95.56
PF06008	264	Laminin_I: Laminin Domain I; InterPro: IPR009254 L	95.5
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	95.4
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	95.33
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	95.25
PF05911	769	DUF869: Plant protein of unknown function (DUF869)	95.22
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	95.18
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	95.05
KOG4673	961	consensus Transcription factor TMF, TATA element m	95.01
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	95.0
PF12795	240	MscS_porin: Mechanosensitive ion channel porin dom	95.0
KOG4674	1822	consensus Uncharacterized conserved coiled-coil pr	94.99
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	94.97
KOG0979	1072	consensus Structural maintenance of chromosome pro	94.92
PF05622	713	HOOK: HOOK protein; InterPro: IPR008636 This famil	94.91
KOG0971	1243	consensus Microtubule-associated protein dynactin	94.89
PRK10929	1109	putative mechanosensitive channel protein; Provisi	94.85
PF05911	769	DUF869: Plant protein of unknown function (DUF869)	94.82
PRK11281	1113	hypothetical protein; Provisional	94.76
COG1382	119	GimC Prefoldin, chaperonin cofactor [Posttranslati	94.75
PRK10884	206	SH3 domain-containing protein; Provisional	94.71
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	94.68
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	94.67
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	94.64
KOG0976	1265	consensus Rho/Rac1-interacting serine/threonine ki	94.64
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	94.64
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	94.63
KOG0018	1141	consensus Structural maintenance of chromosome pro	94.63
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	94.59
PRK10884	206	SH3 domain-containing protein; Provisional	94.56
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	94.55
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	94.51
TIGR02977	219	phageshock_pspA phage shock protein A. Members of	94.46
KOG0018	1141	consensus Structural maintenance of chromosome pro	94.46
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	94.46
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	94.41
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.41
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	94.3
PRK09343	121	prefoldin subunit beta; Provisional	94.27
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	94.22
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	94.21
PRK10698	222	phage shock protein PspA; Provisional	94.17
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	94.15
PF10186	302	Atg14: UV radiation resistance protein and autopha	94.1
PF15450	531	DUF4631: Domain of unknown function (DUF4631)	94.03
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	93.98
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	93.83
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	93.81
PF15397	258	DUF4618: Domain of unknown function (DUF4618)	93.78
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	93.78
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	93.78
PF04582	326	Reo_sigmaC: Reovirus sigma C capsid protein; Inter	93.66
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	93.62
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	93.61
PF14362	301	DUF4407: Domain of unknown function (DUF4407)	93.56
PRK03947	140	prefoldin subunit alpha; Reviewed	93.35
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	93.35
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	93.3
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	93.28
PF06818	202	Fez1: Fez1; InterPro: IPR009638 This family repres	93.28
PF10186	302	Atg14: UV radiation resistance protein and autopha	93.26
PRK10929	1109	putative mechanosensitive channel protein; Provisi	93.22
PF04582	326	Reo_sigmaC: Reovirus sigma C capsid protein; Inter	93.11
PF12777	344	MT: Microtubule-binding stalk of dynein motor; Int	93.11
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	93.06
PF01576	859	Myosin_tail_1: Myosin tail; InterPro: IPR002928 Mu	93.03
KOG1853	333	consensus LIS1-interacting protein NUDE [Cytoskele	92.76
COG1842	225	PspA Phage shock protein A (IM30), suppresses sigm	92.66
PF05335	188	DUF745: Protein of unknown function (DUF745); Inte	92.61
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	92.44
PF14662	193	CCDC155: Coiled-coil region of CCDC155	92.36
COG2433	652	Uncharacterized conserved protein [Function unknow	92.29
COG1730	145	GIM5 Predicted prefoldin, molecular chaperone impl	92.29
PF13514	1111	AAA_27: AAA domain	92.25
PRK10803	263	tol-pal system protein YbgF; Provisional	92.23
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	92.2
KOG1853	333	consensus LIS1-interacting protein NUDE [Cytoskele	92.15
KOG0979	1072	consensus Structural maintenance of chromosome pro	92.09
TIGR02338	110	gimC_beta prefoldin, beta subunit, archaeal. Chape	92.0
KOG0963	629	consensus Transcription factor/CCAAT displacement	91.88
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	91.84
PF13166	712	AAA_13: AAA domain	91.77
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	91.69
PF10481	307	CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR0	91.51
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	91.45
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	91.38
PF14282	106	FlxA: FlxA-like protein	91.19
KOG0971	1243	consensus Microtubule-associated protein dynactin	91.18
PF09403	126	FadA: Adhesion protein FadA; InterPro: IPR018543 F	91.11
COG5185	622	HEC1 Protein involved in chromosome segregation, i	91.09
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	90.95
PRK03947	140	prefoldin subunit alpha; Reviewed	90.93
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	90.68
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	90.68
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	90.67
PF06160	560	EzrA: Septation ring formation regulator, EzrA ; I	90.63
COG2433	652	Uncharacterized conserved protein [Function unknow	90.57
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	90.52
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	90.37
PF06008	264	Laminin_I: Laminin Domain I; InterPro: IPR009254 L	90.05
PF05384	159	DegS: Sensor protein DegS; InterPro: IPR008595 Thi	89.95
PRK15396	78	murein lipoprotein; Provisional	89.82
KOG4360	596	consensus Uncharacterized coiled coil protein [Fun	89.75
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	89.57
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	89.52
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	89.47
PF10498	359	IFT57: Intra-flagellar transport protein 57 ; Inte	89.46
PF03148	384	Tektin: Tektin family; InterPro: IPR000435 Tektin	89.42
KOG1899	861	consensus LAR transmembrane tyrosine phosphatase-i	89.38
PRK04406	75	hypothetical protein; Provisional	89.31
COG1842	225	PspA Phage shock protein A (IM30), suppresses sigm	89.22
PF02994	370	Transposase_22: L1 transposable element; InterPro:	89.2
PF10481	307	CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR0	89.19
PF13166	712	AAA_13: AAA domain	89.1
PRK09841	726	cryptic autophosphorylating protein tyrosine kinas	89.08
PF05335	188	DUF745: Protein of unknown function (DUF745); Inte	88.99
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	88.93
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	88.86
PRK02119	73	hypothetical protein; Provisional	88.82
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	88.79
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	88.76
PRK04406	75	hypothetical protein; Provisional	88.76
PF10368	204	YkyA: Putative cell-wall binding lipoprotein; Inte	88.74
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	88.74
KOG4673	961	consensus Transcription factor TMF, TATA element m	88.67
PRK02119	73	hypothetical protein; Provisional	88.64
KOG2129	552	consensus Uncharacterized conserved protein H4 [Fu	88.52
PRK02793	72	phi X174 lysis protein; Provisional	88.45
KOG1899	861	consensus LAR transmembrane tyrosine phosphatase-i	88.29
PF04912	388	Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamit	88.25
PRK00295	68	hypothetical protein; Provisional	88.17
PRK00736	68	hypothetical protein; Provisional	88.09
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	87.96
PRK04325	74	hypothetical protein; Provisional	87.95
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	87.71
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	87.6
PRK04325	74	hypothetical protein; Provisional	87.5
COG5185	622	HEC1 Protein involved in chromosome segregation, i	87.42
PF10212	518	TTKRSYEDQ: Predicted coiled-coil domain-containing	87.26
KOG4809	654	consensus Rab6 GTPase-interacting protein involved	87.25
COG3206	458	GumC Uncharacterized protein involved in exopolysa	87.18
PF10267	395	Tmemb_cc2: Predicted transmembrane and coiled-coil	87.12
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	87.02
PF05384	159	DegS: Sensor protein DegS; InterPro: IPR008595 Thi	87.0
PF12072	201	DUF3552: Domain of unknown function (DUF3552); Int	86.65
KOG2991	330	consensus Splicing regulator [RNA processing and m	86.43
PF05010	207	TACC: Transforming acidic coiled-coil-containing p	86.4
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	86.35
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	86.17
PF09755	310	DUF2046: Uncharacterized conserved protein H4 (DUF	86.01
PRK00846	77	hypothetical protein; Provisional	85.96
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	85.86
PF05010	207	TACC: Transforming acidic coiled-coil-containing p	85.82
PF14282	106	FlxA: FlxA-like protein	85.61
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	85.6
PRK09841	726	cryptic autophosphorylating protein tyrosine kinas	85.34
KOG0962	1294	consensus DNA repair protein RAD50, ABC-type ATPas	85.26
PF05483	786	SCP-1: Synaptonemal complex protein 1 (SCP-1); Int	85.24
PRK11519	719	tyrosine kinase; Provisional	85.21
cd00584	129	Prefoldin_alpha Prefoldin alpha subunit; Prefoldin	85.19
KOG4360	596	consensus Uncharacterized coiled coil protein [Fun	85.06
PRK10476	346	multidrug resistance protein MdtN; Provisional	85.05
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	85.0
PF11570	136	E2R135: Coiled-coil receptor-binding R-domain of c	84.87
TIGR02338	110	gimC_beta prefoldin, beta subunit, archaeal. Chape	84.85
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	84.75
TIGR02231	525	conserved hypothetical protein. This family consis	84.74
COG3206	458	GumC Uncharacterized protein involved in exopolysa	84.69
PRK00846	77	hypothetical protein; Provisional	84.62
PF15450	531	DUF4631: Domain of unknown function (DUF4631)	84.54
PRK02793	72	phi X174 lysis protein; Provisional	84.26
PF05622	713	HOOK: HOOK protein; InterPro: IPR008636 This famil	84.26
PF10267	395	Tmemb_cc2: Predicted transmembrane and coiled-coil	84.18
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	83.92
PRK10361	475	DNA recombination protein RmuC; Provisional	83.91
TIGR00293	126	prefoldin, archaeal alpha subunit/eukaryotic subun	83.72
PF05557	722	MAD: Mitotic checkpoint protein; InterPro: IPR0086	83.66
PF09755	310	DUF2046: Uncharacterized conserved protein H4 (DUF	83.5
PRK00295	68	hypothetical protein; Provisional	83.5
COG1730	145	GIM5 Predicted prefoldin, molecular chaperone impl	83.46
PHA03332	1328	membrane glycoprotein; Provisional	83.24
PRK00736	68	hypothetical protein; Provisional	82.99
PRK10780	165	periplasmic chaperone; Provisional	82.79
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	82.52
KOG0243	1041	consensus Kinesin-like protein [Cytoskeleton]	82.51
PRK00409	782	recombination and DNA strand exchange inhibitor pr	82.39
TIGR03545	555	conserved hypothetical protein TIGR03545. This mod	82.28
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	82.17
PF06120	301	Phage_HK97_TLTM: Tail length tape measure protein;	82.11
TIGR02231	525	conserved hypothetical protein. This family consis	82.05
PRK06975	656	bifunctional uroporphyrinogen-III synthetase/uropo	81.95
PF15066	527	CAGE1: Cancer-associated gene protein 1 family	81.76
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	81.67
TIGR01010	362	BexC_CtrB_KpsE polysaccharide export inner-membran	81.66
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	81.61
PF09728	309	Taxilin: Myosin-like coiled-coil protein; InterPro	81.3
PRK11546	143	zraP zinc resistance protein; Provisional	81.3
KOG0288	459	consensus WD40 repeat protein TipD [General functi	81.25
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	81.23
COG2900	72	SlyX Uncharacterized protein conserved in bacteria	81.23
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	81.12
TIGR02977	219	phageshock_pspA phage shock protein A. Members of	80.96
KOG3091	508	consensus Nuclear pore complex, p54 component (sc	80.92
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	80.68
KOG0244	913	consensus Kinesin-like protein [Cytoskeleton]	80.6
KOG1003	205	consensus Actin filament-coating protein tropomyos	80.53
PF06120	301	Phage_HK97_TLTM: Tail length tape measure protein;	80.52
KOG4809	654	consensus Rab6 GTPase-interacting protein involved	80.5
PF02994	370	Transposase_22: L1 transposable element; InterPro:	80.4
TIGR00414	418	serS seryl-tRNA synthetase. This model represents	80.25
PF10779	71	XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemoly	80.23
PF05483	786	SCP-1: Synaptonemal complex protein 1 (SCP-1); Int	80.22
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	80.2
PF11180	192	DUF2968: Protein of unknown function (DUF2968); In	80.11

>PRK11637 AmiB activator; Provisional

Probab=99.29  E-value=1.7e-09  Score=108.05  Aligned_cols=154  Identities=15%  Similarity=0.253  Sum_probs=96.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK---ETLNAAEQVDKAH  115 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~---~~~~~eeq~~~~~  115 (321)
                      ....+++++++++.++..++++++++..+|..++.+|..++..|+.++.+|..++.+|+.++.+   .+.+++.+...+.
T Consensus        48 ~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~  127 (428)
T PRK11637         48 QLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLA  127 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5566677777777777777777777777777777777777777777777777777777777664   3455666666677


Q ss_pred             HHHHH----------------------------HH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---
Q 020809          116 ARADE----------------------------LE-------KQIDNLKKESEKQQKEKEALEARAIEAEKKISDLS---  157 (321)
Q Consensus       116 ~Rire----------------------------L~-------k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~---  157 (321)
                      .|++.                            |+       ..|+.+.....++...+..++....+++..+.++.   
T Consensus       128 ~rlra~Y~~g~~~~l~vLl~a~~~~~~~r~~~~l~~i~~~d~~~l~~l~~~~~~L~~~k~~le~~~~~l~~~~~e~~~~k  207 (428)
T PRK11637        128 AQLDAAFRQGEHTGLQLILSGEESQRGERILAYFGYLNQARQETIAELKQTREELAAQKAELEEKQSQQKTLLYEQQAQQ  207 (428)
T ss_pred             HHHHHHHHcCCCcHHHHHhcCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77776                            11       12555555555555555555544444444444444   


Q ss_pred             -----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          158 -----------AKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAK  192 (321)
Q Consensus       158 -----------~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~  192 (321)
                                 ..+..|.....++...+.++++..+.++..|.+++
T Consensus       208 ~~L~~~k~e~~~~l~~L~~~~~~~~~~l~~l~~~~~~L~~~I~~l~  253 (428)
T PRK11637        208 QKLEQARNERKKTLTGLESSLQKDQQQLSELRANESRLRDSIARAE  253 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                       44444555555555566666666666666666553

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=98.94  E-value=8.4e-07  Score=83.30  Aligned_cols=143  Identities=18%  Similarity=0.268  Sum_probs=81.3

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH-----
Q 020809           46 ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE-----  120 (321)
Q Consensus        46 el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire-----  120 (321)
                      +++++......++.+++.+..++.+...+++..+.++.....+|..|+.+|+.+    .....+|.+.+++|+|.     
T Consensus        39 ~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~----~~~I~~r~~~l~~raRAmq~nG  114 (265)
T COG3883          39 KLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAEL----KENIVERQELLKKRARAMQVNG  114 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHcC
Confidence            333333333333333333333333333333333333333333344444444333    24556667788888888     


Q ss_pred             ------------------------HHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          121 ------------------------LEKQ-------IDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDE  169 (321)
Q Consensus       121 ------------------------L~k~-------Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~E  169 (321)
                                              +..+       |+..+.+...+..+...++.....+.....++...+..|+..+.+
T Consensus       115 ~~t~Yidvil~SkSfsD~IsRvtAi~~iv~aDk~ile~qk~dk~~Le~kq~~l~~~~e~l~al~~e~e~~~~~L~~qk~e  194 (265)
T COG3883         115 TATSYIDVILNSKSFSDLISRVTAISVIVDADKKILEQQKEDKKSLEEKQAALEDKLETLVALQNELETQLNSLNSQKAE  194 (265)
T ss_pred             ChhHHHHHHHccCcHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                    2222       555555555555555666666666666777777777778888888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 020809          170 QKSKIRKTERALKVAEEEMMRAK  192 (321)
Q Consensus       170 qk~~l~elE~~lq~~Eeei~kl~  192 (321)
                      ++..+..+......+..+...+.
T Consensus       195 ~~~l~~~~aa~~a~~~~e~a~l~  217 (265)
T COG3883         195 KNALIAALAAKEASALGEKAALE  217 (265)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHH
Confidence            88888877777777777766664

>PRK11637 AmiB activator; Provisional

Probab=98.60  E-value=4.8e-05  Score=76.21  Aligned_cols=83  Identities=18%  Similarity=0.238  Sum_probs=70.7

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE  120 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire  120 (321)
                      ++++.++++++.+|.++++.+.++..+++....+|+.++..|.....+|+.++.+|..++. ....++.++..++.++..
T Consensus        43 ~~~~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~-ei~~l~~eI~~~q~~l~~  121 (428)
T PRK11637         43 SDNRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNK-QIDELNASIAKLEQQQAA  121 (428)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence            4579999999999999999999999999999999999999999999999999999988866 556777777777777777


Q ss_pred             HHHH
Q 020809          121 LEKQ  124 (321)
Q Consensus       121 L~k~  124 (321)
                      ++..
T Consensus       122 ~~~~  125 (428)
T PRK11637        122 QERL  125 (428)
T ss_pred             HHHH
Confidence            5554

>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

Probab=98.56  E-value=3.4e-05  Score=76.78  Aligned_cols=79  Identities=18%  Similarity=0.285  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 020809          124 QIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKEL  202 (321)
Q Consensus       124 ~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~ql  202 (321)
                      .|+.|.+++..+..-...+++.+.++...+.+.......+.....|++..+.+++..+..-+..+..+......+.+.|
T Consensus       162 ~i~~l~~~~~~l~~~~~~iaaeq~~l~~~~~eq~~q~~kl~~~~~E~kk~~~~l~~~l~~~q~~l~eL~~~~~~L~~~I  240 (420)
T COG4942         162 RIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELSADQKKLEELRANESRLKNEI  240 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            3888888888888888888888888888888888888888888888888888888888777777777766666555544

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=98.42  E-value=0.0002  Score=67.40  Aligned_cols=153  Identities=19%  Similarity=0.224  Sum_probs=95.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           71 KDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAE  150 (321)
Q Consensus        71 kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~e  150 (321)
                      .|..|..+++....++.+|.+|+++|++++. +..+.+++.+..+..+..|+.+|+.++..|.+++   ..|..|++.+.
T Consensus        36 ~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~-k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~r~---~~l~~raRAmq  111 (265)
T COG3883          36 QDSKLSELQKEKKNIQNEIESLDNQIEEIQS-KIDELQKEIDQSKAEIKKLQKEIAELKENIVERQ---ELLKKRARAMQ  111 (265)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH
Confidence            3444444455555555555555555555544 3344555555555666666677777777777777   77788888777


Q ss_pred             ----------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh-------hh
Q 020809          151 ----------------------KKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRS-------KE  201 (321)
Q Consensus       151 ----------------------kk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a-------~q  201 (321)
                                            .|+..++..++...++...++.+-..++.....+++.+..+..-.....       .+
T Consensus       112 ~nG~~t~Yidvil~SkSfsD~IsRvtAi~~iv~aDk~ile~qk~dk~~Le~kq~~l~~~~e~l~al~~e~e~~~~~L~~q  191 (265)
T COG3883         112 VNGTATSYIDVILNSKSFSDLISRVTAISVIVDADKKILEQQKEDKKSLEEKQAALEDKLETLVALQNELETQLNSLNSQ  191 (265)
T ss_pred             HcCChhHHHHHHHccCcHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                  4777788888888888888888888888888888888777744333332       22


Q ss_pred             hhhhhccCchhHHHHHHHHHHHHHHhHH
Q 020809          202 LTEVHSAWLPPWLAVHLLQCQSLIETHW  229 (321)
Q Consensus       202 l~e~~g~~l~Pwla~~~~~~~~~~~~~~  229 (321)
                      ..+  ..-+.--++...+.....+....
T Consensus       192 k~e--~~~l~~~~aa~~a~~~~e~a~l~  217 (265)
T COG3883         192 KAE--KNALIAALAAKEASALGEKAALE  217 (265)
T ss_pred             HHH--HHHHHHHHHHHHHHhHHHHHHHH
Confidence            222  22444455555555555555444

>PRK09039 hypothetical protein; Validated

Probab=98.31  E-value=0.00036  Score=68.37  Aligned_cols=82  Identities=21%  Similarity=0.257  Sum_probs=40.0

Q ss_pred             hhHHHHHHHHHHHHhhhhhhcccCCCCCCcccccCCCCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHH
Q 020809            3 ASKLVIFSLFFALILTAADVSIQGEDVPPLTASDAVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAI   82 (321)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i   82 (321)
                      .+-||++++|+++||..+..+-..            .....+.+|++++.+|.+|-..++--......++..|.++...+
T Consensus        23 ~~~ll~~~~f~l~~f~~~q~fLs~------------~i~~~~~eL~~L~~qIa~L~e~L~le~~~~~~l~~~l~~l~~~l   90 (343)
T PRK09039         23 LSTLLLVIMFLLTVFVVAQFFLSR------------EISGKDSALDRLNSQIAELADLLSLERQGNQDLQDSVANLRASL   90 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH------------HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            456777777766677663332111            11223345555555555544444444444444555555555444


Q ss_pred             HHHHHHHHHHHHHH
Q 020809           83 QDKSERIVSLQKEL   96 (321)
Q Consensus        83 ~e~~~~I~~Lq~eI   96 (321)
                      ...+.....|++.+
T Consensus        91 ~~a~~~r~~Le~~~  104 (343)
T PRK09039         91 SAAEAERSRLQALL  104 (343)
T ss_pred             HHHHHHHHHHHHHH
Confidence            44444444444433

>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=98.29  E-value=0.00026  Score=61.09  Aligned_cols=60  Identities=23%  Similarity=0.371  Sum_probs=43.7

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      +++.+.+.+..+...++.++..++++...++..|..++..+..++.++..++..+...+.
T Consensus         4 ~lk~E~d~a~~r~e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~   63 (143)
T PF12718_consen    4 ALKLEADNAQDRAEELEAKVKQLEQENEQKEQEITSLQKKNQQLEEELDKLEEQLKEAKE   63 (143)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456666777777777777777777777777777777777777777777777777776644

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].

>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=98.11  E-value=0.0011  Score=57.21  Aligned_cols=54  Identities=22%  Similarity=0.322  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           47 LDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      |+.|+..........+.+..+++.++....+++.+|..++..+..|+.+|+.++
T Consensus         2 m~~lk~E~d~a~~r~e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld~~~   55 (143)
T PF12718_consen    2 MQALKLEADNAQDRAEELEAKVKQLEQENEQKEQEITSLQKKNQQLEEELDKLE   55 (143)
T ss_pred             hHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555555555555555555555555555543

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=98.06  E-value=0.0014  Score=72.37  Aligned_cols=41  Identities=37%  Similarity=0.513  Sum_probs=17.1

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAI   82 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i   82 (321)
                      .+..++..++.++..++..+.....++..+...+...+..+
T Consensus       291 ~l~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~  331 (1164)
T TIGR02169       291 RVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEI  331 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444433333333333333

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]

Probab=98.02  E-value=0.0039  Score=68.03  Aligned_cols=102  Identities=20%  Similarity=0.250  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccCchhHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLL  219 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~ql~e~~g~~l~Pwla~~~~  219 (321)
                      ..+..++.+++.+++.++..++.++.........++++..+....+++....+.....+.+.|..         -..+..
T Consensus       390 ~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~---------~~~~l~  460 (1074)
T KOG0250|consen  390 NELGSELEERENKLEQLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIEN---------ISEELK  460 (1074)
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH---------HHHHHH
Confidence            33334444444444444444444444444444444444443333333333333333333332321         112344


Q ss_pred             HHHHHHHhHHHhhCcchHHHHHHHHHHHHHhh
Q 020809          220 QCQSLIETHWNAHGKPAMDVAIQKALEKKAQA  251 (321)
Q Consensus       220 ~~~~~~~~~~~~hg~p~~~~~~~~~~~k~~~~  251 (321)
                      .+....++..+-.| |-|-.+++--...+.++
T Consensus       461 ~lk~~k~dkvs~FG-~~m~~lL~~I~r~~~~f  491 (1074)
T KOG0250|consen  461 DLKKTKTDKVSAFG-PNMPQLLRAIERRKRRF  491 (1074)
T ss_pred             HHHhcccchhhhcc-hhhHHHHHHHHHHHhcC
Confidence            56666788999999 99988887655554443

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=98.00  E-value=0.0016  Score=71.61  Aligned_cols=17  Identities=24%  Similarity=0.161  Sum_probs=7.2

Q ss_pred             HHHHHhhhhhcCchhHH
Q 020809          293 IEACEATKTAVTPHIIR  309 (321)
Q Consensus       293 ~~~~~~~~~~~~ph~~k  309 (321)
                      ...|+.+...+.-+|.+
T Consensus      1031 ~~~F~~v~~~f~~~F~~ 1047 (1179)
T TIGR02168      1031 RERFKDTFDQVNENFQR 1047 (1179)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            44444444444444433

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=97.99  E-value=0.0017  Score=71.30  Aligned_cols=54  Identities=20%  Similarity=0.329  Sum_probs=25.1

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQK   94 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~   94 (321)
                      ..+..++..++..+..++..+..+..++......+.++...+..+...+..+..
T Consensus       673 ~~l~~e~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~  726 (1179)
T TIGR02168       673 LERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSR  726 (1179)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445555555555555555555444444444444444444443333333333

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.

>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=97.96  E-value=0.0049  Score=57.23  Aligned_cols=46  Identities=20%  Similarity=0.353  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERI   89 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I   89 (321)
                      ..++..++.+|..++..++.....|......+..+++...+.+...
T Consensus        35 E~e~~~l~rri~~lE~~le~~eerL~~~~~kL~~~e~~~de~er~~   80 (237)
T PF00261_consen   35 EAEVASLQRRIQLLEEELERAEERLEEATEKLEEAEKRADESERAR   80 (237)
T ss_dssp             HHHHHHHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHHHHCHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444455555555554444444444444444444444444443333

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=97.96  E-value=0.0072  Score=56.39  Aligned_cols=17  Identities=18%  Similarity=-0.009  Sum_probs=12.4

Q ss_pred             CchhHHHHHHHHHHHHH
Q 020809          209 WLPPWLAVHLLQCQSLI  225 (321)
Q Consensus       209 ~l~Pwla~~~~~~~~~~  225 (321)
                      -++|-|...|.++....
T Consensus       171 ~l~~ell~~yeri~~~~  187 (239)
T COG1579         171 KLDPELLSEYERIRKNK  187 (239)
T ss_pred             hcCHHHHHHHHHHHhcC
Confidence            47888888888776544

>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=97.95  E-value=0.0014  Score=60.75  Aligned_cols=53  Identities=25%  Similarity=0.412  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           47 LDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      |..++..+...+..+......|+........++..+..+...|..|+.+++.+
T Consensus         3 ~~~l~~eld~~~~~~~~~~~~l~~~~~~~~~aE~e~~~l~rri~~lE~~le~~   55 (237)
T PF00261_consen    3 IQQLKDELDEAEERLEEAEEKLKEAEKRAEKAEAEVASLQRRIQLLEEELERA   55 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            44444455555555555555555555555555555555555555555555444

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=97.84  E-value=0.033  Score=62.71  Aligned_cols=89  Identities=25%  Similarity=0.402  Sum_probs=44.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          107 AAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEE  186 (321)
Q Consensus       107 ~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Ee  186 (321)
                      +..++..+..++.+++..+..+...+.........+......+...+..++..+...+....+....++.++..+..+..
T Consensus       826 ~~~ei~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~l~~~~~~~~~l~~~l~~~~~~~~~~~~  905 (1163)
T COG1196         826 LEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKE  905 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444444444444444555555555555555555555555555555555555


Q ss_pred             HHHHHHHHH
Q 020809          187 EMMRAKFEA  195 (321)
Q Consensus       187 ei~kl~~ea  195 (321)
                      .+.++....
T Consensus       906 ~~~~~~~~~  914 (1163)
T COG1196         906 EIEKLRERL  914 (1163)
T ss_pred             HHHHHHHHH
Confidence            555554333

>PRK03918 chromosome segregation protein; Provisional

Probab=97.75  E-value=0.022  Score=61.72  Aligned_cols=38  Identities=21%  Similarity=0.323  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          151 KKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEM  188 (321)
Q Consensus       151 kk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei  188 (321)
                      ..+..++..+..+..........+..++..+..++..+
T Consensus       666 ~~~~~l~~~l~~l~~~~~~l~~~i~~l~~~i~~~~~~~  703 (880)
T PRK03918        666 EEYLELSRELAGLRAELEELEKRREEIKKTLEKLKEEL  703 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444444444443333

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=97.74  E-value=0.01  Score=66.76  Aligned_cols=28  Identities=11%  Similarity=0.192  Sum_probs=12.8

Q ss_pred             hHHHHhHhHHHHHhhhhhcCchhHHHHh
Q 020809          285 VQTLKTKTIEACEATKTAVTPHIIRVQE  312 (321)
Q Consensus       285 ~q~~~~~~~~~~~~~~~~~~ph~~k~~~  312 (321)
                      +..+..+..+.+..+-+.|.=||..+=.
T Consensus      1000 i~~~d~~~~~~f~~~f~~In~~F~~if~ 1027 (1163)
T COG1196        1000 IEELDKEKRERFKETFDKINENFSEIFK 1027 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444444433

>PHA02562 46 endonuclease subunit; Provisional

Probab=97.66  E-value=0.0067  Score=62.29  Aligned_cols=25  Identities=16%  Similarity=0.189  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          165 KINDEQKSKIRKTERALKVAEEEMM  189 (321)
Q Consensus       165 k~~~Eqk~~l~elE~~lq~~Eeei~  189 (321)
                      ......+..+..++......+.++.
T Consensus       358 ~~~~~l~~ei~~l~~~~~~~~~~l~  382 (562)
T PHA02562        358 DKAKKVKAAIEELQAEFVDNAEELA  382 (562)
T ss_pred             HHHHHHHHHHHHHHhhhhchHHHHH
Confidence            3333333334433333333333333

>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

Probab=97.66  E-value=0.025  Score=56.70  Aligned_cols=47  Identities=11%  Similarity=0.145  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          146 AIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAK  192 (321)
Q Consensus       146 a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~  192 (321)
                      ...+...+.+....+.+++......+..+.++......+...|.+++
T Consensus       198 ~~kl~~~~~E~kk~~~~l~~~l~~~q~~l~eL~~~~~~L~~~Ias~e  244 (420)
T COG4942         198 QAKLAQLLEERKKTLAQLNSELSADQKKLEELRANESRLKNEIASAE  244 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            33334444555555555555555555555555555555555555554

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes

Probab=97.65  E-value=0.015  Score=62.01  Aligned_cols=105  Identities=23%  Similarity=0.364  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH--------------
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAA--------------  108 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~e--------------  108 (321)
                      ++.+|.+++.+-.+|++++..+++....=...|..+|+.+.+-...-..++.++..-++.+..+.+              
T Consensus       458 lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DKq~l~~LEkrL~eE~~~R~~lEkQL~eErk~r~~ee~~aar~~~~~~~~r~  537 (697)
T PF09726_consen  458 LKSELSQLRQENEQLQNKLQNLVQARQQDKQSLQQLEKRLAEERRQRASLEKQLQEERKARKEEEEKAARALAQAQATRQ  537 (697)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhccccchhccc
Confidence            344455555555555555555555555555555666666666666666666666555443211100              


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          109 EQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAI  147 (321)
Q Consensus       109 eq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~  147 (321)
                      +-.+..+.|.++|+.++..|+.++...+..+..+|....
T Consensus       538 e~~e~~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~  576 (697)
T PF09726_consen  538 ECAESCRQRRRQLESELKKLRRELKQKEEQIRELESELQ  576 (697)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            222335556677777777777777666666666665553

; GO: 0016021 integral to membrane

>PRK02224 chromosome segregation protein; Provisional

Probab=97.59  E-value=0.022  Score=61.90  Aligned_cols=30  Identities=17%  Similarity=0.426  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKD   72 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd   72 (321)
                      +...++.+...+..++..++++..++..+.
T Consensus       473 ~~~~~~~~~~~~~~le~~l~~~~~~~e~l~  502 (880)
T PRK02224        473 DRERVEELEAELEDLEEEVEEVEERLERAE  502 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444455555555555555555554444333

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]

Probab=97.59  E-value=0.033  Score=61.06  Aligned_cols=88  Identities=24%  Similarity=0.355  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          106 NAAEQVDKAHARADELEKQIDNLKKES-EKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVA  184 (321)
Q Consensus       106 ~~eeq~~~~~~RireL~k~Ie~Lk~el-e~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~  184 (321)
                      +.+..+...+.+++.|+++|..++++. .....++.+.+.+...++..+..++..+..|.....+....+..-+.+.-.+
T Consensus       362 ~~~n~i~~~k~~~d~l~k~I~~~~~~~~~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i  441 (1074)
T KOG0250|consen  362 EIENSIRKLKKEVDRLEKQIADLEKQTNNELGSELEERENKLEQLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHI  441 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            344455555556666666676666666 5555556666666666666666666666666666666666666666655555


Q ss_pred             HHHHHHHHH
Q 020809          185 EEEMMRAKF  193 (321)
Q Consensus       185 Eeei~kl~~  193 (321)
                      +.++..+..
T Consensus       442 ~~~i~~l~k  450 (1074)
T KOG0250|consen  442 EGEILQLRK  450 (1074)
T ss_pred             HHHHHHHHH
Confidence            555555533

>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT)

Probab=97.57  E-value=0.053  Score=56.05  Aligned_cols=95  Identities=22%  Similarity=0.337  Sum_probs=55.9

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------hhHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK------ETLNAAEQVDKAH  115 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~------~~~~~eeq~~~~~  115 (321)
                      -++.+++.......+|......+.++...+...+..++..+.........|..+...+...      ....+..+...+.
T Consensus       140 ~lQ~qlE~~qkE~eeL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~ee~e~L~~~~kel~~~~e~l~~E~~~L~~q~~e~~  219 (546)
T PF07888_consen  140 LLQNQLEECQKEKEELLKENEQLEEEVEQLREEVERLEAELEQEEEEMEQLKQQQKELTESSEELKEERESLKEQLAEAR  219 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3566666666666666666666666666666666666666666555555555554444332      2233445556666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 020809          116 ARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus       116 ~RireL~k~Ie~Lk~ele~~~  136 (321)
                      .||+.|+..|..+.....+..
T Consensus       220 ~ri~~LEedi~~l~qk~~E~e  240 (546)
T PF07888_consen  220 QRIRELEEDIKTLTQKEKEQE  240 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            677777777666665554333

This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=97.56  E-value=0.024  Score=52.92  Aligned_cols=113  Identities=27%  Similarity=0.401  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK-ETLNAAEQVDKAHARADEL  121 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~-~~~~~eeq~~~~~~RireL  121 (321)
                      .+..+..++..+..+...+..+..++..++.++.+.+..|.+++.++..++..+...... ...+++-..+.++.|...|
T Consensus        29 ~~~~l~k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ak~r~~~l  108 (239)
T COG1579          29 IRKALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSL  108 (239)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHH
Confidence            344555556666666666666666666666666666666666666666666665333222 2344555555566666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          122 EKQIDNLKKESEKQQKEKEALEARAIEAEKKISD  155 (321)
Q Consensus       122 ~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~e  155 (321)
                      +.+|..+...++....++..+..+....+..+.+
T Consensus       109 e~el~~l~~~~~~l~~~i~~l~~~~~~~e~~~~e  142 (239)
T COG1579         109 EDELAELMEEIEKLEKEIEDLKERLERLEKNLAE  142 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6665555555555554444444444444443333

>TIGR00606 rad50 rad50

Probab=97.53  E-value=0.18  Score=57.61  Aligned_cols=59  Identities=10%  Similarity=-0.064  Sum_probs=30.9

Q ss_pred             chhHHHHHHHHHHHHHHhHHHhhCcchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhh
Q 020809          210 LPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPA  269 (321)
Q Consensus       210 l~Pwla~~~~~~~~~~~~~~~~hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~  269 (321)
                      -.|-+...+..+....+.+...++...= .+-+.-..=..--..|-+|....+..+....
T Consensus      1048 ~~~~~~~e~~~l~~~~~~l~~~~a~l~g-~~k~le~qi~~l~~eL~e~~yk~a~~ryrka 1106 (1311)
T TIGR00606      1048 QVLQMKQEHQKLEENIDLIKRNHVLALG-RQKGYEKEIKHFKKELREPQFRDAEEKYREM 1106 (1311)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHcchHHHHHHHHHHHH
Confidence            3477888888888877777766554221 1111111111122334456666666665544

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK09039 hypothetical protein; Validated

Probab=97.49  E-value=0.06  Score=52.82  Aligned_cols=141  Identities=24%  Similarity=0.273  Sum_probs=67.9

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELE  122 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~  122 (321)
                      +..++...+.++..|+++|.++..-+.--......++..+.++..++..++..-..++..- .........++.|+..|.
T Consensus        44 Ls~~i~~~~~eL~~L~~qIa~L~e~L~le~~~~~~l~~~l~~l~~~l~~a~~~r~~Le~~~-~~~~~~~~~~~~~~~~l~  122 (343)
T PRK09039         44 LSREISGKDSALDRLNSQIAELADLLSLERQGNQDLQDSVANLRASLSAAEAERSRLQALL-AELAGAGAAAEGRAGELA  122 (343)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH-hhhhhhcchHHHHHHHHH
Confidence            5666666677777777776666666655556666666666666666666655555554320 000011112333333333


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          123 KQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVA  184 (321)
Q Consensus       123 k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~  184 (321)
                      ..+...+....+.+.+...|......+..++..++..++..+....+++.+|+.+...+..+
T Consensus       123 ~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a  184 (343)
T PRK09039        123 QELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVA  184 (343)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333344444444444444444444444444444433

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=97.48  E-value=0.083  Score=55.14  Aligned_cols=124  Identities=16%  Similarity=0.189  Sum_probs=72.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 020809          118 ADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATS  197 (321)
Q Consensus       118 ireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~  197 (321)
                      ++.+++++..+.+..................++..+.++...++.+++...+....+..+......+...+.++......
T Consensus       350 ~~~lekeL~~Le~~~~~~~~~i~~~~~~ysel~e~leel~e~leeie~eq~ei~e~l~~Lrk~E~eAr~kL~~~~~~L~~  429 (569)
T PRK04778        350 VRQLEKQLESLEKQYDEITERIAEQEIAYSELQEELEEILKQLEEIEKEQEKLSEMLQGLRKDELEAREKLERYRNKLHE  429 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555555554444444444445566677777777888888888888888888888888888887777666665


Q ss_pred             hhhhhhhhhccCchhHHHHHHHHHHHHHHhHHHhh--CcchHHHHH
Q 020809          198 RSKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAH--GKPAMDVAI  241 (321)
Q Consensus       198 ~a~ql~e~~g~~l~Pwla~~~~~~~~~~~~~~~~h--g~p~~~~~~  241 (321)
                      ..+.+...+---+|..+-..+......+......-  |..=|+.+.
T Consensus       430 ikr~l~k~~lpgip~~y~~~~~~~~~~i~~l~~~L~~g~VNm~ai~  475 (569)
T PRK04778        430 IKRYLEKSNLPGLPEDYLEMFFEVSDEIEALAEELEEKPINMEAVN  475 (569)
T ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHH
Confidence            55545443312255555444444443333332221  554444443

>PHA02562 46 endonuclease subunit; Provisional

Probab=97.44  E-value=0.05  Score=55.85  Aligned_cols=38  Identities=18%  Similarity=0.126  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          157 SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFE  194 (321)
Q Consensus       157 ~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~e  194 (321)
                      ...+..++....+....+..+......++.++.+++..
T Consensus       336 ~~~i~el~~~i~~~~~~i~~~~~~~~~l~~ei~~l~~~  373 (562)
T PHA02562        336 SKKLLELKNKISTNKQSLITLVDKAKKVKAAIEELQAE  373 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            33333333344444444444444444444444444333

>PRK03918 chromosome segregation protein; Provisional

Probab=97.39  E-value=0.04  Score=59.72  Aligned_cols=39  Identities=28%  Similarity=0.457  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          141 ALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTER  179 (321)
Q Consensus       141 ~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~  179 (321)
                      .++.....++..+.++...+..++.........+..++.
T Consensus       663 ~l~~~~~~l~~~l~~l~~~~~~l~~~i~~l~~~i~~~~~  701 (880)
T PRK03918        663 ELREEYLELSRELAGLRAELEELEKRREEIKKTLEKLKE  701 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444444444444433

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=97.39  E-value=0.091  Score=58.15  Aligned_cols=167  Identities=21%  Similarity=0.224  Sum_probs=75.8

Q ss_pred             HHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           55 RSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK---ETLNAAEQVDKAHARADELEKQIDNLKKE  131 (321)
Q Consensus        55 ~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~---~~~~~eeq~~~~~~RireL~k~Ie~Lk~e  131 (321)
                      ..+.+.+..+.++|.....++.++++....-+..|..++.+|+.++..   ....+++....++.+-..+...+..++++
T Consensus       408 K~~~~k~kKleke~ek~~~~~~e~e~~pe~~~~~i~~~~~ei~~L~~~~~~~~~~l~e~~~~l~~~t~~~~~e~~~~eke  487 (1293)
T KOG0996|consen  408 KRLTSKIKKLEKEIEKARRKKSELEKAPEKARIEIQKCQTEIEQLEELLEKEERELDEILDSLKQETEGIREEIEKLEKE  487 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHhCchhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHH
Confidence            333344444444444444444444444444555666666666666443   22344555555555444444444444444


Q ss_pred             HHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 020809          132 SEKQQKEK--------------EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATS  197 (321)
Q Consensus       132 le~~~~kk--------------~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~  197 (321)
                      +..-..+.              ..|..+.....+++.++...+..+.....+-+..+..+...+.....++.....+...
T Consensus       488 l~~~~~~~n~~~~e~~vaesel~~L~~~~~~~~~~~e~lk~~L~~~~~~~~e~~~~l~~~k~~l~~~k~e~~~~~k~l~~  567 (1293)
T KOG0996|consen  488 LMPLLKQVNEARSELDVAESELDILLSRHETGLKKVEELKGKLLASSESLKEKKTELDDLKEELPSLKQELKEKEKELPK  567 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHH
Confidence            44333333              3333333333344444555555544445555555555444444444444443333222


Q ss_pred             hhhhhhhhhccCchhHHHHHHHHHHHHHH
Q 020809          198 RSKELTEVHSAWLPPWLAVHLLQCQSLIE  226 (321)
Q Consensus       198 ~a~ql~e~~g~~l~Pwla~~~~~~~~~~~  226 (321)
                      ..+   +.+  -+-+.+...-.+..+..+
T Consensus       568 ~~~---e~~--~~~~~~~~~rqrveE~ks  591 (1293)
T KOG0996|consen  568 LRK---EER--NLKSQLNKLRQRVEEAKS  591 (1293)
T ss_pred             HHH---HHH--HHHHHHHHHHHHHHHHHH
Confidence            211   111  244555555555555544

>TIGR00606 rad50 rad50

Probab=97.35  E-value=0.12  Score=59.09  Aligned_cols=57  Identities=12%  Similarity=0.212  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHHHH--------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           86 SERIVSLQKELSSLQKK--------ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEAL  142 (321)
Q Consensus        86 ~~~I~~Lq~eI~~~qk~--------~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~L  142 (321)
                      ..++..++.+|.++..+        ...+++..+...+..++.|...++.+..+.+..+.++..|
T Consensus       798 ~~ei~~l~~qie~l~~~l~~~~~~~s~~ele~ei~~~~~el~~l~~~~e~l~~e~e~~~~eI~~L  862 (1311)
T TIGR00606       798 QMELKDVERKIAQQAAKLQGSDLDRTVQQVNQEKQEKQHELDTVVSKIELNRKLIQDQQEQIQHL  862 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555555554433        1244566666666666666555555555555555444444

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=97.34  E-value=0.16  Score=56.27  Aligned_cols=159  Identities=21%  Similarity=0.259  Sum_probs=113.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARA  118 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Ri  118 (321)
                      -+..|+++-...+++-..++...+.+..-|.+.|.....++.-|+.....|...+..|+..+.+ ....|.....+..|+
T Consensus      1543 ra~~L~s~A~~a~~~A~~v~~~ae~V~eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~~-t~~aE~~~~~a~q~~ 1621 (1758)
T KOG0994|consen 1543 RAENLQSEAERARSRAEDVKGQAEDVVEALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQEE-TAAAEKLATSATQQL 1621 (1758)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence            3456677777788888888889999999999999999999999999999999999999998774 466788888899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 020809          119 DELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSR  198 (321)
Q Consensus       119 reL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~  198 (321)
                      ++|...++.|+.....+-......+.-+..+...-..++..++.+++..+.....+.+--.....+.+....+..++.++
T Consensus      1622 ~eL~~~~e~lk~~~~qns~~A~~a~~~a~sa~~~A~~a~q~~~~lq~~~~~~~~l~~~r~~g~~~ar~rAe~L~~eA~~L 1701 (1758)
T KOG0994|consen 1622 GELETRMEELKHKAAQNSAEAKQAEKTAGSAKEQALSAEQGLEILQKYYELVDRLLEKRMEGSQAARERAEQLRTEAEKL 1701 (1758)
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHH
Confidence            99999999999888777766555555555555444455555555555555555555444444444444444444444433

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=97.27  E-value=0.077  Score=61.97  Aligned_cols=57  Identities=28%  Similarity=0.410  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          125 IDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERAL  181 (321)
Q Consensus       125 Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~l  181 (321)
                      +..++..++.....+...+.....+..++.+.+..+..+++.+.+....|.++...+
T Consensus      1057 ~~~~~~~~~el~~~l~kke~El~~l~~k~e~e~~~~~~l~k~i~eL~~~i~el~e~l 1113 (1930)
T KOG0161|consen 1057 IEELKKQKEELDNQLKKKESELSQLQSKLEDEQAEVAQLQKQIKELEARIKELEEEL 1113 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444444445555555555555555555555555555555544443

>PRK04863 mukB cell division protein MukB; Provisional

Probab=97.26  E-value=0.31  Score=56.33  Aligned_cols=38  Identities=18%  Similarity=0.222  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKA   81 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~   81 (321)
                      +.+..+...++...+..+..+...+.++...+..++.+
T Consensus       292 r~rk~eA~kkLe~tE~nL~rI~diL~ELe~rL~kLEkQ  329 (1486)
T PRK04863        292 RRELYTSRRQLAAEQYRLVEMARELAELNEAESDLEQD  329 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444433333333333333333

>COG4372 Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

Probab=97.25  E-value=0.13  Score=50.87  Aligned_cols=28  Identities=18%  Similarity=0.240  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          164 QKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       164 ek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .+...+++.+++.+|.+...+|.+..++
T Consensus       251 ~e~I~~re~~lq~lEt~q~~leqeva~l  278 (499)
T COG4372         251 AEQIRERERQLQRLETAQARLEQEVAQL  278 (499)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444444444

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins

Probab=97.13  E-value=0.28  Score=55.59  Aligned_cols=98  Identities=21%  Similarity=0.350  Sum_probs=54.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGK-------DEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQV  111 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~k-------d~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~  111 (321)
                      +-..++.+++.+...+..+....+++.+.|...       ...+..++..+.....++..+.++-..++.+.....+++.
T Consensus       601 ~ee~L~~~l~~~~~~l~~~~~~~~~~e~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  680 (1201)
T PF12128_consen  601 SEEELRERLEQAEDQLQSAEERQEELEKQLKQINKKIEELKREITQAEQELKQAEQDLQRLKNEREQLKQEIEEAKEERK  680 (1201)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334566666666666655555555554444444       4444444444444455555555555555444445566666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          112 DKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus       112 ~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      ...+.++..++..+..+..+++...
T Consensus       681 ~~~~~~l~~l~~~l~~~~~e~~~~~  705 (1201)
T PF12128_consen  681 EQIEEQLNELEEELKQLKQELEELL  705 (1201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666666666666666555554

>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion

Probab=97.07  E-value=0.15  Score=45.24  Aligned_cols=16  Identities=44%  Similarity=0.669  Sum_probs=6.0

Q ss_pred             HHHHHHHHHHHHHHHH
Q 020809          117 RADELEKQIDNLKKES  132 (321)
Q Consensus       117 RireL~k~Ie~Lk~el  132 (321)
                      |+..++..+..+..+.
T Consensus       131 ~l~~l~~~~~~~~~e~  146 (191)
T PF04156_consen  131 RLDSLDESIKELEKEI  146 (191)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333333333333333

The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].

>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT)

Probab=97.02  E-value=0.26  Score=51.07  Aligned_cols=50  Identities=16%  Similarity=0.255  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           50 LKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        50 lk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ++.++...+....++.+....+.....+++..+..++..+.....+...+
T Consensus       141 lQ~qlE~~qkE~eeL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~ee~e~L  190 (546)
T PF07888_consen  141 LQNQLEECQKEKEELLKENEQLEEEVEQLREEVERLEAELEQEEEEMEQL  190 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444444444444444444444444444444444444333

This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].

>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family

Probab=96.99  E-value=0.41  Score=46.92  Aligned_cols=27  Identities=19%  Similarity=0.388  Sum_probs=17.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKT   65 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~   65 (321)
                      +...+..++..++.++..++.....+.
T Consensus        75 d~~~~~~~l~~l~~~~~~l~a~~~~l~  101 (423)
T TIGR01843        75 DATDVEADAAELESQVLRLEAEVARLR  101 (423)
T ss_pred             ccchhhhHHHHHHHHHHHHHHHHHHHH
Confidence            455567777777777776666555433

Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.

>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function

Probab=96.94  E-value=0.2  Score=52.65  Aligned_cols=58  Identities=28%  Similarity=0.377  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .-.+++++++.++.++...+..+..+++.+...+.++..++.+.......++.++.-.
T Consensus       325 ~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l~  382 (594)
T PF05667_consen  325 EQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKLK  382 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456677777777777777777777777777777777777776666666666666543

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=96.92  E-value=0.2  Score=55.64  Aligned_cols=48  Identities=15%  Similarity=0.383  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           50 LKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS   97 (321)
Q Consensus        50 lk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~   97 (321)
                      ++.+...+.+.......+....+..=...+..+....++|..|..+|+
T Consensus       375 ~~e~~~~~kn~~~~~k~~~~~~e~~~vk~~E~lK~~~~k~kKleke~e  422 (1293)
T KOG0996|consen  375 IKERAKELKNKFESLKKKFQDLEREDVKREEKLKRLTSKIKKLEKEIE  422 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333344444444333333333333333333333333333

>PRK01156 chromosome segregation protein; Provisional

Probab=96.92  E-value=0.45  Score=52.02  Aligned_cols=32  Identities=16%  Similarity=0.295  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          151 KKISDLSAKLEKLQKINDEQKSKIRKTERALK  182 (321)
Q Consensus       151 kk~~el~~~le~Lek~~~Eqk~~l~elE~~lq  182 (321)
                      ..+..+...++.++....+...++..+...+.
T Consensus       688 ~~l~~l~~~~~~l~~~i~~l~~~~~~l~eel~  719 (895)
T PRK01156        688 KALDDAKANRARLESTIEILRTRINELSDRIN  719 (895)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            33333333333333333333333333333333

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope

Probab=96.89  E-value=0.12  Score=49.30  Aligned_cols=34  Identities=15%  Similarity=0.145  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          156 LSAKLEKLQKINDEQKSKIRKTERALKVAEEEMM  189 (321)
Q Consensus       156 l~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~  189 (321)
                      +...+..+......+-..++.+-.-.-.++.+|.
T Consensus       267 le~el~~l~~~~~~~~~ey~~Ll~~K~~Ld~EIa  300 (312)
T PF00038_consen  267 LEEELAELREEMARQLREYQELLDVKLALDAEIA  300 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            3333333333333344444444444444444443

They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....

>PRK04863 mukB cell division protein MukB; Provisional

Probab=96.88  E-value=0.41  Score=55.35  Aligned_cols=36  Identities=6%  Similarity=0.098  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKE   79 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~e   79 (321)
                      ..+|...+.++..+...+.++..++..+..++..+.
T Consensus       299 ~kkLe~tE~nL~rI~diL~ELe~rL~kLEkQaEkA~  334 (1486)
T PRK04863        299 RRQLAAEQYRLVEMARELAELNEAESDLEQDYQAAS  334 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444444443

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=96.83  E-value=0.31  Score=47.38  Aligned_cols=54  Identities=26%  Similarity=0.439  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          125 IDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTE  178 (321)
Q Consensus       125 Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE  178 (321)
                      +..++.++.....++........+++.++..++..++.+...+.+....|.+++
T Consensus       211 L~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~  264 (325)
T PF08317_consen  211 LEALRQELAEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEIAEAE  264 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444333333333333333444444444444444444444444444

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=96.81  E-value=1.1  Score=49.23  Aligned_cols=173  Identities=18%  Similarity=0.248  Sum_probs=77.1

Q ss_pred             ccCCCCCCc-ccc-cCCCCchH--HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHH---HHHHHHHHHHHHHHHHHHHHH
Q 020809           24 IQGEDVPPL-TAS-DAVDSSPL--KIELDQLKSKIRSLESHIDEKTQELKGKDEVV---AQKEKAIQDKSERIVSLQKEL   96 (321)
Q Consensus        24 ~~~~~~~~~-~~~-~~~~~~~l--~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I---~q~ek~i~e~~~~I~~Lq~eI   96 (321)
                      +|..||.+. +.+ +..+++.+  -+.+.+++.++...++.++.++.+|..+...-   ..+.++++-+..+.+-+...+
T Consensus       652 GDV~dP~GtlTGGs~~~~a~~L~~l~~l~~~~~~~~~~q~el~~le~eL~~le~~~~kf~~l~~ql~l~~~~l~l~~~r~  731 (1174)
T KOG0933|consen  652 GDVYDPSGTLTGGSRSKGADLLRQLQKLKQAQKELRAIQKELEALERELKSLEAQSQKFRDLKQQLELKLHELALLEKRL  731 (1174)
T ss_pred             CceeCCCCcccCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455554 332 33343322  23466666677777777777766666654432   223333333333333333333


Q ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           97 SSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK  176 (321)
Q Consensus        97 ~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~e  176 (321)
                      +.+.-   ..+-+....+..++.+++.+|......+..-..+...+|....+...   .....+.++++.....+..+++
T Consensus       732 ~~~e~---~~~~~~~~~~~e~v~e~~~~Ike~~~~~k~~~~~i~~lE~~~~d~~~---~re~rlkdl~keik~~k~~~e~  805 (1174)
T KOG0933|consen  732 EQNEF---HKLLDDLKELLEEVEESEQQIKEKERALKKCEDKISTLEKKMKDAKA---NRERRLKDLEKEIKTAKQRAEE  805 (1174)
T ss_pred             hcChH---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhh---hhHhHHHHHHHHHHHHHHHHHH
Confidence            32211   22222233333333333333333333333333333333333333322   2344455555555555555555


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhh
Q 020809          177 TERALKVAEEEMMRAKFEATSRSKEL  202 (321)
Q Consensus       177 lE~~lq~~Eeei~kl~~ea~~~a~ql  202 (321)
                      ....+...+.+..+++.+.....+.+
T Consensus       806 ~~~~~ek~~~e~e~l~lE~e~l~~e~  831 (1174)
T KOG0933|consen  806 SSKELEKRENEYERLQLEHEELEKEI  831 (1174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55555555555555555555444333

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=96.76  E-value=0.26  Score=51.47  Aligned_cols=141  Identities=17%  Similarity=0.229  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------hhHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK---------ETLNAAEQVDKAH  115 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~---------~~~~~eeq~~~~~  115 (321)
                      ..++.+..+|..|-..+..-..-.+..+..+..+...+.....+...|..+|+.++..         .-..++++...+.
T Consensus       282 ~~~~~i~~~Id~Lyd~lekE~~A~~~vek~~~~l~~~l~~~~e~~~~l~~Ei~~l~~sY~l~~~e~~~~~~lekeL~~Le  361 (569)
T PRK04778        282 EKNEEIQERIDQLYDILEREVKARKYVEKNSDTLPDFLEHAKEQNKELKEEIDRVKQSYTLNESELESVRQLEKQLESLE  361 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHccccCchhHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333334444444555555555555666666655443         0223333344444


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          116 ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAE  185 (321)
Q Consensus       116 ~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~E  185 (321)
                      .++..+...+................+..+...++....++...+..+.+.-.+-+..+..+...+..+.
T Consensus       362 ~~~~~~~~~i~~~~~~ysel~e~leel~e~leeie~eq~ei~e~l~~Lrk~E~eAr~kL~~~~~~L~~ik  431 (569)
T PRK04778        362 KQYDEITERIAEQEIAYSELQEELEEILKQLEEIEKEQEKLSEMLQGLRKDELEAREKLERYRNKLHEIK  431 (569)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444333332222222233333333344444444444444444444444444444444444444444333

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes

Probab=96.75  E-value=0.54  Score=50.40  Aligned_cols=98  Identities=15%  Similarity=0.254  Sum_probs=66.8

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE  120 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire  120 (321)
                      .-++.++..++..+....+.=.++..+|..++..=..+..+|..+..+.+.|++++..+....+.|. ..+..+++|+++
T Consensus       421 ~rLE~dvkkLraeLq~~Rq~E~ELRsqis~l~~~Er~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DK-q~l~~LEkrL~e  499 (697)
T PF09726_consen  421 SRLEADVKKLRAELQSSRQSEQELRSQISSLTNNERSLKSELSQLRQENEQLQNKLQNLVQARQQDK-QSLQQLEKRLAE  499 (697)
T ss_pred             HHHHHHHHHHHHHHHhhhhhHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence            3466777778888877777777777776666666566777777777888888888877766544442 335567777777


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKESEKQQKEK  139 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk  139 (321)
                      ..+.=..+++++.+.+..+
T Consensus       500 E~~~R~~lEkQL~eErk~r  518 (697)
T PF09726_consen  500 ERRQRASLEKQLQEERKAR  518 (697)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            7766666666665555433

; GO: 0016021 integral to membrane

>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function

Probab=96.72  E-value=0.43  Score=50.22  Aligned_cols=58  Identities=12%  Similarity=0.263  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      ..+..+-...+.+|+.+++++..++..++.++..+...+..+..++.....+...++.
T Consensus       320 ~~~~~~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~  377 (594)
T PF05667_consen  320 EDEQEEQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEE  377 (594)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555666666666666666666666666666665555555555555555544433

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=96.67  E-value=1  Score=49.39  Aligned_cols=65  Identities=18%  Similarity=0.212  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh-------hhhhcc---C--chhHHHHHHHHHHHHHHhHHHhhCc
Q 020809          170 QKSKIRKTERALKVAEEEMMRAKFEATSRSKEL-------TEVHSA---W--LPPWLAVHLLQCQSLIETHWNAHGK  234 (321)
Q Consensus       170 qk~~l~elE~~lq~~Eeei~kl~~ea~~~a~ql-------~e~~g~---~--l~Pwla~~~~~~~~~~~~~~~~hg~  234 (321)
                      ...-|+.+......++.++..++.+..++.+++       .+.+|.   +  ..-.+-..++-++..-..+|.+-.+
T Consensus       402 l~~~i~~~ke~e~~lq~e~~~~e~~l~~~~e~i~~l~~si~e~~~r~~~~~~~~~~~k~~~del~~~Rk~lWREE~~  478 (1200)
T KOG0964|consen  402 LKRGINDTKEQENILQKEIEDLESELKEKLEEIKELESSINETKGRMEEFDAENTELKRELDELQDKRKELWREEKK  478 (1200)
T ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444455555555555555555555444333       111111   1  2334445566667777788877443

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins

Probab=96.61  E-value=0.69  Score=52.53  Aligned_cols=96  Identities=15%  Similarity=0.304  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH--
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE--  120 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire--  120 (321)
                      +...-++++.++..++..+........+++..|....+.++....++.....++...+.. ...+......++.++..  
T Consensus       598 ~~~~ee~L~~~l~~~~~~l~~~~~~~~~~e~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~~~~  676 (1201)
T PF12128_consen  598 YAASEEELRERLEQAEDQLQSAEERQEELEKQLKQINKKIEELKREITQAEQELKQAEQD-LQRLKNEREQLKQEIEEAK  676 (1201)
T ss_pred             hhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH-HHHHHHHHHHHHHHHHHHH
Confidence            444455777778888888887777777777777777777777777777777766666442 22222222333333322  


Q ss_pred             ------HHHHHHHHHHHHHHHHHHH
Q 020809          121 ------LEKQIDNLKKESEKQQKEK  139 (321)
Q Consensus       121 ------L~k~Ie~Lk~ele~~~~kk  139 (321)
                            ++..+..+..++.....++
T Consensus       677 ~~~~~~~~~~l~~l~~~l~~~~~e~  701 (1201)
T PF12128_consen  677 EERKEQIEEQLNELEEELKQLKQEL  701 (1201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                  4444666666665555544

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope

Probab=96.60  E-value=0.7  Score=44.03  Aligned_cols=58  Identities=21%  Similarity=0.296  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      +..++.+++..|..+......+.-++..+...++.....+.........++++|..+.
T Consensus        52 ye~el~~lr~~id~~~~eka~l~~e~~~l~~e~~~~r~k~e~e~~~~~~le~el~~lr  109 (312)
T PF00038_consen   52 YEEELRELRRQIDDLSKEKARLELEIDNLKEELEDLRRKYEEELAERKDLEEELESLR  109 (312)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHhHHhhhhHHHHhhHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            4455555555555555555555555555555555544444444444444444444443

They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....

>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family

Probab=96.58  E-value=0.85  Score=44.72  Aligned_cols=20  Identities=20%  Similarity=0.418  Sum_probs=10.9

Q ss_pred             CCchHHHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLE   58 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Le   58 (321)
                      +...++.++..++.++..++
T Consensus        82 ~l~~l~~~~~~l~a~~~~l~  101 (423)
T TIGR01843        82 DAAELESQVLRLEAEVARLR  101 (423)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            44555666665555554443

Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.

>PF10174 Cast: RIM-binding protein of the cytomatrix active zone; InterPro: IPR019323 This entry represents a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion []

Probab=96.48  E-value=0.75  Score=49.83  Aligned_cols=32  Identities=22%  Similarity=0.356  Sum_probs=11.7

Q ss_pred             HHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHH
Q 020809           57 LESHIDEKTQELKGKDEVVAQKEKAIQDKSER   88 (321)
Q Consensus        57 Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~   88 (321)
                      |++.++.+..++..+...|++.+..+..++..
T Consensus       341 Lqsdve~Lr~rle~k~~~l~kk~~~~~~~qeE  372 (775)
T PF10174_consen  341 LQSDVEALRFRLEEKNSQLEKKQAQIEKLQEE  372 (775)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333333

Located at the C terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). These proteins also contain four coiled-coil domains [].

>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=96.47  E-value=0.076  Score=47.81  Aligned_cols=101  Identities=24%  Similarity=0.316  Sum_probs=26.3

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE  120 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire  120 (321)
                      .++...+-.++..+.++.....+..++|..+...+..++..+......|..|..++..++. +..++++       .+++
T Consensus        70 ~~le~~~~~l~~ELael~r~~~el~~~L~~~~~~l~~l~~~~~~~~~~l~~l~~~~~~L~~-~~~~l~~-------~l~e  141 (194)
T PF08614_consen   70 SSLEQKLAKLQEELAELYRSKGELAQQLVELNDELQELEKELSEKERRLAELEAELAQLEE-KIKDLEE-------ELKE  141 (194)
T ss_dssp             --------------------------------------------HHHHHHHHHHHHHHHHH-HHHHHHH-------HHHH
T ss_pred             cccccccccccccccccccccccccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHH-HHHHHHH-------HHHH
Confidence            3444555556666666666666666666666666666666666666666666666555533 1122222       4444


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKESEKQQKEKEALEARAIEA  149 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk~~LEa~a~e~  149 (321)
                      +++.++.++.++...+-....+|.+...+
T Consensus       142 k~k~~e~l~DE~~~L~l~~~~~e~k~~~l  170 (194)
T PF08614_consen  142 KNKANEILQDELQALQLQLNMLEEKLRKL  170 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445555555444444444444433333

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.

>PRK11281 hypothetical protein; Provisional

Probab=96.44  E-value=0.6  Score=52.50  Aligned_cols=21  Identities=19%  Similarity=0.393  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 020809          170 QKSKIRKTERALKVAEEEMMR  190 (321)
Q Consensus       170 qk~~l~elE~~lq~~Eeei~k  190 (321)
                      ....++.++...+.+++.+..
T Consensus       232 ~~~~~~~~~~~~~~lq~~in~  252 (1113)
T PRK11281        232 LTARIQRLEHQLQLLQEAINS  252 (1113)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444443

>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]

Probab=96.42  E-value=0.54  Score=40.59  Aligned_cols=52  Identities=25%  Similarity=0.288  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL   96 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI   96 (321)
                      .+|...+++...|+..+..+..+|.........+..........|..|+.+|
T Consensus        10 ~kLK~~~~e~dsle~~v~~LEreLe~~q~~~e~~~~daEn~k~eie~L~~el   61 (140)
T PF10473_consen   10 EKLKESESEKDSLEDHVESLERELEMSQENKECLILDAENSKAEIETLEEEL   61 (140)
T ss_pred             HHHHHHHHhHhhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444443333333333333333333333333333

There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding

>PF13851 GAS: Growth-arrest specific micro-tubule binding

Probab=96.40  E-value=0.74  Score=41.91  Aligned_cols=100  Identities=28%  Similarity=0.353  Sum_probs=57.3

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELE  122 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~  122 (321)
                      +..++.+++.+....+..+.++..+.+.+.+-|..++.+..++..++...+..-            .....++.|+..++
T Consensus        32 LKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~y~kdK------------~~L~~~k~rl~~~e   99 (201)
T PF13851_consen   32 LKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKNYEKDK------------QSLQNLKARLKELE   99 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHH
Confidence            344445555555555555555555555555555444444444444433322221            22334666888888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          123 KQIDNLKKESEKQQKEKEALEARAIEAEKKIS  154 (321)
Q Consensus       123 k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~  154 (321)
                      +++..|+-+-+....+...++..+.++..+..
T Consensus       100 k~l~~Lk~e~evL~qr~~kle~ErdeL~~kf~  131 (201)
T PF13851_consen  100 KELKDLKWEHEVLEQRFEKLEQERDELYRKFE  131 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888877777777777777776544

>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold)

Probab=96.38  E-value=0.43  Score=39.21  Aligned_cols=55  Identities=29%  Similarity=0.407  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          108 AEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK  162 (321)
Q Consensus       108 eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~  162 (321)
                      ..+......|+++|+..|..+...++..+.-+-.|+.+....++-.+.++-++..
T Consensus        50 ~~q~~s~~qr~~eLqaki~ea~~~le~eK~ak~~l~~r~~k~~~dka~lel~l~e  104 (107)
T PF09304_consen   50 QAQNASRNQRIAELQAKIDEARRNLEDEKQAKLELESRLLKAQKDKAILELKLAE  104 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHh
Confidence            3344455668888999999988888887766667888888877777766666554

The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.

>PF15070 GOLGA2L5: Putative golgin subfamily A member 2-like protein 5

Probab=96.34  E-value=0.23  Score=52.51  Aligned_cols=124  Identities=19%  Similarity=0.357  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-HHHHHHHHHHHHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKET-LNAAEQVDKAHARADELEKQIDN  127 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~-~~~eeq~~~~~~RireL~k~Ie~  127 (321)
                      .++.....++..+..++.++..+..+.......+.+++..|..|.+.+........ ..-.+.-..++.+++.|.++++.
T Consensus        19 ~lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eLk~q~~~~~~~~~pa~pse~E~~Lq~E~~~L~kElE~   98 (617)
T PF15070_consen   19 QLKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSELKNQMAEPPPPEPPAGPSEVEQQLQAEAEHLRKELES   98 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCccccccchHHHHHHHHHHHHHHHHHHH
Confidence            34555566777777888888888888888888888888888888877765432200 00001112344455555555555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          128 LKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKS  172 (321)
Q Consensus       128 Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~  172 (321)
                      |..++..+..+...|-....+.+.++.+++..+..+.....++..
T Consensus        99 L~~qlqaqv~~ne~Ls~L~~EqEerL~ELE~~le~~~e~~~D~~k  143 (617)
T PF15070_consen   99 LEEQLQAQVENNEQLSRLNQEQEERLAELEEELERLQEQQEDRQK  143 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555555544444333333333444444444444444443333333

>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]

Probab=96.33  E-value=1.1  Score=43.17  Aligned_cols=58  Identities=17%  Similarity=0.264  Sum_probs=32.9

Q ss_pred             CchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           40 SSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS   97 (321)
Q Consensus        40 ~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~   97 (321)
                      .+.++.+..++..++.++.++.++++.++.++...-++....++++-..+..+-..++
T Consensus        43 Rdeln~kvrE~~e~~~elr~~rdeineev~elK~kR~ein~kl~eL~~~~~~l~e~~~  100 (294)
T COG1340          43 RDELNAKVRELREKAQELREERDEINEEVQELKEKRDEINAKLQELRKEYRELKEKRN  100 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3445555566666666666666666666666665555555555555555444444444

>PRK01156 chromosome segregation protein; Provisional

Probab=96.31  E-value=1.3  Score=48.54  Aligned_cols=61  Identities=25%  Similarity=0.319  Sum_probs=30.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHH---HHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEK---TQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~---~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +...+..-.+.++..+..++..++.+   ...+......|...+..+.++...+..+..++..+
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~ei~~le~~~~~l~~~e~eL~~~~~~i~el~~~~~~l~~~i~~~  223 (895)
T PRK01156        160 EINSLERNYDKLKDVIDMLRAEISNIDYLEEKLKSSNLELENIKKQIADDEKSHSITLKEIERL  223 (895)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55566555566666666555544333   23334444444444444444444444444444333

>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []

Probab=96.31  E-value=1.4  Score=47.34  Aligned_cols=146  Identities=20%  Similarity=0.303  Sum_probs=104.0

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hh-HHHH------------
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK---ET-LNAA------------  108 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~---~~-~~~e------------  108 (321)
                      .++..+++++.+.+.+...+...|.+....++..+..+.+....|..|-..++.+..-   ++ ....            
T Consensus       265 ~EiqKL~qQL~qve~EK~~L~~~L~e~Q~qLe~a~~als~q~eki~~L~e~l~aL~~l~~~ke~~~~~d~~~~~~s~~d~  344 (717)
T PF09730_consen  265 SEIQKLKQQLLQVEREKSSLLSNLQESQKQLEHAQGALSEQQEKINRLTEQLDALRKLQEDKEQQSAEDSEKERDSHEDG  344 (717)
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccchhhhhhhhccccccccccc
Confidence            4678889999999999999999999999999999999999999999999998888661   10 0000            


Q ss_pred             -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          109 -------EQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEA----EKKISDLSAKLEKLQKINDEQKSKIRKT  177 (321)
Q Consensus       109 -------eq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~----ekk~~el~~~le~Lek~~~Eqk~~l~el  177 (321)
                             .....++.+.+....++..|+.++...+.+...++.+....    ...+..+..++..+++...+-...+..+
T Consensus       345 ~~ye~Di~~~eiLe~Ky~vav~Ev~~Lk~ELk~Lk~k~~~~~~~~~~ek~~~~~e~q~L~ekl~~lek~~re~qeri~~L  424 (717)
T PF09730_consen  345 DYYEVDINGLEILECKYKVAVSEVIQLKAELKALKSKYNELEERYKQEKDRLESEVQNLKEKLMSLEKSSREDQERISEL  424 (717)
T ss_pred             chhhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence                   01234566777777778888888888877776666655443    3455667777777777666666666666


Q ss_pred             HHHHHHHHHHHHH
Q 020809          178 ERALKVAEEEMMR  190 (321)
Q Consensus       178 E~~lq~~Eeei~k  190 (321)
                      +.++..+-..-..
T Consensus       425 E~ELr~l~~~A~E  437 (717)
T PF09730_consen  425 EKELRALSKLAGE  437 (717)
T ss_pred             HHHHHHHHHHHHh
Confidence            6666555444443

Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=96.28  E-value=0.87  Score=48.88  Aligned_cols=62  Identities=21%  Similarity=0.309  Sum_probs=40.5

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK  102 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~  102 (321)
                      ..++.+++.|+.++.+|...+-++.-.|-.....|+...+.+.-.-++|.+|+.+|.+.|..
T Consensus       440 ~ql~~eletLn~k~qqls~kl~Dvr~~~tt~kt~ie~~~~q~e~~isei~qlqarikE~q~k  501 (1118)
T KOG1029|consen  440 KQLQQELETLNFKLQQLSGKLQDVRVDITTQKTEIEEVTKQRELMISEIDQLQARIKELQEK  501 (1118)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhheeccchHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556666666666666666666666666666666666666666667777777777776654

>PF05701 WEMBL: Weak chloroplast movement under blue light; InterPro: IPR008545 This family consists of several plant proteins of unknown function

Probab=96.27  E-value=1.6  Score=45.17  Aligned_cols=23  Identities=17%  Similarity=0.426  Sum_probs=10.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHI   61 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i   61 (321)
                      ++..+...+.+.+.++..|...+
T Consensus       212 ~~~~~~~~leeae~~l~~L~~e~  234 (522)
T PF05701_consen  212 DAEEWEKELEEAEEELEELKEEL  234 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444555555554444444

Several sequences in this family are described as being myosin heavy chain-like.

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=96.25  E-value=0.91  Score=44.13  Aligned_cols=47  Identities=21%  Similarity=0.360  Sum_probs=26.6

Q ss_pred             HHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           55 RSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        55 ~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      ..|+...+.+..+...+...+..+...+..+...-+.|..++..++.
T Consensus       152 ~~L~~~~~~L~~D~~~L~~~~~~l~~~~~~l~~~~~~L~~e~~~Lk~  198 (325)
T PF08317_consen  152 EGLEENLELLQEDYAKLDKQLEQLDELLPKLRERKAELEEELENLKQ  198 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555555555555555555555566666655544

>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion

Probab=96.24  E-value=0.51  Score=41.88  Aligned_cols=19  Identities=16%  Similarity=0.288  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 020809           72 DEVVAQKEKAIQDKSERIV   90 (321)
Q Consensus        72 d~~I~q~ek~i~e~~~~I~   90 (321)
                      +..+...++.+........
T Consensus       101 ~~~~~~~~~~l~~~~~~~~  119 (191)
T PF04156_consen  101 QERIQELESELEKLKEDLQ  119 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333

The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].

>KOG4674 consensus Uncharacterized conserved coiled-coil protein [Function unknown]

Probab=96.19  E-value=1  Score=52.44  Aligned_cols=54  Identities=20%  Similarity=0.240  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS   98 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~   98 (321)
                      .+++..-.++.++...++.++.++-.++..+.++...++.....+..|+.+.+.
T Consensus      1236 ee~~~~~~k~qEl~~~i~kl~~el~plq~~l~el~~e~~~~~ael~~l~~e~~~ 1289 (1822)
T KOG4674|consen 1236 EENEANLEKIQELRDKIEKLNFELAPLQNELKELKAELQEKVAELKKLEEENDR 1289 (1822)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444444444444444444444444444444444333

>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]

Probab=96.14  E-value=1.4  Score=42.50  Aligned_cols=43  Identities=28%  Similarity=0.317  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 020809          156 LSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSR  198 (321)
Q Consensus       156 l~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~  198 (321)
                      +.+....+.....+....+..+-...+..-.+|.++..++...
T Consensus       163 l~aei~~lk~~~~e~~eki~~la~eaqe~he~m~k~~~~~De~  205 (294)
T COG1340         163 LKAEIDELKKKAREIHEKIQELANEAQEYHEEMIKLFEEADEL  205 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444444444444444433333

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=96.12  E-value=1  Score=40.80  Aligned_cols=35  Identities=23%  Similarity=0.253  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          152 KISDLSAKLEKLQKINDEQKSKIRKTERALKVAEE  186 (321)
Q Consensus       152 k~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Ee  186 (321)
                      .+.+.+...+.+.....++..-.+++......+|+
T Consensus       152 ~l~e~t~~i~eL~~~ieEy~~~teeLR~e~s~LEe  186 (193)
T PF14662_consen  152 ILSERTQQIEELKKTIEEYRSITEELRLEKSRLEE  186 (193)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444444444444444444433333333

>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=96.12  E-value=0.075  Score=49.64  Aligned_cols=57  Identities=14%  Similarity=0.288  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .+.++++...+...|...+..+..++..+..+.++++..+...+.+|..|+.+|+..
T Consensus        40 sQ~~id~~~~e~~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~   96 (251)
T PF11932_consen   40 SQKRIDQWDDEKQELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQI   96 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445555555555555555555555555555555555555555555555444444

However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.

>PF12795 MscS_porin: Mechanosensitive ion channel porin domain

Probab=96.08  E-value=0.69  Score=42.88  Aligned_cols=133  Identities=17%  Similarity=0.267  Sum_probs=98.4

Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hHHHHHHHHHHH
Q 020809           37 AVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE-TLNAAEQVDKAH  115 (321)
Q Consensus        37 ~~~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~-~~~~eeq~~~~~  115 (321)
                      .-....+++.|.+....+..++..+...+..+.........+...|.+....+..+...+......+ ..-.+.+...+.
T Consensus        77 ~~s~~eLeq~l~~~~~~L~~~q~~l~~~~~~l~~~~~~p~~aq~~l~~~~~~l~ei~~~L~~~~~~~~~~l~~a~~~~l~  156 (240)
T PF12795_consen   77 NLSLEELEQRLSQEQAQLQELQEQLQQENSQLIEIQTRPERAQQQLSEARQRLQEIRNQLQNLPPNGESPLSEAQRWLLQ  156 (240)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchhhHHHHHHHH
Confidence            3477788888888888888888888888888888888888888888888888888888777653323 344566777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          116 ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDE  169 (321)
Q Consensus       116 ~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~E  169 (321)
                      ++...|+.++.-++.++........-+..++.....++..+...+..|+.....
T Consensus       157 ae~~~l~~~~~~le~el~s~~~rq~L~~~qrdl~~~~~~~l~~~l~~Lq~~ln~  210 (240)
T PF12795_consen  157 AELAALEAQIEMLEQELLSNNNRQELLQLQRDLLKARIQRLQQQLQALQNLLNQ  210 (240)
T ss_pred             HHHHHHHHHHHHHHHHHHCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777777777777777777776666666666666666666666666666554443

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=96.07  E-value=3.1  Score=46.00  Aligned_cols=14  Identities=29%  Similarity=0.612  Sum_probs=6.4

Q ss_pred             HHHHHHHhhccccc
Q 020809          243 KALEKKAQAGKWVQ  256 (321)
Q Consensus       243 ~~~~k~~~~~~~~~  256 (321)
                      +..++...=..|..
T Consensus       927 k~v~~l~~k~~wi~  940 (1174)
T KOG0933|consen  927 KEVEKLLKKHEWIG  940 (1174)
T ss_pred             HHHHHHHHhccchh
Confidence            33444444455554

>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT)

Probab=96.07  E-value=0.76  Score=38.88  Aligned_cols=52  Identities=23%  Similarity=0.403  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          112 DKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKI  166 (321)
Q Consensus       112 ~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~  166 (321)
                      ..++..+..|+..++..+..+...+   ..++.+...+++.+.++...+++|...
T Consensus        69 ~~~~~~~~~l~~~~~~a~~~l~~~e---~sw~~qk~~le~e~~~~~~r~~dL~~Q  120 (132)
T PF07926_consen   69 QELQQEINELKAEAESAKAELEESE---ASWEEQKEQLEKELSELEQRIEDLNEQ  120 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH---HhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344444444444444333333   444444555555555555555544443

These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore

>COG4372 Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

Probab=96.05  E-value=1.8  Score=43.14  Aligned_cols=33  Identities=30%  Similarity=0.419  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          120 ELEKQIDNLKKESEKQQKEKEALEARAIEAEKK  152 (321)
Q Consensus       120 eL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk  152 (321)
                      .|+.++.+|+..-+.+..+-..|-.+++.++.+
T Consensus       183 Qlk~~~~~L~~r~~~ieQ~~~~la~r~~a~q~r  215 (499)
T COG4372         183 QLKSQVLDLKLRSAQIEQEAQNLATRANAAQAR  215 (499)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445555544444444444455555544443

>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=96.03  E-value=0.18  Score=45.36  Aligned_cols=60  Identities=20%  Similarity=0.343  Sum_probs=11.2

Q ss_pred             CchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           40 SSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        40 ~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ...++.++.++.....++...+...+.++..++..+......|..+...+..|+.+|..+
T Consensus        76 ~~~l~~ELael~r~~~el~~~L~~~~~~l~~l~~~~~~~~~~l~~l~~~~~~L~~~~~~l  135 (194)
T PF08614_consen   76 LAKLQEELAELYRSKGELAQQLVELNDELQELEKELSEKERRLAELEAELAQLEEKIKDL  135 (194)
T ss_dssp             --------------------------------------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444455555555555555555555555555555555555555555555555555444

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.

>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]

Probab=95.97  E-value=3.1  Score=45.09  Aligned_cols=19  Identities=37%  Similarity=0.372  Sum_probs=13.3

Q ss_pred             hHHHHHHHHHHHHHhhccc
Q 020809          236 AMDVAIQKALEKKAQAGKW  254 (321)
Q Consensus       236 ~~~~~~~~~~~k~~~~~~~  254 (321)
                      ++.+-++.|.+|....++.
T Consensus       414 ~~kneL~~a~ekld~mgth  432 (1265)
T KOG0976|consen  414 AAKNELQEALEKLDLMGTH  432 (1265)
T ss_pred             HHHHHHHHHHHHHHHHhHH
Confidence            3566788888887766654

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=95.97  E-value=0.66  Score=49.79  Aligned_cols=56  Identities=7%  Similarity=0.125  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      .+++--+.++.++..+...-...+--+.....+++.++..+..+++.|...|-+..
T Consensus       409 RqlewErar~qem~~Qk~reqe~iv~~nak~~ql~~eletLn~k~qqls~kl~Dvr  464 (1118)
T KOG1029|consen  409 RQLEWERARRQEMLNQKNREQEWIVYLNAKKKQLQQELETLNFKLQQLSGKLQDVR  464 (1118)
T ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhe
Confidence            33444445556666665555555555666666666666666666666666555443

>PF05701 WEMBL: Weak chloroplast movement under blue light; InterPro: IPR008545 This family consists of several plant proteins of unknown function

Probab=95.96  E-value=1.5  Score=45.45  Aligned_cols=133  Identities=22%  Similarity=0.297  Sum_probs=55.6

Q ss_pred             HHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---
Q 020809           58 ESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEK---  134 (321)
Q Consensus        58 es~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~---  134 (321)
                      ...+..+..+|......|.....++..+...+..|.++|...+. ....+.++...+..-|..|+.++...+.+++.   
T Consensus       280 ~~~l~s~~~ELe~ak~~L~~~k~E~~~L~~~vesL~~ELe~~K~-el~~lke~e~~a~~~v~~L~~eL~~~r~eLea~~~  358 (522)
T PF05701_consen  280 QSSLASAKKELEEAKKELEKAKEEASSLRASVESLRSELEKEKE-ELERLKEREKEASSEVSSLEAELNKTRSELEAAKA  358 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhHHhhHHHHHHHHHHHHHHHHh
Confidence            33344444444444444444444444444444444444433322 22222333333333333344443333333322   


Q ss_pred             -----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          135 -----------QQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       135 -----------~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                                 +...++.+-.....+..........+..+.......+..+..++..+..+..++...
T Consensus       359 ~e~~~k~~~~~l~~~Lqql~~Eae~Ak~ea~~~~~E~~~~k~E~e~~ka~i~t~E~rL~aa~ke~eaa  426 (522)
T PF05701_consen  359 EEEKAKEAMSELPKALQQLSSEAEEAKKEAEEAKEEVEKAKEEAEQTKAAIKTAEERLEAALKEAEAA  426 (522)
T ss_pred             hhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                       222223333333333334444444444444444555555555555555555555544

Several sequences in this family are described as being myosin heavy chain-like.

>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily

Probab=95.92  E-value=2.3  Score=43.25  Aligned_cols=57  Identities=9%  Similarity=0.147  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhh--------hcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQEL--------KGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eL--------k~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      +.++.+++.++.+.+..+.....+-        ......|..++..+...+.++..++..++.++
T Consensus       167 ~~ql~~~~~~L~~ae~~l~~f~~~~~~~~~~~~~~~~~~l~~l~~~l~~~~~~l~~~~a~~~~l~  231 (498)
T TIGR03007       167 DEQIKTYEKKLEAAENRLKAFKQENGGILPDQEGDYYSEISEAQEELEAARLELNEAIAQRDALK  231 (498)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcccCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455556666655555555432211        11233444444444444444444444444443

Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene.

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=95.91  E-value=1.3  Score=40.22  Aligned_cols=133  Identities=17%  Similarity=0.274  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDE-------VVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHAR  117 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~-------~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~R  117 (321)
                      -++.+++..+.+++..++++..+-+-+..       .|+..+..=++++.-|+.-.++|..++. ......++...+..+
T Consensus        12 ~ki~~L~n~l~elq~~l~~l~~ENk~Lk~lq~Rq~kAL~k~e~~e~~Lpqll~~h~eEvr~Lr~-~LR~~q~~~r~~~~k   90 (194)
T PF15619_consen   12 HKIKELQNELAELQRKLQELRKENKTLKQLQKRQEKALQKYEDTEAELPQLLQRHNEEVRVLRE-RLRKSQEQERELERK   90 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence            35566666666666666666655544433       3444444446666667777777777744 444445555555556


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          118 ADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVA  184 (321)
Q Consensus       118 ireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~  184 (321)
                      +++.+.+|..+..++.....    |-...+ +. ...++...+..++....+....+..+++.+...
T Consensus        91 lk~~~~el~k~~~~l~~L~~----L~~dkn-L~-eReeL~~kL~~~~~~l~~~~~ki~~Lek~leL~  151 (194)
T PF15619_consen   91 LKDKDEELLKTKDELKHLKK----LSEDKN-LA-EREELQRKLSQLEQKLQEKEKKIQELEKQLELE  151 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHH----HHHcCC-ch-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66555555544444443221    100000 00 124445555555555555555555555544333

>KOG0963 consensus Transcription factor/CCAAT displacement protein CDP1 [Transcription]

Probab=95.91  E-value=1.8  Score=45.40  Aligned_cols=87  Identities=22%  Similarity=0.312  Sum_probs=59.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------H----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          111 VDKAHARADELEKQIDNLKKESEKQQKEK--------E----ALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTE  178 (321)
Q Consensus       111 ~~~~~~RireL~k~Ie~Lk~ele~~~~kk--------~----~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE  178 (321)
                      .+.++.||+.|+++++.|..++...+...        +    .|-.+=+.+.....++......+.+.......+|..++
T Consensus       244 Le~aq~ri~~lE~e~e~L~~ql~~~N~~~~~~~~~~i~~~~~~L~~kd~~i~~L~~di~~~~~S~~~e~e~~~~qI~~le  323 (629)
T KOG0963|consen  244 LEDAQQRIVFLEREVEQLREQLAKANSSKKLAKIDDIDALGSVLNQKDSEIAQLSNDIERLEASLVEEREKHKAQISALE  323 (629)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCchHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45678899999999999999988877554        1    22222233334444555555666677777888888888


Q ss_pred             HHHHHHHHHHHHHHHHHhh
Q 020809          179 RALKVAEEEMMRAKFEATS  197 (321)
Q Consensus       179 ~~lq~~Eeei~kl~~ea~~  197 (321)
                      +.+...-..+.++....+.
T Consensus       324 ~~l~~~~~~leel~~kL~~  342 (629)
T KOG0963|consen  324 KELKAKISELEELKEKLNS  342 (629)
T ss_pred             HHHHHHHHHHHHHHHHHhh
Confidence            8888877777777555543

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=95.89  E-value=1.5  Score=47.01  Aligned_cols=71  Identities=14%  Similarity=0.193  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKESEKQQKEK-EALEARAIEAEKKISDLSAKLEKLQKIND---EQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk-~~LEa~a~e~ekk~~el~~~le~Lek~~~---Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ++.+|+.+++++....... ..+......+..+.+.++..+++++....   .....+..++++....+..+..+
T Consensus       321 l~~qi~~l~~~i~~e~~~~~~~~~~~~~~a~~~~~~L~~~l~~~~~~~~~~~~~~~e~~~L~Re~~~~~~~Y~~l  395 (754)
T TIGR01005       321 AKSSLADLDAQIRSELQKITKSLLMQADAAQARESQLVSDVNQLKAASAQAGEQQVDLDALQRDAAAKRQLYESY  395 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcHhHHHHHHHHHHHHHHHHHHHHH
Confidence            4444555554443322221 22333333333333344444444433332   23455555555555555555544

The model describes the exopolysaccharide transport protein family in bacteria. The transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed atleast seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]

Probab=95.79  E-value=3.4  Score=44.22  Aligned_cols=101  Identities=24%  Similarity=0.211  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 020809          121 LEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSK  200 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~  200 (321)
                      +..++..+..-++..+.+..++...+..+...+...++.+++++....+-...+...-.....+++++.++........+
T Consensus       543 l~~el~~~~~~le~~kk~~~e~~~~~~~Lq~~~ek~~~~le~i~~~~~e~~~ele~~~~k~~rleEE~e~L~~kle~~k~  622 (698)
T KOG0978|consen  543 LIKELTTLTQSLEMLKKKAQEAKQSLEDLQIELEKSEAKLEQIQEQYAELELELEIEKFKRKRLEEELERLKRKLERLKK  622 (698)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            33334444444455555555555556666666666666667776666666677776766677777777777555544432


Q ss_pred             hhhhhhccCchhHHHHHHHHHHHH
Q 020809          201 ELTEVHSAWLPPWLAVHLLQCQSL  224 (321)
Q Consensus       201 ql~e~~g~~l~Pwla~~~~~~~~~  224 (321)
                      ..+   |.-..|.|+.+...|...
T Consensus       623 ~~~---~~s~d~~L~EElk~yK~~  643 (698)
T KOG0978|consen  623 EES---GASADEVLAEELKEYKEL  643 (698)
T ss_pred             ccc---cccccHHHHHHHHHHHhc
Confidence            222   334567777777666654

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=95.77  E-value=3  Score=44.26  Aligned_cols=46  Identities=9%  Similarity=0.297  Sum_probs=25.8

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSE   87 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~   87 (321)
                      .+..++++++.++..++...+.+.+++..++..++.++..+.+++.
T Consensus       206 ~~~~~~~~le~el~~l~~~~e~l~~~i~~l~~ele~a~~~l~~l~~  251 (650)
T TIGR03185       206 SILSEIEALEAELKEQSEKYEDLAQEIAHLRNELEEAQRSLESLEK  251 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555566666666555555555555555555555555554444

This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=95.76  E-value=2.1  Score=47.14  Aligned_cols=72  Identities=24%  Similarity=0.314  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 020809          125 IDNLKKESEKQQKEKEALEARAIEAEK-------KISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEAT  196 (321)
Q Consensus       125 Ie~Lk~ele~~~~kk~~LEa~a~e~ek-------k~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~  196 (321)
                      ++.+..++.+...++.+++...++...       ...++...++.+.....+.|+.-..+...+..+++.+.+.+....
T Consensus       420 ~~~~e~~l~~~~e~i~~l~~si~e~~~r~~~~~~~~~~~k~~~del~~~Rk~lWREE~~l~~~i~~~~~dl~~~~~~L~  498 (1200)
T KOG0964|consen  420 IEDLESELKEKLEEIKELESSINETKGRMEEFDAENTELKRELDELQDKRKELWREEKKLRSLIANLEEDLSRAEKNLR  498 (1200)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444444444443332       334445556666666666777666666666666666666654444

>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures

Probab=95.71  E-value=0.21  Score=38.35  Aligned_cols=65  Identities=23%  Similarity=0.364  Sum_probs=37.0

Q ss_pred             HHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           64 KTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLK  129 (321)
Q Consensus        64 ~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk  129 (321)
                      +...|.++|..|+++..+-..++.+...+.+.|..+.. ...+.+..+..++.|+..+...++.|+
T Consensus         3 l~~~l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~-~~~e~e~~~~~l~~~~~~~e~~~~~l~   67 (74)
T PF12329_consen    3 LEKKLAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRA-KIKELEKQIKELKKKLEELEKELESLE   67 (74)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556667777777777777777776666666666644 334444444444444444444444433

The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.

>PF15070 GOLGA2L5: Putative golgin subfamily A member 2-like protein 5

Probab=95.60  E-value=3.3  Score=43.94  Aligned_cols=93  Identities=24%  Similarity=0.362  Sum_probs=40.0

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhh-------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELK-------GKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKA  114 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk-------~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~  114 (321)
                      .++.++..|+..+..|..++.....+-.       +.+..|.+++..+........+...-+..++..+     .-+..+
T Consensus        84 ~Lq~E~~~L~kElE~L~~qlqaqv~~ne~Ls~L~~EqEerL~ELE~~le~~~e~~~D~~kLLe~lqsdk-----~t~SRA  158 (617)
T PF15070_consen   84 QLQAEAEHLRKELESLEEQLQAQVENNEQLSRLNQEQEERLAELEEELERLQEQQEDRQKLLEQLQSDK-----ATASRA  158 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc-----hHHHHH
Confidence            4555566666666666655544433333       3334444444444443333333222223332221     011222


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          115 HARADELEKQIDNLKKESEKQQKEK  139 (321)
Q Consensus       115 ~~RireL~k~Ie~Lk~ele~~~~kk  139 (321)
                      -...++|+.++..++.--..+..++
T Consensus       159 lsQN~eLK~QL~Elq~~Fv~ltne~  183 (617)
T PF15070_consen  159 LSQNRELKEQLAELQDAFVKLTNEN  183 (617)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHhh
Confidence            2333455555555555444444444

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=95.59  E-value=1.3  Score=48.85  Aligned_cols=141  Identities=25%  Similarity=0.321  Sum_probs=70.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hhHHHHHHH-----
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK--ETLNAAEQV-----  111 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~--~~~~~eeq~-----  111 (321)
                      ...++.-.+-+++.+|.-|+.++++....+..+..+|+.++.++..+..+|.....+-.+...-  ....+-++.     
T Consensus       171 ~~~hL~velAdle~kir~LrqElEEK~enll~lr~eLddleae~~klrqe~~e~l~ea~ra~~yrdeldalre~aer~d~  250 (1195)
T KOG4643|consen  171 KNLHLEVELADLEKKIRTLRQELEEKFENLLRLRNELDDLEAEISKLRQEIEEFLDEAHRADRYRDELDALREQAERPDT  250 (1195)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHhhhcCCC
Confidence            4556666677777777777777777666666666666655555555555555444433322111  111111111     


Q ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          112 ---------DKAHARADELEKQIDNLKKESEKQQKEKEALEARA--IEAEKKISDLSAKLEKLQKINDEQKSKIRKTER  179 (321)
Q Consensus       112 ---------~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a--~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~  179 (321)
                               +-++.|+.+|+..=..|.++.+-.+..++.+.++-  ...+..+=.++++++.|+....--+.++.++-.
T Consensus       251 ~ykerlmDs~fykdRveelkedN~vLleekeMLeeQLq~lrarse~~tleseiiqlkqkl~dm~~erdtdr~kteeL~e  329 (1195)
T KOG4643|consen  251 TYKERLMDSDFYKDRVEELKEDNRVLLEEKEMLEEQLQKLRARSEGATLESEIIQLKQKLDDMRSERDTDRHKTEELHE  329 (1195)
T ss_pred             ccchhhhhhHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence                     11344444444444444444444444444444333  334445555555555555555555555544443

>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site

Probab=95.56  E-value=3.7  Score=42.95  Aligned_cols=166  Identities=18%  Similarity=0.235  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 020809          121 LEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSK  200 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~  200 (321)
                      |+++|..+.+...........-..--..+...+.+....++.+++...+....++.+..+...+.+.+.++.......-+
T Consensus       349 l~~~l~~l~~~~~~~~~~i~~~~~~yS~i~~~l~~~~~~l~~ie~~q~~~~~~l~~L~~dE~~Ar~~l~~~~~~l~~ikR  428 (560)
T PF06160_consen  349 LEKQLKELEKRYEDLEERIEEQQVPYSEIQEELEEIEEQLEEIEEEQEEINESLQSLRKDEKEAREKLQKLKQKLREIKR  428 (560)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444444443333344455567777778888888888888888888888888888888888777776666


Q ss_pred             hhhhhhccCchh----HHHHHHHHHHHHHHhHHHhhCcchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhhhhhhHHH
Q 020809          201 ELTEVHSAWLPP----WLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVV  276 (321)
Q Consensus       201 ql~e~~g~~l~P----wla~~~~~~~~~~~~~~~~hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~~~~~~~~  276 (321)
                      .+...+---+|-    .+..-...+..+...+  .+...=|+.+.+....        +...|+++..++.-.|..-  .
T Consensus       429 ~lek~nLPGlp~~y~~~~~~~~~~i~~l~~~L--~~~pinm~~v~~~l~~--------a~~~v~~L~~~t~~li~~A--~  496 (560)
T PF06160_consen  429 RLEKSNLPGLPEDYLDYFFDVSDEIEELSDEL--NQVPINMDEVNKQLEE--------AEDDVETLEEKTEELIDNA--T  496 (560)
T ss_pred             HHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHH--hcCCcCHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHH--H
Confidence            554433111222    2222223333322221  1222334444333222        4556777777776653321  1


Q ss_pred             HHh----------ccchhhHHHHhHhHHHHHh
Q 020809          277 FTT----------NVEPHVQTLKTKTIEACEA  298 (321)
Q Consensus       277 ~~~----------~~~p~~q~~~~~~~~~~~~  298 (321)
                      +.+          .-.|-|...-+.+-.+|+.
T Consensus       497 L~E~~iQYaNRYR~~~~~v~~al~~Ae~~F~~  528 (560)
T PF06160_consen  497 LAEQLIQYANRYRSDNPEVDEALTEAEDLFRN  528 (560)
T ss_pred             HHHHHHHHHhcccCCCHHHHHHHHHHHHHHHh
Confidence            111          4566677777777666665

EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane

>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells

Probab=95.50  E-value=2.2  Score=40.03  Aligned_cols=144  Identities=19%  Similarity=0.310  Sum_probs=84.6

Q ss_pred             HHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 020809           47 LDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQID  126 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie  126 (321)
                      +.-+...+..+..........+......++..++.+..+..++..|+.+....-. ....+....+....|+.+|...|.
T Consensus        19 ~~~l~~~~e~~~~~L~~~~~~~~~~~~~~~~~e~~l~~L~~d~~~L~~k~~~~~~-~~~~l~~~t~~t~~~a~~L~~~i~   97 (264)
T PF06008_consen   19 PYKLLSSIEDLTNQLRSYRSKLNPQKQQLDPLEKELESLEQDVENLQEKATKVSR-KAQQLNNNTERTLQRAQDLEQFIQ   97 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444555555554445555555666666666666666666666665533 345566667777778888888888


Q ss_pred             HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          127 NLKKESEKQQKEKEALEA-----RAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKF  193 (321)
Q Consensus       127 ~Lk~ele~~~~kk~~LEa-----~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~  193 (321)
                      .+...+..+-.+...+-.     .-.++...+.++...+..|++..  -.......+.++..++.-+.+...
T Consensus        98 ~l~~~i~~l~~~~~~l~~~~~~~~~~~l~~~l~ea~~mL~emr~r~--f~~~~~~Ae~El~~A~~LL~~v~~  167 (264)
T PF06008_consen   98 NLQDNIQELIEQVESLNENGDQLPSEDLQRALAEAQRMLEEMRKRD--FTPQRQNAEDELKEAEDLLSRVQK  167 (264)
T ss_pred             HHHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHHHHHHHHHHhcc--chhHHHHHHHHHHHHHHHHHHHHH
Confidence            888777777766644443     33444556666666666665542  444445555555555555555533

Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex

>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures

Probab=95.40  E-value=0.25  Score=37.92  Aligned_cols=71  Identities=39%  Similarity=0.499  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           77 QKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIE  148 (321)
Q Consensus        77 q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e  148 (321)
                      .+++.|.++..+|+.|..+-..+-+ .+......+-++.+.+.+++..+..+...++....+...|+.++..
T Consensus         2 sl~~~l~EKDe~Ia~L~eEGekLSk-~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~l~~   72 (74)
T PF12329_consen    2 SLEKKLAEKDEQIAQLMEEGEKLSK-KELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESLEERLKR   72 (74)
T ss_pred             hHHHHHHhHHHHHHHHHHHHHHHHH-HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3567888889999999988888854 6667777788888888888888888888888877777777666543

The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.

>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]

Probab=95.33  E-value=1.7  Score=37.56  Aligned_cols=99  Identities=17%  Similarity=0.307  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           81 AIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKL  160 (321)
Q Consensus        81 ~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~l  160 (321)
                      .-..+.+.|..|+.++...+. ....+....+..++-+..|+.+|..+-..+.....+...+-.....+.+.+...+.++
T Consensus        18 e~dsle~~v~~LEreLe~~q~-~~e~~~~daEn~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv   96 (140)
T PF10473_consen   18 EKDSLEDHVESLERELEMSQE-NKECLILDAENSKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEKV   96 (140)
T ss_pred             hHhhHHHHHHHHHHHHHHHHH-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333444444444444433 1122233333334444444444444444444444444444444444444444444444


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 020809          161 EKLQKINDEQKSKIRKTERA  180 (321)
Q Consensus       161 e~Lek~~~Eqk~~l~elE~~  180 (321)
                      ..|+.........|...+..
T Consensus        97 ~eLE~~~~~~~~~l~~~E~e  116 (140)
T PF10473_consen   97 SELESLNSSLENLLQEKEQE  116 (140)
T ss_pred             HHHHHHhHHHHHHHHHHHHH
Confidence            44444444444444444433

There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding

>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily

Probab=95.25  E-value=3.9  Score=41.61  Aligned_cols=57  Identities=9%  Similarity=0.229  Sum_probs=27.0

Q ss_pred             CchHHHHHHHHHHHHHHHHH--------hHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           40 SSPLKIELDQLKSKIRSLES--------HIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL   96 (321)
Q Consensus        40 ~~~l~~el~qlk~ki~~Les--------~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI   96 (321)
                      ...++.++++.+.++.....        .......++..++..+.+.+.++...+..+..++..+
T Consensus       170 l~~~~~~L~~ae~~l~~f~~~~~~~~~~~~~~~~~~l~~l~~~l~~~~~~l~~~~a~~~~l~~~l  234 (498)
T TIGR03007       170 IKTYEKKLEAAENRLKAFKQENGGILPDQEGDYYSEISEAQEELEAARLELNEAIAQRDALKRQL  234 (498)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcccCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34455555555555544432        1122344555555555555555555555555554433

Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene.

>PF05911 DUF869: Plant protein of unknown function (DUF869); InterPro: IPR008587 This family consists of a number of sequences found in plants

Probab=95.22  E-value=3.6  Score=44.67  Aligned_cols=58  Identities=22%  Similarity=0.362  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      ......+..++..+++....+...+......|......+.+.+..|..|+.++...++
T Consensus       588 ~~~~~el~eelE~le~eK~~Le~~L~~~~d~lE~~~~qL~E~E~~L~eLq~eL~~~ke  645 (769)
T PF05911_consen  588 TSEKKELEEELEKLESEKEELEMELASCQDQLESLKNQLKESEQKLEELQSELESAKE  645 (769)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555666666666666666666666666666666666666666666666666543

The function of this family is unknown.

>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=95.18  E-value=0.61  Score=45.27  Aligned_cols=68  Identities=21%  Similarity=0.231  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          124 QIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       124 ~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ++..|+.+.+.+..++..++.....++......-.....+.-...+.....+.+..........+.++
T Consensus        65 eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~~q~~~~~~~L~~L  132 (314)
T PF04111_consen   65 ELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLKNQYEYASNQLDRL  132 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444444455555555555555555666666666666665

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=95.05  E-value=2.7  Score=44.54  Aligned_cols=74  Identities=23%  Similarity=0.370  Sum_probs=30.6

Q ss_pred             HhHHHHHHhhhcHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           59 SHIDEKTQELKGKDEVVAQKEKAIQDK--SERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESE  133 (321)
Q Consensus        59 s~i~e~~~eLk~kd~~I~q~ek~i~e~--~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele  133 (321)
                      +.+.....++..++.+|+.+...|...  ...|..+..++..+++ ....+....+....++..+++.|+.+++++.
T Consensus       391 ~~~~~~~~~~~~~e~el~~l~~~l~~~~~~e~i~~l~e~l~~l~~-~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~~  466 (650)
T TIGR03185       391 DAKSQLLKELRELEEELAEVDKKISTIPSEEQIAQLLEELGEAQN-ELFRSEAEIEELLRQLETLKEAIEALRKTLD  466 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444332  2344444444444432 2223333333333344444444444444443

This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.

>KOG4673 consensus Transcription factor TMF, TATA element modulatory factor [Transcription]

Probab=95.01  E-value=6  Score=42.27  Aligned_cols=84  Identities=18%  Similarity=0.226  Sum_probs=41.2

Q ss_pred             CchHHHHHHHHHHHHHHHHHhHHHHHH----------------hhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 020809           40 SSPLKIELDQLKSKIRSLESHIDEKTQ----------------ELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKE  103 (321)
Q Consensus        40 ~~~l~~el~qlk~ki~~Les~i~e~~~----------------eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~  103 (321)
                      .+.+-+.+..+..|+..+-..-+.+..                +|.++|+.|+++..+=..+++++-.-.+-|..+.. +
T Consensus       404 ~~e~~QRva~lEkKvqa~~kERDalr~e~kslk~ela~~l~~DeLaEkdE~I~~lm~EGEkLSK~ql~qs~iIkKLRA-k  482 (961)
T KOG4673|consen  404 REEYHQRVATLEKKVQALTKERDALRREQKSLKKELAAALLKDELAEKDEIINQLMAEGEKLSKKQLAQSAIIKKLRA-K  482 (961)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH-H
Confidence            334445555555555444444444433                44555666666665555555555555555555544 2


Q ss_pred             hHHHHHHHHHHHHHHHHHHHH
Q 020809          104 TLNAAEQVDKAHARADELEKQ  124 (321)
Q Consensus       104 ~~~~eeq~~~~~~RireL~k~  124 (321)
                      .+..+.-..+.+..|..|..+
T Consensus       483 ~ke~etl~~K~ge~i~~L~sE  503 (961)
T KOG4673|consen  483 IKEAETLEEKKGELITKLQSE  503 (961)
T ss_pred             hhhhhHHHHHhhhHHHHHHHH
Confidence            233333333444444444444

>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=95.00  E-value=0.73  Score=44.74  Aligned_cols=51  Identities=22%  Similarity=0.261  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          134 KQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVA  184 (321)
Q Consensus       134 ~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~  184 (321)
                      ....++..||....++...+..+......+.....+.+.....+...+-..
T Consensus        61 ~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~  111 (314)
T PF04111_consen   61 ELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEF  111 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333344444433334444444433333333

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.

>PF12795 MscS_porin: Mechanosensitive ion channel porin domain

Probab=95.00  E-value=3  Score=38.63  Aligned_cols=25  Identities=16%  Similarity=0.314  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          167 NDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       167 ~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .+.....++.++..+..++..+...
T Consensus       187 rdl~~~~~~~l~~~l~~Lq~~ln~~  211 (240)
T PF12795_consen  187 RDLLKARIQRLQQQLQALQNLLNQK  211 (240)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444445555555555555544

>KOG4674 consensus Uncharacterized conserved coiled-coil protein [Function unknown]

Probab=94.99  E-value=6.9  Score=46.05  Aligned_cols=69  Identities=13%  Similarity=0.204  Sum_probs=40.7

Q ss_pred             HHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 020809           55 RSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQ  124 (321)
Q Consensus        55 ~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~  124 (321)
                      ..|....+.....+.++...|+.++..+..++..+..|..+|....+ ...-++...+.-+.|..+|-..
T Consensus      1232 ~~LRee~~~~~~k~qEl~~~i~kl~~el~plq~~l~el~~e~~~~~a-el~~l~~e~~~wK~R~q~L~~k 1300 (1822)
T KOG4674|consen 1232 KVLREENEANLEKIQELRDKIEKLNFELAPLQNELKELKAELQEKVA-ELKKLEEENDRWKQRNQDLLEK 1300 (1822)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhHhhHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555566666666666666666666666666665544 3355566666777777774443

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=94.97  E-value=4.7  Score=40.81  Aligned_cols=32  Identities=9%  Similarity=0.110  Sum_probs=21.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhc
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKG   70 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~   70 (321)
                      +...+..+++.++.++..++.++..+..+++.
T Consensus        91 d~~~~~~~~~~~~~~~~~~~~~~~rL~a~~~~  122 (457)
T TIGR01000        91 DNGNEENQKQLLEQQLDNLKDQKKSLDTLKQS  122 (457)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55566777777777777777776666555543

This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.

>KOG0979 consensus Structural maintenance of chromosome protein SMC5/Spr18, SMC superfamily [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=94.92  E-value=7.7  Score=43.01  Aligned_cols=110  Identities=25%  Similarity=0.337  Sum_probs=65.4

Q ss_pred             cCCCCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------hh
Q 020809           36 DAVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK-----------ET  104 (321)
Q Consensus        36 ~~~~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~-----------~~  104 (321)
                      ++.++...-.+|-+++..-.+|+...+.-...|+.+...++.+.+..+.... -....+.|+.+.++           .-
T Consensus       172 g~~~ll~~h~eL~~lr~~e~~Le~~~~~~~~~l~~L~~~~~~l~kdVE~~re-r~~~~~~Ie~l~~k~~~v~y~~~~~ey  250 (1072)
T KOG0979|consen  172 GAEELLQYHIELMDLREDEKSLEDKLTTKTEKLNRLEDEIDKLEKDVERVRE-RERKKSKIELLEKKKKWVEYKKHDREY  250 (1072)
T ss_pred             CchhhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhccccchHhhhHHH
Confidence            4445556667788888888888888888877777777777777777755543 34456777777554           11


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARA  146 (321)
Q Consensus       105 ~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a  146 (321)
                      ..+-.-.+.+++.+|.|.+.+..+...++.++..+.++.++-
T Consensus       251 ~~~k~~~~r~k~~~r~l~k~~~pi~~~~eeLe~~~~et~~~~  292 (1072)
T KOG0979|consen  251 NAYKQAKDRAKKELRKLEKEIKPIEDKKEELESEKKETRSKI  292 (1072)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhhhhhHHhHHHhHHHHH
Confidence            223334455555566666654444444444433333333333

>PF05622 HOOK: HOOK protein; InterPro: IPR008636 This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms

Probab=94.91  E-value=0.0071  Score=64.62  Aligned_cols=106  Identities=20%  Similarity=0.363  Sum_probs=0.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH--hhHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKS---ERIVSLQKELSSLQKK--ETLNAAEQVDK  113 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~---~~I~~Lq~eI~~~qk~--~~~~~eeq~~~  113 (321)
                      ....++.++++++.++..++...++...++..++..|..+++...++.   .....|..+++.+..+  +-..++..++.
T Consensus       240 ~~~~l~~ql~~L~~el~~~e~~~~d~~~~~e~le~ei~~L~q~~~eL~~~A~~a~~LrDElD~lR~~a~r~~klE~~ve~  319 (713)
T PF05622_consen  240 ELADLRAQLRRLREELERLEEQRDDLKIELEELEKEIDELRQENEELQAEAREARALRDELDELREKADRADKLENEVEK  319 (713)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence            445566677777777766666666666666666666666665555544   5566666777776543  33446667777


Q ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          114 AHARADE---LEKQIDNLKKESEKQQKEKEALEA  144 (321)
Q Consensus       114 ~~~Rire---L~k~Ie~Lk~ele~~~~kk~~LEa  144 (321)
                      +++|+.+   |+++|..|+.+....-..+..||.
T Consensus       320 YKkKLed~~~lk~qvk~Lee~N~~l~e~~~~LEe  353 (713)
T PF05622_consen  320 YKKKLEDLEDLKRQVKELEEDNAVLLETKAMLEE  353 (713)
T ss_dssp             ----------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7777777   444455555544433333333333

The different members of the Homo sapiens gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three Homo sapiens HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerisation and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes [], whereas both HOOK1 and HOOK2 are localised to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head [].; GO: 0008017 microtubule binding, 0000226 microtubule cytoskeleton organization, 0005737 cytoplasm; PDB: 1WIX_A.

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=94.89  E-value=6.9  Score=43.04  Aligned_cols=15  Identities=27%  Similarity=0.259  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHHHHH
Q 020809          177 TERALKVAEEEMMRA  191 (321)
Q Consensus       177 lE~~lq~~Eeei~kl  191 (321)
                      +|.....+++.+..+
T Consensus       460 lEekVklLeetv~dl  474 (1243)
T KOG0971|consen  460 LEEKVKLLEETVGDL  474 (1243)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            333444444444443

>PRK10929 putative mechanosensitive channel protein; Provisional

Probab=94.85  E-value=9  Score=43.40  Aligned_cols=29  Identities=17%  Similarity=0.335  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          108 AEQVDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus       108 eeq~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      ..+.+.++.++..++..++.|+..+...+
T Consensus       207 ~~q~dl~~~~~~~l~~~~~~Lq~~in~kR  235 (1109)
T PRK10929        207 RLRSELAKKRSQQLDAYLQALRNQLNSQR  235 (1109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444445555555555554444

>PF05911 DUF869: Plant protein of unknown function (DUF869); InterPro: IPR008587 This family consists of a number of sequences found in plants

Probab=94.82  E-value=3.4  Score=44.88  Aligned_cols=78  Identities=19%  Similarity=0.255  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          117 RADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFE  194 (321)
Q Consensus       117 RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~e  194 (321)
                      .+..+++-=..+..++...+.....++.+...++..+..+..++..|+.....-+..-.++...-..++.++.+...+
T Consensus       639 eL~~~keS~s~~E~ql~~~~e~~e~le~~~~~~e~E~~~l~~Ki~~Le~Ele~er~~~~e~~~kc~~Le~el~r~~~~  716 (769)
T PF05911_consen  639 ELESAKESNSLAETQLKAMKESYESLETRLKDLEAEAEELQSKISSLEEELEKERALSEELEAKCRELEEELERMKKE  716 (769)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhHHHHHHHHHHhhhcc
Confidence            333333333344445555555556677777777777777777777777777776666666676677777777766433

The function of this family is unknown.

>PRK11281 hypothetical protein; Provisional

Probab=94.76  E-value=2.1  Score=48.26  Aligned_cols=18  Identities=17%  Similarity=0.335  Sum_probs=7.9

Q ss_pred             chHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLE   58 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Le   58 (321)
                      .+..+++.+++.++..+.
T Consensus        90 ~~Ap~~l~~a~~~Le~Lk  107 (1113)
T PRK11281         90 AQAPAKLRQAQAELEALK  107 (1113)
T ss_pred             HHhHHHHHHHHHHHHHhh
Confidence            333444444444444433

>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]

Probab=94.75  E-value=2  Score=36.03  Aligned_cols=94  Identities=17%  Similarity=0.216  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH--HhhHHHHHHHHHHHHHH
Q 020809           46 ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSE-----RIVSLQKELSSLQK--KETLNAAEQVDKAHARA  118 (321)
Q Consensus        46 el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~-----~I~~Lq~eI~~~qk--~~~~~~eeq~~~~~~Ri  118 (321)
                      ++.+.=.+..+|+++++.+..+...++..|.+.++-+++++.     .|...-+.+-.-..  +...+++++.+-++.||
T Consensus         7 ~~q~~l~q~QqLq~ql~~~~~qk~~le~qL~E~~~al~Ele~l~eD~~vYk~VG~llvk~~k~~~~~eL~er~E~Le~ri   86 (119)
T COG1382           7 EVQAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKEEAVDELEERKETLELRI   86 (119)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHhhhHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence            444445555666666666666666677777777666666652     44444444322221  13455666666666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 020809          119 DELEKQIDNLKKESEKQQKEK  139 (321)
Q Consensus       119 reL~k~Ie~Lk~ele~~~~kk  139 (321)
                      ..|+++.+.++..+++.+..+
T Consensus        87 ~tLekQe~~l~e~l~eLq~~i  107 (119)
T COG1382          87 KTLEKQEEKLQERLEELQSEI  107 (119)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666666444

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.71  E-value=0.68  Score=42.40  Aligned_cols=22  Identities=23%  Similarity=0.502  Sum_probs=8.9

Q ss_pred             HHHHHHHHHhHHHHHHhhhcHH
Q 020809           51 KSKIRSLESHIDEKTQELKGKD   72 (321)
Q Consensus        51 k~ki~~Les~i~e~~~eLk~kd   72 (321)
                      +.++..++.+++++..++.+.+
T Consensus        92 ~~rlp~le~el~~l~~~l~~~~  113 (206)
T PRK10884         92 RTRVPDLENQVKTLTDKLNNID  113 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444433333333

>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch

Probab=94.68  E-value=2.5  Score=36.24  Aligned_cols=95  Identities=12%  Similarity=0.205  Sum_probs=62.6

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE  120 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire  120 (321)
                      ..+-+=+..|=.....--...+.++..+..++..+..++..+..+..++..++.++...+. ....+..+...+...++.
T Consensus        34 ~~vin~i~~Ll~~~~r~~~~~e~l~~~~~~l~~d~~~l~~~~~rL~~~~~~~ere~~~~~~-~~~~l~~~~~~~~~~~k~  112 (151)
T PF11559_consen   34 VRVINCIYDLLQQRDRDMEQREDLSDKLRRLRSDIERLQNDVERLKEQLEELERELASAEE-KERQLQKQLKSLEAKLKQ  112 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence            3344455666666666666777777777777888888887777777777777777776654 445555555555555665


Q ss_pred             HHHHHHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKESEKQQ  136 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~  136 (321)
                      .+.++..++..+...+
T Consensus       113 ~kee~~klk~~~~~~~  128 (151)
T PF11559_consen  113 EKEELQKLKNQLQQRK  128 (151)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            6666666665555555

pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=94.67  E-value=4.9  Score=40.66  Aligned_cols=26  Identities=27%  Similarity=0.367  Sum_probs=19.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEK   64 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~   64 (321)
                      +...++.++..++.++..|+..++.+
T Consensus        98 ~~~~~~~~~~~~~~~~~rL~a~~~~~  123 (457)
T TIGR01000        98 QKQLLEQQLDNLKDQKKSLDTLKQSI  123 (457)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66677888888888888887766543

This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.

>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]

Probab=94.64  E-value=6.7  Score=40.97  Aligned_cols=87  Identities=21%  Similarity=0.288  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADEL  121 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL  121 (321)
                      ..+.-+++.......++..+..+..+++++.......++....-..++.....-|        .+++.....++.|++.|
T Consensus        96 ~ar~~l~e~~~~ra~~e~ei~kl~~e~~elr~~~~~~~k~~~~~re~~~~~~~~l--------~~leAe~~~~krr~~~l  167 (546)
T KOG0977|consen   96 TARKLLDETARERAKLEIEITKLREELKELRKKLEKAEKERRGAREKLDDYLSRL--------SELEAEINTLKRRIKAL  167 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhhh--------hhhhhHHHHHHHHHHHH
Confidence            3334444444444444444444444444444444433333333333333333333        33444455555566665


Q ss_pred             HHHHHHHHHHHHHHH
Q 020809          122 EKQIDNLKKESEKQQ  136 (321)
Q Consensus       122 ~k~Ie~Lk~ele~~~  136 (321)
                      +.++..|+++...+.
T Consensus       168 e~e~~~Lk~en~rl~  182 (546)
T KOG0977|consen  168 EDELKRLKAENSRLR  182 (546)
T ss_pred             HHHHHHHHHHhhhhH
Confidence            555555555554444

>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]

Probab=94.64  E-value=6.3  Score=42.83  Aligned_cols=55  Identities=20%  Similarity=0.259  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---------hhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           75 VAQKEKAIQDKSERIVSLQKELSSLQKK---------ETLNAAEQVDKAHARADELEKQIDNLK  129 (321)
Q Consensus        75 I~q~ek~i~e~~~~I~~Lq~eI~~~qk~---------~~~~~eeq~~~~~~RireL~k~Ie~Lk  129 (321)
                      +..+-....+++.+|+.+.+.|..+..-         ......++.+.+++...++..++..++
T Consensus       381 lqsL~~l~aerqeQidelKn~if~~e~~~~dhe~~kneL~~a~ekld~mgthl~mad~Q~s~fk  444 (1265)
T KOG0976|consen  381 LQSLLELQAERQEQIDELKNHIFRLEQGKKDHEAAKNELQEALEKLDLMGTHLSMADYQLSNFK  444 (1265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhHH
Confidence            3333333444445555555555544331         134456666666666666666644443

>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]

Probab=94.64  E-value=6.7  Score=40.96  Aligned_cols=14  Identities=21%  Similarity=0.562  Sum_probs=5.3

Q ss_pred             HHHHHHHHHHHHHH
Q 020809          153 ISDLSAKLEKLQKI  166 (321)
Q Consensus       153 ~~el~~~le~Lek~  166 (321)
                      +...+..++.+.+.
T Consensus       348 l~~i~~~~d~l~k~  361 (581)
T KOG0995|consen  348 LNKIQSELDRLSKE  361 (581)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333333333333

>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]

Probab=94.63  E-value=5.6  Score=41.52  Aligned_cols=46  Identities=13%  Similarity=0.176  Sum_probs=21.7

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKS   86 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~   86 (321)
                      ..++---.+=+..|.+|.+.+...-..++.++.+=..++.+|+.+.
T Consensus        31 s~ir~sR~rEK~El~~LNDRLA~YIekVR~LEaqN~~L~~di~~lr   76 (546)
T KOG0977|consen   31 SPIRDSREREKKELQELNDRLAVYIEKVRFLEAQNRKLEHDINLLR   76 (546)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344333444455555555555554444444444444444444443

>KOG0018 consensus Structural maintenance of chromosome protein 1 (sister chromatid cohesion complex Cohesin, subunit SMC1) [Cell cycle control, cell division, chromosome partitioning]

Probab=94.63  E-value=7  Score=43.58  Aligned_cols=34  Identities=12%  Similarity=0.141  Sum_probs=15.5

Q ss_pred             chhHHhhhhhhhhhhhhhHHHHHhccchhhHHHH
Q 020809          256 QPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLK  289 (321)
Q Consensus       256 ~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~  289 (321)
                      .--+.+||++=-..+-+-+..|-.++||-|..++
T Consensus       981 k~~F~~VK~~R~~~F~~~F~~va~~Id~IYK~Lt 1014 (1141)
T KOG0018|consen  981 KNAFNKVKKKRYERFMACFEHVADNIDRIYKELT 1014 (1141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3344444444444444444444444555444444

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=94.59  E-value=10  Score=42.86  Aligned_cols=52  Identities=21%  Similarity=0.222  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 020809          151 KKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKEL  202 (321)
Q Consensus       151 kk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~ql  202 (321)
                      .-+++.....-..++.+.+-...++..+..+..+++++...+.-++..+.++
T Consensus      1570 eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~~t~~aE~~~~~a~q~~ 1621 (1758)
T KOG0994|consen 1570 EALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQEETAAAEKLATSATQQL 1621 (1758)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333444444444444444455555555555554444444444444

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.56  E-value=0.96  Score=41.43  Aligned_cols=48  Identities=15%  Similarity=0.279  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          144 ARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       144 a~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .+..+++.++...+.....|+..+++...++..+......++.++..+
T Consensus       118 ~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~  165 (206)
T PRK10884        118 QRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDDK  165 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444444444444544444444444444444

>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]

Probab=94.55  E-value=10  Score=42.83  Aligned_cols=37  Identities=27%  Similarity=0.338  Sum_probs=21.1

Q ss_pred             HhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           66 QELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK  102 (321)
Q Consensus        66 ~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~  102 (321)
                      .+++..++.+.+.+..++.++..+..++.+++.+++.
T Consensus       494 ~~~ke~~ek~~~~~~~~~~l~~~~~~~~eele~~q~~  530 (1317)
T KOG0612|consen  494 HEQKEVEEKLSEEEAKKRKLEALVRQLEEELEDAQKK  530 (1317)
T ss_pred             HhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555555566666666666666666555443

>PF04849 HAP1_N: HAP1 N-terminal conserved region; InterPro: IPR006933 This family is defined by an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues

Probab=94.51  E-value=5  Score=38.94  Aligned_cols=125  Identities=23%  Similarity=0.303  Sum_probs=56.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARA  118 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Ri  118 (321)
                      ....-..+++.++.|+..|+..-..+-.+...+.......+       .+=..|-.           +--++...++..|
T Consensus       154 ~~~~~~~~le~Lq~Klk~LEeEN~~LR~Ea~~L~~et~~~E-------ekEqqLv~-----------dcv~QL~~An~qi  215 (306)
T PF04849_consen  154 LSSQKCIQLEALQEKLKSLEEENEQLRSEASQLKTETDTYE-------EKEQQLVL-----------DCVKQLSEANQQI  215 (306)
T ss_pred             cccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhcc-------HHHHHHHH-----------HHHHHhhhcchhH
Confidence            33344456677777777776654444333333332222221       11111111           1122334445555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          119 DELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERAL  181 (321)
Q Consensus       119 reL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~l  181 (321)
                      ..|..+|.....+...+..++..|-++.-+++.+...+....+.+......-+..-+.+...+
T Consensus       216 a~LseELa~k~Ee~~rQQEEIt~LlsqivdlQ~r~k~~~~EnEeL~q~L~~ske~Q~~L~aEL  278 (306)
T PF04849_consen  216 ASLSEELARKTEENRRQQEEITSLLSQIVDLQQRCKQLAAENEELQQHLQASKESQRQLQAEL  278 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            555555555555555555555555555555555444444444444443333333333333333

HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [].

>TIGR02977 phageshock_pspA phage shock protein A

Probab=94.46  E-value=3.9  Score=37.48  Aligned_cols=46  Identities=11%  Similarity=0.234  Sum_probs=23.5

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSE   87 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~   87 (321)
                      .+++=+.+++..+......+......-+.....+++.+..+...+.
T Consensus        28 ~l~q~irem~~~l~~ar~~lA~~~a~~k~~e~~~~~~~~~~~~~~~   73 (219)
T TIGR02977        28 MIRLIIQEMEDTLVEVRTTSARTIADKKELERRVSRLEAQVADWQE   73 (219)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555566555555555555544444444444444444444433

Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.

>KOG0018 consensus Structural maintenance of chromosome protein 1 (sister chromatid cohesion complex Cohesin, subunit SMC1) [Cell cycle control, cell division, chromosome partitioning]

Probab=94.46  E-value=10  Score=42.35  Aligned_cols=34  Identities=21%  Similarity=0.166  Sum_probs=22.3

Q ss_pred             ccchhhHHHHhHhHHHHHhhhhhcCchhHHHHhh
Q 020809          280 NVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEV  313 (321)
Q Consensus       280 ~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~~~  313 (321)
                      .+.--|..|+++=.+.|..|-++|+-|++.+=..
T Consensus       979 ~ak~~F~~VK~~R~~~F~~~F~~va~~Id~IYK~ 1012 (1141)
T KOG0018|consen  979 KAKNAFNKVKKKRYERFMACFEHVADNIDRIYKE 1012 (1141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444566677777777777777777777765443

>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription

Probab=94.46  E-value=3.7  Score=37.27  Aligned_cols=47  Identities=9%  Similarity=0.185  Sum_probs=25.4

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSER   88 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~   88 (321)
                      -+++-|.+++..+..++..+..+...-+.+...+++.+..+...+.+
T Consensus        27 ~l~q~ird~e~~l~~a~~~~a~~~a~~~~le~~~~~~~~~~~~~~~~   73 (221)
T PF04012_consen   27 MLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQ   73 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555666666666666655555555555555555555444444444

The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].

>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]

Probab=94.41  E-value=9.8  Score=43.04  Aligned_cols=84  Identities=15%  Similarity=0.215  Sum_probs=44.9

Q ss_pred             HhhhcHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           66 QELKGKDEVVAQKEKAIQDKS-ERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEA  144 (321)
Q Consensus        66 ~eLk~kd~~I~q~ek~i~e~~-~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa  144 (321)
                      ...+++++.|.++.....+++ .++.-+|.++...+. .-...+++...+..++++++++++.+++...........+.+
T Consensus       465 ~~~keL~e~i~~lk~~~~el~~~q~~l~q~~~ke~~e-k~~~~~~~~~~l~~~~~~~~eele~~q~~~~~~~~~~~kv~~  543 (1317)
T KOG0612|consen  465 EMDKELEETIEKLKSEESELQREQKALLQHEQKEVEE-KLSEEEAKKRKLEALVRQLEEELEDAQKKNDNAADSLEKVNS  543 (1317)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence            445555555555555555555 355555555555533 334455566666666777666666665555555444444444


Q ss_pred             HHHHHH
Q 020809          145 RAIEAE  150 (321)
Q Consensus       145 ~a~e~e  150 (321)
                      .++.++
T Consensus       544 ~rk~le  549 (1317)
T KOG0612|consen  544 LRKQLE  549 (1317)
T ss_pred             HHHHHH
Confidence            444444

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.41  E-value=4.4  Score=41.13  Aligned_cols=75  Identities=17%  Similarity=0.219  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           48 DQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDN  127 (321)
Q Consensus        48 ~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~  127 (321)
                      .+++++..-.++.+.++++      .++.......+.+..+...|..+.+.+++ ..+..+.+...++.++..+.+++..
T Consensus       328 sqleSqr~y~e~~~~e~~q------sqlen~k~~~e~~~~e~~~l~~~~~~~e~-~kk~~e~k~~q~q~k~~k~~kel~~  400 (493)
T KOG0804|consen  328 SQLESQRKYYEQIMSEYEQ------SQLENQKQYYELLITEADSLKQESSDLEA-EKKIVERKLQQLQTKLKKCQKELKE  400 (493)
T ss_pred             hhhhHHHHHHHHHHHHHHH------HHHHhHHHHHHHHHHHHHhhhhhhhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555556666666655      23333333333333444444444444433 2244455555555555555555555


Q ss_pred             HH
Q 020809          128 LK  129 (321)
Q Consensus       128 Lk  129 (321)
                      ++
T Consensus       401 ~~  402 (493)
T KOG0804|consen  401 ER  402 (493)
T ss_pred             HH
Confidence            44

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=94.30  E-value=10  Score=43.80  Aligned_cols=21  Identities=19%  Similarity=0.346  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHhHHHHHH
Q 020809           46 ELDQLKSKIRSLESHIDEKTQ   66 (321)
Q Consensus        46 el~qlk~ki~~Les~i~e~~~   66 (321)
                      ++++++.++..++..+..+..
T Consensus       231 ~~~~~~~~le~l~~~~~~l~~  251 (1353)
T TIGR02680       231 QLDEYRDELERLEALERALRN  251 (1353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            345555555555555544433

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.

>PRK09343 prefoldin subunit beta; Provisional

Probab=94.27  E-value=2.8  Score=35.07  Aligned_cols=44  Identities=14%  Similarity=0.234  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKS   86 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~   86 (321)
                      +..++.+.-.+...++.++..+..++..++..+.+++.-+.+++
T Consensus         5 ~~~~~q~~~~~~q~lq~~l~~~~~q~~~le~q~~e~~~~~~EL~   48 (121)
T PRK09343          5 IPPEVQAQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELE   48 (121)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555566666666665555555665555555554443

>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]

Probab=94.22  E-value=10  Score=41.48  Aligned_cols=55  Identities=9%  Similarity=0.171  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFE  194 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~e  194 (321)
                      .+.+.....+...+.++......++..-+++...+..+++++..+..++.+++..
T Consensus       462 ~~~~~~~~~L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~~l~~e~~~lq~~  516 (980)
T KOG0980|consen  462 DDVEEENTNLNDQLEELQRAAGRAETKTESQAKALESLRQELALLLIELEELQRT  516 (980)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333344444444444444444444445555555555555555555555443

>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold)

Probab=94.21  E-value=2.7  Score=34.64  Aligned_cols=69  Identities=16%  Similarity=0.273  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          108 AEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK  176 (321)
Q Consensus       108 eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~e  176 (321)
                      +.+.+....|+..|+..|+..+........++..|++..+.+......++..+..|+..+.+-.+.++.
T Consensus         8 ~as~~el~n~La~Le~slE~~K~S~~eL~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~   76 (107)
T PF09304_consen    8 EASQNELQNRLASLERSLEDEKTSQGELAKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLED   76 (107)
T ss_dssp             ------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444555555555555555544444444444444444444444444444444444444444433

The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.

>PRK10698 phage shock protein PspA; Provisional

Probab=94.17  E-value=4.6  Score=37.25  Aligned_cols=44  Identities=11%  Similarity=0.163  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKS   86 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~   86 (321)
                      +++=+.+++..+.++...+..+...-+.....+++++..+...+
T Consensus        29 l~q~i~em~~~l~~~r~alA~~~A~~k~~er~~~~~~~~~~~~e   72 (222)
T PRK10698         29 VRLMIQEMEDTLVEVRSTSARALAEKKQLTRRIEQAEAQQVEWQ   72 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555556666666555555554444444555554444444443

>smart00787 Spc7 Spc7 kinetochore protein

Probab=94.15  E-value=6  Score=38.48  Aligned_cols=39  Identities=28%  Similarity=0.218  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          153 ISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       153 ~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      +......+++++....+....|+........+..+|..+
T Consensus       220 i~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~a  258 (312)
T smart00787      220 IMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEA  258 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333444444444444444444444444444444444

This domain is found in cell division proteins which are required for kinetochore-spindle association.

>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking

Probab=94.10  E-value=5.1  Score=37.43  Aligned_cols=17  Identities=29%  Similarity=0.503  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHhHHH
Q 020809           47 LDQLKSKIRSLESHIDE   63 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e   63 (321)
                      +..++..+..+....+.
T Consensus        22 L~~~~~~l~~~~~~~~~   38 (302)
T PF10186_consen   22 LLELRSELQQLKEENEE   38 (302)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            33444444444333333

In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy

>PF15450 DUF4631: Domain of unknown function (DUF4631)

Probab=94.03  E-value=8.6  Score=39.79  Aligned_cols=95  Identities=21%  Similarity=0.269  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAI----QDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE  120 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i----~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire  120 (321)
                      ..++-++.+.+-++..+......|+.++..|..+...+    ..+...|..+.+++.+...+....+..=...+.+.+++
T Consensus       337 ~~ld~LqEksqile~sv~~l~~~lkDLd~~~~aLs~rld~qEqtL~~rL~e~~~e~~~~~r~~lekl~~~q~e~~~~l~~  416 (531)
T PF15450_consen  337 SELDLLQEKSQILEDSVAELMRQLKDLDDHILALSWRLDLQEQTLNLRLSEAKNEWESDERKSLEKLDQWQNEMEKHLKE  416 (531)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555666666666666666677777777766665543    23334444455555544444445555555666667777


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKESEKQQKEK  139 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk  139 (321)
                      +..-|+.|..+|+.+..+.
T Consensus       417 v~eKVd~LpqqI~~vs~Kc  435 (531)
T PF15450_consen  417 VQEKVDSLPQQIEEVSDKC  435 (531)
T ss_pred             HHHHHHhhhHHHHHHHHHH
Confidence            7777777777777777555

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=93.98  E-value=4.7  Score=36.59  Aligned_cols=25  Identities=20%  Similarity=0.292  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          169 EQKSKIRKTERALKVAEEEMMRAKF  193 (321)
Q Consensus       169 Eqk~~l~elE~~lq~~Eeei~kl~~  193 (321)
                      +....+..++..++..+..+..+..
T Consensus       122 eL~~kL~~~~~~l~~~~~ki~~Lek  146 (194)
T PF15619_consen  122 ELQRKLSQLEQKLQEKEKKIQELEK  146 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444455555555555544433

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=93.83  E-value=12  Score=43.34  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=15.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHID   62 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~   62 (321)
                      ..+.++.+++.++..+..|+.-..
T Consensus       231 ~~~~~~~~le~l~~~~~~l~~i~~  254 (1353)
T TIGR02680       231 QLDEYRDELERLEALERALRNFLQ  254 (1353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555666677777777666655444

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.

>PF04849 HAP1_N: HAP1 N-terminal conserved region; InterPro: IPR006933 This family is defined by an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues

Probab=93.81  E-value=6.9  Score=37.98  Aligned_cols=61  Identities=16%  Similarity=0.259  Sum_probs=38.3

Q ss_pred             cCCCCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           36 DAVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        36 ~~~~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .....+.++.++..++..-..|.++...+..+-...+++=   +..|.+--.++.....+|..+
T Consensus       158 ~~~~le~Lq~Klk~LEeEN~~LR~Ea~~L~~et~~~EekE---qqLv~dcv~QL~~An~qia~L  218 (306)
T PF04849_consen  158 KCIQLEALQEKLKSLEEENEQLRSEASQLKTETDTYEEKE---QQLVLDCVKQLSEANQQIASL  218 (306)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhccHHH---HHHHHHHHHHhhhcchhHHHH
Confidence            4447788899999888888888888887776666555542   223333444444444444444

HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [].

>PF15397 DUF4618: Domain of unknown function (DUF4618)

Probab=93.78  E-value=6.3  Score=37.39  Aligned_cols=39  Identities=15%  Similarity=0.129  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 020809          158 AKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEAT  196 (321)
Q Consensus       158 ~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~  196 (321)
                      .....|.+....+...|++++.....+..++..+.....
T Consensus       186 ~~N~~m~kei~~~re~i~el~e~I~~L~~eV~~L~~~~~  224 (258)
T PF15397_consen  186 LENQVMQKEIVQFREEIDELEEEIPQLRAEVEQLQAQAQ  224 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            344455666666666666666666666666665544443

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=93.78  E-value=8  Score=38.60  Aligned_cols=24  Identities=8%  Similarity=0.076  Sum_probs=10.0

Q ss_pred             HHHHHHhHHHHHHhhhcHHHHHHH
Q 020809           54 IRSLESHIDEKTQELKGKDEVVAQ   77 (321)
Q Consensus        54 i~~Les~i~e~~~eLk~kd~~I~q   77 (321)
                      +.-++.++.++.+++...+..+..
T Consensus       173 ~~fl~~ql~~~~~~l~~ae~~l~~  196 (444)
T TIGR03017       173 ALWFVQQIAALREDLARAQSKLSA  196 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444333

Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.

>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []

Probab=93.78  E-value=3.6  Score=34.58  Aligned_cols=16  Identities=31%  Similarity=0.696  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHhHH
Q 020809           47 LDQLKSKIRSLESHID   62 (321)
Q Consensus        47 l~qlk~ki~~Les~i~   62 (321)
                      ++.+.+.|..+++++.
T Consensus        18 ve~L~s~lr~~E~E~~   33 (120)
T PF12325_consen   18 VERLQSQLRRLEGELA   33 (120)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4444444444433333

The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].

>PF04582 Reo_sigmaC: Reovirus sigma C capsid protein; InterPro: IPR007662 Protein sigmaC in its native state was shown to be a homotrimer

Probab=93.66  E-value=0.15  Score=49.55  Aligned_cols=44  Identities=20%  Similarity=0.311  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          107 AAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAE  150 (321)
Q Consensus       107 ~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~e  150 (321)
                      ....+..++..+..+.-.|..|+..+-.+--.+..|+.|.+.+|
T Consensus       110 h~ssIS~Lqs~v~~lsTdvsNLksdVSt~aL~ItdLe~RV~~LE  153 (326)
T PF04582_consen  110 HSSSISDLQSSVSALSTDVSNLKSDVSTQALNITDLESRVKALE  153 (326)
T ss_dssp             --------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHhhhhhhhhhhhhhhhhhhhcchHhhHHHHHHHHh
Confidence            34444455555555666666666666555555555555555544

It was demonstrated that the sigmaC subunits are not covalently bound via disulphide linkages and the formation of an intrachain disulphide bond between the two cysteine residues of the sigmaC polypeptide may have a negative effect on oligomer stability. The susceptibility of the trimer to pH, temperature, ionic strength, chemical denaturants and detergents indicates that hydrophobic interactions contribute much more to oligomer stability than do ionic interactions and hydrogen bonding [].; PDB: 2VRS_C 2JJL_A 2BSF_A 2BT7_A 2BT8_A.

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs

Probab=93.62  E-value=3.9  Score=44.18  Aligned_cols=12  Identities=25%  Similarity=0.434  Sum_probs=4.8

Q ss_pred             HHHHHHHHHHHH
Q 020809          109 EQVDKAHARADE  120 (321)
Q Consensus       109 eq~~~~~~Rire  120 (321)
                      ++.+.+.+|+..
T Consensus       607 d~Qe~L~~R~~~  618 (717)
T PF10168_consen  607 DKQEKLMKRVDR  618 (717)
T ss_pred             HHHHHHHHHHHH
Confidence            333344444443

It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]

Probab=93.61  E-value=5.1  Score=42.93  Aligned_cols=122  Identities=19%  Similarity=0.217  Sum_probs=54.4

Q ss_pred             HHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           54 IRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESE  133 (321)
Q Consensus        54 i~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele  133 (321)
                      ...|....+.+..++..+....+.....|..++.+...+++....+-+ ....+.......++.+-++...++.|+-..+
T Consensus       498 ~k~L~~ek~~l~~~i~~l~~~~~~~~~~i~~leeq~~~lt~~~~~l~~-el~~~~~~le~~kk~~~e~~~~~~~Lq~~~e  576 (698)
T KOG0978|consen  498 HKLLREEKSKLEEQILTLKASVDKLELKIGKLEEQERGLTSNESKLIK-ELTTLTQSLEMLKKKAQEAKQSLEDLQIELE  576 (698)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444444444444444444422 2223333333444444444444444544444


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          134 KQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK  176 (321)
Q Consensus       134 ~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~e  176 (321)
                      ....+...++..-++....+.....+...++.......+.+..
T Consensus       577 k~~~~le~i~~~~~e~~~ele~~~~k~~rleEE~e~L~~kle~  619 (698)
T KOG0978|consen  577 KSEAKLEQIQEQYAELELELEIEKFKRKRLEEELERLKRKLER  619 (698)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444444444444444444444443

>PF14362 DUF4407: Domain of unknown function (DUF4407)

Probab=93.56  E-value=6.7  Score=37.40  Aligned_cols=15  Identities=27%  Similarity=0.231  Sum_probs=7.6

Q ss_pred             hccCchhHHHHHHHH
Q 020809          206 HSAWLPPWLAVHLLQ  220 (321)
Q Consensus       206 ~g~~l~Pwla~~~~~  220 (321)
                      ++.|+|.|+-.=.-.
T Consensus       259 ~~~~~~~~~i~llfi  273 (301)
T PF14362_consen  259 PSALLASLFIFLLFI  273 (301)
T ss_pred             CcHHHHHHHHHHHHH
Confidence            355666665544333

>PRK03947 prefoldin subunit alpha; Reviewed

Probab=93.35  E-value=3.9  Score=34.60  Aligned_cols=45  Identities=20%  Similarity=0.320  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          106 NAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAE  150 (321)
Q Consensus       106 ~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~e  150 (321)
                      ..++-...+++|+..|++.++.+..++...+.....+......+.
T Consensus        91 ~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~l~  135 (140)
T PRK03947         91 DLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQLAQELQQLQ  135 (140)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567777777778888888877777777777766655555444443

>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]

Probab=93.35  E-value=12  Score=39.19  Aligned_cols=28  Identities=32%  Similarity=0.423  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           72 DEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        72 d~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +..|..+..+|.+++.+|..|+.+++++
T Consensus       293 ~~~l~~l~~Eie~kEeE~e~lq~~~d~L  320 (581)
T KOG0995|consen  293 EKKLEMLKSEIEEKEEEIEKLQKENDEL  320 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444444

>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription

Probab=93.30  E-value=6.2  Score=35.83  Aligned_cols=52  Identities=17%  Similarity=0.230  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           48 DQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        48 ~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ..++.-|.+++..+......+...-..-..++..+.+....+..++......
T Consensus        26 ~~l~q~ird~e~~l~~a~~~~a~~~a~~~~le~~~~~~~~~~~~~~~~A~~A   77 (221)
T PF04012_consen   26 KMLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQAELA   77 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5566666666666666666666555555556666666666666555555444

The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].

>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]

Probab=93.28  E-value=15  Score=40.28  Aligned_cols=31  Identities=16%  Similarity=0.214  Sum_probs=19.0

Q ss_pred             HHHhhCcc-hHHHHHHHHHHHHHhhcc-ccchh
Q 020809          228 HWNAHGKP-AMDVAIQKALEKKAQAGK-WVQPH  258 (321)
Q Consensus       228 ~~~~hg~p-~~~~~~~~~~~k~~~~~~-~~~ph  258 (321)
                      ||+--+-| .+=+....+|.-..++.+ |..|-
T Consensus       613 ~~~~~~~p~~Llst~~~~s~n~~~~e~~~~~yl  645 (980)
T KOG0980|consen  613 HWRCLTSPDFLLSTAENASVNATQFETSFNNYL  645 (980)
T ss_pred             ccCcCCCHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            44433333 556677778887777776 65543

>PF06818 Fez1: Fez1; InterPro: IPR009638 This family represents the eukaryotic Fez1 protein

Probab=93.28  E-value=6.5  Score=35.99  Aligned_cols=17  Identities=24%  Similarity=0.384  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 020809          118 ADELEKQIDNLKKESEK  134 (321)
Q Consensus       118 ireL~k~Ie~Lk~ele~  134 (321)
                      +..|+.++..|+..+..
T Consensus        89 l~~le~El~~Lr~~l~~  105 (202)
T PF06818_consen   89 LGQLEAELAELREELAC  105 (202)
T ss_pred             hhhhHHHHHHHHHHHHh
Confidence            33344444444443333

Fez1 contains a leucine-zipper region with similarity to the DNA-binding domain of the cAMP-responsive activating-transcription factor 5 []. There is evidence that Fez1 inhibits cancer cell growth through regulation of mitosis, and that its alterations result in abnormal cell growth []. Note that some family members contain more than one copy of this region.; GO: 0005737 cytoplasm, 0016020 membrane

>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking

Probab=93.26  E-value=7.1  Score=36.42  Aligned_cols=10  Identities=40%  Similarity=0.451  Sum_probs=3.5

Q ss_pred             HHHHHHHHHH
Q 020809           49 QLKSKIRSLE   58 (321)
Q Consensus        49 qlk~ki~~Le   58 (321)
                      +++.....+.
T Consensus        31 ~~~~~~~~l~   40 (302)
T PF10186_consen   31 QLKEENEELR   40 (302)
T ss_pred             HHHHHHHHHH
Confidence            3333333333

In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy

>PRK10929 putative mechanosensitive channel protein; Provisional

Probab=93.22  E-value=18  Score=41.02  Aligned_cols=29  Identities=7%  Similarity=0.115  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          163 LQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       163 Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .+...+....+++.++...+.+++.+...
T Consensus       206 ~~~q~dl~~~~~~~l~~~~~~Lq~~in~k  234 (1109)
T PRK10929        206 ARLRSELAKKRSQQLDAYLQALRNQLNSQ  234 (1109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444455555555555555555543

>PF04582 Reo_sigmaC: Reovirus sigma C capsid protein; InterPro: IPR007662 Protein sigmaC in its native state was shown to be a homotrimer

Probab=93.11  E-value=0.21  Score=48.61  Aligned_cols=42  Identities=19%  Similarity=0.222  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          143 EARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVA  184 (321)
Q Consensus       143 Ea~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~  184 (321)
                      ......+...+..+...+..|...+.-+.-.|-.++...+.+
T Consensus       111 ~ssIS~Lqs~v~~lsTdvsNLksdVSt~aL~ItdLe~RV~~L  152 (326)
T PF04582_consen  111 SSSISDLQSSVSALSTDVSNLKSDVSTQALNITDLESRVKAL  152 (326)
T ss_dssp             -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHhhhhhhhhhhhhhhhhhhhcchHhhHHHHHHHH
Confidence            333333444444444444455555555555555555444433

It was demonstrated that the sigmaC subunits are not covalently bound via disulphide linkages and the formation of an intrachain disulphide bond between the two cysteine residues of the sigmaC polypeptide may have a negative effect on oligomer stability. The susceptibility of the trimer to pH, temperature, ionic strength, chemical denaturants and detergents indicates that hydrophobic interactions contribute much more to oligomer stability than do ionic interactions and hydrogen bonding [].; PDB: 2VRS_C 2JJL_A 2BSF_A 2BT7_A 2BT8_A.

>PF12777 MT: Microtubule-binding stalk of dynein motor; InterPro: IPR024743 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=93.11  E-value=9.4  Score=37.37  Aligned_cols=58  Identities=16%  Similarity=0.093  Sum_probs=33.4

Q ss_pred             chhHHHHHHHHHHHHHHhHHHhhCcchHHHHHHHHHHHHHhhccccchhHHhhh-hhhhhh
Q 020809          210 LPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIK-AKWIPA  269 (321)
Q Consensus       210 l~Pwla~~~~~~~~~~~~~~~~hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~-~k~~p~  269 (321)
                      |..-|..+..||......+-..+.-.+-+.++--|.-  +-+.=|-.+|=+.+- ..|+||
T Consensus       285 Li~~L~~E~~RW~~~~~~l~~~~~~l~GD~llaaa~i--sY~G~f~~~~R~~l~~~~W~~~  343 (344)
T PF12777_consen  285 LISGLSGEKERWSEQIEELEEQLKNLVGDSLLAAAFI--SYLGPFTPEYRQELLKKMWKPY  343 (344)
T ss_dssp             HHHCCHHHHHCCHCHHHHHHHHHHHHHHHHHHHHHHH--HCCCCTSHHHHHHHHHHH----
T ss_pred             HHhhhcchhhhHHHHHHHHHHHhcccHHHHHHHHHHH--HHcCCCCHHHHHHHHHHhcccc
Confidence            5555777888888888888888888888888755443  223333333333332 235554

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules (D1-6), of which four correspond to the ATP binding sites with P-loop signatures, and two are modules in which the P loop has been lost in evolution. This domain occurs between D4 and D5 and includes the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [].; PDB: 3VKH_A 3VKG_A 3ERR_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 2RR7_A.

>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []

Probab=93.06  E-value=4.8  Score=33.84  Aligned_cols=34  Identities=12%  Similarity=0.184  Sum_probs=14.1

Q ss_pred             HHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           65 TQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS   98 (321)
Q Consensus        65 ~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~   98 (321)
                      ...|+.++.++..++.++..++.+-+.+..+|-.
T Consensus        22 ~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~   55 (120)
T PF12325_consen   22 QSQLRRLEGELASLQEELARLEAERDELREEIVK   55 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333334444444444444444444444444433

The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].

>PF01576 Myosin_tail_1: Myosin tail; InterPro: IPR002928 Muscle contraction is caused by sliding between the thick and thin filaments of the myofibril

Probab=93.03  E-value=0.028  Score=61.48  Aligned_cols=40  Identities=30%  Similarity=0.312  Sum_probs=0.0

Q ss_pred             HHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           62 DEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        62 ~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      .+++.+|..+...-..+++.-..+...+..|.+.++.+++
T Consensus       134 ~eL~eqle~lqk~k~~lEK~k~~l~~e~~dL~~~l~~~~k  173 (859)
T PF01576_consen  134 AELNEQLEQLQKQKAKLEKEKSQLEAELDDLQAQLDSLQK  173 (859)
T ss_dssp             ----------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            3333333333333344444444444444444444444443

Myosin is a major component of thick filaments and exists as a hexamer of 2 heavy chains [], 2 alkali light chains, and 2 regulatory light chains. The heavy chain can be subdivided into the N-terminal globular head and the C-terminal coiled-coil rod-like tail, although some forms have a globular region in their C-terminal. There are many cell-specific isoforms of myosin heavy chains, coded for by a multi-gene family []. Myosin interacts with actin to convert chemical energy, in the form of ATP, to mechanical energy []. The 3-D structure of the head portion of myosin has been determined [] and a model for actin-myosin complex has been constructed []. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament []. The coiled-coil region provides the structural backbone of the thick filament [].; GO: 0003774 motor activity, 0016459 myosin complex; PDB: 2LNK_C 3ZWH_Q.

>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]

Probab=92.76  E-value=9.1  Score=36.31  Aligned_cols=127  Identities=17%  Similarity=0.190  Sum_probs=84.6

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELE  122 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~  122 (321)
                      +.+.-.+++..+.+.+....++..+   ++.+++++++...++....+.|.-+...++    ...+.+...+...+..|+
T Consensus        25 ykq~f~~~reEl~EFQegSrE~Eae---lesqL~q~etrnrdl~t~nqrl~~E~e~~K----ek~e~q~~q~y~q~s~Le   97 (333)
T KOG1853|consen   25 YKQHFLQMREELNEFQEGSREIEAE---LESQLDQLETRNRDLETRNQRLTTEQERNK----EKQEDQRVQFYQQESQLE   97 (333)
T ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
Confidence            4556677788888888777777654   477888899999888888888888887773    334555556666677777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          123 KQIDNLKKESEKQQKEKEALEARAIEAEK-------KISDLSAKLEKLQKINDEQKSKIRK  176 (321)
Q Consensus       123 k~Ie~Lk~ele~~~~kk~~LEa~a~e~ek-------k~~el~~~le~Lek~~~Eqk~~l~e  176 (321)
                      +.+....+..+.++..+.+||..-.+++.       .++.+.+.+++....++-.+..|++
T Consensus        98 ddlsqt~aikeql~kyiReLEQaNDdLErakRati~sleDfeqrLnqAIErnAfLESELdE  158 (333)
T KOG1853|consen   98 DDLSQTHAIKEQLRKYIRELEQANDDLERAKRATIYSLEDFEQRLNQAIERNAFLESELDE  158 (333)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            77777777777777777666666555553       3444555555544444444444443

>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]

Probab=92.66  E-value=8.5  Score=35.74  Aligned_cols=37  Identities=8%  Similarity=0.210  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKE   79 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~e   79 (321)
                      +++-|.++++.+..+...+..+...-+....++++++
T Consensus        29 l~Q~ird~~~~l~~ar~~~A~~~a~~k~~e~~~~~~~   65 (225)
T COG1842          29 LEQAIRDMESELAKARQALAQAIARQKQLERKLEEAQ   65 (225)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444333333333333333

>PF05335 DUF745: Protein of unknown function (DUF745); InterPro: IPR007999 This family consists of several uncharacterised Drosophila melanogaster proteins of unknown function

Probab=92.61  E-value=7.7  Score=35.10  Aligned_cols=94  Identities=21%  Similarity=0.371  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------hhHHHHHH--
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK----------ETLNAAEQ--  110 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~----------~~~~~eeq--  110 (321)
                      -++-+++|+..+.+.+..+.+....|..-...+............++..|..-+...+..          ...++.++  
T Consensus        65 Kq~iveqLe~ev~EAe~vV~ee~~sL~~aq~na~aA~~aa~~A~~q~~~L~~~l~~a~~nl~~a~~~a~~AQ~el~eK~q  144 (188)
T PF05335_consen   65 KQQIVEQLEQEVREAEAVVQEEKASLQQAQANAQAAQRAAQQAQQQLETLKAALKAAQANLANAEQVAEGAQQELAEKTQ  144 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445567777777777777777777776666666666555555555555555554444332          22333333  


Q ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          111 -VDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus       111 -~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                       ++.++.|+..|.+++...+.+.+..+
T Consensus       145 LLeaAk~Rve~L~~QL~~Ar~D~~~tk  171 (188)
T PF05335_consen  145 LLEAAKRRVEELQRQLQAARADYEKTK  171 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             44455555555555555555555444

>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []

Probab=92.44  E-value=18  Score=39.06  Aligned_cols=61  Identities=13%  Similarity=0.191  Sum_probs=38.3

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      +.+..+|.+++..+.++...++....+...+......+......++.+...|..+|...+.
T Consensus        30 ~~~~~~i~~l~~elk~~~~~~~~~~~e~~rl~~~~~~~~~~~~~~e~~~~~lr~e~ke~K~   90 (717)
T PF09730_consen   30 AYLQQRILELENELKQLRQELSNVQAENERLSQLNQELRKECEDLELERKRLREEIKEYKF   90 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455666666666666666666666666666666666666666666666666666666533

Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=92.36  E-value=8.4  Score=34.96  Aligned_cols=51  Identities=29%  Similarity=0.278  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          106 NAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL  156 (321)
Q Consensus       106 ~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el  156 (321)
                      .+++....+-++.+.++++...|-..++..+.+...+-.....+.++..++
T Consensus        78 ~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL  128 (193)
T PF14662_consen   78 SLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKEL  128 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHH
Confidence            344444444444444444433333333333333333333333333333333

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=92.29  E-value=3.6  Score=43.24  Aligned_cols=29  Identities=31%  Similarity=0.487  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          118 ADELEKQIDNLKKESEKQQKEKEALEARA  146 (321)
Q Consensus       118 ireL~k~Ie~Lk~ele~~~~kk~~LEa~a  146 (321)
                      ++.+...|+.|...+.........|+.+.
T Consensus       476 i~~~~~~I~~L~~~L~e~~~~ve~L~~~l  504 (652)
T COG2433         476 IRARDRRIERLEKELEEKKKRVEELERKL  504 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444333

>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]

Probab=92.29  E-value=7.1  Score=33.92  Aligned_cols=44  Identities=30%  Similarity=0.392  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIE  148 (321)
Q Consensus       105 ~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e  148 (321)
                      .+.++-++.+++|+.+|++.++.+...+...-.....++..+..
T Consensus        90 ~~~~eAie~l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q~  133 (145)
T COG1730          90 KSADEAIEFLKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQ  133 (145)
T ss_pred             ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556566666666666666655555555555444444444333

>PF13514 AAA_27: AAA domain

Probab=92.25  E-value=24  Score=39.94  Aligned_cols=32  Identities=25%  Similarity=0.391  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          145 RAIEAEKKISDLSAKLEKLQKINDEQKSKIRK  176 (321)
Q Consensus       145 ~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~e  176 (321)
                      ....++..+..++..+..+.......+..+..
T Consensus       897 ~l~~l~~~l~~l~~~~~~l~~~~~~~~~~l~~  928 (1111)
T PF13514_consen  897 ELEELEEELEELEEELEELQEERAELEQELEA  928 (1111)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333444444444433333333333

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=92.23  E-value=1.9  Score=40.81  Aligned_cols=51  Identities=16%  Similarity=0.235  Sum_probs=30.2

Q ss_pred             HHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           51 KSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        51 k~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      +.++..|+..+...++-+-++...|+.++.+|.++..+|..++.+|+.++.
T Consensus        39 ~~r~~~le~~~~~~~~~~~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~   89 (263)
T PRK10803         39 EDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVE   89 (263)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            455566666666655555555666666666666666666666666655533

>KOG0946 consensus ER-Golgi vesicle-tethering protein p115 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.20  E-value=21  Score=39.06  Aligned_cols=55  Identities=13%  Similarity=0.125  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccCchhHHHHHHHHHHH
Q 020809          167 NDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLLQCQS  223 (321)
Q Consensus       167 ~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~ql~e~~g~~l~Pwla~~~~~~~~  223 (321)
                      ..+....++.+.......++++..+-....+.+..+..-|  -.-|-+++...+...
T Consensus       801 l~e~~~~l~~~q~e~~~~keq~~t~~~~tsa~a~~le~m~--~~~~~la~e~~~ieq  855 (970)
T KOG0946|consen  801 LSEESTRLQELQSELTQLKEQIQTLLERTSAAADSLESMG--STEKNLANELKLIEQ  855 (970)
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHhh--ccccchhhHHHHHHH
Confidence            4444444555555555555555544333333443333322  234555555544443

>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]

Probab=92.15  E-value=8.2  Score=36.59  Aligned_cols=79  Identities=24%  Similarity=0.341  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVA  184 (321)
Q Consensus       105 ~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~  184 (321)
                      ..++.+.+.++.|.|+|......|.-+.+.++   +.++.....--..+..+..-+.++..+..++..-|.+++++-+.+
T Consensus        48 aelesqL~q~etrnrdl~t~nqrl~~E~e~~K---ek~e~q~~q~y~q~s~Leddlsqt~aikeql~kyiReLEQaNDdL  124 (333)
T KOG1853|consen   48 AELESQLDQLETRNRDLETRNQRLTTEQERNK---EKQEDQRVQFYQQESQLEDDLSQTHAIKEQLRKYIRELEQANDDL  124 (333)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHH
Confidence            34555666666677777776666666666655   444555555555555666666666666666666666666665555


Q ss_pred             HH
Q 020809          185 EE  186 (321)
Q Consensus       185 Ee  186 (321)
                      |.
T Consensus       125 Er  126 (333)
T KOG1853|consen  125 ER  126 (333)
T ss_pred             HH
Confidence            43

>KOG0979 consensus Structural maintenance of chromosome protein SMC5/Spr18, SMC superfamily [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=92.09  E-value=23  Score=39.45  Aligned_cols=37  Identities=27%  Similarity=0.346  Sum_probs=21.8

Q ss_pred             HHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           65 TQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        65 ~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      -.+|.++...-.+++.........|..|..+|+.+.+
T Consensus       180 h~eL~~lr~~e~~Le~~~~~~~~~l~~L~~~~~~l~k  216 (1072)
T KOG0979|consen  180 HIELMDLREDEKSLEDKLTTKTEKLNRLEDEIDKLEK  216 (1072)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            3445555555666666666666666666666665544

>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal

Probab=92.00  E-value=5.9  Score=32.35  Aligned_cols=34  Identities=12%  Similarity=0.277  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAI   82 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i   82 (321)
                      ++-.+.+.++.++..+..++..++..+.+.+.-+
T Consensus         7 ~~~~~~q~~q~~~~~l~~q~~~le~~~~E~~~v~   40 (110)
T TIGR02338         7 NQLAQLQQLQQQLQAVATQKQQVEAQLKEAEKAL   40 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444444444333

Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.

>KOG0963 consensus Transcription factor/CCAAT displacement protein CDP1 [Transcription]

Probab=91.88  E-value=19  Score=38.03  Aligned_cols=57  Identities=19%  Similarity=0.258  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           89 IVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEAR  145 (321)
Q Consensus        89 I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~  145 (321)
                      +..++.......++.+..+.+..+..+.+++.+++-|..++..++....+...+++.
T Consensus       169 a~~~e~~~~q~~~e~e~~L~~~~~~~~~q~~~le~ki~~lq~a~~~t~~el~~~~s~  225 (629)
T KOG0963|consen  169 ANETEEKLEQEWAEREAGLKDEEQNLQEQLEELEKKISSLQSAIEDTQNELFDLKSK  225 (629)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHh
Confidence            445555555555556666777777777777777777777777777666665555544

>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT)

Probab=91.84  E-value=7  Score=32.94  Aligned_cols=22  Identities=23%  Similarity=0.289  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 020809          159 KLEKLQKINDEQKSKIRKTERA  180 (321)
Q Consensus       159 ~le~Lek~~~Eqk~~l~elE~~  180 (321)
                      ....+++.+.+.+..++++...
T Consensus        99 qk~~le~e~~~~~~r~~dL~~Q  120 (132)
T PF07926_consen   99 QKEQLEKELSELEQRIEDLNEQ  120 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444433

These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore

>PF13166 AAA_13: AAA domain

Probab=91.77  E-value=20  Score=38.12  Aligned_cols=18  Identities=6%  Similarity=-0.324  Sum_probs=10.4

Q ss_pred             HHHhhCcchHHHHHHHHH
Q 020809          228 HWNAHGKPAMDVAIQKAL  245 (321)
Q Consensus       228 ~~~~hg~p~~~~~~~~~~  245 (321)
                      +.-.|.-+.|..+.....
T Consensus       565 iIlTHn~~F~~~l~~~~~  582 (712)
T PF13166_consen  565 IILTHNLYFFKELKKWFE  582 (712)
T ss_pred             EEEeCcHHHHHHHHHHhh
Confidence            444566666666655544

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=91.69  E-value=15  Score=36.56  Aligned_cols=19  Identities=11%  Similarity=0.382  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHHhHHH
Q 020809           45 IELDQLKSKIRSLESHIDE   63 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e   63 (321)
                      .++++++.++...+.+..+
T Consensus       215 ~~l~~l~~~l~~~~~~~~~  233 (444)
T TIGR03017       215 ARLNELSAQLVAAQAQVMD  233 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            4555555555555544433

Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.

>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []

Probab=91.51  E-value=13  Score=35.51  Aligned_cols=76  Identities=22%  Similarity=0.272  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 020809          117 RADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEAT  196 (321)
Q Consensus       117 RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~  196 (321)
                      .+..|+++...|-...+........|...+..-+..+.-++       .....-+.+|+.++..+.....++.+.+..+.
T Consensus        61 e~s~LkREnq~l~e~c~~lek~rqKlshdlq~Ke~qv~~lE-------gQl~s~Kkqie~Leqelkr~KsELErsQ~~~~  133 (307)
T PF10481_consen   61 EYSALKRENQSLMESCENLEKTRQKLSHDLQVKESQVNFLE-------GQLNSCKKQIEKLEQELKRCKSELERSQQAAS  133 (307)
T ss_pred             hhhhhhhhhhhHHHHHHHHHHHHHHhhHHHhhhHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34445555555555555554444555555555444444444       44444556888888888888888888877766


Q ss_pred             hhh
Q 020809          197 SRS  199 (321)
Q Consensus       197 ~~a  199 (321)
                      ...
T Consensus       134 ~~~  136 (307)
T PF10481_consen  134 SGD  136 (307)
T ss_pred             cCC
Confidence            443

Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].

>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences

Probab=91.45  E-value=1.7  Score=38.11  Aligned_cols=63  Identities=19%  Similarity=0.349  Sum_probs=38.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVV--AQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I--~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      +...+..++.+++.++.+++.....+..+|..+...+  .++...|..++.+|..+++.+..++.
T Consensus        73 el~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~  137 (169)
T PF07106_consen   73 ELAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS  137 (169)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4455566666666666666666666666666665554  44555666666666666666665544

TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].

>PF00769 ERM: Ezrin/radixin/moesin family; InterPro: IPR011259 The ERM family consists of three closely-related proteins, ezrin, radixin and moesin []

Probab=91.38  E-value=13  Score=34.94  Aligned_cols=115  Identities=23%  Similarity=0.393  Sum_probs=54.0

Q ss_pred             HHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           58 ESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQK  137 (321)
Q Consensus        58 es~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~  137 (321)
                      +....++...|....+.....+..+.+....+..|..+....+.        ....+..+..++...+..|..+......
T Consensus         4 Er~k~Ele~rL~q~eee~~~a~~~L~e~e~~a~~Leek~k~aee--------ea~~Le~k~~eaee~~~rL~~~~~~~~e   75 (246)
T PF00769_consen    4 EREKQELEERLRQMEEEMRRAQEALEESEETAEELEEKLKQAEE--------EAEELEQKRQEAEEEKQRLEEEAEMQEE   75 (246)
T ss_dssp             HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHH-------
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444555555555666666666666666666666665544432        2334445666666666666666666665


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          138 EKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEE  187 (321)
Q Consensus       138 kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eee  187 (321)
                      .+..|+.+..+.+..+..       |..........-..+...+..+...
T Consensus        76 Ek~~Le~e~~e~~~~i~~-------l~ee~~~ke~Ea~~lq~el~~ar~~  118 (246)
T PF00769_consen   76 EKEQLEQELREAEAEIAR-------LEEESERKEEEAEELQEELEEARED  118 (246)
T ss_dssp             -----HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555555555555544444       4444444444444444444333333

Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain; an extended alpha-helical domain; and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament-plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains [].; GO: 0008092 cytoskeletal protein binding, 0005737 cytoplasm, 0019898 extrinsic to membrane; PDB: 2I1J_A 2I1K_A 1E5W_A 1EF1_C.

>PF14282 FlxA: FlxA-like protein

Probab=91.19  E-value=2.3  Score=34.78  Aligned_cols=58  Identities=21%  Similarity=0.357  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHh----hhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQE----LKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~e----Lk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +....+..|+.+|..|+.++.++...    -+.+...+..++..|..++.+|..++.+...-
T Consensus        16 ~~~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~~   77 (106)
T PF14282_consen   16 SSDSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAEQ   77 (106)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34788999999999999999888772    23455555555555555555555555554333

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=91.18  E-value=28  Score=38.58  Aligned_cols=39  Identities=13%  Similarity=0.240  Sum_probs=20.4

Q ss_pred             HHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           62 DEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        62 ~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      ....+++..+..++.++...-+.++.+++.+++.|..++
T Consensus       399 qK~~kelE~k~sE~~eL~r~kE~Lsr~~d~aEs~iadlk  437 (1243)
T KOG0971|consen  399 QKLQKELEKKNSELEELRRQKERLSRELDQAESTIADLK  437 (1243)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334445555555555555555555555555555555553

>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices

Probab=91.11  E-value=8.7  Score=32.59  Aligned_cols=59  Identities=19%  Similarity=0.248  Sum_probs=35.9

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .++..+++.+..+...|...=+...++.+...+.+...=....++...|...-..|...
T Consensus        23 ~~v~~~l~~LEae~q~L~~kE~~r~~~~k~~ae~a~~~L~~~~~~~~~i~e~~~kl~~~   81 (126)
T PF09403_consen   23 ASVESELNQLEAEYQQLEQKEEARYNEEKQEAEAAEAELAELKELYAEIEEKIEKLKQD   81 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Confidence            34667888888888888888777766666655544444444444444444444444333

; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.

>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]

Probab=91.09  E-value=20  Score=36.84  Aligned_cols=51  Identities=6%  Similarity=0.138  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHHhHHHHHHhhh---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELK---GKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk---~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .+...|..|+++-+.+-..|.   ..+..|..+...-..+.+..+.+++-....
T Consensus       268 ~i~~~i~~lk~~n~~l~e~i~ea~k~s~~i~~l~ek~r~l~~D~nk~~~~~~~m  321 (622)
T COG5185         268 IINTDIANLKTQNDNLYEKIQEAMKISQKIKTLREKWRALKSDSNKYENYVNAM  321 (622)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            333444444444333333322   234444444444555555555555555444

>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea

Probab=90.95  E-value=7.3  Score=31.43  Aligned_cols=19  Identities=16%  Similarity=0.307  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHhHHHH
Q 020809           46 ELDQLKSKIRSLESHIDEK   64 (321)
Q Consensus        46 el~qlk~ki~~Les~i~e~   64 (321)
                      ++++++.++..+.+++..+
T Consensus         7 ~~q~l~~~~~~l~~~~~~l   25 (105)
T cd00632           7 QLQQLQQQLQAYIVQRQKV   25 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444333

Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st

>PRK03947 prefoldin subunit alpha; Reviewed

Probab=90.93  E-value=8.9  Score=32.39  Aligned_cols=39  Identities=21%  Similarity=0.408  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAI   82 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i   82 (321)
                      +.+++++......++..++.+...+..+...|.+...-+
T Consensus         5 ~~~l~~l~~~~~~l~~~~~~l~~~~~~l~~~~~e~~~~~   43 (140)
T PRK03947          5 EQELEELAAQLQALQAQIEALQQQLEELQASINELDTAK   43 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566666666666666655555555555555444444

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=90.68  E-value=11  Score=33.12  Aligned_cols=29  Identities=14%  Similarity=0.002  Sum_probs=21.3

Q ss_pred             hhhhhccCchhHHHHHHHHHHHHHHhHHH
Q 020809          202 LTEVHSAWLPPWLAVHLLQCQSLIETHWN  230 (321)
Q Consensus       202 l~e~~g~~l~Pwla~~~~~~~~~~~~~~~  230 (321)
                      +...||.+--|-|--.|..+......+..
T Consensus       131 l~~~~~~~~~P~ll~Dy~~~~~~~~~l~~  159 (177)
T PF13870_consen  131 LRQQGGLLGVPALLRDYDKTKEEVEELRK  159 (177)
T ss_pred             HHHhcCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            44567888889998888888877665543

>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea

Probab=90.68  E-value=5.6  Score=32.13  Aligned_cols=37  Identities=8%  Similarity=0.232  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHH
Q 020809           50 LKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKS   86 (321)
Q Consensus        50 lk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~   86 (321)
                      +-.+.+.++..+..+..++..++..+.+...-+.++.
T Consensus         4 ~~~~~q~l~~~~~~l~~~~~~l~~~~~E~~~v~~EL~   40 (105)
T cd00632           4 QLAQLQQLQQQLQAYIVQRQKVEAQLNENKKALEELE   40 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566666666666666666666655555554444

Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st

>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP

Probab=90.67  E-value=2.5  Score=30.90  Aligned_cols=45  Identities=20%  Similarity=0.339  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q 020809           74 VVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARAD  119 (321)
Q Consensus        74 ~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rir  119 (321)
                      +|+++...+..+..+|+.|.++|..++.+ -....+....++.||.
T Consensus         4 kid~Ls~dVq~L~~kvdqLs~dv~~lr~~-v~~ak~EAaRAN~RlD   48 (56)
T PF04728_consen    4 KIDQLSSDVQTLNSKVDQLSSDVNALRAD-VQAAKEEAARANQRLD   48 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence            34444444444445555555555444332 1222333445555554

The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.

>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site

Probab=90.63  E-value=24  Score=36.92  Aligned_cols=38  Identities=16%  Similarity=0.224  Sum_probs=24.3

Q ss_pred             HHHHhhccccchhHHhhhhhhhhh--hhhhHHHHHhccch
Q 020809          246 EKKAQAGKWVQPHVETIKAKWIPA--VKEQWVVFTTNVEP  283 (321)
Q Consensus       246 ~k~~~~~~~~~ph~~~~~~k~~p~--~~~~~~~~~~~~~p  283 (321)
                      .......+....-.+.+..+-+||  +.+.|..+...++.
T Consensus       351 ~~l~~l~~~~~~~~~~i~~~~~~yS~i~~~l~~~~~~l~~  390 (560)
T PF06160_consen  351 KQLKELEKRYEDLEERIEEQQVPYSEIQEELEEIEEQLEE  390 (560)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHHHHHH
Confidence            445566677777777888888886  55555555444433

EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=90.57  E-value=8.7  Score=40.48  Aligned_cols=80  Identities=25%  Similarity=0.432  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          106 NAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAI---EAEKKISDLSAKLEKLQKINDEQKSKIRKTERALK  182 (321)
Q Consensus       106 ~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~---e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq  182 (321)
                      .+++....++.+++.|+..|+.++++++..+.+...+..+..   -....+..+...++.|+....+....+++|++.+.
T Consensus       426 ~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~~~~~~~rei~~~~~~I~~L~~~L~e~~~~ve~L~~~l~  505 (652)
T COG2433         426 KLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLA  505 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444444433322222211   11124445556666666666666666666666665


Q ss_pred             HHH
Q 020809          183 VAE  185 (321)
Q Consensus       183 ~~E  185 (321)
                      .+.
T Consensus       506 ~l~  508 (652)
T COG2433         506 ELR  508 (652)
T ss_pred             HHH
Confidence            554

>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast)

Probab=90.52  E-value=9.8  Score=34.23  Aligned_cols=62  Identities=23%  Similarity=0.395  Sum_probs=33.6

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           70 GKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESE  133 (321)
Q Consensus        70 ~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele  133 (321)
                      .+...++.+++.+..+...|..|+..|....... .+- ..+..+-.++.+|+.++..|+++++
T Consensus        66 ~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~~~~r-~~~-~eR~~~l~~l~~l~~~~~~l~~el~  127 (188)
T PF03962_consen   66 KRQNKLEKLQKEIEELEKKIEELEEKIEEAKKGR-EES-EEREELLEELEELKKELKELKKELE  127 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccc-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555666666666666666666663322 111 2233344455666666666666665

The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].

>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences

Probab=90.37  E-value=2.2  Score=37.33  Aligned_cols=28  Identities=25%  Similarity=0.423  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           72 DEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        72 d~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      |.+|.+++.++.++...+..|.+++..+
T Consensus        78 d~ei~~L~~el~~l~~~~k~l~~eL~~L  105 (169)
T PF07106_consen   78 DAEIKELREELAELKKEVKSLEAELASL  105 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444444444

TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].

>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells

Probab=90.05  E-value=17  Score=34.11  Aligned_cols=31  Identities=16%  Similarity=0.233  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          161 EKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       161 e~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..+.....++..+++.+...+..+.....+.
T Consensus       181 ~~i~~~L~~~~~kL~Dl~~~l~eA~~~~~ea  211 (264)
T PF06008_consen  181 EAIRDDLNDYNAKLQDLRDLLNEAQNKTREA  211 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444445555555555554444444433

Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex

>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins

Probab=89.95  E-value=13  Score=32.75  Aligned_cols=51  Identities=18%  Similarity=0.276  Sum_probs=30.0

Q ss_pred             HHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           51 KSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        51 k~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      +.-|..+++.++++..--.....+...+.+++.++..++...-.+++.++.
T Consensus         5 ~~ti~~ie~sK~qIf~I~E~~R~E~~~l~~EL~evk~~v~~~I~evD~Le~   55 (159)
T PF05384_consen    5 KKTIDTIESSKEQIFEIAEQARQEYERLRKELEEVKEEVSEVIEEVDKLEK   55 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555666666665555555666666666666666666666555555543

The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction

>PRK15396 murein lipoprotein; Provisional

Probab=89.82  E-value=2.8  Score=32.70  Aligned_cols=13  Identities=31%  Similarity=0.488  Sum_probs=7.1

Q ss_pred             CchhHHHHHHHHH
Q 020809            1 MAASKLVIFSLFF   13 (321)
Q Consensus         1 ~~~~~~~~~~~~~   13 (321)
                      |...+|++.++.+
T Consensus         1 m~~~kl~l~av~l   13 (78)
T PRK15396          1 MNRTKLVLGAVIL   13 (78)
T ss_pred             CchhHHHHHHHHH
Confidence            5555666654443

>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]

Probab=89.75  E-value=28  Score=36.20  Aligned_cols=18  Identities=17%  Similarity=0.135  Sum_probs=8.4

Q ss_pred             hhhhcc-CchhHHHHHHHH
Q 020809          203 TEVHSA-WLPPWLAVHLLQ  220 (321)
Q Consensus       203 ~e~~g~-~l~Pwla~~~~~  220 (321)
                      ...||. |-+--++++...
T Consensus       314 ~~~~~~~fp~~~~aae~i~  332 (596)
T KOG4360|consen  314 ALSHGHHFPQLSLAAEKIE  332 (596)
T ss_pred             HHHhhhhCChhhHHHHHHH
Confidence            345564 444445555333

>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins

Probab=89.57  E-value=7.5  Score=36.63  Aligned_cols=54  Identities=24%  Similarity=0.309  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          107 AAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKL  160 (321)
Q Consensus       107 ~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~l  160 (321)
                      .-.|++.++.|+.+|+.++.....++...+.+...|.++--.+-.++.-+++--
T Consensus        84 VtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqSY~  137 (248)
T PF08172_consen   84 VTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQSYN  137 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc
Confidence            567888889999999988888888888888777777777666666666655544

These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane

>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6

Probab=89.52  E-value=4.2  Score=32.75  Aligned_cols=71  Identities=20%  Similarity=0.328  Sum_probs=44.8

Q ss_pred             HHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           61 IDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus        61 i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      ......+|..+|.+-.++...++.+..+.+.+..+|......+     +..+.+..+++.|+.+|..+..++....
T Consensus        24 ~~~~vd~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~-----~~~~~l~~e~~~lk~~i~~le~~~~~~e   94 (108)
T PF02403_consen   24 DEEDVDEIIELDQERRELQQELEELRAERNELSKEIGKLKKAG-----EDAEELKAEVKELKEEIKELEEQLKELE   94 (108)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTT-----CCTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCc-----ccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455677778888888888888888888888888887775433     2223344455555555555554444444

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....

>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function

Probab=89.47  E-value=2.5  Score=31.82  Aligned_cols=51  Identities=27%  Similarity=0.400  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          142 LEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAK  192 (321)
Q Consensus       142 LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~  192 (321)
                      ++.+..+++.++.-+...++.|.+.+.+|+..|+.+++.+..+...+..+.
T Consensus         2 le~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen    2 LEERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            577788888888888899999999999999999999998888877777663

It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.

>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms

Probab=89.46  E-value=17  Score=36.16  Aligned_cols=101  Identities=15%  Similarity=0.275  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           72 DEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEK  151 (321)
Q Consensus        72 d~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ek  151 (321)
                      ..-+++..+....++.....+...++.+..    ++....++...|=.-|+.+++.+-.+-.....+..+...+.+.+..
T Consensus       219 R~hleqm~~~~~~I~~~~~~~~~~L~kl~~----~i~~~lekI~sREk~iN~qle~l~~eYr~~~~~ls~~~~~y~~~s~  294 (359)
T PF10498_consen  219 RSHLEQMKQHKKSIESALPETKSQLDKLQQ----DISKTLEKIESREKYINNQLEPLIQEYRSAQDELSEVQEKYKQASE  294 (359)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            344444444444444444444444444432    3333344445555556666666666666666666666666666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          152 KISDLSAKLEKLQKINDEQKSKIRK  176 (321)
Q Consensus       152 k~~el~~~le~Lek~~~Eqk~~l~e  176 (321)
                      -+.++...+..+.....+.+..+++
T Consensus       295 ~V~~~t~~L~~IseeLe~vK~emee  319 (359)
T PF10498_consen  295 GVSERTRELAEISEELEQVKQEMEE  319 (359)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666665555555555555555544

Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.

>PF03148 Tektin: Tektin family; InterPro: IPR000435 Tektin heteropolymers form unique protofilaments of flagellar microtubules []

Probab=89.42  E-value=24  Score=35.12  Aligned_cols=54  Identities=15%  Similarity=0.291  Sum_probs=29.9

Q ss_pred             HhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 020809           66 QELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE  120 (321)
Q Consensus        66 ~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire  120 (321)
                      +.|.+......+++..+.....+|..++..|..+++ ...+.+.-.-.+..|+..
T Consensus       251 ~Ri~et~~ak~~Le~ql~~~~~ei~~~e~~i~~L~~-ai~~k~~~lkvaqTRL~~  304 (384)
T PF03148_consen  251 KRIHETQEAKNELEWQLKKTLQEIAEMEKNIEDLEK-AIRDKEGPLKVAQTRLEN  304 (384)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH-HHHHHHhhHHHHHHHHhh
Confidence            334444555555556666666666666666666644 444444555555566555

The proteins are predicted to form extended rods composed of 2 alpha- helical segments (~180 residues long) capable of forming coiled coils, interrupted by non-helical linkers []. The 2 segments are similar in sequence, indicating a gene duplication event. Along each tektin rod, cysteine residues occur with a periodicity of ~8nm, coincident with the axial repeat of tubulin dimers in microtubules []. It is proposed that the assembly of tektin heteropolymers produces filaments with repeats of 8, 16, 24, 32, 40, 48 and 96nm, generating the basis for the complex spatial arrangements of axonemal components [].; GO: 0000226 microtubule cytoskeleton organization, 0005874 microtubule

>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]

Probab=89.38  E-value=18  Score=38.47  Aligned_cols=110  Identities=18%  Similarity=0.265  Sum_probs=63.9

Q ss_pred             CCCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hhHHHHHHHHHHH
Q 020809           38 VDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK--ETLNAAEQVDKAH  115 (321)
Q Consensus        38 ~~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~--~~~~~eeq~~~~~  115 (321)
                      .+-..++-.|..|......|.=+.+-++.++..--++|..+|.-|.+...+++..+.-+   |.+  ....+|.|.-.+-
T Consensus       104 ~~~~~yQerLaRLe~dkesL~LQvsvLteqVeaQgEKIrDLE~cie~kr~kLnatEEmL---QqellsrtsLETqKlDLm  180 (861)
T KOG1899|consen  104 PEYPEYQERLARLEMDKESLQLQVSVLTEQVEAQGEKIRDLETCIEEKRNKLNATEEML---QQELLSRTSLETQKLDLM  180 (861)
T ss_pred             CcchHHHHHHHHHhcchhhheehHHHHHHHHHHhhhhHHHHHHHHHHHHhhhchHHHHH---HHHHHhhhhHHHHHhHHH
Confidence            35556777777777777777777777777777777788888888877777766555433   222  2234454444444


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          116 ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLS  157 (321)
Q Consensus       116 ~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~  157 (321)
                      +.|.+|+-.+..++++.       .+.|.+.+..+..+.+++
T Consensus       181 aevSeLKLkltalEkeq-------~e~E~K~R~se~l~qevn  215 (861)
T KOG1899|consen  181 AEVSELKLKLTALEKEQ-------NETEKKLRLSENLMQEVN  215 (861)
T ss_pred             HHHHHhHHHHHHHHHHh-------hhHHHHHHhHHHHHHHHH
Confidence            45554444444443333       334444444444444444

>PRK04406 hypothetical protein; Provisional

Probab=89.31  E-value=4.3  Score=31.26  Aligned_cols=51  Identities=22%  Similarity=0.241  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMR  190 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~k  190 (321)
                      ..+++|..++|.++.-....++.|.+.+.+|+..|+.+.+.++.+-..+..
T Consensus         7 ~~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~   57 (75)
T PRK04406          7 EQLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKN   57 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            457888888888888999999999999999999999999887777555443

>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]

Probab=89.22  E-value=19  Score=33.50  Aligned_cols=47  Identities=19%  Similarity=0.241  Sum_probs=20.9

Q ss_pred             HHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           55 RSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        55 ~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      .-|+.-|.+...++......+.+.-..-..++.+++.++..+...+.
T Consensus        27 ~~l~Q~ird~~~~l~~ar~~~A~~~a~~k~~e~~~~~~~~~~~k~e~   73 (225)
T COG1842          27 KMLEQAIRDMESELAKARQALAQAIARQKQLERKLEEAQARAEKLEE   73 (225)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444444444444444444444433

>PF02994 Transposase_22: L1 transposable element; InterPro: IPR004244 Many human L1 elements are capable of retrotransposition

Probab=89.20  E-value=1.5  Score=43.49  Aligned_cols=11  Identities=45%  Similarity=0.709  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHH
Q 020809           88 RIVSLQKELSS   98 (321)
Q Consensus        88 ~I~~Lq~eI~~   98 (321)
                      .+..+..+|..
T Consensus       106 ~~~elkkEie~  116 (370)
T PF02994_consen  106 RIKELKKEIEN  116 (370)
T ss_dssp             -----------
T ss_pred             HHHHHHHHHHH
Confidence            33333333333

Some of these have been shown to exhibit reverse transcriptase (RT) activity [] although the function of many are, as yet, unknown. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 2LDY_A 3SOO_A 2YKQ_A 2YKO_C 2YKP_B 2W7A_B 2JRB_A.

>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []

Probab=89.19  E-value=21  Score=34.17  Aligned_cols=48  Identities=25%  Similarity=0.388  Sum_probs=24.3

Q ss_pred             HHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           52 SKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        52 ~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .+|.+|+++.+.+.++-..+.-.|+.++.-+..-..+...-.+++..+
T Consensus        18 qKIqelE~QldkLkKE~qQrQfQleSlEAaLqKQKqK~e~ek~e~s~L   65 (307)
T PF10481_consen   18 QKIQELEQQLDKLKKERQQRQFQLESLEAALQKQKQKVEEEKNEYSAL   65 (307)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence            456666666666655555555555555544444444433333333333

Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].

>PF13166 AAA_13: AAA domain

Probab=89.10  E-value=34  Score=36.34  Aligned_cols=14  Identities=29%  Similarity=0.430  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHHHH
Q 020809           84 DKSERIVSLQKELS   97 (321)
Q Consensus        84 e~~~~I~~Lq~eI~   97 (321)
                      ++...+..+...|+
T Consensus       326 ~~~~~~~~l~~~l~  339 (712)
T PF13166_consen  326 ELKSAIEALKEELE  339 (712)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333333443333

>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional

Probab=89.08  E-value=29  Score=37.47  Aligned_cols=47  Identities=11%  Similarity=0.232  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          141 ALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       141 ~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .|..+.+.++.+++.++..+..+-.    .+..+..++++.+..+..+..+
T Consensus       343 ~l~~~~~~L~~~~~~l~~~~~~~p~----~e~~~~~L~R~~~~~~~lY~~l  389 (726)
T PRK09841        343 ALLEKRQTLEQERKRLNKRVSAMPS----TQQEVLRLSRDVEAGRAVYLQL  389 (726)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccH----HHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444443332    3444445555555555544443

>PF05335 DUF745: Protein of unknown function (DUF745); InterPro: IPR007999 This family consists of several uncharacterised Drosophila melanogaster proteins of unknown function

Probab=88.99  E-value=17  Score=32.84  Aligned_cols=106  Identities=19%  Similarity=0.282  Sum_probs=46.0

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           68 LKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAI  147 (321)
Q Consensus        68 Lk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~  147 (321)
                      |.++...+++++.++.+-+.-+......|..++. .-.....       -......++..|+.-+..-+......+.-..
T Consensus        62 L~GKq~iveqLe~ev~EAe~vV~ee~~sL~~aq~-na~aA~~-------aa~~A~~q~~~L~~~l~~a~~nl~~a~~~a~  133 (188)
T PF05335_consen   62 LAGKQQIVEQLEQEVREAEAVVQEEKASLQQAQA-NAQAAQR-------AAQQAQQQLETLKAALKAAQANLANAEQVAE  133 (188)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555554444444444433 1122222       2222333344444444444444444444444


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          148 EAEKKISDLSAKLEKLQKINDEQKSKIRKTERAL  181 (321)
Q Consensus       148 e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~l  181 (321)
                      .+...+.+-...++......+....++.....++
T Consensus       134 ~AQ~el~eK~qLLeaAk~Rve~L~~QL~~Ar~D~  167 (188)
T PF05335_consen  134 GAQQELAEKTQLLEAAKRRVEELQRQLQAARADY  167 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444445444444444444444444333

>TIGR00634 recN DNA repair protein RecN

Probab=88.93  E-value=32  Score=35.88  Aligned_cols=43  Identities=5%  Similarity=0.017  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDK   85 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~   85 (321)
                      +..+..++..+...+...+.+...+.......++.++-.+.++
T Consensus       159 ~~~~~~~~~~~~~~~~~~L~~l~~~~~~~~~eld~L~~ql~EL  201 (563)
T TIGR00634       159 KVKAYRELYQAWLKARQQLKDRQQKEQELAQRLDFLQFQLEEL  201 (563)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444333334444444443333333

All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.

>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=88.86  E-value=42  Score=37.12  Aligned_cols=75  Identities=33%  Similarity=0.484  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          117 RADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       117 RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      |.+.+...++.+...+...-.....+.........+.......+..+.....+....+..+...+......+..+
T Consensus       362 ~~~~l~~~~~~l~~~~~~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~~~~~~~~  436 (908)
T COG0419         362 RLKELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEELEEEIKKL  436 (908)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444442222222233333333333333344444444444444444444444444444444433

>PRK02119 hypothetical protein; Provisional

Probab=88.82  E-value=2.9  Score=32.02  Aligned_cols=51  Identities=16%  Similarity=0.268  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           48 DQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS   98 (321)
Q Consensus        48 ~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~   98 (321)
                      ..+..+|.+||..+.=...-|.+++..+..-++.|..+..++..|...+..
T Consensus         5 ~~~e~Ri~~LE~rla~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~~rl~~   55 (73)
T PRK02119          5 QNLENRIAELEMKIAFQENLLEELNQALIEQQFVIDKMQVQLRYMANKLKD   55 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            334444444444444444444444555555555555555555555444443

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=88.79  E-value=45  Score=37.38  Aligned_cols=12  Identities=17%  Similarity=0.047  Sum_probs=4.3

Q ss_pred             hhhcHHHHHHHH
Q 020809           67 ELKGKDEVVAQK   78 (321)
Q Consensus        67 eLk~kd~~I~q~   78 (321)
                      ++..+.+.|.+.
T Consensus       416 k~e~Leeri~ql  427 (1195)
T KOG4643|consen  416 KHEILEERINQL  427 (1195)
T ss_pred             HHHHHHHHHHHH
Confidence            333333333333

>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length

Probab=88.76  E-value=9  Score=33.45  Aligned_cols=48  Identities=21%  Similarity=0.278  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHhHHHHHHhhhcHHHHHHHHHH---HHHHHHHHHHHHHHHHH
Q 020809           50 LKSKIRSLESHIDEKTQELKGKDEVVAQKEK---AIQDKSERIVSLQKELS   97 (321)
Q Consensus        50 lk~ki~~Les~i~e~~~eLk~kd~~I~q~ek---~i~e~~~~I~~Lq~eI~   97 (321)
                      .+.+...++.+.+.+..+|...+..|..+.+   .+.+++.+|..|+....
T Consensus        18 ~K~~~~~~~~e~~~~k~ql~~~d~~i~~Lk~~~~d~eeLk~~i~~lq~~~~   68 (155)
T PF06810_consen   18 PKAKVDKVKEERDNLKTQLKEADKQIKDLKKSAKDNEELKKQIEELQAKNK   68 (155)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHH
Confidence            4444445555555555555555555555554   55555555555555554

The function of this family is unknown.; GO: 0005198 structural molecule activity

>PRK04406 hypothetical protein; Provisional

Probab=88.76  E-value=3.6  Score=31.68  Aligned_cols=51  Identities=16%  Similarity=0.335  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .+..+|.+||..+.=...-|.+++..+.+-++.|..+..++..|...+.+.
T Consensus         8 ~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~   58 (75)
T PRK04406          8 QLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKNM   58 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            344444445444444444444445555555555555555555555444443

>PF10368 YkyA: Putative cell-wall binding lipoprotein; InterPro: IPR019454 The YkyA family of proteins contain a lipoprotein signal and a hydrolase domain

Probab=88.74  E-value=13  Score=33.86  Aligned_cols=70  Identities=17%  Similarity=0.231  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          109 EQVDKAHARADELEKQIDNLKKESEKQQKEKEAL---EARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTE  178 (321)
Q Consensus       109 eq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~L---Ea~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE  178 (321)
                      +-...++.|-.........+.+-+...+.==..|   +.....+..++..+|.....+.+..........+-.
T Consensus       119 ~l~~~~~~ry~~~~~l~~~Y~~~l~~ekely~~L~~~d~~~~~l~~ki~~iN~~y~~~~~~~~~fn~~t~~yN  191 (204)
T PF10368_consen  119 ELNEAMKKRYKSYDKLYKAYKKALELEKELYEMLKDKDTTQKQLDEKIKAINQSYKEVNKQKEKFNEYTKKYN  191 (204)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444455555555555555554333111111   122334444555555555555554444444444433

They are similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely that they function in pathways important for pathogenicity []. ; PDB: 2AP3_A.

>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure

Probab=88.74  E-value=8  Score=28.70  Aligned_cols=44  Identities=34%  Similarity=0.546  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           92 LQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus        92 Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      ++.++..++. .....+.+...+..|.++|..+|+.|+.+++..+
T Consensus        16 ~~eEL~kvk~-~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r   59 (61)
T PF08826_consen   16 IQEELTKVKS-ANLAFESKLQEAEKRNRELEQEIERLKKEMEELR   59 (61)
T ss_dssp             HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4445544422 4466677777788888888888888888887765

It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.

>KOG4673 consensus Transcription factor TMF, TATA element modulatory factor [Transcription]

Probab=88.67  E-value=39  Score=36.46  Aligned_cols=45  Identities=22%  Similarity=0.218  Sum_probs=28.9

Q ss_pred             HHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           57 LESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        57 Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      |-.++-..+..|+.+..++.+.++....+-..|..|+++...++.
T Consensus       465 LSK~ql~qs~iIkKLRAk~ke~etl~~K~ge~i~~L~sE~~~lk~  509 (961)
T KOG4673|consen  465 LSKKQLAQSAIIKKLRAKIKEAETLEEKKGELITKLQSEENKLKS  509 (961)
T ss_pred             hHHHHHHHHHHHHHHHHHhhhhhHHHHHhhhHHHHHHHHHHHHHH
Confidence            333344444556677777777777777777777778777766643

>PRK02119 hypothetical protein; Provisional

Probab=88.64  E-value=4.1  Score=31.20  Aligned_cols=52  Identities=29%  Similarity=0.260  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..+++|..++|.++.-....++.|.+.+.+|+..|+.+.+.+..+-..+..+
T Consensus         5 ~~~e~Ri~~LE~rla~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~~rl~~~   56 (73)
T PRK02119          5 QNLENRIAELEMKIAFQENLLEELNQALIEQQFVIDKMQVQLRYMANKLKDM   56 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4578888888888899999999999999999999999998877775555443

>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]

Probab=88.52  E-value=30  Score=35.08  Aligned_cols=19  Identities=37%  Similarity=0.531  Sum_probs=10.1

Q ss_pred             chHHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLES   59 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les   59 (321)
                      ..+-.++++|+.+.-.||.
T Consensus       132 n~Lsrkl~qLr~ek~~lEq  150 (552)
T KOG2129|consen  132 NPLSRKLKQLRHEKLPLEQ  150 (552)
T ss_pred             CchhHHHHHHHhhhccHHH
Confidence            3455566677655444433

>PRK02793 phi X174 lysis protein; Provisional

Probab=88.45  E-value=4.4  Score=30.90  Aligned_cols=51  Identities=22%  Similarity=0.308  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          141 ALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       141 ~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .+++|..++|.++.-....++.|.+.+.+|+..|+.+.+.+..+-..+..+
T Consensus         5 ~~e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~   55 (72)
T PRK02793          5 SLEARLAELESRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLKAS   55 (72)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            477888888889999999999999999999999999998877776655543

>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]

Probab=88.29  E-value=34  Score=36.46  Aligned_cols=83  Identities=19%  Similarity=0.285  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQ  124 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~  124 (321)
                      -+......||.+||.-|.+-...|...++.+.+.=-.+..++.+--+|..+|.+++- +...+|......+++.|.-+..
T Consensus       132 eqVeaQgEKIrDLE~cie~kr~kLnatEEmLQqellsrtsLETqKlDLmaevSeLKL-kltalEkeq~e~E~K~R~se~l  210 (861)
T KOG1899|consen  132 EQVEAQGEKIRDLETCIEEKRNKLNATEEMLQQELLSRTSLETQKLDLMAEVSELKL-KLTALEKEQNETEKKLRLSENL  210 (861)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHhhhchHHHHHHHHHHhhhhHHHHHhHHHHHHHHhHH-HHHHHHHHhhhHHHHHHhHHHH
Confidence            344555666666777776666666666666655544455556666666666666633 3344554444555555554444


Q ss_pred             HHHH
Q 020809          125 IDNL  128 (321)
Q Consensus       125 Ie~L  128 (321)
                      ++.+
T Consensus       211 ~qev  214 (861)
T KOG1899|consen  211 MQEV  214 (861)
T ss_pred             HHHH
Confidence            4443

>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []

Probab=88.25  E-value=29  Score=34.50  Aligned_cols=18  Identities=22%  Similarity=0.348  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHhH
Q 020809           44 KIELDQLKSKIRSLESHI   61 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i   61 (321)
                      -..+-++..+|..||+.+
T Consensus       208 la~~a~LE~RL~~LE~~l  225 (388)
T PF04912_consen  208 LARAADLEKRLARLESAL  225 (388)
T ss_pred             HHHHHHHHHHHHHHHHHh
Confidence            345566666666666544

It is also thought to modulate cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organisation during mitosis. Dynamitin is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development []. ; GO: 0007017 microtubule-based process, 0005869 dynactin complex

>PRK00295 hypothetical protein; Provisional

Probab=88.17  E-value=4.9  Score=30.30  Aligned_cols=50  Identities=18%  Similarity=0.191  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          142 LEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       142 LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ++++..++|.++.-....++.|.+.+.+|+..|+.+.+.+..+-..+..+
T Consensus         3 ~e~Ri~~LE~kla~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~~   52 (68)
T PRK00295          3 LEERVTELESRQAFQDDTIQALNDVLVEQQRVIERLQLQMAALIKRQEEM   52 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            56777788888888888899999999999999999998877776655554

>PRK00736 hypothetical protein; Provisional

Probab=88.09  E-value=4.2  Score=30.68  Aligned_cols=50  Identities=20%  Similarity=0.299  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          142 LEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       142 LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ++.+..++|.++......++.|.+.+.+|+..|+.+.+.+..+-+.+...
T Consensus         3 ~e~Ri~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~   52 (68)
T PRK00736          3 AEERLTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSL   52 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            56677788888888888999999999999999999998877776665443

>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function

Probab=87.96  E-value=11  Score=32.04  Aligned_cols=56  Identities=13%  Similarity=0.309  Sum_probs=37.5

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      ++-++|+++-..   |.+....++++|+.+|.+|++.....+.+.+++..+...++...
T Consensus        47 ~v~kql~~vs~~---l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~  102 (126)
T PF07889_consen   47 SVSKQLEQVSES---LSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIG  102 (126)
T ss_pred             HHHHHHHHHHHH---HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            445566555544   44555566677888888888887777777777777777666663

The region featured in this family is approximately 100 amino acids long.

>PRK04325 hypothetical protein; Provisional

Probab=87.95  E-value=5.2  Score=30.69  Aligned_cols=51  Identities=18%  Similarity=0.221  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          141 ALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       141 ~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .++.+..++|.++.-....++.|.+.+.+|+..|+.+.+.+..+-..+..+
T Consensus         6 ~~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~~   56 (74)
T PRK04325          6 EMEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQMRDA   56 (74)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            467777788888888888899999999999999999998877775555443

>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function

Probab=87.71  E-value=3  Score=31.39  Aligned_cols=48  Identities=23%  Similarity=0.414  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ..|.+|+.++.-.+..++++       +..+..-+..|..+..++..|...|.+.
T Consensus         4 ~Ri~~LE~~la~qe~~ie~L-------n~~v~~Qq~~I~~L~~~l~~L~~rl~~~   51 (69)
T PF04102_consen    4 ERIEELEIKLAFQEDTIEEL-------NDVVTEQQRQIDRLQRQLRLLRERLREL   51 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHT----
T ss_pred             HHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444444444444444444       4444444444444444444444444443

It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=87.60  E-value=36  Score=34.83  Aligned_cols=63  Identities=14%  Similarity=0.308  Sum_probs=30.1

Q ss_pred             HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           73 EVVAQKEK-AIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus        73 ~~I~q~ek-~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      ..+.+.++ +++........+-.+.++++. .+.+++........|+..|+..+.++.+++...+
T Consensus       339 ~~~~e~~qsqlen~k~~~e~~~~e~~~l~~-~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~~  402 (493)
T KOG0804|consen  339 QIMSEYEQSQLENQKQYYELLITEADSLKQ-ESSDLEAEKKIVERKLQQLQTKLKKCQKELKEER  402 (493)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHhhhh-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333 444444444444444444433 3444555555555555555555555555554444

>PRK04325 hypothetical protein; Provisional

Probab=87.50  E-value=4.1  Score=31.26  Aligned_cols=48  Identities=15%  Similarity=0.281  Sum_probs=23.4

Q ss_pred             HHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           52 SKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        52 ~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .+|.+||..+.=...-|..++..|.+-++.|..+..++..|..++.+.
T Consensus         9 ~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~~   56 (74)
T PRK04325          9 DRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQMRDA   56 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            334444444444434444445555555555555555555555555444

>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]

Probab=87.42  E-value=38  Score=34.95  Aligned_cols=15  Identities=27%  Similarity=0.454  Sum_probs=6.0

Q ss_pred             HHHHHHHHHHHHHHH
Q 020809           85 KSERIVSLQKELSSL   99 (321)
Q Consensus        85 ~~~~I~~Lq~eI~~~   99 (321)
                      ++..|..|...-..+
T Consensus       293 ~s~~i~~l~ek~r~l  307 (622)
T COG5185         293 ISQKIKTLREKWRAL  307 (622)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            334444444433333

>PF10212 TTKRSYEDQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019348 This entry represents a C-terminal 500 residue region, which contains a conserved TTKRSYEDQ motif

Probab=87.26  E-value=19  Score=37.37  Aligned_cols=21  Identities=14%  Similarity=0.291  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 020809          142 LEARAIEAEKKISDLSAKLEK  162 (321)
Q Consensus       142 LEa~a~e~ekk~~el~~~le~  162 (321)
                      .|...+.+-..+..+|.++..
T Consensus       485 YE~QLs~MSEHLasmNeqL~~  505 (518)
T PF10212_consen  485 YEEQLSMMSEHLASMNEQLAK  505 (518)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333

It is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain an N-terminal domain with a KLRAQ motif (IPR019343 from INTERPRO). The function of these proteins is not known.

>KOG4809 consensus Rab6 GTPase-interacting protein involved in endosome-to-TGN transport [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.25  E-value=42  Score=35.22  Aligned_cols=77  Identities=26%  Similarity=0.335  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE  120 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire  120 (321)
                      .+.+...|..+|+.++....+....+..+.+...++-.-+..+.+.+.+++--|++- ++.-.+.+.+.-+++.+..+
T Consensus       336 ~~ke~kdLkEkv~~lq~~l~eke~sl~dlkehassLas~glk~ds~Lk~leIalEqk-kEec~kme~qLkkAh~~~dd  412 (654)
T KOG4809|consen  336 FRKENKDLKEKVNALQAELTEKESSLIDLKEHASSLASAGLKRDSKLKSLEIALEQK-KEECSKMEAQLKKAHNIEDD  412 (654)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHH-HHHHHHHHHHHHHHHHhhHh
Confidence            333344444444444443333333333333333333333333333333333322222 22233344444444444443

>COG3206 GumC Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]

Probab=87.18  E-value=30  Score=34.94  Aligned_cols=61  Identities=18%  Similarity=0.265  Sum_probs=31.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHH---HHHHHHHH-HHHHHHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKD---EVVAQKEK-AIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd---~~I~q~ek-~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ...+++.++...+.+....+.......+.+....   ........ .|+.+..++..+...|...
T Consensus       240 ~~~~ln~ql~~~~~~~~~~~a~l~~~~~~~~~~~~~~~~~~~~~s~~i~~Lr~~~~~~~~~~~~l  304 (458)
T COG3206         240 QLSALNTQLQSARARLAQAEARLASLLQLLPLGREAAALREVLESPTIQDLRQQYAQVRQQIADL  304 (458)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhHHhccHHHHHHHHHHHHHHHHHHHH
Confidence            4445566666666666666665555555554444   22222222 2555555555555555555

>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans

Probab=87.12  E-value=36  Score=34.32  Aligned_cols=41  Identities=22%  Similarity=0.245  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          124 QIDNLKKESEKQQKEK-EALEARAIEAEKKISDLSAKLEKLQ  164 (321)
Q Consensus       124 ~Ie~Lk~ele~~~~kk-~~LEa~a~e~ekk~~el~~~le~Le  164 (321)
                      +|..|+.++..+..+. -....|++++.+-++..+..+..|+
T Consensus       277 Ei~~LKqeLa~~EEK~~Yqs~eRaRdi~E~~Es~qtRisklE  318 (395)
T PF10267_consen  277 EIYNLKQELASMEEKMAYQSYERARDIWEVMESCQTRISKLE  318 (395)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            3666666666666544 3445666666666666666666666

Its function is unknown.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=87.02  E-value=11  Score=28.49  Aligned_cols=23  Identities=26%  Similarity=0.419  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 020809          111 VDKAHARADELEKQIDNLKKESE  133 (321)
Q Consensus       111 ~~~~~~RireL~k~Ie~Lk~ele  133 (321)
                      .+.+-.++.+|+.+++.|+++++
T Consensus        42 l~~a~~e~~~Lk~E~e~L~~el~   64 (69)
T PF14197_consen   42 LGDAYEENNKLKEENEALRKELE   64 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444444433

>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins

Probab=87.00  E-value=21  Score=31.48  Aligned_cols=33  Identities=12%  Similarity=0.328  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVA   76 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~   76 (321)
                      +++.+.++..+.++...+..+-.+.+.+...-.
T Consensus        26 R~E~~~l~~EL~evk~~v~~~I~evD~Le~~er   58 (159)
T PF05384_consen   26 RQEYERLRKELEEVKEEVSEVIEEVDKLEKRER   58 (159)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444333333333333

The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction

>PF12072 DUF3552: Domain of unknown function (DUF3552); InterPro: IPR022711 This presumed domain is functionally uncharacterised

Probab=86.65  E-value=24  Score=31.87  Aligned_cols=106  Identities=21%  Similarity=0.369  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH--H
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE--L  121 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire--L  121 (321)
                      +.++..+..++..-+..++.....|......|...+..|......+.....+++.+.......++.-.+-...-++.  |
T Consensus        77 ~~el~~~E~rl~~rE~~L~~~~~~L~~~e~~l~~~~~~l~~~~~~l~~~~~e~~~~~~~~~~~Le~iAglT~eEAk~~Ll  156 (201)
T PF12072_consen   77 RKELQRLEKRLQQREEQLDRRLEQLEKREEELEKKEEELEQRKEELEEREEELEELIEEQQQELEEIAGLTAEEAKEILL  156 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHH


Q ss_pred             HHHHHHHHHHHHHHHHHH-----HHHHHHHHHH
Q 020809          122 EKQIDNLKKESEKQQKEK-----EALEARAIEA  149 (321)
Q Consensus       122 ~k~Ie~Lk~ele~~~~kk-----~~LEa~a~e~  149 (321)
                      +..-+.++.+....-.+.     ...+.+++.+
T Consensus       157 ~~le~e~~~e~a~~ir~~eeeak~~A~~~Ar~I  189 (201)
T PF12072_consen  157 EKLEEEARREAAALIRRIEEEAKEEADKKARRI  189 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH

This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with PF00013 from PFAM, PF01966 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity

>KOG2991 consensus Splicing regulator [RNA processing and modification]

Probab=86.43  E-value=31  Score=32.90  Aligned_cols=66  Identities=18%  Similarity=0.246  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          125 IDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMR  190 (321)
Q Consensus       125 Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~k  190 (321)
                      |..|..++.-++...++|.+...++.+-+.++..-++-++..+-=...+|.+.++.++.++.....
T Consensus       238 ia~Le~eLAmQKs~seElkssq~eL~dfm~eLdedVEgmqsTiliLQq~Lketr~~Iq~l~k~~~q  303 (330)
T KOG2991|consen  238 IAELEIELAMQKSQSEELKSSQEELYDFMEELDEDVEGMQSTILILQQKLKETRKEIQRLKKGLEQ  303 (330)
T ss_pred             HHHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            778888888888777888888888888777777777777776666666666666555555444433

>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules

Probab=86.40  E-value=27  Score=32.12  Aligned_cols=34  Identities=12%  Similarity=0.192  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 020809          167 NDEQKSKIRKTERALKVAEEEMMRAKFEATSRSK  200 (321)
Q Consensus       167 ~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~  200 (321)
                      .......+..+...+...+..+..++.....+.+
T Consensus       156 ~~~~~~e~~aLqa~lkk~e~~~~SLe~~LeQK~k  189 (207)
T PF05010_consen  156 RSKHQAELLALQASLKKEEMKVQSLEESLEQKTK  189 (207)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444555555555555555444444433

The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].

>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.35  E-value=28  Score=32.41  Aligned_cols=36  Identities=22%  Similarity=0.176  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 020809          163 LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSR  198 (321)
Q Consensus       163 Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~  198 (321)
                      |+.+..+.+..............+++..+..+.+.+
T Consensus        65 lE~iIkqa~~er~~~~~~i~r~~eey~~Lk~~in~~  100 (230)
T PF10146_consen   65 LENIIKQAESERNKRQEKIQRLYEEYKPLKDEINEL  100 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333334444444444444433

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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.

>PF00769 ERM: Ezrin/radixin/moesin family; InterPro: IPR011259 The ERM family consists of three closely-related proteins, ezrin, radixin and moesin []

Probab=86.17  E-value=30  Score=32.44  Aligned_cols=14  Identities=21%  Similarity=0.359  Sum_probs=6.7

Q ss_pred             hhhhHHHHHhccch
Q 020809          270 VKEQWVVFTTNVEP  283 (321)
Q Consensus       270 ~~~~~~~~~~~~~p  283 (321)
                      +..++..++.-+++
T Consensus       187 lq~QL~~L~~EL~~  200 (246)
T PF00769_consen  187 LQEQLKELKSELEQ  200 (246)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHH
Confidence            44455555544443

Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain; an extended alpha-helical domain; and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament-plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains [].; GO: 0008092 cytoskeletal protein binding, 0005737 cytoplasm, 0019898 extrinsic to membrane; PDB: 2I1J_A 2I1K_A 1E5W_A 1EF1_C.

>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain

Probab=86.01  E-value=36  Score=33.21  Aligned_cols=17  Identities=29%  Similarity=0.407  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHhHHHH
Q 020809           48 DQLKSKIRSLESHIDEK   64 (321)
Q Consensus        48 ~qlk~ki~~Les~i~e~   64 (321)
                      +++...+..|+++-..+
T Consensus        23 ~~l~~~~~sL~qen~~L   39 (310)
T PF09755_consen   23 EQLRKRIESLQQENRVL   39 (310)
T ss_pred             HHHHHHHHHHHHHhHHH
Confidence            44444444444443333

>PRK00846 hypothetical protein; Provisional

Probab=85.96  E-value=7.4  Score=30.24  Aligned_cols=52  Identities=21%  Similarity=0.276  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..+++|..++|.++.-....++.|.+.+..|+..|+.+.+.+..+-+.+..+
T Consensus         9 ~~le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~   60 (77)
T PRK00846          9 QALEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKV   60 (77)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5678888888888888888999999999999999999998877776666554

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.86  E-value=3.9  Score=38.89  Aligned_cols=18  Identities=39%  Similarity=0.671  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHhHHHH
Q 020809           47 LDQLKSKIRSLESHIDEK   64 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e~   64 (321)
                      +.+++++|..|+..++++
T Consensus        58 ~~~l~~Ql~~l~g~i~~L   75 (262)
T COG1729          58 LTQLEQQLRQLQGKIEEL   75 (262)
T ss_pred             cHHHHHHHHHHHhhHHHH
Confidence            444444444444444443

>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules

Probab=85.82  E-value=28  Score=31.92  Aligned_cols=32  Identities=22%  Similarity=0.352  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          106 NAAEQVDKAHARADELEKQIDNLKKESEKQQK  137 (321)
Q Consensus       106 ~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~  137 (321)
                      .++.....+..|..-++..|+.++..=+..+.
T Consensus        87 s~E~sfsdl~~ryek~K~vi~~~k~NEE~Lkk  118 (207)
T PF05010_consen   87 SLEKSFSDLHKRYEKQKEVIEGYKKNEETLKK  118 (207)
T ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            34444444444555455555555444444443

The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].

>PF14282 FlxA: FlxA-like protein

Probab=85.61  E-value=3.6  Score=33.60  Aligned_cols=20  Identities=25%  Similarity=0.424  Sum_probs=7.9

Q ss_pred             HHHHHHHHhHHHHHHhhhcH
Q 020809           52 SKIRSLESHIDEKTQELKGK   71 (321)
Q Consensus        52 ~ki~~Les~i~e~~~eLk~k   71 (321)
                      ..|..|+.+|..+.++|..+
T Consensus        19 ~~I~~L~~Qi~~Lq~ql~~l   38 (106)
T PF14282_consen   19 SQIEQLQKQIKQLQEQLQEL   38 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33444444444443333333

>PF13851 GAS: Growth-arrest specific micro-tubule binding

Probab=85.60  E-value=28  Score=31.63  Aligned_cols=38  Identities=29%  Similarity=0.371  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSA  158 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~  158 (321)
                      ++..+..+..++...+-+-+.|+.+-..++....++..
T Consensus        91 ~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~  128 (201)
T PF13851_consen   91 LKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELYR  128 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444444444444333

>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional

Probab=85.34  E-value=44  Score=36.07  Aligned_cols=37  Identities=8%  Similarity=0.064  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHH
Q 020809           50 LKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKS   86 (321)
Q Consensus        50 lk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~   86 (321)
                      ++.+.....+.++=+.+++..+..+++..|..+++..
T Consensus       258 l~~k~~~a~~a~~fL~~qL~~l~~~L~~aE~~l~~fr  294 (726)
T PRK09841        258 IARQAAQDSQSLEFLQRQLPEVRSELDQAEEKLNVYR  294 (726)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444455555555555555555555444443

>KOG0962 consensus DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair]

Probab=85.26  E-value=76  Score=36.61  Aligned_cols=50  Identities=20%  Similarity=0.315  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           48 DQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS   97 (321)
Q Consensus        48 ~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~   97 (321)
                      ..++..|.+.+..++....+..+.+..+...++.|.++...+..++..+.
T Consensus       219 e~~~l~i~~~~~ki~~~ke~v~e~e~e~~~~~~~i~ei~~~~~el~k~~~  268 (1294)
T KOG0962|consen  219 EVLRLNIHSGQRKIEKSKEEVSELENELGPIEAKIEEIEKSLKELEKLLK  268 (1294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555556655555555566665555555555554444444433

>PF05483 SCP-1: Synaptonemal complex protein 1 (SCP-1); InterPro: IPR008827 Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex

Probab=85.24  E-value=59  Score=35.04  Aligned_cols=58  Identities=22%  Similarity=0.336  Sum_probs=28.6

Q ss_pred             HHHHH-HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELD-QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        44 ~~el~-qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      ++++. .++.....++.--++...++..++.++.-++..+.+++..|..|...+..++.
T Consensus       210 r~EM~fKlKE~~~k~~~leeey~~E~n~kEkqvs~L~~q~~eKen~~kdl~~~l~es~~  268 (786)
T PF05483_consen  210 RQEMHFKLKEDYEKFEDLEEEYKKEVNDKEKQVSLLQTQLKEKENKIKDLLLLLQESQD  268 (786)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHH
Confidence            34443 34443444444444444555555555555555555555555555555554443

Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase [].; GO: 0007130 synaptonemal complex assembly, 0000795 synaptonemal complex

>PRK11519 tyrosine kinase; Provisional

Probab=85.21  E-value=59  Score=35.04  Aligned_cols=45  Identities=16%  Similarity=0.299  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          142 LEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMR  190 (321)
Q Consensus       142 LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~k  190 (321)
                      +..+.+.++.+++.++..+..+-.    .+..+..++++.+..+..+..
T Consensus       344 l~~~~~~L~~~~~~l~~~~~~lp~----~e~~~~~L~Re~~~~~~lY~~  388 (719)
T PRK11519        344 LLEKRKALEDEKAKLNGRVTAMPK----TQQEIVRLTRDVESGQQVYMQ  388 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccH----HHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444333    233444444444444444433

>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly

Probab=85.19  E-value=20  Score=29.65  Aligned_cols=42  Identities=31%  Similarity=0.423  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARA  146 (321)
Q Consensus       105 ~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a  146 (321)
                      ...++-...++.|+..|++.++.+.+++...+.....++...
T Consensus        83 ~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~l  124 (129)
T cd00584          83 KDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAEL  124 (129)
T ss_pred             ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555667777777777777777777777776665555443

The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.

>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]

Probab=85.06  E-value=52  Score=34.26  Aligned_cols=14  Identities=36%  Similarity=0.703  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHHh
Q 020809           47 LDQLKSKIRSLESH   60 (321)
Q Consensus        47 l~qlk~ki~~Les~   60 (321)
                      ++.|+.++..++++
T Consensus       161 ~EaL~ekLk~~~ee  174 (596)
T KOG4360|consen  161 LEALQEKLKPLEEE  174 (596)
T ss_pred             HHHHHhhcCChHHH
Confidence            44445554444443

>PRK10476 multidrug resistance protein MdtN; Provisional

Probab=85.05  E-value=38  Score=32.71  Aligned_cols=30  Identities=13%  Similarity=0.345  Sum_probs=18.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhh
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQEL   68 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eL   68 (321)
                      +...++.++++++.++...+..++.....+
T Consensus        80 d~~~~~~~l~~a~a~l~~a~a~l~~~~~~~  109 (346)
T PRK10476         80 DPRPYELTVAQAQADLALADAQIMTTQRSV  109 (346)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445566677777777777666666554333

>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function

Probab=85.00  E-value=41  Score=32.98  Aligned_cols=31  Identities=16%  Similarity=0.208  Sum_probs=14.5

Q ss_pred             HHHHhHhHHHHHhh--hhhcCchhHHHHhhhcc
Q 020809          286 QTLKTKTIEACEAT--KTAVTPHIIRVQEVVDP  316 (321)
Q Consensus       286 q~~~~~~~~~~~~~--~~~~~ph~~k~~~~~~p  316 (321)
                      ..++..+.-..+.+  +..+--|--+.+.+++-
T Consensus       275 sdLksl~~aLle~indK~~al~Hqr~tNkILg~  307 (319)
T PF09789_consen  275 SDLKSLATALLETINDKNLALQHQRKTNKILGN  307 (319)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence            33344444333333  23344566666666543

>PF11570 E2R135: Coiled-coil receptor-binding R-domain of colicin E2; InterPro: IPR024566 Bacteriocins are protein antibiotics that kill bacteria closely related to the producing species

Probab=84.87  E-value=24  Score=30.17  Aligned_cols=45  Identities=24%  Similarity=0.392  Sum_probs=29.9

Q ss_pred             CchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHH
Q 020809           40 SSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQD   84 (321)
Q Consensus        40 ~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e   84 (321)
                      .+..+++|++....|+.+.+.+.....-+.+....++++.+.+.+
T Consensus        10 y~~a~aeL~~a~~~I~~~q~r~a~a~~~~~~r~seldqA~~~~~e   54 (136)
T PF11570_consen   10 YEAARAELDQADEDIATLQERQASAEQALNGRRSELDQANKKVKE   54 (136)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            344566777777777777777777666666666666666665555

Colicins are a subgroup of bacteriocins that are produced by and target Escherichia coli. The lethal action of most colicins is exerted either by formation of a pore in the cytoplasmic membrane of the target cell, or by an enzymatic nuclease digestion mechanism. Most colicins are able to translocate the outer membrane by a two-receptor system, where one receptor is used for the initial binding and the second for translocation. The initial binding is to cell surface receptors such as the porins OmpF, FepA, BtuB, Cir and FhuA. The presence of specific periplasmic proteins, such as TolA, TolB, TolC, or TonB, are required for translocation across the membrane []. Colicins are composed of domains with distinct functional roles. In general they contain a central R (receptor) domain that mediates receptor binding, an N-terminal T (translocation) domain that mediates translocation of the protein from the outer membrane receptor to the colicin's target within the cell, and a C-terminal C (catalytic) domain that performs the catalytic cleavage []. This entry represents the central R domain found in colicin-E2 and other colicins.; PDB: 2YSU_B 1UJW_B 2B5U_C 1JCH_A.

>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal

Probab=84.85  E-value=20  Score=29.22  Aligned_cols=28  Identities=14%  Similarity=0.391  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHhHHHHHHhhhcHHHHH
Q 020809           48 DQLKSKIRSLESHIDEKTQELKGKDEVV   75 (321)
Q Consensus        48 ~qlk~ki~~Les~i~e~~~eLk~kd~~I   75 (321)
                      ++++.++..+.+++..+..++.+...-+
T Consensus        13 q~~q~~~~~l~~q~~~le~~~~E~~~v~   40 (110)
T TIGR02338        13 QQLQQQLQAVATQKQQVEAQLKEAEKAL   40 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333333

Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.

>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility

Probab=84.75  E-value=29  Score=31.16  Aligned_cols=18  Identities=11%  Similarity=0.281  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 020809           78 KEKAIQDKSERIVSLQKE   95 (321)
Q Consensus        78 ~ek~i~e~~~~I~~Lq~e   95 (321)
                      ++.++.++..++..+...
T Consensus       132 L~~e~~~L~~~~~~l~~~  149 (189)
T PF10211_consen  132 LEEEKEELEKQVQELKNK  149 (189)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            333333333333333333

Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].

>TIGR02231 conserved hypothetical protein

Probab=84.74  E-value=15  Score=37.80  Aligned_cols=31  Identities=19%  Similarity=0.276  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           71 KDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        71 kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      .+..+.+++.+|..++.++..++.+++.++.
T Consensus        69 ~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~   99 (525)
T TIGR02231        69 DPERLAELRKQIRELEAELRDLEDRGDALKA   99 (525)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4666777776666666666666666555533

This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.

>COG3206 GumC Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]

Probab=84.69  E-value=48  Score=33.53  Aligned_cols=143  Identities=17%  Similarity=0.293  Sum_probs=69.8

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHH---HHHHHHHHH-HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKE---KAIQDKSER-IVSLQKELSSLQKKETLNAAEQVDKAHARAD  119 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~e---k~i~e~~~~-I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rir  119 (321)
                      .+++..++.++.............+......+..-.   .......+. |..|..+...+.. ...++........-++.
T Consensus       238 ~~~~~~ln~ql~~~~~~~~~~~a~l~~~~~~~~~~~~~~~~~~~~~s~~i~~Lr~~~~~~~~-~~~~l~~~~~~~~p~~~  316 (458)
T COG3206         238 EQQLSALNTQLQSARARLAQAEARLASLLQLLPLGREAAALREVLESPTIQDLRQQYAQVRQ-QIADLSTELGAKHPQLV  316 (458)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhHHhccHHHHHHHHHHHHHHH-HHHHHHHhhcccChHHH
Confidence            555666666666666666666666555555555443   222333333 5666666555533 22334443434444444


Q ss_pred             HHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          120 ELEKQIDNLKKESEKQQKEK--------EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       120 eL~k~Ie~Lk~ele~~~~kk--------~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .++.++..+...+...-...        ..++.+.+.+++.+..++..+..+-..    ...+.+++++.+.....+..+
T Consensus       317 ~~~~q~~~~~~~~~~e~~~~~~~~~~~~~~l~~~~~~L~~~~~~l~~~~~~~~~~----~~~l~~L~Re~~~~r~~ye~l  392 (458)
T COG3206         317 ALEAQLAELRQQIAAELRQILASLPNELALLEQQEAALEKELAQLKGRLSKLPKL----QVQLRELEREAEAARSLYETL  392 (458)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHHHHHHHHHHHHHHHHHHhhchHh----hhHHHHHHHHHHHHHHHHHHH
Confidence            46666555555554333222        334444444444444444444444443    344444454444444444444

>PRK00846 hypothetical protein; Provisional

Probab=84.62  E-value=7.4  Score=30.25  Aligned_cols=50  Identities=22%  Similarity=0.301  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           50 LKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        50 lk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +..+|.+||..+.=...-|.+++..+...+..|..+..++..|...+.+.
T Consensus        11 le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~   60 (77)
T PRK00846         11 LEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKV   60 (77)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44445555555544444444445555555555555555555555555444

>PF15450 DUF4631: Domain of unknown function (DUF4631)

Probab=84.54  E-value=55  Score=34.09  Aligned_cols=92  Identities=18%  Similarity=0.208  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Q 020809          113 KAHARADELEKQ-IDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRK-TERALKVAEEEMMR  190 (321)
Q Consensus       113 ~~~~RireL~k~-Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~e-lE~~lq~~Eeei~k  190 (321)
                      .++.|+.++..+ ....++.++.+..=..+++....++..++..+-..++.+.....-.+.+++. +-...+.-+.++..
T Consensus       380 tL~~rL~e~~~e~~~~~r~~lekl~~~q~e~~~~l~~v~eKVd~LpqqI~~vs~Kc~~~Ksd~d~kIdtE~k~R~~eV~~  459 (531)
T PF15450_consen  380 TLNLRLSEAKNEWESDERKSLEKLDQWQNEMEKHLKEVQEKVDSLPQQIEEVSDKCDLHKSDSDTKIDTEGKAREREVGA  459 (531)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhhhhccHHHHHHHHHHHH
Confidence            444455555444 3333344444443335555555555555555555555555544444444433 22233444445555


Q ss_pred             HHHHHhhhhhhhhh
Q 020809          191 AKFEATSRSKELTE  204 (321)
Q Consensus       191 l~~ea~~~a~ql~e  204 (321)
                      +..+.+++...+-.
T Consensus       460 vRqELa~lLssvQ~  473 (531)
T PF15450_consen  460 VRQELATLLSSVQL  473 (531)
T ss_pred             HHHHHHHHHHHHHH
Confidence            55555555544433

>PRK02793 phi X174 lysis protein; Provisional

Probab=84.26  E-value=8.1  Score=29.46  Aligned_cols=48  Identities=21%  Similarity=0.313  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS   98 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~   98 (321)
                      +..|.+|+.++.-.+..|+++       +..+.+-++.|..+..++..|..++.+
T Consensus         7 e~Ri~~LE~~lafQe~tIe~L-------n~~v~~Qq~~I~~L~~~l~~L~~rl~~   54 (72)
T PRK02793          7 EARLAELESRLAFQEITIEEL-------NVTVTAHEMEMAKLRDHLRLLTEKLKA   54 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344444444444444444444       444444444444444444444444443

>PF05622 HOOK: HOOK protein; InterPro: IPR008636 This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms

Probab=84.26  E-value=0.31  Score=52.23  Aligned_cols=39  Identities=18%  Similarity=0.245  Sum_probs=0.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQ   77 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q   77 (321)
                      +.+.+.+...++..++..|....+.+..+...+...+++
T Consensus       187 e~d~l~q~~~el~~~i~~L~~e~~~L~~e~~~l~~~~~~  225 (713)
T PF05622_consen  187 ERDELAQRCHELEKQISDLQEEKESLQSENEELQERLSQ  225 (713)
T ss_dssp             ---------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHhhhhhhhhhcccCC
Confidence            344455555555555555555544444444444333333

The different members of the Homo sapiens gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three Homo sapiens HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerisation and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes [], whereas both HOOK1 and HOOK2 are localised to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head [].; GO: 0008017 microtubule binding, 0000226 microtubule cytoskeleton organization, 0005737 cytoplasm; PDB: 1WIX_A.

>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans

Probab=84.18  E-value=31  Score=34.80  Aligned_cols=47  Identities=13%  Similarity=0.106  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q 020809          125 IDNLKKESEKQQKEKEALEARAIEA-EKKISDLSAKLEKLQKINDEQK  171 (321)
Q Consensus       125 Ie~Lk~ele~~~~kk~~LEa~a~e~-ekk~~el~~~le~Lek~~~Eqk  171 (321)
                      ++.-++++...+.+++..|.+..-. ..+..++...++..+..+...+
T Consensus       271 ~elHq~Ei~~LKqeLa~~EEK~~Yqs~eRaRdi~E~~Es~qtRisklE  318 (395)
T PF10267_consen  271 TELHQNEIYNLKQELASMEEKMAYQSYERARDIWEVMESCQTRISKLE  318 (395)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            4445555666665555555544432 2344455555555554444444

Its function is unknown.

>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length

Probab=83.92  E-value=9.9  Score=33.22  Aligned_cols=33  Identities=18%  Similarity=0.314  Sum_probs=12.8

Q ss_pred             HHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHH
Q 020809           54 IRSLESHIDEKTQELKGKDEVVAQKEKAIQDKS   86 (321)
Q Consensus        54 i~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~   86 (321)
                      +....+..+....+++.+..+|....+.|..+.
T Consensus        15 i~~~K~~~~~~~~e~~~~k~ql~~~d~~i~~Lk   47 (155)
T PF06810_consen   15 IEAPKAKVDKVKEERDNLKTQLKEADKQIKDLK   47 (155)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333334444443333333333333333333333

The function of this family is unknown.; GO: 0005198 structural molecule activity

>PRK10361 DNA recombination protein RmuC; Provisional

Probab=83.91  E-value=56  Score=33.74  Aligned_cols=143  Identities=10%  Similarity=0.177  Sum_probs=60.6

Q ss_pred             HhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------
Q 020809           66 QELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEK------  139 (321)
Q Consensus        66 ~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk------  139 (321)
                      .++..+...+......+..+......++..++..+.    ..+++...+..--..|..+-+.|-.++=+.+.+.      
T Consensus        60 ~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~le~~~~----~~~ek~~~l~~~~~~L~~~F~~LA~~ile~k~~~f~~~~~  135 (475)
T PRK10361         60 AECELLNNEVRSLQSINTSLEADLREVTTRMEAAQQ----HADDKIRQMINSEQRLSEQFENLANRIFEHSNRRVDEQNR  135 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444455554444445555555544444332    1222222222222224444444444443333332      


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh---hhhccCchhHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELT---EVHSAWLPPWLA  215 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~ql~---e~~g~~l~Pwla  215 (321)
                      ..|+.-..=+...+.....+++++.+........|..   .+..+.+.-.++..++..+++-|.   .+.|.|----|.
T Consensus       136 ~~l~~ll~Pl~e~l~~f~~~v~~~~~~~~~~~~~L~~---qi~~L~~~n~~i~~ea~nLt~ALkgd~K~rG~WGE~qLe  211 (475)
T PRK10361        136 QSLNSLLSPLREQLDGFRRQVQDSFGKEAQERHTLAH---EIRNLQQLNAQMAQEAINLTRALKGDNKTQGNWGEVVLT  211 (475)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHcCCCCcCcchHHHHHH
Confidence            3333334444455555555555555544444333333   333333333444445555554441   233666444443

>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5

Probab=83.72  E-value=23  Score=29.15  Aligned_cols=41  Identities=27%  Similarity=0.400  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEAR  145 (321)
Q Consensus       105 ~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~  145 (321)
                      ...++-...++.|+..|++.++.+...+...+.....+...
T Consensus        82 ~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i~~~  122 (126)
T TIGR00293        82 KDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQE  122 (126)
T ss_pred             ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667777777788888887777777777777666555443

This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.

>PF05557 MAD: Mitotic checkpoint protein; InterPro: IPR008672 This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins

Probab=83.66  E-value=1.4  Score=47.26  Aligned_cols=14  Identities=36%  Similarity=0.237  Sum_probs=7.7

Q ss_pred             HhHhHHHHHhhhhh
Q 020809          289 KTKTIEACEATKTA  302 (321)
Q Consensus       289 ~~~~~~~~~~~~~~  302 (321)
                      +.+|.+|-++|...
T Consensus       630 ~~ks~eFr~av~~l  643 (722)
T PF05557_consen  630 KAKSQEFREAVYSL  643 (722)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            45566666555443

The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in Saccharomyces cerevisiae and higher eukaryotes. In Saccharomyces cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated [].; PDB: 1GO4_F 4DZO_A.

>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain

Probab=83.50  E-value=46  Score=32.44  Aligned_cols=37  Identities=16%  Similarity=0.259  Sum_probs=21.8

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQ   77 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q   77 (321)
                      ..+...+..++++-..|....+-.....+.+...+..
T Consensus        23 ~~l~~~~~sL~qen~~Lk~El~~ek~~~~~L~~e~~~   59 (310)
T PF09755_consen   23 EQLRKRIESLQQENRVLKRELETEKARCKHLQEENRA   59 (310)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5666667777776666666666554444444444443

>PRK00295 hypothetical protein; Provisional

Probab=83.50  E-value=8.9  Score=28.88  Aligned_cols=48  Identities=15%  Similarity=0.277  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS   98 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~   98 (321)
                      +..+.+|+.++.-.+..|+++       +..+.+-++.|..+..++..|...+.+
T Consensus         4 e~Ri~~LE~kla~qE~tie~L-------n~~v~~Qq~~I~~L~~ql~~L~~rl~~   51 (68)
T PRK00295          4 EERVTELESRQAFQDDTIQAL-------NDVLVEQQRVIERLQLQMAALIKRQEE   51 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555554       444444444444444444444444433

>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]

Probab=83.46  E-value=29  Score=30.12  Aligned_cols=12  Identities=42%  Similarity=0.487  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHHH
Q 020809          125 IDNLKKESEKQQ  136 (321)
Q Consensus       125 Ie~Lk~ele~~~  136 (321)
                      |+.|++.++++.
T Consensus        96 ie~l~k~~~~l~  107 (145)
T COG1730          96 IEFLKKRIEELE  107 (145)
T ss_pred             HHHHHHHHHHHH
Confidence            444444333333

>PHA03332 membrane glycoprotein; Provisional

Probab=83.24  E-value=57  Score=36.84  Aligned_cols=22  Identities=18%  Similarity=0.173  Sum_probs=13.2

Q ss_pred             HHHHHHHHhHHHhhCcchHHHHHH
Q 020809          219 LQCQSLIETHWNAHGKPAMDVAIQ  242 (321)
Q Consensus       219 ~~~~~~~~~~~~~hg~p~~~~~~~  242 (321)
                      ..+++..+++-  .|=|.=+.+++
T Consensus      1011 TCl~Sl~aG~L--~GCP~~~pfl~ 1032 (1328)
T PHA03332       1011 TCLKSLLAGTL--AGCPTDAPFLR 1032 (1328)
T ss_pred             HHHHHhhcccc--cCCCCCChhhh
Confidence            35555555543  67777766664

>PRK00736 hypothetical protein; Provisional

Probab=82.99  E-value=8.5  Score=28.99  Aligned_cols=48  Identities=19%  Similarity=0.340  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS   98 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~   98 (321)
                      +..|.+|+.++.-.+..|+++       +..+.+-++.|..+..++..|..++.+
T Consensus         4 e~Ri~~LE~klafqe~tie~L-------n~~v~~Qq~~i~~L~~ql~~L~~rl~~   51 (68)
T PRK00736          4 EERLTELEIRVAEQEKTIEEL-------SDQLAEQWKTVEQMRKKLDALTERFLS   51 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555       444444444444444444444444433

>PRK10780 periplasmic chaperone; Provisional

Probab=82.79  E-value=31  Score=30.00  Aligned_cols=19  Identities=16%  Similarity=0.274  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHHHHhHHHH
Q 020809           46 ELDQLKSKIRSLESHIDEK   64 (321)
Q Consensus        46 el~qlk~ki~~Les~i~e~   64 (321)
                      +..+.+.-...|+...+..
T Consensus        37 ~~p~~k~~~~~le~~~~~~   55 (165)
T PRK10780         37 QVPQRTGVSKQLENEFKGR   55 (165)
T ss_pred             HCHHHHHHHHHHHHHHHHH
Confidence            3333333334444444443

>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=82.52  E-value=42  Score=31.27  Aligned_cols=11  Identities=27%  Similarity=0.389  Sum_probs=4.1

Q ss_pred             HHHHHHHHHHh
Q 020809           50 LKSKIRSLESH   60 (321)
Q Consensus        50 lk~ki~~Les~   60 (321)
                      ++.+..+++..
T Consensus         6 ir~K~~~lek~   16 (230)
T PF10146_consen    6 IRNKTLELEKL   16 (230)
T ss_pred             HHHHHHHHHHH
Confidence            33333333333

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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.

>KOG0243 consensus Kinesin-like protein [Cytoskeleton]

Probab=82.51  E-value=92  Score=35.16  Aligned_cols=68  Identities=15%  Similarity=0.222  Sum_probs=27.9

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           68 LKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus        68 Lk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      .+.....|.+++.+++.+..+|..++........ --..+.++.+.++.++..-..++..++.++.+.+
T Consensus       443 ~~~~~~~ieele~el~~~~~~l~~~~e~~~~~~~-~~~~l~~~~~~~k~~L~~~~~el~~~~ee~~~~~  510 (1041)
T KOG0243|consen  443 KKEMAEQIEELEEELENLEKQLKDLTELYMNQLE-IKELLKEEKEKLKSKLQNKNKELESLKEELQQAK  510 (1041)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444443321111 1133444444444444444444444444443333

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=82.39  E-value=51  Score=36.09  Aligned_cols=40  Identities=10%  Similarity=0.120  Sum_probs=15.0

Q ss_pred             hHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           60 HIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        60 ~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      -++.++++....+....+++....+.+.....++.+.+.+
T Consensus       521 li~~l~~~~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l  560 (782)
T PRK00409        521 LIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKL  560 (782)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333333333333333333

>TIGR03545 conserved hypothetical protein TIGR03545

Probab=82.28  E-value=36  Score=35.77  Aligned_cols=14  Identities=7%  Similarity=0.368  Sum_probs=8.6

Q ss_pred             hHHHhhCcchHHHH
Q 020809          227 THWNAHGKPAMDVA  240 (321)
Q Consensus       227 ~~~~~hg~p~~~~~  240 (321)
                      -.|-..+.|++...
T Consensus       298 ~~~y~~~~p~i~~~  311 (555)
T TIGR03545       298 LKYYDQAEPLLNKS  311 (555)
T ss_pred             HHHHHHHhHhhccc
Confidence            35666666666665

This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.

>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility

Probab=82.17  E-value=35  Score=30.72  Aligned_cols=21  Identities=29%  Similarity=0.450  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 020809           79 EKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        79 ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +..|..++.++..|..++..+
T Consensus       126 ~~~i~~L~~e~~~L~~~~~~l  146 (189)
T PF10211_consen  126 EEEIEELEEEKEELEKQVQEL  146 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333

Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].

>PF06120 Phage_HK97_TLTM: Tail length tape measure protein; InterPro: IPR009302 This entry consists of the tail length tape measure protein from Bacteriophage HK97 and related sequences from Escherichia coli (strain K12)

Probab=82.11  E-value=52  Score=32.00  Aligned_cols=55  Identities=25%  Similarity=0.364  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhc-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKG-----KDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~-----kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ++.++.+..--+.-+.++++...+++     +...|+.+...|.+....|..++.+|+++
T Consensus        41 Q~~EQAr~~A~~fA~~ld~~~~kl~~Ms~~ql~~~~~k~~~si~~q~~~i~~l~~~i~~l  100 (301)
T PF06120_consen   41 QNAEQARQEAIEFADSLDELKEKLKEMSSTQLRANIAKAEESIAAQKRAIEDLQKKIDSL  100 (301)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444444444444332     33444444444444444444444444444

>TIGR02231 conserved hypothetical protein

Probab=82.05  E-value=22  Score=36.71  Aligned_cols=28  Identities=18%  Similarity=0.184  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           72 DEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        72 d~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +.+|.+++.++...+.+++.++..+.-+
T Consensus        77 ~~~l~~l~~~~~~~~~~~~~~~~~~~~l  104 (525)
T TIGR02231        77 RKQIRELEAELRDLEDRGDALKALAKFL  104 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333334444444444333

This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.

>PRK06975 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed

Probab=81.95  E-value=78  Score=33.93  Aligned_cols=68  Identities=18%  Similarity=0.258  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKA  114 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~  114 (321)
                      .++++..++.++..+..+.+....+.+.   .+.+.+..+.+.+.++..|+.++..++. ....++..+..+
T Consensus       344 ~~q~~~~~~~~l~~~~~~~~~~~~e~~~---~~~~~~~~~~~~~~~l~~le~~l~~~~~-~~~~L~~~~~~l  411 (656)
T PRK06975        344 LNRKVDRLDQELVQRQQANDAQTAELRV---KTEQAQASVHQLDSQFAQLDGKLADAQS-AQQALEQQYQDL  411 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence            4567778888887777777777666633   3455666667777777777777766654 444555555444

>PF15066 CAGE1: Cancer-associated gene protein 1 family

Probab=81.76  E-value=67  Score=33.08  Aligned_cols=14  Identities=21%  Similarity=0.688  Sum_probs=8.1

Q ss_pred             hhhcccCCCCCCcc
Q 020809           20 ADVSIQGEDVPPLT   33 (321)
Q Consensus        20 ~~~~~~~~~~~~~~   33 (321)
                      -++.++|.+.|..+
T Consensus       262 kev~~e~~e~p~~~  275 (527)
T PF15066_consen  262 KEVTVEGVESPEIA  275 (527)
T ss_pred             hhcchhcccCcccc
Confidence            34556666666653

>PF05266 DUF724: Protein of unknown function (DUF724); InterPro: IPR007930 This family contains several uncharacterised proteins found exclusively in Arabidopsis thaliana

Probab=81.67  E-value=40  Score=30.46  Aligned_cols=37  Identities=19%  Similarity=0.298  Sum_probs=18.2

Q ss_pred             HHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           63 EKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        63 e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ....+.+.++..|.+...+...++..|..|+..|-.+
T Consensus       107 ~~~e~~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el  143 (190)
T PF05266_consen  107 KLLEERKKLEKKIEEKEAELKELESEIKELEMKILEL  143 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence            4444444555555555444444455555555555444

>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family

Probab=81.66  E-value=54  Score=31.94  Aligned_cols=20  Identities=10%  Similarity=0.172  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 020809          172 SKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       172 ~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..+..++++...++..+..+
T Consensus       278 ~~~~~L~re~~~a~~~y~~~  297 (362)
T TIGR01010       278 ADYQRLVLQNELAQQQLKAA  297 (362)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444433

This family contains gamma proteobacterial proteins involved in capsule polysaccharide export.

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=81.61  E-value=6.1  Score=41.40  Aligned_cols=13  Identities=15%  Similarity=0.197  Sum_probs=8.1

Q ss_pred             ccCchhHHHHHHH
Q 020809          207 SAWLPPWLAVHLL  219 (321)
Q Consensus       207 g~~l~Pwla~~~~  219 (321)
                      |..+-|||-.-.-
T Consensus       209 G~~~d~~lk~~fq  221 (907)
T KOG2264|consen  209 GQSEDEWLKQVFQ  221 (907)
T ss_pred             ccchHHHHHHHHH
Confidence            5667777765443

>PF09728 Taxilin: Myosin-like coiled-coil protein; InterPro: IPR019132 Taxilin contains an extraordinarily long coiled-coil domain in its C-terminal half and is ubiquitously expressed

Probab=81.30  E-value=55  Score=31.77  Aligned_cols=97  Identities=16%  Similarity=0.236  Sum_probs=66.1

Q ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           95 ELSSLQKKETLNAAEQVDKAHARADELEKQ-------IDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKIN  167 (321)
Q Consensus        95 eI~~~qk~~~~~~eeq~~~~~~RireL~k~-------Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~  167 (321)
                      .+..+.. .+..+..+.+.+..+-.+++.-       ...++.+++....+...||........+-...+..+-.|-...
T Consensus       203 ~~~~~~~-~E~~Lr~QL~~Y~~Kf~efq~tL~kSNe~F~tfk~Emekm~Kk~kklEKE~~~~k~k~e~~n~~l~~m~eer  281 (309)
T PF09728_consen  203 QVQTLKE-TEKELREQLNLYSEKFEEFQDTLNKSNEVFETFKKEMEKMSKKIKKLEKENQTWKSKWEKSNKALIEMAEER  281 (309)
T ss_pred             HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            4444422 4556666666666666664443       6777788888888888888888888888888888887777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          168 DEQKSKIRKTERALKVAEEEMMRAK  192 (321)
Q Consensus       168 ~Eqk~~l~elE~~lq~~Eeei~kl~  192 (321)
                      ......+..+......++.-...++
T Consensus       282 ~~~~~~~~~~~~k~~kLe~LcRaLQ  306 (309)
T PF09728_consen  282 QKLEKELEKLKKKIEKLEKLCRALQ  306 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7777777777776666655544443

It is a novel binding partner of several syntaxin family members and is possibly involved in Ca(2+)-dependent exocytosis in neuroendocrine cells []. Gamma-taxilin, described as leucine zipper protein Factor Inhibiting ATF4-mediated Transcription (FIAT), localises to the nucleus in osteoblasts and dimerises with ATF4 to form inactive dimers, thus inhibiting ATF4-mediated transcription [].

>PRK11546 zraP zinc resistance protein; Provisional

Probab=81.30  E-value=20  Score=31.08  Aligned_cols=20  Identities=15%  Similarity=0.499  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 020809          117 RADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus       117 RireL~k~Ie~Lk~ele~~~  136 (321)
                      +|+.|.++|..|+..+.+++
T Consensus        90 kI~aL~kEI~~Lr~kL~e~r  109 (143)
T PRK11546         90 KINAVAKEMENLRQSLDELR  109 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444443

>KOG0288 consensus WD40 repeat protein TipD [General function prediction only]

Probab=81.25  E-value=66  Score=32.65  Aligned_cols=50  Identities=16%  Similarity=0.124  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQK   94 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~   94 (321)
                      +.+-+++.++++-++..+.+..++..+..+-...-..+..++..|+.|+.
T Consensus        13 qr~~~~~~~laq~~k~~s~~~aq~~~~~a~~~ai~a~~~~~E~~l~~Lq~   62 (459)
T KOG0288|consen   13 QRLIDLNTELAQCEKAQSRLSAQLVILRAESRAIKAKLQEKELELNRLQE   62 (459)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444555555555544444444444444333333333333333333

>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function

Probab=81.23  E-value=57  Score=31.95  Aligned_cols=70  Identities=20%  Similarity=0.238  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          124 QIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLE--------------KLQKINDEQKSKIRKTERALKVAEEEMM  189 (321)
Q Consensus       124 ~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le--------------~Lek~~~Eqk~~l~elE~~lq~~Eeei~  189 (321)
                      .+..|+.++...-.+++++...+..-..+...+|..+.              .+--.+.-+..+|..++.+..-+..-+.
T Consensus       141 q~~qLe~d~qs~lDEkeEl~~ERD~yk~K~~RLN~ELn~~L~g~~~rivDIDaLi~ENRyL~erl~q~qeE~~l~k~~i~  220 (319)
T PF09789_consen  141 QIEQLERDLQSLLDEKEELVTERDAYKCKAHRLNHELNYILNGDENRIVDIDALIMENRYLKERLKQLQEEKELLKQTIN  220 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444444443              3333334445555555555555555555


Q ss_pred             HHHH
Q 020809          190 RAKF  193 (321)
Q Consensus       190 kl~~  193 (321)
                      +...
T Consensus       221 KYK~  224 (319)
T PF09789_consen  221 KYKS  224 (319)
T ss_pred             HHHH
Confidence            5433

>COG2900 SlyX Uncharacterized protein conserved in bacteria [Function unknown]

Probab=81.23  E-value=15  Score=28.14  Aligned_cols=52  Identities=29%  Similarity=0.332  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..+|+|..++|-+++.....++.|.....+|+..++++...+..+-+.+..+
T Consensus         4 ~~lE~Ri~eLE~r~AfQE~tieeLn~~laEq~~~i~k~q~qlr~L~~kl~~~   55 (72)
T COG2900           4 MELEARIIELEIRLAFQEQTIEELNDALAEQQLVIDKLQAQLRLLTEKLKDL   55 (72)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3577888888888888888888888888899988888888777775555544

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=81.12  E-value=21  Score=36.72  Aligned_cols=12  Identities=17%  Similarity=0.277  Sum_probs=4.5

Q ss_pred             HHHHHHHHHHHH
Q 020809          120 ELEKQIDNLKKE  131 (321)
Q Consensus       120 eL~k~Ie~Lk~e  131 (321)
                      +|+.++..|+.+
T Consensus       108 eLEaE~~~Lk~Q  119 (475)
T PRK13729        108 KLGQDNAALAEQ  119 (475)
T ss_pred             HHHHHHHHHHHH
Confidence            333333333333

>TIGR02977 phageshock_pspA phage shock protein A

Probab=80.96  E-value=44  Score=30.49  Aligned_cols=48  Identities=10%  Similarity=0.118  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL   96 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI   96 (321)
                      .++.-|.+++..+.+....+...-..-..++..+.+....+...+...
T Consensus        28 ~l~q~irem~~~l~~ar~~lA~~~a~~k~~e~~~~~~~~~~~~~~~~A   75 (219)
T TIGR02977        28 MIRLIIQEMEDTLVEVRTTSARTIADKKELERRVSRLEAQVADWQEKA   75 (219)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444444444444444444443

Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.

>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]

Probab=80.92  E-value=73  Score=32.98  Aligned_cols=78  Identities=15%  Similarity=0.195  Sum_probs=41.4

Q ss_pred             cCCCCCCcccccCCCCchHHHHHH-------HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           25 QGEDVPPLTASDAVDSSPLKIELD-------QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS   97 (321)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~l~~el~-------qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~   97 (321)
                      |..+++-....-..+-.+|++.++       +-+-.|+.+.+.+.++.+.=-.--.+|.+....+-+++..|-.+--.+.
T Consensus       321 dnp~s~kliPVpvvGF~dL~~R~K~Q~q~~~~~r~ri~~i~e~v~eLqk~~ad~~~KI~~~k~r~~~Ls~RiLRv~ikqe  400 (508)
T KOG3091|consen  321 DNPPSNKLIPVPVVGFEDLRQRLKVQDQEVKQHRIRINAIGERVTELQKHHADAVAKIEEAKNRHVELSHRILRVMIKQE  400 (508)
T ss_pred             cCCCcccccceeccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            443333324444555555555443       3333444444444444433333345666777777777777777766666


Q ss_pred             HHHHH
Q 020809           98 SLQKK  102 (321)
Q Consensus        98 ~~qk~  102 (321)
                      -+.+.
T Consensus       401 ilr~~  405 (508)
T KOG3091|consen  401 ILRKR  405 (508)
T ss_pred             HHhcc
Confidence            66554

>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation

Probab=80.68  E-value=23  Score=27.05  Aligned_cols=25  Identities=40%  Similarity=0.384  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           75 VAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        75 I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +++++..|...-..|..|+.+|+.+
T Consensus         6 l~~LE~ki~~aveti~~Lq~e~eeL   30 (72)
T PF06005_consen    6 LEQLEEKIQQAVETIALLQMENEEL   30 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444445555555555444

It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.

>KOG0244 consensus Kinesin-like protein [Cytoskeleton]

Probab=80.60  E-value=70  Score=35.50  Aligned_cols=11  Identities=27%  Similarity=0.244  Sum_probs=5.0

Q ss_pred             HHHHHHhhccc
Q 020809          244 ALEKKAQAGKW  254 (321)
Q Consensus       244 ~~~k~~~~~~~  254 (321)
                      -++-++.+.||
T Consensus       651 kt~eas~~~kr  661 (913)
T KOG0244|consen  651 KTEEASAANKR  661 (913)
T ss_pred             HHHHHHHHHHH
Confidence            33444445555

>KOG1003 consensus Actin filament-coating protein tropomyosin [Cytoskeleton]

Probab=80.53  E-value=46  Score=30.42  Aligned_cols=57  Identities=12%  Similarity=0.293  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ++..+..++......+.......+.|.+....-++.+.-+..++..-.++...++..
T Consensus         9 lnrri~~leeele~aqErl~~a~~KL~Eaeq~~dE~er~~Kv~enr~~kdEE~~e~~   65 (205)
T KOG1003|consen    9 LNRRIQLLEEELDRAQERLATALQKLEEAEQAADESERGMKVIENRAQKLEEKMEAQ   65 (205)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhHHHHHHH
Confidence            333333333333333333333333333333333333444444444444444444444

>PF06120 Phage_HK97_TLTM: Tail length tape measure protein; InterPro: IPR009302 This entry consists of the tail length tape measure protein from Bacteriophage HK97 and related sequences from Escherichia coli (strain K12)

Probab=80.52  E-value=59  Score=31.62  Aligned_cols=57  Identities=25%  Similarity=0.435  Sum_probs=31.0

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      -.+...|++++.++..+-.  -++...+......|.+....|.++.++|..|+..|...
T Consensus        51 ~~fA~~ld~~~~kl~~Ms~--~ql~~~~~k~~~si~~q~~~i~~l~~~i~~l~~~i~~y  107 (301)
T PF06120_consen   51 IEFADSLDELKEKLKEMSS--TQLRANIAKAEESIAAQKRAIEDLQKKIDSLKDQIKNY  107 (301)
T ss_pred             HHHHHhhHHHHHHHHhcCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455667777777654422  12333444445555555555566666666666666443

>KOG4809 consensus Rab6 GTPase-interacting protein involved in endosome-to-TGN transport [Intracellular trafficking, secretion, and vesicular transport]

Probab=80.50  E-value=81  Score=33.19  Aligned_cols=45  Identities=27%  Similarity=0.234  Sum_probs=34.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQ   83 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~   83 (321)
                      +......++.-+++.+.+.+..|+...+.|+.+|+.|.++.-.+.
T Consensus       237 e~~~~~~e~~llr~t~~~~e~riEtqkqtl~ardesIkkLlEmLq  281 (654)
T KOG4809|consen  237 ELLTTKEEQFLLRSTDPSGEQRIETQKQTLDARDESIKKLLEMLQ  281 (654)
T ss_pred             HhhhHHHHHHHHHhcCchHHHHHHHHHhhhhhHHHHHHHHHHHHH
Confidence            555666677778888888888888888888888888887765544

>PF02994 Transposase_22: L1 transposable element; InterPro: IPR004244 Many human L1 elements are capable of retrotransposition

Probab=80.40  E-value=5.7  Score=39.46  Aligned_cols=83  Identities=20%  Similarity=0.331  Sum_probs=19.4

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           68 LKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKET---LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEA  144 (321)
Q Consensus        68 Lk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~---~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa  144 (321)
                      +.++...+.++.+++..+...+.....+|....+...   ..+..+++.++.||.+|+..++.+...+......+..++.
T Consensus       100 l~el~~~~~elkkEie~IKk~q~e~~~~i~~~~~~~~~~~~~l~~Ri~e~Eeris~lEd~~~~i~~~~~~~~k~i~~l~~  179 (370)
T PF02994_consen  100 LNELKKRIKELKKEIENIKKNQSEMKLEIENLKKKLENIDESLNSRIDELEERISELEDRIEEIEQAIKELEKRIKKLED  179 (370)
T ss_dssp             ------------------H-------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            3344444444455555554444444445544432110   1233444444444444444444444444444433344444


Q ss_pred             HHHHHH
Q 020809          145 RAIEAE  150 (321)
Q Consensus       145 ~a~e~e  150 (321)
                      +..+++
T Consensus       180 kl~DlE  185 (370)
T PF02994_consen  180 KLDDLE  185 (370)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443

Some of these have been shown to exhibit reverse transcriptase (RT) activity [] although the function of many are, as yet, unknown. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 2LDY_A 3SOO_A 2YKQ_A 2YKO_C 2YKP_B 2W7A_B 2JRB_A.

>TIGR00414 serS seryl-tRNA synthetase

Probab=80.25  E-value=21  Score=36.09  Aligned_cols=68  Identities=12%  Similarity=0.240  Sum_probs=39.3

Q ss_pred             HHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           65 TQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus        65 ~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      ..+|-.+|.+-.++..+++.+..+.+.+..+|....+.+. +   ..+.+..+++.|+.+|..+.+++....
T Consensus        29 vd~i~~ld~~~r~~~~~~~~l~~erN~~sk~i~~~~~~~~-~---~~~~l~~~~~~l~~~~~~~~~~~~~~~   96 (418)
T TIGR00414        29 LEKLIALDDERKKLLSEIEELQAKRNELSKQIGKAKGQKK-D---KIEEIKKELKELKEELTELSAALKALE   96 (418)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCc-c---hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4667777777788888888887777777777765422121 0   023344455555554444444444443

This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.

>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes []

Probab=80.23  E-value=10  Score=28.54  Aligned_cols=44  Identities=18%  Similarity=0.413  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSL   92 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~L   92 (321)
                      +++.++...+..+++..+.++.++...+..+..+..+..+|..+
T Consensus         3 ~i~e~l~~ie~~l~~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I   46 (71)
T PF10779_consen    3 DIKEKLNRIETKLDNHEERIDKLEKRDAANEKDIKNLNKQLEKI   46 (71)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555444444444444444444444443433333

>PF05483 SCP-1: Synaptonemal complex protein 1 (SCP-1); InterPro: IPR008827 Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex

Probab=80.22  E-value=92  Score=33.66  Aligned_cols=11  Identities=36%  Similarity=0.090  Sum_probs=4.2

Q ss_pred             HHhhhhhhhhh
Q 020809          259 VETIKAKWIPA  269 (321)
Q Consensus       259 ~~~~~~k~~p~  269 (321)
                      |+.++.-...+
T Consensus       677 veK~k~~a~EA  687 (786)
T PF05483_consen  677 VEKAKLTADEA  687 (786)
T ss_pred             HHHHHHHHHHH
Confidence            33333333333

Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase [].; GO: 0007130 synaptonemal complex assembly, 0000795 synaptonemal complex

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=80.20  E-value=23  Score=26.79  Aligned_cols=59  Identities=24%  Similarity=0.269  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      ++..+..|+.++..+..+++.....++.+..+=+.....+...-..+..|..+++.+++
T Consensus         3 Lea~~~~Lr~rLd~~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~   61 (69)
T PF14197_consen    3 LEAEIATLRNRLDSLTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRK   61 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555555555555555555555566666666666666666643

>PF11180 DUF2968: Protein of unknown function (DUF2968); InterPro: IPR021350 This family of proteins has no known function

Probab=80.11  E-value=47  Score=30.22  Aligned_cols=84  Identities=18%  Similarity=0.231  Sum_probs=38.7

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE  120 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire  120 (321)
                      ++.+..--.|+.+...++..|..-..++..+...|+-....-......-.....+.        ..++.+...+..+++.
T Consensus       101 A~~eirR~~LeAQka~~eR~ia~~~~ra~~LqaDl~~~~~Q~~~va~~Q~q~r~ea--------~aL~~e~~aaqaQL~~  172 (192)
T PF11180_consen  101 ADVEIRRAQLEAQKAQLERLIAESEARANRLQADLQIARQQQQQVAARQQQARQEA--------QALEAERRAAQAQLRQ  172 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHH
Confidence            33334444455555555555555544444444444444333333333333333333        3344444455556666


Q ss_pred             HHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKES  132 (321)
Q Consensus       121 L~k~Ie~Lk~el  132 (321)
                      |..+|..|+.+.
T Consensus       173 lQ~qv~~Lq~q~  184 (192)
T PF11180_consen  173 LQRQVRQLQRQA  184 (192)
T ss_pred             HHHHHHHHHHHh
Confidence            666666555543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	321
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-15
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	5e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	5e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-13
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-12
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-11
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-11
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-11
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-10
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-10
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-10
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-10
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	4e-07
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-06
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	5e-05
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	8e-05
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	1e-04
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	2e-04
2xs1_A	704	Programmed cell death 6-interacting protein; prote	2e-04
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	2e-04

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 74.8 bits (184), Expect = 6e-15
 Identities = 35/160 (21%), Positives = 69/160 (43%), Gaps = 8/160 (5%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
             K     L++KI  L+  IDE+ +E K    ++ +        S     L+ ++  L+  
Sbjct: 919  YKKLHIGLENKIMQLQRKIDEQNKEYK---SLLEKMNNLEITYSTETEKLRSDVERLRMS 975

Query: 103  ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
            E     E+   A  R   L+++I  L+KE  + Q EK+ +E  A + + +   L ++L++
Sbjct: 976  E-----EEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKE 1030

Query: 163  LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKEL 202
               +   +K ++ +          E M  K    ++  EL
Sbjct: 1031 QNTLLKTEKEELNRRIHDQAKEITETMEKKLVEETKQLEL 1070

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 62.8 bits (153), Expect = 5e-11
 Identities = 31/141 (21%), Positives = 63/141 (44%), Gaps = 12/141 (8%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK- 101
               E   L  K+ +LE     +T++L+   E +   E+  ++ + R++SLQ+E++ L+K 
Sbjct: 940  QNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKE 999

Query: 102  -----KETLNAAEQVDKAHARAD----ELEKQIDNLKKESEKQQKEKEALEARAIEAEKK 152
                  E     E  DK     +    EL++Q   LK E E+  +          E  +K
Sbjct: 1000 LHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETMEK 1059

Query: 153  ISDLSAKLEKLQKINDEQKSK 173
               L  + ++L+   ++++ +
Sbjct: 1060 --KLVEETKQLELDLNDERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 62.0 bits (151), Expect = 7e-11
 Identities = 28/162 (17%), Positives = 58/162 (35%), Gaps = 7/162 (4%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETL 105
               ++    +L++ +       K +  +   K   IQ      ++      +L+    L
Sbjct: 834 RYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYL 893

Query: 106 NAAEQVDKAHARADEL---EKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
               +   A     +L    + ++  KK     + +   L+ +  E  K+   L  K+  
Sbjct: 894 QCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNN 953

Query: 163 LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
           L+     +  K+R     L+++EEE       AT+R   L E
Sbjct: 954 LEITYSTETEKLRSDVERLRMSEEE----AKNATNRVLSLQE 991

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 58.2 bits (141), Expect = 1e-09
 Identities = 29/171 (16%), Positives = 62/171 (36%), Gaps = 12/171 (7%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQK-------EKAIQDKSERIVSLQKE 95
            ++     L++ +R      ++    L+    ++ QK               + IV LQ  
Sbjct: 838  MRDATIALQALLRGYLVR-NKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCC 896

Query: 96   LSSLQKKETLN----AAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEK 151
               +  K  L      A  V++       LE +I  L+++ ++Q KE ++L  +    E 
Sbjct: 897  YRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEI 956

Query: 152  KISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKEL 202
              S  + KL    +     + + +     +   +EE+ + + E      E 
Sbjct: 957  TYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEK 1007

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 50.1 bits (120), Expect = 5e-07
 Identities = 22/168 (13%), Positives = 59/168 (35%), Gaps = 14/168 (8%)

Query: 44   KIELDQLKSKIRSLESHIDEKT-----QELKGKDEVVAQKEKAIQDKSERIVSLQKELSS 98
            ++   +    I  L+            ++LK +   V + +K       +I+ LQ+++  
Sbjct: 880  RVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDE 939

Query: 99   LQKKETLNAAEQVDKAHARADELEKQIDNLKKESE---KQQKEKEALEARAIEAEKKISD 155
              K+        ++K +        + + L+ + E     ++E +    R +  +++I+ 
Sbjct: 940  QNKE----YKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAK 995

Query: 156  LSAKLEKLQKINDEQKSKIRKTERAL--KVAEEEMMRAKFEATSRSKE 201
            L  +L + Q      +    K +      V+E +      +       
Sbjct: 996  LRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELN 1043

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 41.2 bits (97), Expect = 4e-04
 Identities = 21/132 (15%), Positives = 51/132 (38%), Gaps = 6/132 (4%)

Query: 74  VVAQKEKAIQDKSERIVSLQKELSSLQKKETL--NAAEQVDKAHARADELEKQIDNLKKE 131
           VV ++ + ++D +  + +L +      K + +       + + H R            K 
Sbjct: 830 VVRKRYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKA 889

Query: 132 SEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA 191
               Q     + A+     KK+   +  +E+ +K++   ++KI + +R  K+ E+     
Sbjct: 890 IVYLQCCYRRMMAK--RELKKLKIEARSVERYKKLHIGLENKIMQLQR--KIDEQNKEYK 945

Query: 192 KFEATSRSKELT 203
                  + E+T
Sbjct: 946 SLLEKMNNLEIT 957

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 67.9 bits (166), Expect = 9e-13
 Identities = 29/162 (17%), Positives = 67/162 (41%), Gaps = 1/162 (0%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
            L+ E  +++ ++  LE  ++E+    +         +  I+   + I+ ++ + + L K 
Sbjct: 946  LQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTK- 1004

Query: 103  ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
            E     E+V        E E++  NL K   K +     LE R  + EK   +L     K
Sbjct: 1005 ERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRK 1064

Query: 163  LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
            L+  + +   +I + +  +   + ++ + + E  +    L +
Sbjct: 1065 LEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLED 1106

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 66.4 bits (162), Expect = 3e-12
 Identities = 29/162 (17%), Positives = 74/162 (45%), Gaps = 1/162 (0%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
            L  +  +L+  +  +E+ I+E+ +  +       + ++ + D  E++   +     LQ  
Sbjct: 918  LAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQL- 976

Query: 103  ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
            E + A  ++ K       +E Q + L KE +  ++    L     E E+K  +L+    K
Sbjct: 977  EKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNK 1036

Query: 163  LQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
             + +  E + +++K E++ +  E+   + + E++   +++ E
Sbjct: 1037 HESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAE 1078

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 64.1 bits (156), Expect = 2e-11
 Identities = 36/172 (20%), Positives = 78/172 (45%), Gaps = 12/172 (6%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
            L  E   L+ ++  L +++ E+ ++ K   ++  + E  I +   R+   +K    L+K 
Sbjct: 1002 LTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKI 1061

Query: 103  ------ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
                  E+ +  EQ+ +  A+  EL+ Q+   ++E +      E   ++   A KKI +L
Sbjct: 1062 KRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIREL 1121

Query: 157  SAKLEKLQKINDEQKSKIRKTERALKVAEEEM------MRAKFEATSRSKEL 202
             + +  LQ+  + +K+   K E+  +   EE+      +    + T+  +EL
Sbjct: 1122 ESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTELEDTLDTTATQQEL 1173

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 63.7 bits (155), Expect = 2e-11
 Identities = 31/162 (19%), Positives = 72/162 (44%), Gaps = 6/162 (3%)

Query: 48   DQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNA 107
            +++++K   L+   + + +      E+  +  +  ++K+     LQ E     + E +  
Sbjct: 857  EEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRV 916

Query: 108  AEQVDKAH--ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQK 165
                 K        E+E +I+  ++ S++ Q EK+ ++ + ++ E+++ +  A  +KLQ 
Sbjct: 917  RLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQL 976

Query: 166  INDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHS 207
                   KI+K E  + + E++      + T   K L E  S
Sbjct: 977  EKVTADGKIKKMEDDILIMEDQNN----KLTKERKLLEERVS 1014

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 63.7 bits (155), Expect = 2e-11
 Identities = 30/165 (18%), Positives = 62/165 (37%), Gaps = 11/165 (6%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
            L  E + L+ K+++      E  +          + E+ + +   RI   ++    LQ +
Sbjct: 890  LCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAE 949

Query: 103  ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
            +         K   +  +LE+Q++  +   +K Q EK   + +  + E  I  +  +  K
Sbjct: 950  K--------KKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNK 1001

Query: 163  LQKINDEQKSKIRKTERALKVAEE---EMMRAKFEATSRSKELTE 204
            L K     + ++      L   EE    + + K +  S   EL  
Sbjct: 1002 LTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEV 1046

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 61.8 bits (150), Expect = 1e-10
 Identities = 25/146 (17%), Positives = 61/146 (41%), Gaps = 8/146 (5%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
            L++ L + +   + LE    +   E     E +A+ +  I +   ++   ++EL +   +
Sbjct: 1044 LEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALAR 1103

Query: 103  ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK 162
                    ++   ++ +   K+I  L+      Q++ E+ +A   +AEK+  DLS +LE 
Sbjct: 1104 --------LEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEELEA 1155

Query: 163  LQKINDEQKSKIRKTERALKVAEEEM 188
            L+   ++        +       ++ 
Sbjct: 1156 LKTELEDTLDTTATQQELRGSDYKDD 1181

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 61.4 bits (149), Expect = 1e-10
 Identities = 27/168 (16%), Positives = 70/168 (41%), Gaps = 6/168 (3%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ-- 100
               ++ +++  I  +E   ++ T+E K  +E V+     + ++ E+  +L K  +  +  
Sbjct: 981  ADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESM 1040

Query: 101  ----KKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
                +       +   +      +LE +  +L ++  + Q +   L+A+  + E+++   
Sbjct: 1041 ISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAA 1100

Query: 157  SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
             A+LE      +    KIR+ E  +   +E++   K       K+  +
Sbjct: 1101 LARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRD 1148

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 61.0 bits (148), Expect = 2e-10
 Identities = 22/168 (13%), Positives = 61/168 (36%), Gaps = 6/168 (3%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ-- 100
            L   L + + K ++L    ++    +   +  + ++EK+ Q+  +    L+ E S L   
Sbjct: 1016 LTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQ 1075

Query: 101  ----KKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
                + +      Q+ K          ++++   +     K+   LE+   + ++ +   
Sbjct: 1076 IAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESE 1135

Query: 157  SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
             A   K +K   +   ++   +  L+   +     +    S  K+  +
Sbjct: 1136 KAARNKAEKQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDDD 1183

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 59.1 bits (143), Expect = 7e-10
 Identities = 31/168 (18%), Positives = 72/168 (42%), Gaps = 13/168 (7%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK 102
            L+ +L++ ++  + L+        ++K  ++ +   E      ++    L++ +S L   
Sbjct: 960  LEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTN 1019

Query: 103  ------ETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL 156
                  +  N  +  +K  +   ELE ++   +K  ++ +K K  L       E + SDL
Sbjct: 1020 LAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKL-------EGESSDL 1072

Query: 157  SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
              ++ +LQ    E K+++ K E  L+ A   +     +  +  K++ E
Sbjct: 1073 HEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRE 1120

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori} Length = 256

 Score = 49.3 bits (117), Expect = 4e-07
 Identities = 36/160 (22%), Positives = 80/160 (50%), Gaps = 1/160 (0%)

Query: 43  LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK- 101
            + +LD+  +   +    I    +E       V++ E+ +QD + +I S+QK++S ++  
Sbjct: 30  KRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKSE 89

Query: 102 KETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLE 161
           +E  +   + D A  R+++  ++I+NL+ E +++ +++E L+   +E EK   +L + +E
Sbjct: 90  RELRSLNIEEDIAKERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLALELESLVE 149

Query: 162 KLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKE 201
              K   E +  I K +  L    E  + + +E   R  +
Sbjct: 150 NEVKNIKETQQIIFKKKEDLVEKTEPKIYSFYERIRRWAK 189

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori} Length = 256

 Score = 47.0 bits (111), Expect = 3e-06
 Identities = 23/154 (14%), Positives = 72/154 (46%), Gaps = 3/154 (1%)

Query: 53  KIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVD 112
           +I  L+  ID     ++ K + + +     + K++ I++L++E  +L K +     + + 
Sbjct: 12  EISHLDKEIDSLEPLIREKRKDLDKALNDKEAKNKAILNLEEEKLAL-KLQVSKNEQTLQ 70

Query: 113 KAHARADELEKQIDNLK--KESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQ 170
             +A+   ++K++  +K  +E      E++  + R+ +A ++I +L  ++++  +  ++ 
Sbjct: 71  DTNAKIASIQKKMSEIKSERELRSLNIEEDIAKERSNQANREIENLQNEIKRKSEKQEDL 130

Query: 171 KSKIRKTERALKVAEEEMMRAKFEATSRSKELTE 204
           K ++ + E+     E  +           + + +
Sbjct: 131 KKEMLELEKLALELESLVENEVKNIKETQQIIFK 164

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.1 bits (116), Expect = 1e-06
 Identities = 46/279 (16%), Positives = 82/279 (29%), Gaps = 80/279 (28%)

Query: 40  SSPLKIELDQLKSKIRSLESHIDEKTQELKGK---------DEV---------------- 74
           SS +K+ +  +++++R L          LK K           V                
Sbjct: 220 SSNIKLRIHSIQAELRRL----------LKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL 269

Query: 75  VAQKEKAIQD----KSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKK 130
           +  + K + D     +   +SL     +L   E                 L  +  + + 
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK--------------SLLLKYLDCRP 315

Query: 131 ESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMR 190
           +   ++         +I AE  I D  A  +  + +N ++ + I   E +L V E    R
Sbjct: 316 QDLPREVLTTNPRRLSIIAE-SIRDGLATWDNWKHVNCDKLTTII--ESSLNVLEPAEYR 372

Query: 191 AKFEATSRSKELTEVHSAWLPP------WLA---------VHLLQCQSLIETHWNAHGKP 235
             F+  S         SA +P       W           V+ L   SL+E         
Sbjct: 373 KMFDRLSVFPP-----SAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS 427

Query: 236 AMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQW 274
              +     LE K +       H   +    IP   +  
Sbjct: 428 IPSI----YLELKVKLENEYALHRSIVDHYNIPKTFDSD 462

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 46.7 bits (110), Expect = 2e-06
 Identities = 16/76 (21%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 116 ARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEK-LQKINDEQKSKI 174
           A+AD L ++ ++++K  E+Q+K    L+     ++    +   K +K L++ N  Q  ++
Sbjct: 75  AQADRLTQEPESIRKWREEQRKR---LQELDAASKVMEQEWREKAKKDLEEWNQRQSEQV 131

Query: 175 RKTERALKVAEEEMMR 190
            K +   ++A++   +
Sbjct: 132 EKNKINNRIADKAFYQ 147

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12 Length = 430

 Score = 43.5 bits (103), Expect = 5e-05
 Identities = 16/156 (10%), Positives = 57/156 (36%), Gaps = 8/156 (5%)

Query: 46  ELDQLKSKIRSLESHIDEKTQELKGKDEVVAQK--EKAIQDKSERIVSLQKELSSLQKKE 103
           ++D      +     ++ +   +K K+ +V Q   E+        +  + +E+S   + +
Sbjct: 120 KIDGKTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSIQYK 179

Query: 104 TLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKL 163
                E++ +   +  +   +    ++    + K  ++     +    + S       + 
Sbjct: 180 KEY--EELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLFQGPRGSRYDEAEGRF 237

Query: 164 QKINDEQKSKIRKTERALKVAEEEM---MRAKFEAT 196
           + I + +  +++  E+ +     ++    +  FE T
Sbjct: 238 EVI-NNETEQLKAEEKKILNQFLKIKKKRKELFEKT 272

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 43.3 bits (101), Expect = 8e-05
 Identities = 30/162 (18%), Positives = 64/162 (39%), Gaps = 7/162 (4%)

Query: 54  IRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDK 113
           ++S+E         L+   ++  +     Q+ + +  + + E  +  + E     +Q + 
Sbjct: 640 VQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEA 699

Query: 114 AHARADELEKQIDNLKKESEKQQKE--KEALEARAIEAEKKISDLSAKLEKLQKINDEQK 171
             AR + LE +  ++  ES    K   +   EA  IE E  +     K + L    + + 
Sbjct: 700 EKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAEL 759

Query: 172 SKIRKT-----ERALKVAEEEMMRAKFEATSRSKELTEVHSA 208
            +++K        A    E E+ +A+  A   +K+  E+  A
Sbjct: 760 ERVKKVREMELIYARAQLELEVSKAQQLANVEAKKFKEMTEA 801

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C* Length = 3245

 Score = 43.0 bits (101), Expect = 1e-04
 Identities = 20/137 (14%), Positives = 45/137 (32%), Gaps = 16/137 (11%)

Query: 43   LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKE------- 95
               ELD    +       + +  Q  + K +   + +  +  +++ I   + +       
Sbjct: 1946 KNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLEK 2005

Query: 96   -LSSLQKKETLNAAEQVDKAHARAD--------ELEKQIDNLKKESEKQQKEKEALEARA 146
               +   +E +   E                   LEK I   K+E     +E E ++  +
Sbjct: 2006 AEPTGPLREEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTES 2065

Query: 147  IEAEKKISDLSAKLEKL 163
             + + K+    A L+ L
Sbjct: 2066 SKVKNKVDRSIALLDNL 2082

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C* Length = 3245

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 27/169 (15%), Positives = 67/169 (39%), Gaps = 15/169 (8%)

Query: 47   LDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK----- 101
            LD +   +  +     EK  +L+ +   +    K ++D   ++  LQ  L+   +     
Sbjct: 1898 LDFINQVVLLIN----EKRDQLEEEQLHLNIGLKKLRDTEAQVKDLQVSLAQKNRELDVK 1953

Query: 102  -KETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARA---IEAEKKISDLS 157
             ++     +Q+ +    A+  +K    L+ + + + KE    + +A   +E  +    L 
Sbjct: 1954 NEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLEKAEPTGPLR 2013

Query: 158  AKLEKLQKINDEQKSKIRKTERALKVAEE--EMMRAKFEATSRSKELTE 204
             ++E+L+   +E K K  +    +   E+     + ++    R  E  +
Sbjct: 2014 EEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIK 2062

>2xs1_A Programmed cell death 6-interacting protein; protein transport-viral protein complex, cell cycle; 2.30A {Homo sapiens} PDB: 2xs8_A 2oev_A 2r05_A 2r02_A 2r03_A 2oex_A 2ojq_A Length = 704

 Score = 42.2 bits (98), Expect = 2e-04
 Identities = 23/160 (14%), Positives = 54/160 (33%), Gaps = 7/160 (4%)

Query: 29  VPPLTASDAVDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSER 88
           +P    +  +  S +   L  L S +  ++   +    +LK  +  +  K      +   
Sbjct: 540 IPSANPAKTMQGSEVVNVLKSLLSNLDEVKKEREGLENDLKSVNFDMTSKFLTALAQDGV 599

Query: 89  IVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLK------KESEKQQKEKEAL 142
           I      ++ L +        +V ++  + + L K I          K+S  +   +E +
Sbjct: 600 INEEALSVTELDRVYG-GLTTKVQESLKKQEGLLKNIQVSHQEFSKMKQSNNEANLREEV 658

Query: 143 EARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALK 182
                 A     +L A L++  K  +E    + + +    
Sbjct: 659 LKNLATAYDNFVELVANLKEGTKFYNELTEILVRFQNKCS 698

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 Length = 854

 Score = 42.1 bits (100), Expect = 2e-04
 Identities = 32/173 (18%), Positives = 72/173 (41%), Gaps = 36/173 (20%)

Query: 38  VDSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS 97
           ++S+P   E+D L+ K   LE  I+   + LK        KEK    + ER+ +++ E++
Sbjct: 396 LESAP--EEIDALERKKLQLE--IER--EALK--------KEKDPDSQ-ERLKAIEAEIA 440

Query: 98  SLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLS 157
            L ++                 +L  + +  ++   K ++ +  L+    E E       
Sbjct: 441 KLTEE---------------IAKLRAEWEREREILRKLREAQHRLDEVRREIELAERQ-- 483

Query: 158 AKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATS-RSKELTEVHSAW 209
             L +  ++   +  ++ K E  ++   E++  A+F       +++ E+ S W
Sbjct: 484 YDLNRAAEL---RYGELPKLEAEVEALSEKLRGARFVRLEVTEEDIAEIVSRW 533

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	321
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	98.52
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	98.4
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	98.05
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	97.66
3s84_A	273	Apolipoprotein A-IV; four helix bundle, transport	97.62
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	97.6
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	97.57
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	97.43
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	97.41
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	97.24
3s84_A	273	Apolipoprotein A-IV; four helix bundle, transport	97.23
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	97.17
2a01_A	243	Apolipoprotein A-I; four-helix bundle, lipid trans	97.16
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	96.96
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	96.92
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	96.73
3r2p_A	185	Apolipoprotein A-I; amphipathic alpha-helix, major	96.73
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	96.64
2a01_A	243	Apolipoprotein A-I; four-helix bundle, lipid trans	96.58
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	96.55
1gs9_A	165	Apolipoprotein E, APOE4; lipid transport, heparin-	96.53
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	96.51
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	96.49
1gs9_A	165	Apolipoprotein E, APOE4; lipid transport, heparin-	96.43
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	96.38
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	96.36
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	96.35
2lem_A	216	Apolipoprotein A-I; lipid transport; NMR {Mus musc	96.33
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	96.3
1nfn_A	191	Apolipoprotein E3; lipid transport, heparin-bindin	96.24
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	96.19
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	96.05
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	95.97
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	95.97
1nfn_A	191	Apolipoprotein E3; lipid transport, heparin-bindin	95.42
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	95.34
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	95.21
2l7b_A	307	Apolipoprotein E, APO-E; lipid transport, atherosc	94.96
3r2p_A	185	Apolipoprotein A-I; amphipathic alpha-helix, major	94.95
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	94.95
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	94.93
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	94.83
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	94.83
2lem_A	216	Apolipoprotein A-I; lipid transport; NMR {Mus musc	94.78
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	94.55
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	94.27
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	94.16
2b9c_A	147	Striated-muscle alpha tropomyosin; alpha-helix, co	94.16
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	93.97
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	93.95
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	93.94
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	93.67
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	93.51
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	93.51
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	93.38
2l7b_A	307	Apolipoprotein E, APO-E; lipid transport, atherosc	93.35
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	92.9
1m1j_A	491	Fibrinogen alpha subunit; coiled coils, disulfide	92.78
3swk_A	86	Vimentin; cytoskeleton, intermediate filament, alp	92.36
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	92.34
3bas_A	89	Myosin heavy chain, striated muscle/general contro	92.23
2oto_A	155	M protein; helical coiled coil, fibrinogen-binding	90.95
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	90.72
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	90.71
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	90.65
3jsv_C	94	NF-kappa-B essential modulator; ubiquitin, coiled-	90.61
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	90.44
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	89.42
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	89.29
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	88.9
1x8y_A	86	Lamin A/C; structural protein, intermediate filame	88.89
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	88.64
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	88.5
3iox_A	497	AGI/II, PA; alpha helix, PPII helix, supersandwich	88.46
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	87.91
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	87.86
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	86.64
1gk4_A	84	Vimentin; intermediate filament, dimer, parallel c	86.2
3htk_A	60	Structural maintenance of chromosomes protein 5; S	85.89
3bas_A	89	Myosin heavy chain, striated muscle/general contro	85.87
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	85.8
1zxa_A	67	CGMP-dependent protein kinase 1, alpha isozyme; pa	84.73
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	84.65
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	84.42
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	84.19
3mov_A	95	Lamin-B1; LMNB1, B-type lamins, intermediate filam	83.89
1m1j_A	491	Fibrinogen alpha subunit; coiled coils, disulfide	83.18
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	82.92
2p22_C	192	Protein SRN2; endosome, trafficking complex, VPS23	82.89
2e7s_A	135	RAB guanine nucleotide exchange factor SEC2; coile	82.67
2nrj_A	346	HBL B protein; enterotoxin, hemolysis, transmembra	82.43
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	82.23
3swk_A	86	Vimentin; cytoskeleton, intermediate filament, alp	82.2
2pms_C	125	Pneumococcal surface protein A (PSPA); lactoferrin	81.98
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	81.37
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	81.29
1fxk_C	133	Protein (prefoldin); archaeal protein, chaperone;	80.67

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=98.52  E-value=7.4e-05  Score=68.66  Aligned_cols=164  Identities=14%  Similarity=0.142  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH--HH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADE--LE  122 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Rire--L~  122 (321)
                      .+++.++..+..+-..+..+..++..+...+..++..+.++..+|..++++|....        .++..++.++..  =+
T Consensus        18 ~~i~~l~~~~~~lp~el~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~--------~ri~~~~~~l~~v~~~   89 (256)
T 3na7_A           18 KEIDSLEPLIREKRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTN--------AKIASIQKKMSEIKSE   89 (256)
T ss_dssp             HHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHCSSS
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHccCCH
Confidence            34444444444444444444444444444444444444444444444444444442        223333333322  12


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHhhh
Q 020809          123 KQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKV----AEEEMMRAKFEATSR  198 (321)
Q Consensus       123 k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~----~Eeei~kl~~ea~~~  198 (321)
                      +++..|..+++....++..++....++..++..++..++.+.....+.+..+......+..    ++.++..+..+....
T Consensus        90 kE~~aL~kEie~~~~~i~~lE~eile~~e~ie~~~~~l~~~~~~l~~~~~~l~~~~~~~~~~~~e~~~e~~~l~~~r~~l  169 (256)
T 3na7_A           90 RELRSLNIEEDIAKERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLALELESLVENEVKNIKETQQIIFKKKEDL  169 (256)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3345555555555555555555555555555555555554444444444444443333322    222222222221111


Q ss_pred             hhhhhhhhccCchhHHHHHHHHHHHH
Q 020809          199 SKELTEVHSAWLPPWLAVHLLQCQSL  224 (321)
Q Consensus       199 a~ql~e~~g~~l~Pwla~~~~~~~~~  224 (321)
                              ..-+||-|-..|.++..-
T Consensus       170 --------~~~i~~~lL~~Yerir~~  187 (256)
T 3na7_A          170 --------VEKTEPKIYSFYERIRRW  187 (256)
T ss_dssp             --------HHTSCHHHHHHHHHHHHH
T ss_pred             --------HhcCCHHHHHHHHHHHHh
Confidence                    124788888888887653

>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1 PDB: 2tma_A 2w49_A 2w4u_A

Probab=98.40  E-value=0.0003  Score=61.98  Aligned_cols=55  Identities=18%  Similarity=0.257  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS   97 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~   97 (321)
                      +..++..++..+..+...++.+..++..+...+..++..+..+...+..+...+.
T Consensus         4 ~~~~~~~l~~~~~~~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   58 (284)
T 1c1g_A            4 IKKKMQMLKLDKENALDRADEAEADKKAAEDRSKQLEDELVSLQKKLKATEDELD   58 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444444444444444444444333333333

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=98.05  E-value=0.0011  Score=60.80  Aligned_cols=136  Identities=15%  Similarity=0.203  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------hhHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK--------ETLNAAEQVDKA  114 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~--------~~~~~eeq~~~~  114 (321)
                      +...+..+...+..++..+..+...+..+...+..++..+..++..|..+...|...+..        .-.++...++.+
T Consensus        23 l~~~~~~lp~el~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~~v~~~kE~~aL~kEie~~  102 (256)
T 3na7_A           23 LEPLIREKRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKSERELRSLNIEEDIA  102 (256)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHH
Confidence            344444445555555555555555555555555555555555555555555555544433        235566777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          115 HARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERAL  181 (321)
Q Consensus       115 ~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~l  181 (321)
                      +.|+..|++.|..+-..++..+.....++.....++..+   ......+.....+....+..+....
T Consensus       103 ~~~i~~lE~eile~~e~ie~~~~~l~~~~~~l~~~~~~l---~~~~~~~~~~~~e~~~e~~~l~~~r  166 (256)
T 3na7_A          103 KERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLA---LELESLVENEVKNIKETQQIIFKKK  166 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777777777777777777776655555554444444332   3333333333344444444443333

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=97.66  E-value=0.0098  Score=52.39  Aligned_cols=130  Identities=15%  Similarity=0.187  Sum_probs=83.3

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK---ETLNAAEQVDKAHARAD  119 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~---~~~~~eeq~~~~~~Rir  119 (321)
                      +.+++.+++....+......++..+   ++..|.++++.+.++...+..|..++++.+.+   ........++.+++.+.
T Consensus        22 ~~q~~~~le~El~EFqesSrELE~E---LE~eL~~~Ek~~~~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~el~   98 (189)
T 2v71_A           22 YKQSFQEARDELVEFQEGSRELEAE---LEAQLVQAEQRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLS   98 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555555555555443   46778888888888888888888888888553   12223344556666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          120 ELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIR  175 (321)
Q Consensus       120 eL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~  175 (321)
                      .|....+.++..+.++......||...+.....+..+..+++..-....-....++
T Consensus        99 ~l~~~~~~l~~~ireLEq~NDdlEr~~R~~~~SleD~e~kln~aiEr~alLE~El~  154 (189)
T 2v71_A           99 QTRAIKEQLHKYVRELEQANDDLERAKRATIMSLEDFEQRLNQAIERNAFLESELD  154 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66666666666666666666666666666666666666666666555555555554

>3s84_A Apolipoprotein A-IV; four helix bundle, transport protein; 2.40A {Homo sapiens}

Probab=97.62  E-value=0.019  Score=53.22  Aligned_cols=83  Identities=13%  Similarity=0.177  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHHhhccccchhHHhhhhhhhhh--------------hhhhHHHHHhccchhhHHHHhHhHHHHHhhhhh
Q 020809          237 MDVAIQKALEKKAQAGKWVQPHVETIKAKWIPA--------------VKEQWVVFTTNVEPHVQTLKTKTIEACEATKTA  302 (321)
Q Consensus       237 ~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~--------------~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~  302 (321)
                      .+.+-.+.......++.|..|+.+.++.+....              +..++..++..+.||+..+...-..-.+..+..
T Consensus       167 a~~L~~~l~~~~eeLr~~L~p~ae~lr~~l~~~~e~l~~~l~~~~~~~~qq~e~f~~~~~p~~e~~~~~l~~~~e~l~~~  246 (273)
T 3s84_A          167 AEELKARISASAEELRQRLAPLAEDVRGNLRGNTEGLQKSLAELGGHLDQQVEEFRRRVEPYGENFNKALVQQMEQLRQK  246 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHH
Confidence            445556666667778888888888888776642              444555555566666666655555555555555


Q ss_pred             cCchhHHHHhhhccccc
Q 020809          303 VTPHIIRVQEVVDPYFQ  319 (321)
Q Consensus       303 ~~ph~~k~~~~~~py~~  319 (321)
                      +.||+..++..++|+-+
T Consensus       247 l~~~~~~~~~~~~~~~~  263 (273)
T 3s84_A          247 LGPHAGDVEGHLSFLEK  263 (273)
T ss_dssp             HSCC-------------
T ss_pred             hCcchhhHHhhhhHHHH
Confidence            56666555555555543

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A

Probab=97.60  E-value=0.00021  Score=78.46  Aligned_cols=61  Identities=16%  Similarity=0.134  Sum_probs=33.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +...++.++.+++.++..++..+.++..++..+..++..++..+......+..++.++..+
T Consensus       858 El~~L~~eL~el~~~L~~le~~l~ele~~l~~Le~e~~~l~~~L~~e~~~l~~~e~~l~~l  918 (1184)
T 1i84_S          858 EMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRL  918 (1184)
T ss_dssp             HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555666666666666666666665555555555555555555444444444444444333

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A

Probab=97.57  E-value=0.00029  Score=77.44  Aligned_cols=53  Identities=11%  Similarity=0.095  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL   96 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI   96 (321)
                      ..++.+++.++..++..+..+...+.+++..+..++.++..+..++......+
T Consensus       856 ~~El~~L~~eL~el~~~L~~le~~l~ele~~l~~Le~e~~~l~~~L~~e~~~l  908 (1184)
T 1i84_S          856 EEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELY  908 (1184)
T ss_dssp             HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555555555555555444444444444444444444444333333

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=97.43  E-value=0.11  Score=62.39  Aligned_cols=97  Identities=20%  Similarity=0.102  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccCchhHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSRSKELTEVHSAWLPPWLAVHLL  219 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~a~ql~e~~g~~l~Pwla~~~~  219 (321)
                      +.+++....++.++.+.+..+..+++..+..+.+++....+.+.++.++...+...... .        -|.--|+.+..
T Consensus      2017 ~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e~~~~~~kl~rA-~--------~Li~gL~~Ek~ 2087 (3245)
T 3vkg_A         2017 EQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRS-I--------ALLDNLNSERG 2087 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H--------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H--------HHHHhhhhccc
Confidence            33444444444444444444444444444444444444444444444433332221111 1        13334777888


Q ss_pred             HHHHHHHhHHHhhCcchHHHHHHHHH
Q 020809          220 QCQSLIETHWNAHGKPAMDVAIQKAL  245 (321)
Q Consensus       220 ~~~~~~~~~~~~hg~p~~~~~~~~~~  245 (321)
                      ||...+..+-......+-+.++--|.
T Consensus      2088 RW~~~~~~l~~~~~~L~GD~LLaaaf 2113 (3245)
T 3vkg_A         2088 RWEQQSENFNTQMSTVVGDVVLASAF 2113 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhccHHHHHHHHH
Confidence            88888888877777777777765544

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=97.41  E-value=0.0049  Score=67.23  Aligned_cols=131  Identities=24%  Similarity=0.277  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQ  124 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~  124 (321)
                      ....+++.++.+|+..+++..++...+.+.+...+   ..+..++..|+.+++.++.     .+.....++.++..|+++
T Consensus       921 ~~~~~LE~kl~eLq~rL~~~e~~n~~L~~~~~~~~---~~~~~e~~~L~~~l~~le~-----~~~e~~~~~~~v~~L~~e  992 (1080)
T 2dfs_A          921 KLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLE---ITYSTETEKLRSDVERLRM-----SEEEAKNATNRVLSLQEE  992 (1080)
T ss_dssp             ------------------------------CHHHH---HHHHHHHHHHHHTHHHHHH-----HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH
Confidence            33445555555555555555444444444444333   2344555566655555543     233333555677777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          125 IDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEE  186 (321)
Q Consensus       125 Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Ee  186 (321)
                      ++.+.+++.....++..++.+...+.   .+++.++..|++.+...+.++++++......++
T Consensus       993 ~~~l~~~~~~~~ke~~~lee~~~~~~---~~L~~kv~~L~~e~~~L~qq~~~l~~~~~~~~~ 1051 (1080)
T 2dfs_A          993 IAKLRKELHQTQTEKKTIEEWADKYK---HETEQLVSELKEQNTLLKTEKEELNRRIHDQAK 1051 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777777766666666555444   355566667777666666666666644444433

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=97.24  E-value=0.079  Score=46.61  Aligned_cols=78  Identities=24%  Similarity=0.306  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          106 NAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAE  185 (321)
Q Consensus       106 ~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~E  185 (321)
                      .++..++.+.+|.++|...+..|..+++..+.+   +..-..+....++.++..+..+..........|.+++..-+.++
T Consensus        46 ELE~eL~~~Ek~~~~L~~~~~~L~~E~e~~k~K---~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~ireLEq~NDdlE  122 (189)
T 2v71_A           46 ELEAQLVQAEQRNRDLQADNQRLKYEVEALKEK---LEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLE  122 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence            344444555555555555555555555555522   22222333333444444444444444444444444444444443


Q ss_pred             H
Q 020809          186 E  186 (321)
Q Consensus       186 e  186 (321)
                      .
T Consensus       123 r  123 (189)
T 2v71_A          123 R  123 (189)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3s84_A Apolipoprotein A-IV; four helix bundle, transport protein; 2.40A {Homo sapiens}

Probab=97.23  E-value=0.037  Score=51.28  Aligned_cols=73  Identities=8%  Similarity=0.153  Sum_probs=34.6

Q ss_pred             HHhhccccchhHHhhhhhhhhhhhh---h----HHHHHhccchh-------hHHHHhHhHHHHHhhhhhcCchhHHHHhh
Q 020809          248 KAQAGKWVQPHVETIKAKWIPAVKE---Q----WVVFTTNVEPH-------VQTLKTKTIEACEATKTAVTPHIIRVQEV  313 (321)
Q Consensus       248 ~~~~~~~~~ph~~~~~~k~~p~~~~---~----~~~~~~~~~p~-------~q~~~~~~~~~~~~~~~~~~ph~~k~~~~  313 (321)
                      +..++.-+.|+++-++.++-|+...   +    |-.+...+.||       ++..+....||.+....++.=.++.++..
T Consensus       167 a~~L~~~l~~~~eeLr~~L~p~ae~lr~~l~~~~e~l~~~l~~~~~~~~qq~e~f~~~~~p~~e~~~~~l~~~~e~l~~~  246 (273)
T 3s84_A          167 AEELKARISASAEELRQRLAPLAEDVRGNLRGNTEGLQKSLAELGGHLDQQVEEFRRRVEPYGENFNKALVQQMEQLRQK  246 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHH
Confidence            3445556667777777777776222   1    22222222222       22223333333333333333344488888


Q ss_pred             hcccccc
Q 020809          314 VDPYFQV  320 (321)
Q Consensus       314 ~~py~~~  320 (321)
                      ++||+-+
T Consensus       247 l~~~~~~  253 (273)
T 3s84_A          247 LGPHAGD  253 (273)
T ss_dssp             HSCC---
T ss_pred             hCcchhh
Confidence            8898753

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=97.17  E-value=0.012  Score=64.06  Aligned_cols=29  Identities=17%  Similarity=0.209  Sum_probs=1.0

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhh
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELK   69 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk   69 (321)
                      ..+++++.+|+.++.+.+....++..++.
T Consensus       924 ~~LE~kl~eLq~rL~~~e~~n~~L~~~~~  952 (1080)
T 2dfs_A          924 IGLENKIMQLQRKIDEQNKEYKSLLEKMN  952 (1080)
T ss_dssp             ---------------------------CH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566666777766666666655555554

>2a01_A Apolipoprotein A-I; four-helix bundle, lipid transport; HET: AC9; 2.40A {Homo sapiens} PDB: 3k2s_A* 1av1_A 3j00_0*

Probab=97.16  E-value=0.0027  Score=57.82  Aligned_cols=101  Identities=12%  Similarity=0.127  Sum_probs=78.4

Q ss_pred             chhHHHHHHHHHHHHHHhHHHhhCcchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhhhhhhHHHHHhccchhhHHHH
Q 020809          210 LPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLK  289 (321)
Q Consensus       210 l~Pwla~~~~~~~~~~~~~~~~hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~  289 (321)
                      |-|....-..++..... ....+..|..+.+-.++.++...++.|+.||++.++.++.|.+..    ++..+.||.+.++
T Consensus       141 L~p~~eelr~kl~~~ve-elk~~l~P~~ee~r~kl~~~~~el~~~l~p~~~e~~~kl~~~~e~----lr~~l~p~~e~lk  215 (243)
T 2a01_A          141 LSPLGEEMRDRARAHVD-ALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLST----LSEKAKPALEDLR  215 (243)
T ss_dssp             CCSSTHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSCCHHHHHHH----HHHHHHHHHHHSS
T ss_pred             HHhHHHHHHHHHHHHHH-HHHHHHHhhHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHH----HHHHhHHHHHHHH
Confidence            44444433334333322 234567789999999999999999999999999999999888555    8888999999999


Q ss_pred             hHhHHHHHhhhhhcCchhHHHHhhhc
Q 020809          290 TKTIEACEATKTAVTPHIIRVQEVVD  315 (321)
Q Consensus       290 ~~~~~~~~~~~~~~~ph~~k~~~~~~  315 (321)
                      .+-.||++..+..+..-+++++..+.
T Consensus       216 ~~l~p~~e~~~~~l~~~~e~~~~~~~  241 (243)
T 2a01_A          216 QGLLPVLESFKVSFLSALEEYTKKLN  241 (243)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHhhc
Confidence            99889999888888888888887764

>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil (dimeric, parallel), familial hypertrophic cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo sapiens} SCOP: h.1.26.1 PDB: 2fxm_A

Probab=96.96  E-value=0.12  Score=42.49  Aligned_cols=59  Identities=22%  Similarity=0.362  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKL  163 (321)
Q Consensus       105 ~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~L  163 (321)
                      .+.+++...+.++=.+|+..|..+...++........|.+..+.++..+.++...++.+
T Consensus        65 ~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~~led~  123 (129)
T 2fxo_A           65 ADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKRDIDDL  123 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45556555555555566666666555555555555555555555554444444444443

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=96.92  E-value=0.032  Score=55.88  Aligned_cols=38  Identities=16%  Similarity=0.225  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          154 SDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       154 ~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..++..+..++...++++.++.++.++...+..++..+
T Consensus       540 ~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l  577 (597)
T 3oja_B          540 EDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQL  577 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            33334444455555555555555554444444444444

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=96.73  E-value=0.11  Score=40.97  Aligned_cols=32  Identities=13%  Similarity=0.205  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHH
Q 020809           47 LDQLKSKIRSLESHIDEKTQELKGKDEVVAQK   78 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~   78 (321)
                      ++.++.++..|....+............+..+
T Consensus         4 MdaIKkKm~~lk~e~e~a~drae~~e~~~k~~   35 (101)
T 3u1c_A            4 MDAIKKKMQMLKLDKENALDRAEQAEADKKAA   35 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555554433333333333333

>3r2p_A Apolipoprotein A-I; amphipathic alpha-helix, major protein of high density lipop (HDL), lipid binding, plasma, lipid transport; 2.20A {Homo sapiens} PDB: 1gw3_A 1gw4_A

Probab=96.73  E-value=0.00097  Score=58.33  Aligned_cols=62  Identities=18%  Similarity=0.249  Sum_probs=34.3

Q ss_pred             chhHHhhhhhhhhhhhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhHHHHhhhccccccC
Q 020809          256 QPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY  321 (321)
Q Consensus       256 ~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~~~~~py~~~~  321 (321)
                      .+|++.++.++-|++.+    +++.+...++.++.+-.||.+..++-+..|++.++..+.||+.+|
T Consensus       110 ~~~~e~lr~~l~Py~~e----l~~~~~~~~e~Lr~~L~p~~e~lr~~l~~~~e~lk~~l~Py~ee~  171 (185)
T 3r2p_A          110 QEEMELYRQKVEPLRAE----LQEGARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDEL  171 (185)
T ss_dssp             HHHHHHHHHHHHHHHHH----HHHHHHHHHTTTTTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHH----HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence            33444444444444332    333344444444455555666666666677777777777877654

>2efr_A General control protein GCN4 and tropomyosin 1 Al; destabilizing cluster, hydrophobic core, contractIle protein; 1.80A {Saccharomyces cerevisiae} PDB: 2efs_A 2d3e_A

Probab=96.64  E-value=0.27  Score=41.91  Aligned_cols=113  Identities=19%  Similarity=0.278  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           71 KDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAE  150 (321)
Q Consensus        71 kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~e  150 (321)
                      ....+...+......+.+|..|+.++...-+ ..+.++.+.+++..|-..++.+|..|.       .+..+.+.|+..++
T Consensus        26 ~E~dLEraEERae~aE~k~~eLEeeL~~v~~-nlKsLE~seekasqrEd~yEeqIk~L~-------~kLKEAE~RAE~AE   97 (155)
T 2efr_A           26 LKKLLERAEERAELSEGKSAELEEELKTVTN-NLKSLEAQAEKYSQKEDKYEEEIKVLS-------DKLKEAETRAEFAE   97 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhccchhhhhHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHH
Confidence            5555555555555555555556655555533 444555555555555444444444433       33445566666777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          151 KKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       151 kk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..+..++..++.++......+.....+...+..+-..+.-+
T Consensus        98 Rsv~kLEk~id~lEd~L~~~Kek~~~i~~eLd~tl~el~~~  138 (155)
T 2efr_A           98 RSVTKLEKSIDDLEDELYAQKLKYKAISEEMKQLEDKVEEL  138 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            77777777777777776666666666666666655555544

>2a01_A Apolipoprotein A-I; four-helix bundle, lipid transport; HET: AC9; 2.40A {Homo sapiens} PDB: 3k2s_A* 1av1_A 3j00_0*

Probab=96.58  E-value=0.0024  Score=58.22  Aligned_cols=87  Identities=9%  Similarity=0.140  Sum_probs=66.2

Q ss_pred             HHhhCcchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhhhhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhH
Q 020809          229 WNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHII  308 (321)
Q Consensus       229 ~~~hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~  308 (321)
                      +..+=.|+++.+-.++.+....++.-..|+++.++.+.    ..++..++..+.||++.+..+-.++++..+..+.|+++
T Consensus       137 l~~~L~p~~eelr~kl~~~veelk~~l~P~~ee~r~kl----~~~~~el~~~l~p~~~e~~~kl~~~~e~lr~~l~p~~e  212 (243)
T 2a01_A          137 LQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRL----AARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALE  212 (243)
T ss_dssp             HCCSCCSSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHTTTSSSCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH----HHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHhHHHHH
Confidence            34466788888888888888888888888888888876    44555688888888777777777777777777777777


Q ss_pred             HHHhhhccccc
Q 020809          309 RVQEVVDPYFQ  319 (321)
Q Consensus       309 k~~~~~~py~~  319 (321)
                      .++.-+.||++
T Consensus       213 ~lk~~l~p~~e  223 (243)
T 2a01_A          213 DLRQGLLPVLE  223 (243)
T ss_dssp             HSSSCSHHHHH
T ss_pred             HHHHHhHHHHH
Confidence            77777777765

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=96.55  E-value=0.22  Score=59.69  Aligned_cols=71  Identities=13%  Similarity=0.228  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ++..++.++++++..+.++...++..++++.+++.++...+.+...++..+..++..+..+..++.-+..|
T Consensus      2012 kr~~l~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e~~~~~~kl~rA~~Li~gL 2082 (3245)
T 3vkg_A         2012 LREEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNL 2082 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            33445566666666666666666666666666666666666665555555566665555555555554444

>1gs9_A Apolipoprotein E, APOE4; lipid transport, heparin-binding, plasma, lipid binding protein; 1.7A {Homo sapiens} SCOP: a.24.1.1 PDB: 1or3_A 1or2_A 1le4_A 1bz4_A 1lpe_A 1le2_A

Probab=96.53  E-value=0.0021  Score=55.51  Aligned_cols=81  Identities=9%  Similarity=0.131  Sum_probs=39.7

Q ss_pred             cchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhhhhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhHHHHhh
Q 020809          234 KPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEV  313 (321)
Q Consensus       234 ~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~~~  313 (321)
                      .|+-+.+..+.+.....++.=+.|+++.++.++-|++.+    ++..+.||+..++.+-.||.+.-++-+..|++-++..
T Consensus        83 ~P~t~el~~~l~~~~e~Lr~~L~~d~EelR~~l~p~~~e----l~~~l~~~~EelR~kl~P~~eeL~~~~~~~~eeLr~k  158 (165)
T 1gs9_A           83 TPVAEETRARLSKELQAAQARLGADMEDVRGRLVQYRGE----VQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKR  158 (165)
T ss_dssp             CCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHTSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            344444444444444444444444555555444444333    4555555555555555555555555555555555555


Q ss_pred             hcccc
Q 020809          314 VDPYF  318 (321)
Q Consensus       314 ~~py~  318 (321)
                      +.||.
T Consensus       159 L~p~~  163 (165)
T 1gs9_A          159 LAVYQ  163 (165)
T ss_dssp             HHHSS
T ss_pred             hhhhc
Confidence            55554

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=96.51  E-value=0.35  Score=41.70  Aligned_cols=42  Identities=19%  Similarity=0.366  Sum_probs=16.3

Q ss_pred             HHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           53 KIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQK   94 (321)
Q Consensus        53 ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~   94 (321)
                      +|..|+.++.+++..++.=.+.-..+-+...++...+..++.
T Consensus         7 Ki~~LekQL~E~n~kLk~EsE~~~rlkK~~tEl~k~~~~~E~   48 (168)
T 3o0z_A            7 KLSQLQKQLEEANDLLRTESDTAVRLRKSHTEMSKSISQLES   48 (168)
T ss_dssp             ---CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444333344444444444333333

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=96.49  E-value=0.17  Score=39.87  Aligned_cols=36  Identities=14%  Similarity=0.219  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHH
Q 020809           47 LDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAI   82 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i   82 (321)
                      ++.++.++..|....+............+..++...
T Consensus         4 md~iKkKm~~lk~e~e~a~d~ae~~e~~~k~~e~~~   39 (101)
T 3u59_A            4 MEAIKKKMQMLKLDKENAIDRAEQAEADKKQAEDRC   39 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555554444444444444333333

>1gs9_A Apolipoprotein E, APOE4; lipid transport, heparin-binding, plasma, lipid binding protein; 1.7A {Homo sapiens} SCOP: a.24.1.1 PDB: 1or3_A 1or2_A 1le4_A 1bz4_A 1lpe_A 1le2_A

Probab=96.43  E-value=0.0029  Score=54.67  Aligned_cols=68  Identities=3%  Similarity=0.097  Sum_probs=43.2

Q ss_pred             cccchhHHhhhhhhhhhh-------hhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhHHHHhhhcccccc
Q 020809          253 KWVQPHVETIKAKWIPAV-------KEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQV  320 (321)
Q Consensus       253 ~~~~ph~~~~~~k~~p~~-------~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~~~~~py~~~  320 (321)
                      .-+.++++.+..++.|+.       ......++..+.|++..++.+..||.+..+.-+.||++.++.-+.||+.+
T Consensus        69 d~l~~~~~~l~~~L~P~t~el~~~l~~~~e~Lr~~L~~d~EelR~~l~p~~~el~~~l~~~~EelR~kl~P~~ee  143 (165)
T 1gs9_A           69 KELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVRGRLVQYRGEVQAMLGQSTEELRVRLASHLRK  143 (165)
T ss_dssp             HHHHHHHHHHTTSCCCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455666666666662       22333356667777777777777777777777777777777777777654

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=96.38  E-value=0.2  Score=39.54  Aligned_cols=60  Identities=13%  Similarity=0.160  Sum_probs=39.9

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      +.+..+|..++..........+....+++.......+++.+|..+...|..++.+++.++
T Consensus         5 daIKkKm~~lk~e~e~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld~~e   64 (101)
T 3u1c_A            5 DAIKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRDQVL   64 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            456666777777766666666666666666666666666666666666666666666553

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=96.36  E-value=0.08  Score=43.50  Aligned_cols=49  Identities=16%  Similarity=0.278  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          108 AEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDL  156 (321)
Q Consensus       108 eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el  156 (321)
                      +.....++..|..|+.++..++.+...+..+-..|-.-.-.++-.+..+
T Consensus        74 ~~~l~~~q~~i~~lE~eL~~~r~e~~~ql~EYq~LlnvKl~Ld~EIatY  122 (129)
T 3tnu_B           74 ELALKDARNKLAELEEALQKAKQDMARLLREYQELMNTKLALDVEIATY  122 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555666666666555555544444433333333333333

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=96.35  E-value=0.085  Score=52.82  Aligned_cols=73  Identities=11%  Similarity=0.061  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 020809          126 DNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEATSR  198 (321)
Q Consensus       126 e~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~~~  198 (321)
                      +.+.+.+...+.+.+.++......++..++.+...+.+++...+.+..++...+....+.+++..+..+....
T Consensus       505 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l  577 (597)
T 3oja_B          505 DNLNKVFTHLKERQAFKLRETQARRTEADAKQKETEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQL  577 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhhhHHHHHHHHHhhhhhhcchhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333344444444444444445555555555555555555555555555555555444444433

>2lem_A Apolipoprotein A-I; lipid transport; NMR {Mus musculus}

Probab=96.33  E-value=0.023  Score=50.74  Aligned_cols=87  Identities=14%  Similarity=0.229  Sum_probs=66.7

Q ss_pred             HhhCcchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhhhhhhHHHHHhccchhhHHHHhHhHHHHHhhhh--------
Q 020809          230 NAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKT--------  301 (321)
Q Consensus       230 ~~hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~--------  301 (321)
                      ..+-.|+++.+-.++.......+.-..|+++.++.++    ..|+..++..+.||++.++++-.+.++..+.        
T Consensus       115 r~~L~Py~~el~~~~~~~~e~Lr~~L~p~~e~lr~kl----~~~~e~lk~~l~P~~ee~~~kl~~~leeL~~~p~~~e~~  190 (216)
T 2lem_A          115 RQKASPQGAELQESARQKLQELQGRLSPVAEEFRDRM----RTHVDSLRTQLAPHSEQMRESLAQRLAELKSNPTLNEYH  190 (216)
T ss_dssp             HHHTSCHHHHHHHHHHCSCCSSCCSCSTHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHhHhhHHHHHHHHHHHHHHHhCCcchHHHH
Confidence            4456688888877777777777777788888777765    4455558888888888888887777777776        


Q ss_pred             -hcCchhHHHHhhhcccccc
Q 020809          302 -AVTPHIIRVQEVVDPYFQV  320 (321)
Q Consensus       302 -~~~ph~~k~~~~~~py~~~  320 (321)
                       -|.||++-++.-+.||++.
T Consensus       191 ~ki~~~~e~Lr~~l~P~~ed  210 (216)
T 2lem_A          191 SSAKSHLKSLGEKARPALED  210 (216)
T ss_dssp             CCSSSHHHHHHHTSCTTTHH
T ss_pred             HHHHHHHHHHHHHhhhhHHH
Confidence             5677999999999999863

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=96.30  E-value=0.079  Score=43.67  Aligned_cols=111  Identities=16%  Similarity=0.198  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQ  124 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~  124 (321)
                      .++.+++.....-...+.....+|.++...|..++.+|..+......|+..|..++    ...+.....++..|..|+.+
T Consensus        17 ~K~eel~~~~~~~~~~l~~~k~Ei~elrr~iq~L~~el~~l~~~~~sLE~~l~e~e----~~~~~~l~~~q~~i~~lE~e   92 (131)
T 3tnu_A           17 TKTEELNREVATNSELVQSGKSEISELRRTMQNLEIELQSQLSMKASLENSLEETK----GRYCMQLAQIQEMIGSVEEQ   92 (131)
T ss_dssp             ------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333334444444444444444444444444444442    23344444555666666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          125 IDNLKKESEKQQKEKEALEARAIEAEKKISDLSAK  159 (321)
Q Consensus       125 Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~  159 (321)
                      +..++.+...+..+-..|-.-.-.++-.+..+...
T Consensus        93 L~~~r~em~~ql~EYq~Ll~vKl~Ld~EIatYRkL  127 (131)
T 3tnu_A           93 LAQLRCEMEQQNQEYKILLDVKTRLEQEIATYRRL  127 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            66666666666544444444444444444444433

>1nfn_A Apolipoprotein E3; lipid transport, heparin-binding, plasma protein, HDL, VLDL; 1.80A {Homo sapiens} SCOP: a.24.1.1 PDB: 1h7i_A 1ea8_A 1b68_A 1nfo_A 2kc3_A 1ya9_A

Probab=96.24  E-value=0.026  Score=49.67  Aligned_cols=106  Identities=8%  Similarity=0.152  Sum_probs=44.4

Q ss_pred             chhHHHHHHHHHHHHHHhHHHhhCcchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhhhhhhHHHHHhccchhhHHHH
Q 020809          210 LPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLK  289 (321)
Q Consensus       210 l~Pwla~~~~~~~~~~~~~~~~hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~  289 (321)
                      |-|....-..++...+..+....++ -|+.+-.+..-....++.-+.+|++.++.+..|++.+    +++.+.-+++.++
T Consensus        82 L~P~~~e~~~~l~~~~e~lr~~l~k-dlEelr~kL~P~~eEL~~~l~~~~Eelr~~L~Py~ee----lr~kl~~~~eeLr  156 (191)
T 1nfn_A           82 LTPVAEETRARLSKELQAAQARLGA-DMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRK----LRKRLLRDADDLQ  156 (191)
T ss_dssp             ----------CHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHH----HHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhhhHHH----HHHHHHHHHHHHH
Confidence            4444443334444444444333322 1344444444555556666777777777777777555    6666666777777


Q ss_pred             hHhHHHHHhhhhhcCchhHHHHhhhcccccc
Q 020809          290 TKTIEACEATKTAVTPHIIRVQEVVDPYFQV  320 (321)
Q Consensus       290 ~~~~~~~~~~~~~~~ph~~k~~~~~~py~~~  320 (321)
                      .+..||.+-.++-+.+||+-++..+.||+.+
T Consensus       157 ~~l~P~~eelk~~l~~~veel~~~L~P~~e~  187 (191)
T 1nfn_A          157 KRLAVYQAGAREGAERGLSAIRERLGPLVEQ  187 (191)
T ss_dssp             HHHHHHTC-----------------------
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Confidence            7777888878888888888888888888754

>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil (dimeric, parallel), familial hypertrophic cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo sapiens} SCOP: h.1.26.1 PDB: 2fxm_A

Probab=96.19  E-value=0.41  Score=39.24  Aligned_cols=33  Identities=27%  Similarity=0.327  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKS  172 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~  172 (321)
                      ..+.++..+.+.....+......++....+.+.
T Consensus        86 ~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~  118 (129)
T 2fxo_A           86 KEMNKRLEDEEEMNAELTAKKRKLEDECSELKR  118 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333333333

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=96.05  E-value=0.63  Score=40.08  Aligned_cols=120  Identities=13%  Similarity=0.167  Sum_probs=53.7

Q ss_pred             chHHHHHHHHHHHHHHHHHhH-------HHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHI-------DEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDK  113 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i-------~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~  113 (321)
                      ..++.++++++.++..-...-       .++...+...+....+++..+..+...-..|+.++..+|.. ...--.-...
T Consensus         9 ~~LekQL~E~n~kLk~EsE~~~rlkK~~tEl~k~~~~~E~~~rELq~~~~~L~~~k~~Leke~~~LQa~-L~qEr~~r~q   87 (168)
T 3o0z_A            9 SQLQKQLEEANDLLRTESDTAVRLRKSHTEMSKSISQLESLNRELQERNRILENSKSQTDKDYYQLQAI-LEAERRDRGH   87 (168)
T ss_dssp             -CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence            456778888877774333322       23333333333333333333333333333333333333321 0000111123


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          114 AHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLE  161 (321)
Q Consensus       114 ~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le  161 (321)
                      ...++.+|+.-|..|..+++..+.....++...+.+..++..+....+
T Consensus        88 ~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a  135 (168)
T 3o0z_A           88 DSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKN  135 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334555666666666666666665555555555554444444443333

>2efr_A General control protein GCN4 and tropomyosin 1 Al; destabilizing cluster, hydrophobic core, contractIle protein; 1.80A {Saccharomyces cerevisiae} PDB: 2efs_A 2d3e_A

Probab=95.97  E-value=0.64  Score=39.53  Aligned_cols=84  Identities=19%  Similarity=0.323  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          106 NAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAE  185 (321)
Q Consensus       106 ~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~E  185 (321)
                      ..+++...+..++++|+..+...-+.+......-.....+-...+.++..+..++...+..-..-.+.+..+++.+..++
T Consensus        32 raEERae~aE~k~~eLEeeL~~v~~nlKsLE~seekasqrEd~yEeqIk~L~~kLKEAE~RAE~AERsv~kLEk~id~lE  111 (155)
T 2efr_A           32 RAEERAELSEGKSAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLE  111 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555556666666666665555544444333222222222233333333333333333333333333333333333333


Q ss_pred             HHHH
Q 020809          186 EEMM  189 (321)
Q Consensus       186 eei~  189 (321)
                      +.+.
T Consensus       112 d~L~  115 (155)
T 2efr_A          112 DELY  115 (155)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            3333

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=95.97  E-value=0.4  Score=37.68  Aligned_cols=59  Identities=14%  Similarity=0.200  Sum_probs=37.5

Q ss_pred             chHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           41 SPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        41 ~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +++..+|..++..........+....+++.......+.+.+|..+...|..|+.+++.+
T Consensus         5 d~iKkKm~~lk~e~e~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~   63 (101)
T 3u59_A            5 EAIKKKMQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKY   63 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            34566666666666666666666666666666666666666666666666666665554

>1nfn_A Apolipoprotein E3; lipid transport, heparin-binding, plasma protein, HDL, VLDL; 1.80A {Homo sapiens} SCOP: a.24.1.1 PDB: 1h7i_A 1ea8_A 1b68_A 1nfo_A 2kc3_A 1ya9_A

Probab=95.42  E-value=0.011  Score=52.19  Aligned_cols=60  Identities=8%  Similarity=0.082  Sum_probs=29.7

Q ss_pred             hHHhhhhhhhhhhhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhHHHHhhhccccccC
Q 020809          258 HVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY  321 (321)
Q Consensus       258 h~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~~~~~py~~~~  321 (321)
                      +++.++.+.-|+..+    ++..+.++++.++.+-.||.+..++-+.-|++-++..+.||.++|
T Consensus       107 dlEelr~kL~P~~eE----L~~~l~~~~Eelr~~L~Py~eelr~kl~~~~eeLr~~l~P~~eel  166 (191)
T 1nfn_A          107 DMEDVCGRLVQYRGE----VQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVYQAGA  166 (191)
T ss_dssp             HHHHHHHHHHHHHHH----HHHTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--
T ss_pred             HHHHHHHHhhHHHHH----HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            344444444443222    444445555555555555555555555555555666666665544

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=95.21  E-value=0.054  Score=40.37  Aligned_cols=47  Identities=32%  Similarity=0.519  Sum_probs=41.6

Q ss_pred             HHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           54 IRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        54 i~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      +.+|+..+.....+|..+|..|..+++.|.++...|..|+++++..+
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfr   67 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKYR   67 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            77788888888888999999999999999999999999999998763

>2l7b_A Apolipoprotein E, APO-E; lipid transport, atherosclerosis, alzheime disease; NMR {Homo sapiens}

Probab=94.96  E-value=0.099  Score=49.27  Aligned_cols=69  Identities=16%  Similarity=0.072  Sum_probs=53.3

Q ss_pred             hhccccchhHHhhhhhhhhhh---------------------hhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhH
Q 020809          250 QAGKWVQPHVETIKAKWIPAV---------------------KEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHII  308 (321)
Q Consensus       250 ~~~~~~~ph~~~~~~k~~p~~---------------------~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~  308 (321)
                      ..+.-+.||++-++.+.-|+.                     +.+..-++..++||+..++....||.+..+..+.|.++
T Consensus       210 ~L~~ki~~~~e~Lr~~L~p~~~~~~~~l~~l~~q~ee~~~ql~~~aeel~~kl~~~~eeLr~~l~P~~e~lk~~l~~l~E  289 (307)
T 2l7b_A          210 PLQERAQAWGERLRARMEEMGSRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAAQARLKSRFEPLAEDMQRQWAGQVE  289 (307)
T ss_dssp             CCSSCSCCHHHHHHHHHHHHHHTCSCSSCCCCSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCHHHHHHTTSSC
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            345556777777777777753                     55556678888888888888888888888888888888


Q ss_pred             HHHhhhcccc
Q 020809          309 RVQEVVDPYF  318 (321)
Q Consensus       309 k~~~~~~py~  318 (321)
                      .++..+.||.
T Consensus       290 ~l~~sl~~~~  299 (307)
T 2l7b_A          290 KVQAAEGTSA  299 (307)
T ss_dssp             CCSSSSCSSS
T ss_pred             HHHHHhcCCC
Confidence            8888888886

>3r2p_A Apolipoprotein A-I; amphipathic alpha-helix, major protein of high density lipop (HDL), lipid binding, plasma, lipid transport; 2.20A {Homo sapiens} PDB: 1gw3_A 1gw4_A

Probab=94.95  E-value=0.024  Score=49.33  Aligned_cols=77  Identities=13%  Similarity=0.150  Sum_probs=37.3

Q ss_pred             chHHHHHHHHHHHHHhhccccchhHHhhhhhhhhhhhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhHHHHhhh
Q 020809          235 PAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVV  314 (321)
Q Consensus       235 p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~~~~  314 (321)
                      |+++-+..+........+.-..||++.++.++..    ++..++..+.||++.++++..+-.+..+.-+.|+++.++.-+
T Consensus       100 P~~~e~~~~~~~~~e~lr~~l~Py~~el~~~~~~----~~e~Lr~~L~p~~e~lr~~l~~~~e~lk~~l~Py~ee~k~kl  175 (185)
T 3r2p_A          100 PYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQ----KLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRL  175 (185)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHTTTTTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence            4444444444444444444455555555554332    223355555555555555555555555555555555554444


Q ss_pred             c
Q 020809          315 D  315 (321)
Q Consensus       315 ~  315 (321)
                      +
T Consensus       176 ~  176 (185)
T 3r2p_A          176 A  176 (185)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1ic2_A Tropomyosin alpha chain, skeletal muscle; alpha-helical coiled coil, alanine, symmetry, axial stagger, BEND, contractIle protein; 2.00A {Gallus gallus} SCOP: h.1.5.1

Probab=94.95  E-value=0.34  Score=36.53  Aligned_cols=57  Identities=16%  Similarity=0.222  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      |...+..++..........+.....++..+....+.+.++..+...|..|+.+++.+
T Consensus         4 ikkKm~~lk~e~d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~   60 (81)
T 1ic2_A            4 IKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKY   60 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence            444444455444444444444444444444444444444444444444444444444

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=94.93  E-value=0.19  Score=41.98  Aligned_cols=61  Identities=21%  Similarity=0.205  Sum_probs=33.4

Q ss_pred             CchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           40 SSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        40 ~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      ....+.+.+.++.++..+...+..+..++.+.+.+++++.+++.++..++..|+.++..++
T Consensus        70 l~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le  130 (138)
T 3hnw_A           70 YFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLE  130 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455555555555555555555555555555555555555555555555555554443

>1ic2_A Tropomyosin alpha chain, skeletal muscle; alpha-helical coiled coil, alanine, symmetry, axial stagger, BEND, contractIle protein; 2.00A {Gallus gallus} SCOP: h.1.5.1

Probab=94.83  E-value=0.31  Score=36.76  Aligned_cols=51  Identities=18%  Similarity=0.261  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .++.++..|+...+....++......+...+......+..|..|+..|..+
T Consensus         3 ~ikkKm~~lk~e~d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~l   53 (81)
T 1ic2_A            3 AIKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGT   53 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            456666666666666655555555555555544444444444444444333

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=94.83  E-value=0.75  Score=46.04  Aligned_cols=98  Identities=11%  Similarity=0.113  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 020809           47 LDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQID  126 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie  126 (321)
                      =.++...|++|..+++++.+.-++.+..+..+-..+.....+.....+.+..    -..+|+.++..++.+|..--..|.
T Consensus        59 ErDltkrINELKnqLEdlsKnsKdseqy~k~~~E~Lr~rq~q~~dNdNtynE----~S~ELRRrIqyLKekVdnQlsnIr  134 (562)
T 3ghg_A           59 NQDFTNRINKLKNSLFEYQKNNKDSHSLTTNIMEILRGDFSSANNRDNTYNR----VSEDLRSRIEVLKRKVIEKVQHIQ  134 (562)
T ss_dssp             HHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHH----TTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcHHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHHhhhccchhHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555555555544455555544444444444444433333322    234667777777777766446677


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 020809          127 NLKKESEKQQKEKEALEARAIE  148 (321)
Q Consensus       127 ~Lk~ele~~~~kk~~LEa~a~e  148 (321)
                      .|+.-|+.+..+++.||.....
T Consensus       135 vLQsnLedq~~kIQRLEvDIdi  156 (562)
T 3ghg_A          135 LLQKNVRAQLVDMKRLEVDIDI  156 (562)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            7777777777777777765443

>2lem_A Apolipoprotein A-I; lipid transport; NMR {Mus musculus}

Probab=94.78  E-value=0.6  Score=41.41  Aligned_cols=88  Identities=15%  Similarity=0.198  Sum_probs=52.4

Q ss_pred             hCcchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhh-------hhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcC
Q 020809          232 HGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPA-------VKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVT  304 (321)
Q Consensus       232 hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~-------~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~  304 (321)
                      .-.|+++.+..+........+.-..||++.+++++..-       +.|+-..++..+..+++.++..-.||.+..++-+.
T Consensus        95 ~l~py~~el~~~~~~~~e~lr~~L~Py~~el~~~~~~~~e~Lr~~L~p~~e~lr~kl~~~~e~lk~~l~P~~ee~~~kl~  174 (216)
T 2lem_A           95 KVQPYLDEFQKKWKEDVELYRQKASPQGAELQESARQKLQELQGRLSPVAEEFRDRMRTHVDSLRTQLAPHSEQMRESLA  174 (216)
T ss_dssp             HTTTTCCHHHHHHHHHHHHHHHHTSCHHHHHHHHHHCSCCSSCCSCSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhHHHHHHHHH
Confidence            35577777777766666667777777776666655442       22222224444445555555555666666666666


Q ss_pred             chhHHHHhhhccccccC
Q 020809          305 PHIIRVQEVVDPYFQVY  321 (321)
Q Consensus       305 ph~~k~~~~~~py~~~~  321 (321)
                      .|+..++..  ||+.+|
T Consensus       175 ~~leeL~~~--p~~~e~  189 (216)
T 2lem_A          175 QRLAELKSN--PTLNEY  189 (216)
T ss_dssp             HHHHHHHHC--CCCCCC
T ss_pred             HHHHHHhCC--cchHHH
Confidence            666666666  776665

>1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1

Probab=94.55  E-value=0.93  Score=35.65  Aligned_cols=75  Identities=16%  Similarity=0.244  Sum_probs=33.9

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H------h----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           69 KGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK-K------E----TLNAAEQVDKAHARADELEKQIDNLKKESEKQQK  137 (321)
Q Consensus        69 k~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk-~------~----~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~  137 (321)
                      .++...|..+...+..+..+|..+...+..+.. .      +    ........+....++..+...+..+..++...+.
T Consensus        13 ~~~~~~l~~L~~~~~~l~~~i~~l~~~l~~l~~~g~~CPvCgs~l~~~~~~~~i~~~~~~l~~l~~~i~~l~~~i~~l~~   92 (112)
T 1l8d_A           13 TTIEEERNEITQRIGELKNKIGDLKTAIEELKKAKGKCPVCGRELTDEHREELLSKYHLDLNNSKNTLAKLIDRKSELER   92 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECTTTCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444455555555555555543 1      1    1222333444444555555555555555544444


Q ss_pred             HHHHHH
Q 020809          138 EKEALE  143 (321)
Q Consensus       138 kk~~LE  143 (321)
                      .+..|.
T Consensus        93 ~~~~l~   98 (112)
T 1l8d_A           93 ELRRID   98 (112)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444333

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=94.27  E-value=1.5  Score=34.35  Aligned_cols=58  Identities=22%  Similarity=0.334  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      .++++.++.++..|++..+.+..++..+...+..-...-...+.....++.+++.+..
T Consensus         4 ~~~~e~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLTa   61 (97)
T 2eqb_B            4 GSNYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTA   61 (97)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567777777777777777777777777777777666666667777777777766644

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=94.16  E-value=0.19  Score=38.09  Aligned_cols=59  Identities=31%  Similarity=0.354  Sum_probs=54.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS   97 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~   97 (321)
                      ++..+-+++++|+.++.+++++.......|+.-.++|..++..+..+...|.-|++++.
T Consensus        20 ~~E~L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~   78 (81)
T 3qh9_A           20 KAEELLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLS   78 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence            45578899999999999999999999999999999999999999999999999988874

>2b9c_A Striated-muscle alpha tropomyosin; alpha-helix, coiled coil, alanine, axial stagger, radius, SIDE-chain packing, crystal packing; 2.30A {Rattus norvegicus} SCOP: h.1.5.1

Probab=94.16  E-value=2.2  Score=35.80  Aligned_cols=6  Identities=17%  Similarity=0.224  Sum_probs=2.1

Q ss_pred             HHHHHH
Q 020809          117 RADELE  122 (321)
Q Consensus       117 RireL~  122 (321)
                      |+..|+
T Consensus        53 r~~~lE   58 (147)
T 2b9c_A           53 KMEIQE   58 (147)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            333333

>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine exchange factor, coiled-coil, endocytosis/exocytosis complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=93.97  E-value=2.5  Score=35.80  Aligned_cols=39  Identities=5%  Similarity=0.022  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          156 LSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFE  194 (321)
Q Consensus       156 l~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~e  194 (321)
                      +|.-+..........+.+.+.++..+...+..+..++.+
T Consensus        99 AN~MVa~ar~~~~~~e~r~~~L~~ql~e~~~~l~~lq~q  137 (154)
T 2ocy_A           99 ANNMVADARKEKYAIEILNKRLTEQLREKDTLLDTLTLQ  137 (154)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333334444444444444444444444333

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=93.95  E-value=2  Score=35.03  Aligned_cols=23  Identities=17%  Similarity=0.359  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 020809           77 QKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        77 q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ....+|.++...|..|+.+|+++
T Consensus        33 ~~k~Ei~elrr~iq~L~~el~~l   55 (129)
T 3tnu_B           33 NTKHEISEMNRMIQRLRAEIDNV   55 (129)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444454444444

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=93.94  E-value=1.5  Score=35.28  Aligned_cols=82  Identities=18%  Similarity=0.210  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           79 EKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSA  158 (321)
Q Consensus        79 ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~  158 (321)
                      ++...++......|..++++...    .+.......+..+..|+++|..|....+.....+..||..-.+++........
T Consensus         2 Ek~~rdL~~~~~~L~~E~e~~k~----K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~R~t~~   77 (111)
T 2v66_B            2 EQRNRDLQADNQRLKYEVEALKE----KLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIV   77 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHh
Confidence            45556666666666666666632    33334444555666666666666666666666666666666666654444444


Q ss_pred             HHHHHH
Q 020809          159 KLEKLQ  164 (321)
Q Consensus       159 ~le~Le  164 (321)
                      -+++++
T Consensus        78 SLeD~E   83 (111)
T 2v66_B           78 SLEDFE   83 (111)
T ss_dssp             HHHHHH
T ss_pred             hHHHHH
Confidence            444443

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=93.67  E-value=0.89  Score=37.83  Aligned_cols=9  Identities=22%  Similarity=0.541  Sum_probs=3.5

Q ss_pred             HHHHHHHHH
Q 020809           50 LKSKIRSLE   58 (321)
Q Consensus        50 lk~ki~~Le   58 (321)
                      +..++.++.
T Consensus        37 vd~km~ei~   45 (138)
T 3hnw_A           37 INNKITEFN   45 (138)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHH
Confidence            333333333

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=93.51  E-value=2.4  Score=34.02  Aligned_cols=87  Identities=18%  Similarity=0.257  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 020809           47 LDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQID  126 (321)
Q Consensus        47 l~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie  126 (321)
                      ..+|+.+...|....++.       ..+..+..   .+-...|+.|+.+|..+...        ...+..++|+|+-.=+
T Consensus         5 ~rdL~~~~~~L~~E~e~~-------k~K~~~~~---~e~~~~~~~Lq~El~~lr~~--------~~~l~~~iReLEq~ND   66 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEAL-------KEKLEHQY---AQSYKQVSVLEDDLSQTRAI--------KEQLHKYVRELEQAND   66 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHH-------HHHHHHHH---HHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH-------HHHHHHHH---HHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHhch
Confidence            444555555555544444       44444333   23345666677777666431        2244556666665555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          127 NLKKESEKQQKEKEALEARAIEAEK  151 (321)
Q Consensus       127 ~Lk~ele~~~~kk~~LEa~a~e~ek  151 (321)
                      +|...-+-...-+..++.+.+.+-.
T Consensus        67 DLER~~R~t~~SLeD~E~k~n~aiE   91 (111)
T 2v66_B           67 DLERAKRATIVSLEDFEQRLNQAIE   91 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            5554444444444444444444333

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=93.51  E-value=1.9  Score=35.28  Aligned_cols=28  Identities=25%  Similarity=0.337  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           72 DEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        72 d~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      ...+.....+|.++...|..|+.+|+++
T Consensus        30 ~~~l~~~k~Ei~elrr~iq~L~~el~~l   57 (131)
T 3tnu_A           30 SELVQSGKSEISELRRTMQNLEIELQSQ   57 (131)
T ss_dssp             -----------CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444445555555555444

>2l7b_A Apolipoprotein E, APO-E; lipid transport, atherosclerosis, alzheime disease; NMR {Homo sapiens}

Probab=93.35  E-value=0.13  Score=48.50  Aligned_cols=62  Identities=6%  Similarity=0.163  Sum_probs=31.4

Q ss_pred             chhHHhhhhhhhhhhhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhHHHHhhhccccccC
Q 020809          256 QPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY  321 (321)
Q Consensus       256 ~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~~~~~py~~~~  321 (321)
                      .-|++.++.+..|+..+    +++.+.-.++.++.+-.||.+-.++-+..||+.++..+.||..+|
T Consensus       135 ~~~~eelr~kL~Py~~E----L~~~~~~~~eeLr~~L~py~eeLr~kl~~~veelr~~L~Py~e~~  196 (307)
T 2l7b_A          135 GQSTEELRVRLASHLRK----LRKRLLRDADDLQKRLAVYQAGAREGAERGLSAIRERLGPLVEQG  196 (307)
T ss_dssp             SCCSHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHTSCCSSHHHHHHHHHHHHCSSSCTTT
T ss_pred             HHHHHHHHHHHHHHHHH----HHHHHHhhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence            33444444444444333    444444444445555555555555555556666666666666543

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=92.90  E-value=1.6  Score=34.93  Aligned_cols=19  Identities=21%  Similarity=0.476  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHhHHHH
Q 020809           46 ELDQLKSKIRSLESHIDEK   64 (321)
Q Consensus        46 el~qlk~ki~~Les~i~e~   64 (321)
                      +++.|+.++...+..+...
T Consensus        25 ei~~L~~~L~~AEeaL~~K   43 (110)
T 2v4h_A           25 QLEDLRQQLQQAEEALVAK   43 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            4455555444444444443

>1m1j_A Fibrinogen alpha subunit; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: h.1.8.1 PDB: 1ei3_A

Probab=92.78  E-value=3.8  Score=40.39  Aligned_cols=102  Identities=12%  Similarity=0.181  Sum_probs=75.8

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 020809           43 LKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELE  122 (321)
Q Consensus        43 l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~  122 (321)
                      +..+=.....+|..|...+.+..+--......+..+-..+.....++...++.+...    ..+++.++..++.+|..==
T Consensus        56 L~kqerdv~~rI~kLkn~L~~~s~s~~~s~~y~~~~~~~lk~~~~q~~dndn~~~e~----S~eLe~ri~yIK~kVd~qi  131 (491)
T 1m1j_A           56 IDDTDQNYSQRIDNIRQQLADSQNKYKTSNRVIVETINILKPGLEGAQQLDENYGHV----STELRRRIVTLKQRVATQV  131 (491)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHhhhccchhHHHHH----HHHHHHHHHHHHHHHHHHH
Confidence            344455667778888888888888778888888888888888888877777777665    3677787888888877722


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          123 KQIDNLKKESEKQQKEKEALEARAIE  148 (321)
Q Consensus       123 k~Ie~Lk~ele~~~~kk~~LEa~a~e  148 (321)
                      ..|..|+.-|+.+..++..||.....
T Consensus       132 ~~IrvLq~~l~~q~skIQRLE~dI~~  157 (491)
T 1m1j_A          132 NRIKALQNSIQEQVVEMKRLEVDIDI  157 (491)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66888888888888888877765443

>3swk_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural; 1.70A {Homo sapiens}

Probab=92.36  E-value=2  Score=32.73  Aligned_cols=51  Identities=14%  Similarity=0.188  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      +|+.+|..+......+.-+++.....++.......+=-..-..++++|..+
T Consensus         4 eLr~qi~~l~~e~~~l~~e~dn~~~~~edfk~KyE~E~~~R~~~E~d~~~L   54 (86)
T 3swk_A            4 ELRRQVDQLTNDKARVEVERDNLAEDIMRLREKLQEEMLQREEAENTLQSF   54 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444333333333333333333333333333333333344444444

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*

Probab=92.34  E-value=4.2  Score=40.26  Aligned_cols=10  Identities=40%  Similarity=0.694  Sum_probs=3.7

Q ss_pred             HHHHHHHHHH
Q 020809          156 LSAKLEKLQK  165 (321)
Q Consensus       156 l~~~le~Lek  165 (321)
                      ++.++..|+.
T Consensus       180 l~~ki~~l~~  189 (464)
T 1m1j_B          180 LHKKIQKLEN  189 (464)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            3333333333

>3bas_A Myosin heavy chain, striated muscle/general control protein GCN4 chimera; alpha-helical coiled coil, disorder, salt links; 2.30A {Argopecten irradians} SCOP: h.1.26.1 PDB: 1nkn_A 3bat_A

Probab=92.23  E-value=2.5  Score=32.35  Aligned_cols=56  Identities=21%  Similarity=0.306  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           73 EVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLK  129 (321)
Q Consensus        73 ~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk  129 (321)
                      ..+...+....+++.....|..+.+.++.. ..+++++...+.++-.+|+.+|..+.
T Consensus        28 e~l~k~e~~rkele~~~~~l~~ek~~L~~q-l~eaEe~~~~L~~~K~eLE~~l~el~   83 (89)
T 3bas_A           28 EDLAKTERIKKELEEQNVTLLEQKNDLFGS-MKQLEDKVEELLSKNYHLENEVARLK   83 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333334444444444443333321 33444444444444444444444443

>2oto_A M protein; helical coiled coil, fibrinogen-binding, virulence factor, S active protein, toxin; 3.04A {Streptococcus pyogenes serotype M1} PDB: 2xny_M

Probab=90.95  E-value=6.2  Score=32.93  Aligned_cols=51  Identities=18%  Similarity=0.242  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .+......|.+........+.........++..+.+++.....|+..+..+
T Consensus        26 ~l~~eN~~Lk~e~e~l~~~~~~~~~~~~eL~~~~~~Le~~n~~L~~~lke~   76 (155)
T 2oto_A           26 RLRHENKDLKARLENAMEVAGRDFKRAEELEKAKQALEDQRKDLETKLKEL   76 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444445555544444444444444455555555555555555444333

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=90.72  E-value=4  Score=34.45  Aligned_cols=56  Identities=27%  Similarity=0.300  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQ  100 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~q  100 (321)
                      +..+.....|..|++....+..+|+.++..|....+.+..+.+++..|+-+.+.++
T Consensus        61 s~~~~~~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE  116 (152)
T 3a7p_A           61 SHDDALLNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQ  116 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555666666666666666666666666666666666666666665555553

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=90.71  E-value=3.5  Score=41.25  Aligned_cols=40  Identities=20%  Similarity=0.224  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          141 ALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERA  180 (321)
Q Consensus       141 ~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~  180 (321)
                      +|+.+...++.++...-+.+..|+..+++|..+|++||-+
T Consensus       114 ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvD  153 (562)
T 3ghg_A          114 DLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVD  153 (562)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444455555555555555555555544

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=90.65  E-value=3.9  Score=34.50  Aligned_cols=59  Identities=22%  Similarity=0.225  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           44 KIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKK  102 (321)
Q Consensus        44 ~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~  102 (321)
                      .+.+..++..+..++..+..+..+++++...+..++.++..+.-+.+.++..+..++.+
T Consensus        67 ~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~kLq~E  125 (152)
T 3a7p_A           67 LNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLSDLKKE  125 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555555555555555555555555555555555555555443

>3jsv_C NF-kappa-B essential modulator; ubiquitin, coiled-coil, cellular signaling, cytoplasm, isopeptide bond, nucleus, phosphoprotein, UBL conjugation; 2.70A {Mus musculus} PDB: 3f89_A 2zvo_B 2zvn_B

Probab=90.61  E-value=2.8  Score=32.67  Aligned_cols=57  Identities=23%  Similarity=0.226  Sum_probs=29.6

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           68 LKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus        68 Lk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      ++.+...+..++..+..++..|+.|..+|...+.    + -       .+|..|+-+++-++.+-..-+
T Consensus         4 ~~~L~~~L~~aEeaL~~kq~~id~lke~~~q~~~----~-~-------E~i~vLk~Qv~IY~~DF~aER   60 (94)
T 3jsv_C            4 LEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKI----V-M-------ETVPVLKAQADIYKADFQAER   60 (94)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-H-------HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH----H-H-------HHHHHHHHHHHHHHHHHHHHH
Confidence            3444555556666666666666666665554422    1 1       245555555555554444443

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=90.44  E-value=4.6  Score=30.59  Aligned_cols=57  Identities=25%  Similarity=0.416  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           75 VAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKES  132 (321)
Q Consensus        75 I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~el  132 (321)
                      +++++..|+..-..|..|+-+|+.++. +-..+....+.+......|..++..|+.+.
T Consensus         8 leqLE~KIq~avdtI~lLqmEieELKe-kN~~L~~e~~e~~~~~~~L~~en~qLk~E~   64 (81)
T 2jee_A            8 FEKLEAKVQQAIDTITLLQMEIEELKE-KNNSLSQEVQNAQHQREELERENNHLKEQQ   64 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            455566666666666666666666633 223333333333333333444444444333

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*

Probab=89.42  E-value=16  Score=36.16  Aligned_cols=9  Identities=56%  Similarity=0.630  Sum_probs=3.5

Q ss_pred             HHHHHHHHH
Q 020809          172 SKIRKTERA  180 (321)
Q Consensus       172 ~~l~elE~~  180 (321)
                      .+|+.++..
T Consensus       182 ~ki~~l~~~  190 (464)
T 1m1j_B          182 KKIQKLENA  190 (464)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            333344333

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=89.29  E-value=6.6  Score=30.71  Aligned_cols=59  Identities=14%  Similarity=0.293  Sum_probs=34.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           39 DSSPLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELS   97 (321)
Q Consensus        39 ~~~~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~   97 (321)
                      ++..++.++.+++.+....+..+..+..++..-...-..+++....++.++..|-..+-
T Consensus         6 ~~e~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLTasLF   64 (97)
T 2eqb_B            6 NYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLF   64 (97)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455556666666666666666666666655555555555555555555555555543

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}

Probab=88.90  E-value=15  Score=35.39  Aligned_cols=25  Identities=24%  Similarity=0.268  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          166 INDEQKSKIRKTERALKVAEEEMMR  190 (321)
Q Consensus       166 ~~~Eqk~~l~elE~~lq~~Eeei~k  190 (321)
                      .+.|++..|-++++.++.++.++.+
T Consensus       444 ~~~~~~~~~~~~~~~~~~~~~~~~~  468 (471)
T 3mq9_A          444 KVEELEGEITTLNHKLQDASAEVER  468 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444433

>1x8y_A Lamin A/C; structural protein, intermediate filament protein; 2.20A {Homo sapiens} SCOP: h.1.20.1 PDB: 3v5b_A 3v4w_A 3v4q_A

Probab=88.89  E-value=4.5  Score=30.70  Aligned_cols=51  Identities=16%  Similarity=0.221  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          110 QVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKL  160 (321)
Q Consensus       110 q~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~l  160 (321)
                      +...++..|..|+.++..++.+++.+..+-..|-.-.-.++..++.+...+
T Consensus        29 ~l~~~q~~i~~lE~el~~~r~e~~~ql~EYq~LlnvK~~Le~EIatYRkLL   79 (86)
T 1x8y_A           29 ERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLL   79 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            334444455555555555555555555444444444444444444444443

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=88.64  E-value=9.7  Score=36.92  Aligned_cols=39  Identities=18%  Similarity=0.091  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          153 ISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       153 ~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      .+......+.+.+..+.++..++++......+.+.+..+
T Consensus       437 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  475 (487)
T 3oja_A          437 WDMYQHKETQLAEENARLKKLNGEADLALASANATLQEL  475 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHhhhhhhhhhhhhhhhHhcccHHHHH
Confidence            333444444444444445555555555554444444444

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=88.50  E-value=5.2  Score=32.44  Aligned_cols=27  Identities=11%  Similarity=0.282  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           75 VAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        75 I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      ..+.+..+..+...|..|+.+++....
T Consensus        35 ~~E~q~~v~ql~~~i~~Le~eL~e~r~   61 (120)
T 3i00_A           35 KTESQRVVLQLKGHVSELEADLAEQQH   61 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566666666666666666666543

>3iox_A AGI/II, PA; alpha helix, PPII helix, supersandwich fold, surface adhesin WALL, peptidoglycan-anchor, cell adhesion; HET: PMS; 1.80A {Streptococcus mutans} PDB: 3ipk_A* 1jmm_A

Probab=88.46  E-value=19  Score=35.74  Aligned_cols=99  Identities=19%  Similarity=0.208  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           86 SERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKLEKLQK  165 (321)
Q Consensus        86 ~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~le~Lek  165 (321)
                      +.+++.-|.++.+.|+... ++   ....++.+.+++..=..++++.+.++.+-+.   ....-+..+...+..++.-++
T Consensus         8 q~~la~yq~elarvqkana-~a---ka~Ye~~~ae~~a~n~~i~aeNeaikkrNa~---aka~Ye~~l~kY~~dlakY~~   80 (497)
T 3iox_A            8 QAKLTAYQTELARVQKANA-DA---KAAYEAAVAANNAANAALTAENTAIKKRNAD---AKADYEAKLAKYQADLAKYQK   80 (497)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-HH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH-HH---HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
Confidence            4566667777777766421 11   2234445555555555566666666633322   223334456677777777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          166 INDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       166 ~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..++++.++..-+..++.+...+.++
T Consensus        81 ~~AeY~~kl~aYe~~~~~~~k~lae~  106 (497)
T 3iox_A           81 DLADYPVKLKAYEDEQTSIKAALAEL  106 (497)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888887777777776665

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=87.91  E-value=8.2  Score=30.08  Aligned_cols=35  Identities=17%  Similarity=0.380  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          108 AEQVDKAHARADELEKQIDNLKKESEKQQKEKEAL  142 (321)
Q Consensus       108 eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~L  142 (321)
                      ++-...++.|+..++..|..|...+.....+..++
T Consensus        69 ~ea~~~L~~~~e~ie~~i~~le~~~~~l~~~l~~l  103 (117)
T 2zqm_A           69 DKAVAELKEKIETLEVRLNALERQEKKLNEKLKEL  103 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444444444444444444444333333

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=87.86  E-value=1.8  Score=32.57  Aligned_cols=52  Identities=19%  Similarity=0.261  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      ..++.|..++|.+++-....++.|...+.+|+..|+.+.+.+..+-..+..+
T Consensus        10 ~~le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~~rl~~~   61 (78)
T 3efg_A           10 QELEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKV   61 (78)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4678888888899999999999999999999999999998887776665554

>1jcd_A Major outer membrane lipoprotein; protein folding, coiled coil, helix capping, alanine-zipper, membrane protein; 1.30A {Escherichia coli} SCOP: h.1.16.1 PDB: 1eq7_A 1t8z_A* 2guv_A 2gus_A 1jcc_A 1kfn_A 1kfm_A

Probab=86.64  E-value=4.2  Score=28.27  Aligned_cols=9  Identities=44%  Similarity=0.656  Sum_probs=4.6

Q ss_pred             HHHHHHHHH
Q 020809          111 VDKAHARAD  119 (321)
Q Consensus       111 ~~~~~~Rir  119 (321)
                      ...++.|+.
T Consensus        41 A~RAN~RlD   49 (52)
T 1jcd_A           41 AARANQRAD   49 (52)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhh
Confidence            345555654

>1gk4_A Vimentin; intermediate filament, dimer, parallel coiled coil, heptad repeat, stutter; 2.3A {Homo sapiens} SCOP: h.1.20.1

Probab=86.20  E-value=9  Score=28.80  Aligned_cols=74  Identities=18%  Similarity=0.263  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           83 QDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEAEKKISDLSAKL  160 (321)
Q Consensus        83 ~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~el~~~l  160 (321)
                      ..+......|++.|..++.    ..+.....++..|..|+.++..++.+.+.+..+-..|-.-.-.++..++.+...+
T Consensus         4 ~~l~~~~~sLE~~l~e~e~----~~~~~~~~~q~~i~~lE~eL~~~r~e~~~q~~EYq~LlnvK~~Ld~EIatYRkLL   77 (84)
T 1gk4_A            4 DALKGTNESLERQMREMEE----NFAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLL   77 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            3444444555555554432    2333344455555556666666666665555444444444444444444444443

>3htk_A Structural maintenance of chromosomes protein 5; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=85.89  E-value=4.1  Score=28.37  Aligned_cols=54  Identities=11%  Similarity=0.164  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSS   98 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~   98 (321)
                      ..+..++..+...+...+.....+.+....+++.-..++.....|..++.+|..
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~   58 (60)
T 3htk_A            5 NTKKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEY   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            455666666666666666666666666667777666666666777766666643

>3bas_A Myosin heavy chain, striated muscle/general control protein GCN4 chimera; alpha-helical coiled coil, disorder, salt links; 2.30A {Argopecten irradians} SCOP: h.1.26.1 PDB: 1nkn_A 3bat_A

Probab=85.87  E-value=9.8  Score=28.93  Aligned_cols=73  Identities=10%  Similarity=0.129  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 020809           45 IELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARA  118 (321)
Q Consensus        45 ~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~Ri  118 (321)
                      .++..+..++..++..+.......+++......+..+.+++..+++..+...+.+.+ ...+++.++..++.|+
T Consensus        14 eEm~~~eeel~~lke~l~k~e~~rkele~~~~~l~~ek~~L~~ql~eaEe~~~~L~~-~K~eLE~~l~el~~rl   86 (89)
T 3bas_A           14 EEMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGSMKQLEDKVEELLS-KNYHLENEVARLKKLV   86 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH-HHHHHHHHHHHHHHHh
Confidence            344445555555555555555555555555555555555555554444444444433 2244455444444443

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=85.80  E-value=11  Score=29.35  Aligned_cols=13  Identities=8%  Similarity=0.248  Sum_probs=4.8

Q ss_pred             HHHHHHHHhHHHH
Q 020809           52 SKIRSLESHIDEK   64 (321)
Q Consensus        52 ~ki~~Les~i~e~   64 (321)
                      .+...+..++..+
T Consensus        13 ~~~~~l~~~~~~l   25 (117)
T 2zqm_A           13 GQLESYQQQLQLV   25 (117)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3333333333333

>1zxa_A CGMP-dependent protein kinase 1, alpha isozyme; parallel coiled coil dimer, transferase; NMR {Homo sapiens}

Probab=84.73  E-value=1.2  Score=32.67  Aligned_cols=41  Identities=27%  Similarity=0.354  Sum_probs=28.4

Q ss_pred             HHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           61 IDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQK  101 (321)
Q Consensus        61 i~e~~~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk  101 (321)
                      .++....|+.+|..|.+++..++.+...|..|.++++..+.
T Consensus        13 ~e~~~~~i~~Kde~I~eLE~~L~~kd~eI~eLr~~LdK~qs   53 (67)
T 1zxa_A           13 EEDFAKILMLKEERIKELEKRLSEKEEEIQELKRKLHKCQS   53 (67)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555667777888888888888888888888888777643

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=84.65  E-value=30  Score=33.41  Aligned_cols=12  Identities=33%  Similarity=0.390  Sum_probs=4.4

Q ss_pred             HHHHHHHHHHHH
Q 020809           72 DEVVAQKEKAIQ   83 (321)
Q Consensus        72 d~~I~q~ek~i~   83 (321)
                      +..+...+..+.
T Consensus       373 e~~~~~~~~~~~  384 (487)
T 3oja_A          373 DEQVSNGRRAHA  384 (487)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            333333333333

>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine exchange factor, coiled-coil, endocytosis/exocytosis complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=84.42  E-value=18  Score=30.59  Aligned_cols=35  Identities=9%  Similarity=0.175  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          157 SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRA  191 (321)
Q Consensus       157 ~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl  191 (321)
                      +.....++..+...+.++.+.+.-+...+.++..+
T Consensus       107 r~~~~~~e~r~~~L~~ql~e~~~~l~~lq~ql~~L  141 (154)
T 2ocy_A          107 RKEKYAIEILNKRLTEQLREKDTLLDTLTLQLKNL  141 (154)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444444444444444444444

>1m1j_A Fibrinogen alpha subunit; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: h.1.8.1 PDB: 1ei3_A

Probab=83.18  E-value=37  Score=33.43  Aligned_cols=42  Identities=17%  Similarity=0.332  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          140 EALEARAIEAEKKISDLSAKLEKLQKINDEQKSKIRKTERAL  181 (321)
Q Consensus       140 ~~LEa~a~e~ekk~~el~~~le~Lek~~~Eqk~~l~elE~~l  181 (321)
                      .+|+.+...+..++...-+.+..|+..+..|..+|+.||.+.
T Consensus       114 ~eLe~ri~yIK~kVd~qi~~IrvLq~~l~~q~skIQRLE~dI  155 (491)
T 1m1j_A          114 TELRRRIVTLKQRVATQVNRIKALQNSIQEQVVEMKRLEVDI  155 (491)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444555666666666666666666554

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=82.92  E-value=3.1  Score=31.18  Aligned_cols=47  Identities=19%  Similarity=0.227  Sum_probs=23.2

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhcHHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSER   88 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~kd~~I~q~ek~i~e~~~~   88 (321)
                      .+...|.+|+.+++-.+..|+++|+.+-.-...|+.++..+..+...
T Consensus        11 ~le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~~r   57 (78)
T 3efg_A           11 ELEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLED   57 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555556666666655555555444444444444444333333333

>2p22_C Protein SRN2; endosome, trafficking complex, VPS23, VPS28, VPS37, MVB12; 2.70A {Saccharomyces cerevisiae} PDB: 2caz_C 2f66_C

Probab=82.89  E-value=23  Score=30.80  Aligned_cols=16  Identities=13%  Similarity=0.333  Sum_probs=13.7

Q ss_pred             HHHHHHHhHHHhhCcc
Q 020809          220 QCQSLIETHWNAHGKP  235 (321)
Q Consensus       220 ~~~~~~~~~~~~hg~p  235 (321)
                      ++..++...|.+.|..
T Consensus       175 H~RreK~~rw~e~~~~  190 (192)
T 2p22_C          175 HLRREKLATWDKQGNL  190 (192)
T ss_dssp             HHHHHHHHHHTTCSCB
T ss_pred             HHHHHHHHHHHhcccc
Confidence            7888899999999864

>2e7s_A RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 3.00A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=82.67  E-value=2.8  Score=34.80  Aligned_cols=26  Identities=8%  Similarity=0.300  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           74 VVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        74 ~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .++++.+.+.....++..|...+..-
T Consensus        33 ~l~~l~~~l~~~~~e~~~L~~~l~eE   58 (135)
T 2e7s_A           33 DYNTLKRELSDRDDEVKRLREDIAKE   58 (135)
T ss_dssp             HHHHHHHHTTTHHHHHHTHHHHHHHT
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            34444444445555555555554433

>2nrj_A HBL B protein; enterotoxin, hemolysis, transmembrane, structural genomics, PSI-2, protein structure initiative; 2.03A {Bacillus cereus} SCOP: h.4.4.2

Probab=82.43  E-value=28  Score=32.83  Aligned_cols=26  Identities=15%  Similarity=-0.020  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHhhccccchhHHhhh
Q 020809          238 DVAIQKALEKKAQAGKWVQPHVETIK  263 (321)
Q Consensus       238 ~~~~~~~~~k~~~~~~~~~ph~~~~~  263 (321)
                      ..-+..|...|..+++.|+-+.+-++
T Consensus       310 ~~~L~~a~~~W~~l~~~a~~l~~~~~  335 (346)
T 2nrj_A          310 KPNLNAAKDSWKTLRTDAVTLKEGIK  335 (346)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHhhh
Confidence            44456666777777777666665554

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}

Probab=82.23  E-value=36  Score=32.61  Aligned_cols=40  Identities=15%  Similarity=0.211  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 020809          157 SAKLEKLQKINDEQKSKIRKTERALKVAEEEMMRAKFEAT  196 (321)
Q Consensus       157 ~~~le~Lek~~~Eqk~~l~elE~~lq~~Eeei~kl~~ea~  196 (321)
                      -.+.+.|++.+.++.++++++|.+...++.++..+.++..
T Consensus       428 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  467 (471)
T 3mq9_A          428 MALMASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVE  467 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566666666666666666666666666655554443

>3swk_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural; 1.70A {Homo sapiens}

Probab=82.20  E-value=14  Score=27.92  Aligned_cols=34  Identities=12%  Similarity=0.315  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          121 LEKQIDNLKKESEKQQKEKEALEARAIEAEKKIS  154 (321)
Q Consensus       121 L~k~Ie~Lk~ele~~~~kk~~LEa~a~e~ekk~~  154 (321)
                      ++..+..|++.+....-.+..||.+..++...+.
T Consensus        47 ~E~d~~~LrkdvD~a~l~r~dLE~kvesL~eEl~   80 (86)
T 3swk_A           47 AENTLQSFRQDVDNASLARLDLERKVESLQEEIA   80 (86)
T ss_dssp             HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444555555444444433

>2pms_C Pneumococcal surface protein A (PSPA); lactoferrin, protein-protein metal transport, hydrolase; HET: NAG; 2.91A {Streptococcus pneumoniae} SCOP: h.4.19.1

Probab=81.98  E-value=11  Score=30.74  Aligned_cols=25  Identities=40%  Similarity=0.497  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHhHHHHHHhhhcHHH
Q 020809           49 QLKSKIRSLESHIDEKTQELKGKDE   73 (321)
Q Consensus        49 qlk~ki~~Les~i~e~~~eLk~kd~   73 (321)
                      .+..++.+++..+..+.+.++..+.
T Consensus        10 ~l~~KvAElekkv~~lek~lk~~~e   34 (125)
T 2pms_C           10 APQAKIAELENQVHRLEQELKEIDE   34 (125)
T ss_dssp             SHHHHHHHHHHHHHHHHHHTTTTCC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcch
Confidence            3455666666666665555555443

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=81.29  E-value=4  Score=30.25  Aligned_cols=23  Identities=17%  Similarity=0.122  Sum_probs=9.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHH
Q 020809           70 GKDEVVAQKEKAIQDKSERIVSL   92 (321)
Q Consensus        70 ~kd~~I~q~ek~i~e~~~~I~~L   92 (321)
                      .++..|++.+..|.++.++++.+
T Consensus        44 eLEk~L~ekd~eI~~LqseLDKf   66 (72)
T 3nmd_A           44 ELELELDQKDELIQMLQNELDKY   66 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Confidence            33333333333333444444433

>1fxk_C Protein (prefoldin); archaeal protein, chaperone; 2.30A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.2.5.1

Probab=80.67  E-value=16  Score=29.32  Aligned_cols=45  Identities=16%  Similarity=0.211  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEA  149 (321)
Q Consensus       105 ~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~  149 (321)
                      ...++-.+.++.|+..|+..++.+.+++...+.....+....+.+
T Consensus        84 ~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~i~~~~~~l~~~  128 (133)
T 1fxk_C           84 KNFEDAMESIKSQKNELESTLQKMGENLRAITDIMMKLSPQAEEL  128 (133)
T ss_dssp             EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eeHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666677777777777777777777777776666555554443

---

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	321
d1gs9a_	144	Apolipoprotein E {Human (Homo sapiens), E4 [TaxId:	97.36
d1gs9a_	144	Apolipoprotein E {Human (Homo sapiens), E4 [TaxId:	96.84
d1fxkc_	133	Prefoldin alpha subunit {Archaeon Methanobacterium	92.54
d2ap3a1	185	Hypothetical protein MW0975 (SA0943) {Staphylococc	91.75
d1fxkc_	133	Prefoldin alpha subunit {Archaeon Methanobacterium	89.13
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	84.99
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	82.39

>d1gs9a_ a.24.1.1 (A:) Apolipoprotein E {Human (Homo sapiens), E4 [TaxId: 9606]}

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: Apolipoprotein
family: Apolipoprotein
domain: Apolipoprotein E
species: Human (Homo sapiens), E4 [TaxId: 9606]

Probab=97.36  E-value=0.0001  Score=59.92  Aligned_cols=83  Identities=8%  Similarity=0.115  Sum_probs=55.2

Q ss_pred             hCcchHHHHHHHHHHHHHhhccccchhHHhhhhhhhhhhhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhHHHH
Q 020809          232 HGKPAMDVAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQ  311 (321)
Q Consensus       232 hg~p~~~~~~~~~~~k~~~~~~~~~ph~~~~~~k~~p~~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~  311 (321)
                      .-.|+.+.+..+.+.....++.-+.|+++.++.+.-|++.+    ++..+.|++..++.+..||.+..++-+.|+++-++
T Consensus        60 ~l~p~~~e~~~~l~~~~e~lr~~l~~~lee~r~kl~~~~ee----l~~~~~~~~ee~r~~l~p~~eel~~~l~~~~eel~  135 (144)
T d1gs9a_          60 QLTPVAEETRARLSKELQAAQARLGADMEDVRGRLVQYRGE----VQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQ  135 (144)
T ss_dssp             SCCCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHTSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34566666666666666666666666666666666665444    66666677777777777777777777777777777


Q ss_pred             hhhcccc
Q 020809          312 EVVDPYF  318 (321)
Q Consensus       312 ~~~~py~  318 (321)
                      .-|.||.
T Consensus       136 ~kL~py~  142 (144)
T d1gs9a_         136 KRLAVYQ  142 (144)
T ss_dssp             HHHHHSS
T ss_pred             HHhhCcc
Confidence            7777765

>d1gs9a_ a.24.1.1 (A:) Apolipoprotein E {Human (Homo sapiens), E4 [TaxId: 9606]}

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: Apolipoprotein
family: Apolipoprotein
domain: Apolipoprotein E
species: Human (Homo sapiens), E4 [TaxId: 9606]

Probab=96.84  E-value=0.0018  Score=52.15  Aligned_cols=67  Identities=1%  Similarity=0.112  Sum_probs=52.0

Q ss_pred             cchhHHhhhhhhhhh-------hhhhHHHHHhccchhhHHHHhHhHHHHHhhhhhcCchhHHHHhhhccccccC
Q 020809          255 VQPHVETIKAKWIPA-------VKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQVY  321 (321)
Q Consensus       255 ~~ph~~~~~~k~~p~-------~~~~~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~ph~~k~~~~~~py~~~~  321 (321)
                      +.+|++.++.++.|+       +.+.-..++..+.|+++.++.+..||.+..+.-+.||++.++..+.||+.+|
T Consensus        50 l~~~~~~l~~~l~p~~~e~~~~l~~~~e~lr~~l~~~lee~r~kl~~~~eel~~~~~~~~ee~r~~l~p~~eel  123 (144)
T d1gs9a_          50 LKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVRGRLVQYRGEVQAMLGQSTEELRVRLASHLRKL  123 (144)
T ss_dssp             HHHHHHHHTTSCCCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666664       3334444888888999999999999999999999999999999999998653

>d1fxkc_ a.2.5.1 (C:) Prefoldin alpha subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin alpha subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=92.54  E-value=0.47  Score=36.50  Aligned_cols=45  Identities=16%  Similarity=0.211  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809          105 LNAAEQVDKAHARADELEKQIDNLKKESEKQQKEKEALEARAIEA  149 (321)
Q Consensus       105 ~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~~kk~~LEa~a~e~  149 (321)
                      ...++-...++.|++.|+..++.+..++...+.....++.....+
T Consensus        84 ~~~~eA~~~l~~ri~~l~~~~~~l~~~~~~~~~~i~~l~~~~~~l  128 (133)
T d1fxkc_          84 KNFEDAMESIKSQKNELESTLQKMGENLRAITDIMMKLSPQAEEL  128 (133)
T ss_dssp             EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346667778888888888888888888888876666665544443

>d2ap3a1 a.24.27.1 (A:12-196) Hypothetical protein MW0975 (SA0943) {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: MW0975(SA0943)-like
family: MW0975(SA0943)-like
domain: Hypothetical protein MW0975 (SA0943)
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.75  E-value=1.4  Score=33.06  Aligned_cols=23  Identities=17%  Similarity=0.351  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHhh
Q 020809           46 ELDQLKSKIRSLESHIDEKTQEL   68 (321)
Q Consensus        46 el~qlk~ki~~Les~i~e~~~eL   68 (321)
                      .+.+...++..++..+.....++
T Consensus        23 ~~~~~~~k~~~~e~~~~~~~~~~   45 (185)
T d2ap3a1          23 PIKTVGKKIAELDEKKKKLTEDV   45 (185)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTTGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444443333

>d1fxkc_ a.2.5.1 (C:) Prefoldin alpha subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin alpha subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=89.13  E-value=3.5  Score=31.19  Aligned_cols=12  Identities=8%  Similarity=0.451  Sum_probs=4.5

Q ss_pred             HHHHHHHHHHHH
Q 020809          125 IDNLKKESEKQQ  136 (321)
Q Consensus       125 Ie~Lk~ele~~~  136 (321)
                      ++-+.+.++..+
T Consensus        90 ~~~l~~ri~~l~  101 (133)
T d1fxkc_          90 MESIKSQKNELE  101 (133)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            333333333333

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=84.99  E-value=2.7  Score=31.05  Aligned_cols=64  Identities=16%  Similarity=0.207  Sum_probs=30.9

Q ss_pred             HhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           66 QELKGKDEVVAQKEKAIQDKSERIVSLQKELSSLQKKETLNAAEQVDKAHARADELEKQIDNLKKESEKQQ  136 (321)
Q Consensus        66 ~eLk~kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~qk~~~~~~eeq~~~~~~RireL~k~Ie~Lk~ele~~~  136 (321)
                      ..+-.+|..-.+++..++.+..+.+.+..+|.....   .    ..+.+..+++.|+.+|..+..++....
T Consensus        28 d~i~~ld~~rr~l~~~~e~l~~~rN~~sk~i~k~~~---~----~~~~l~~~~k~lk~~i~~le~~~~~~~   91 (110)
T d1seta1          28 EALLALDREVQELKKRLQEVQTERNQVAKRVPKAPP---E----EKEALIARGKALGEEAKRLEEALREKE   91 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCH---H----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc---c----chHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555555532211   1    112344455555555555554444444

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=82.39  E-value=4.4  Score=29.81  Aligned_cols=58  Identities=14%  Similarity=0.177  Sum_probs=30.6

Q ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHhhhc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 020809           42 PLKIELDQLKSKIRSLESHIDEKTQELKG-KDEVVAQKEKAIQDKSERIVSLQKELSSL   99 (321)
Q Consensus        42 ~l~~el~qlk~ki~~Les~i~e~~~eLk~-kd~~I~q~ek~i~e~~~~I~~Lq~eI~~~   99 (321)
                      .+..+..++..++.+|.++...++++|.. ..+....+..+...+..+|..++.++..+
T Consensus        32 ~ld~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~   90 (110)
T d1seta1          32 ALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREK   90 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455566666666666666666666632 33334444444444444444444444433