Citrus Sinensis ID: 028376

---

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
Protein Sequence
MTEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSSQSQSLFKCYYS
Secondary Structure (PSIPRED)
ccHHHHcccHHHHHHHHHccccccccccccccccccccEEccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccEEEEcccHHHHHHHHHHHHHccccEEEEEcccccHHHHHHHHHHcccccEEEEEcccccccccEEEcc
Secondary Structure Prediction (SSPRO)
cccEEEEEccHHHHccccccccccccccEEcccccccEEEEccccHHHHHHHHHHHHHHHHccccccccccEcccEccEcccccEEEEccccccccccccccHccccccHHcccEEcccccHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHHHHHHcccEEEEEcccccHHHHHHHccccccEEEEEcccccccccccEEEEcc
Coil and Loop (DISEMBL)
MTEEVVTISNSTKHRIESlskadeetcpicqeklgnqkmvfqcghftcckcffaMTEQRLIhdnkvknewvmcptcrqrtdigniayaddrqdkscnsdmphgvqdcekgeesftvqgsygtkIEAVTRRILWIkstdpkakILVFSSWNDVLDVLEHAFIANNITCIkmkgenhklpsanlQHRNALQKELtrhmpssqsqslfkcyys
Flexible Loop (DISEMBL)
mteevvtisnstkhrieslskadeETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESftvqgsygtkieaVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELtrhmpssqsqslfkcyys
Low Complexity Region (SEG)
MTEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSSQSQSLFKCYYS
Disordered region (IsUnstruct)
**************************CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA*************************FTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMK***************************************
Disordered Region (DISOPRED)
****V*********************CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQR************MCPTCRQRTDIGNIA*****************************VQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE*************ALQKELTRHMPSSQSQSLFKCYY*
Disordered Region (DISEMBL)
**********************DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKE*******************
Disordered Region (DISPRO)
MTEEVVTISNSTKHR********EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQ*****SDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSSQSQSLFKCYYS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSSQSQSLFKCYYS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	210	2.2.26 [Sep-21-2011]
Q149N8	1683	E3 ubiquitin-protein liga	yes	no	0.690	0.086	0.327	2e-19
Q7TPQ3	1674	E3 ubiquitin-protein liga	yes	no	0.690	0.086	0.320	9e-19
Q9UTL9	1375	Uncharacterized ATP-depen	yes	no	0.852	0.130	0.258	3e-12
Q4IJ84	1154	DNA repair protein RAD5 O	yes	no	0.742	0.135	0.262	2e-05
P0CQ67	1198	DNA repair protein RAD5 O	N/A	no	0.709	0.124	0.263	4e-05
P0CQ66	1198	DNA repair protein RAD5 O	no	no	0.809	0.141	0.260	7e-05
Q7S1P9	1222	DNA repair protein rad-5	N/A	no	0.761	0.130	0.234	0.0006

>sp|Q149N8|SHPRH_HUMAN E3 ubiquitin-protein ligase SHPRH OS=Homo sapiens GN=SHPRH PE=1 SV=2

 Score = 95.5 bits (236), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/162 (32%), Positives = 83/162 (51%), Gaps = 17/162 (10%)

Query: 4    EVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHD 63
            +++ ++N  K + ++    + E CPIC  +LG Q  V  CGH  C +C   + EQ  +  
Sbjct: 1409 QLLYLTNLEKSQDKTSGGVNPEPCPICARQLGKQWAVLTCGHCFCNECISIIIEQYSVGS 1468

Query: 64   NKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTK 123
            ++     + C  CRQ T    I+Y    +  +   D+P              V+GS+ TK
Sbjct: 1469 HRSS---IKCAICRQTTSHKEISYVFTSEKANQEEDIP--------------VKGSHSTK 1511

Query: 124  IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNI 165
            +EAV R ++ I+  DP AK LVFS+W DVLD++  A   NN+
Sbjct: 1512 VEAVVRTLMKIQLRDPGAKALVFSTWQDVLDIISKALTDNNM 1553

E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'.
Homo sapiens (taxid: 9606)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q7TPQ3|SHPRH_MOUSE E3 ubiquitin-protein ligase SHPRH OS=Mus musculus GN=Shprh PE=1 SV=1

 Score = 93.6 bits (231), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 52/162 (32%), Positives = 83/162 (51%), Gaps = 17/162 (10%)

Query: 4    EVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHD 63
            +++ ++N  K + ++    + E CPIC  +LG Q  V  CGH  C +C   + EQ  +  
Sbjct: 1400 QLLYLTNLEKSQDKTSGGINPEPCPICARQLGKQWAVLTCGHCFCNECTSIIIEQYSVGS 1459

Query: 64   NKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTK 123
            ++     + C  CRQ T    ++Y    +  +   D+P              V+GS+ TK
Sbjct: 1460 HRSS---IKCAICRQTTSHKEVSYVFTSEKANQEDDIP--------------VKGSHSTK 1502

Query: 124  IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNI 165
            +EAV R ++ I+  DP AK LVFS+W DVLD++  A   NN+
Sbjct: 1503 VEAVVRTLMKIQLRDPGAKALVFSTWQDVLDIISKALTDNNM 1544

E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9UTL9|YIV5_SCHPO Uncharacterized ATP-dependent helicase C144.05 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC144.05 PE=3 SV=1

 Score = 72.0 bits (175), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 92/205 (44%), Gaps = 26/205 (12%)

Query: 8    ISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVK 67
            ++N  +H +  L     + C IC++ +  Q  +  CGH  C  C     E  L H +   
Sbjct: 1075 LTNLYEHIV--LKAESHQICIICRDII-KQGFITTCGHLYCSFCL----EAWLKHSSS-- 1125

Query: 68   NEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEE-----------SFTV 116
                 CP C+ + +  N  Y  + +D     +   G    ++  E           +  +
Sbjct: 1126 -----CPMCKTKLNKNNAYYIGESRDIYSRQEFVTGFNKRDERLEILDDEAYRQISNMEL 1180

Query: 117  QGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHK 176
            + S+G+KI+ +++ +L++K  +   K++VFS W DVLDVL  +F AN I  I+  G++  
Sbjct: 1181 KESFGSKIDTISKHLLYLKHNELYPKVVVFSQWLDVLDVLHKSFEANGIVFIRFDGKSKN 1240

Query: 177  LPSANLQHRNALQKELTRHMPSSQS 201
                  +   +LQ  LT H  S  S
Sbjct: 1241 TCLKRFKEERSLQV-LTLHARSQSS 1264

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q4IJ84|RAD5_GIBZE DNA repair protein RAD5 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=RAD5 PE=3 SV=1

 Score = 49.3 bits (116), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 75/179 (41%), Gaps = 23/179 (12%)

Query: 1    MTEEVVTISNST--KHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQ 58
            +T++    SN T   H +E +    E  CP+C E+  N + V  C H  C KC       
Sbjct: 872  VTDKASKESNQTFGAHALEQIRDEAENECPLCFEEPMNDQTVTGCWHSACKKCLLD---- 927

Query: 59   RLIHDNKVKNEWVMCPTCRQ---RTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFT 115
              I     K E   C +CR+   + D+  +   DD      +SDM       +K   S  
Sbjct: 928  -YIKHQTDKAEVPRCFSCREPINKRDLFEVVRHDD------DSDM-----MSKKPRISLQ 975

Query: 116  VQG--SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
              G  +   K+ A+   +  ++   PK K +VFS +   L ++E A    NI  +++ G
Sbjct: 976  RVGVNASSAKVVALMSELRALRREHPKMKSVVFSQFTSFLSLIEPALTRANIKFLRLDG 1034

Probable helicase, member of the UBC2/RAD6 epistasis group. Functions with DNA repair protein RAD18 in error-free postreplication DNA repair. Involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. Seems to be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs.

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (taxid: 229533)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|P0CQ67|RAD5_CRYNB DNA repair protein RAD5 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=RAD5 PE=3 SV=1

 Score = 48.1 bits (113), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 45/171 (26%), Positives = 70/171 (40%), Gaps = 22/171 (12%)

Query: 23   DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82
            D   C +C  ++ ++ ++  C H +C  C         I   + +N+   CP+C +    
Sbjct: 916  DTPICELCSNEMFDE-VLLPCYHRSCQDCIV-----EWIGTCEDQNKIASCPSCGK---- 965

Query: 83   GNIAYAD----DRQDKSCNS---DMPHGVQDCEKGEESFTVQGS-----YGTKIEAVTRR 130
            G I  AD     R+ K  N      P G     K     TV          TK+ A+ R+
Sbjct: 966  GPIKLADLRSVQRRHKRVNPITDAYPGGRDPNSKSSNDTTVTLGKVDLVTSTKLRALLRQ 1025

Query: 131  ILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSAN 181
            +  I+  DPKAK LVFS +   LD++E       I  ++  G   +   AN
Sbjct: 1026 LEEIRQEDPKAKALVFSQFTSFLDLIEATLTKQGIRWLRFDGTMSQAQRAN 1076

Probable helicase, member of the UBC2/RAD6 epistasis group. Functions with DNA repair protein RAD18 in error-free postreplication DNA repair. Involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. Seems to be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs.

Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) (taxid: 283643)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|P0CQ66|RAD5_CRYNJ DNA repair protein RAD5 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=RAD5 PE=3 SV=1

 Score = 47.4 bits (111), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 78/192 (40%), Gaps = 22/192 (11%)

Query: 2    TEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLI 61
            T E V  + + K   E   + D   C +C  ++ ++ ++  C H +C  C         I
Sbjct: 895  TPEDVDKAYAAKVLKELGEQEDTPICELCSNEMFDE-VLLPCYHRSCQDCIV-----EWI 948

Query: 62   HDNKVKNEWVMCPTCRQRTDIGNIAYAD----DRQDKSCNS---DMPHGVQDCEKGEESF 114
               + +N+   CP+C +    G I  AD     R+ K  N      P G     K     
Sbjct: 949  GTCEDQNKIASCPSCGK----GPIKLADLRSVQRRHKRVNPITDAYPGGRDPNLKSSNDT 1004

Query: 115  TVQGS-----YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIK 169
            TV          TK+ A+ R++  I+  DPKAK LVFS +   LD++E       I  ++
Sbjct: 1005 TVTLGKVDLVTSTKLRALLRQLEEIRQEDPKAKALVFSQFTSFLDLIEATLTKQGIRWLR 1064

Query: 170  MKGENHKLPSAN 181
              G   +   AN
Sbjct: 1065 FDGTMSQAQRAN 1076

Probable helicase, member of the UBC2/RAD6 epistasis group. Functions with DNA repair protein RAD18 in error-free postreplication DNA repair. Involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. Seems to be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs.

Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (taxid: 214684)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q7S1P9|RAD5_NEUCR DNA repair protein rad-5 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=rad-5 PE=3 SV=2

 Score = 44.3 bits (103), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 39/166 (23%), Positives = 62/166 (37%), Gaps = 6/166 (3%)

Query: 7    TISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKV 66
            T +N   H +  +       CPIC E+    + V  C H  C KC         I     
Sbjct: 941  TNNNFGAHVLRQIRDEAVNECPICAEEPMIDQAVTGCWHSACKKCLLDY-----IKHQTD 995

Query: 67   KNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTKIEA 126
            +NE   C  CR+  +I +I       D    S  P    +     +      S   KI A
Sbjct: 996  RNEVPRCFQCREHINIRDIFEVIRHDDDLETSSTPGASPEPRISLQRVGANDS-SAKIVA 1054

Query: 127  VTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            +   +  ++   PK K LV S +   L ++  A   + I+ +++ G
Sbjct: 1055 LISHLRTLRQEHPKMKSLVISQFTSFLSLISSALTRHKISFLRLDG 1100

Probable helicase, member of the UBC2/RAD6 epistasis group. Functions with DNA repair protein RAD18 in error-free postreplication DNA repair. Involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. Seems to be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

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	210
224127896	169	SW2/SNF2 family-like protein [Populus tr	0.795	0.988	0.708	2e-65
255559737	1588	snf2 histone linker phd ring helicase, p	0.876	0.115	0.654	1e-64
359486454	1704	PREDICTED: E3 ubiquitin-protein ligase S	0.819	0.100	0.649	7e-63
297736470	1717	unnamed protein product [Vitis vinifera]	0.819	0.100	0.649	8e-63
147860973	2416	hypothetical protein VITISV_013126 [Viti	0.819	0.071	0.649	1e-62
356500801	1600	PREDICTED: E3 ubiquitin-protein ligase S	0.809	0.106	0.668	2e-61
449499151	1520	PREDICTED: LOW QUALITY PROTEIN: E3 ubiqu	0.804	0.111	0.645	1e-59
449441236	1520	PREDICTED: E3 ubiquitin-protein ligase S	0.804	0.111	0.645	1e-59
297827713	1635	SNF2 domain-containing protein [Arabidop	0.761	0.097	0.639	2e-55
240254615	1664	RING-finger, DEAD-like helicase, PHD and	0.761	0.096	0.639	3e-55

>gi|224127896|ref|XP_002329204.1| SW2/SNF2 family-like protein [Populus trichocarpa] gi|222870985|gb|EEF08116.1| SW2/SNF2 family-like protein [Populus trichocarpa]

 Score =  254 bits (649), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 119/168 (70%), Positives = 136/168 (80%), Gaps = 1/168 (0%)

Query: 5   VVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDN 64
           +  +  +T+   E L K DEE CPICQEKL NQKMVF CGH TCCKCFFAMTE+++ HDN
Sbjct: 1   MAAVPMTTEKISEYLPKDDEEACPICQEKLNNQKMVFPCGHVTCCKCFFAMTERKM-HDN 59

Query: 65  KVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTKI 124
           + + +WVMCPTCRQ TD GNIAYADDR+DKSC+S M   +Q CEK E S  VQGSYGTK+
Sbjct: 60  RFQRKWVMCPTCRQHTDFGNIAYADDRRDKSCSSAMLDAIQGCEKTEASLAVQGSYGTKV 119

Query: 125 EAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
           EAVTRRILWIKS+DPKAK+LVFSSWNDVLDVLEHA  AN IT I+MKG
Sbjct: 120 EAVTRRILWIKSSDPKAKVLVFSSWNDVLDVLEHALNANEITYIRMKG 167

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559737|ref|XP_002520888.1| snf2 histone linker phd ring helicase, putative [Ricinus communis] gi|223540019|gb|EEF41597.1| snf2 histone linker phd ring helicase, putative [Ricinus communis]

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 125/191 (65%), Positives = 145/191 (75%), Gaps = 7/191 (3%)

Query: 1    MTEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRL 60
            +T+E+ T+S S +   + L K DEE CPICQEK+ NQKMVFQCGH TCCKC FAMTE   
Sbjct: 1264 LTQEMATMSTSEEKMSDDLPKDDEEACPICQEKMHNQKMVFQCGHVTCCKCLFAMTEH-- 1321

Query: 61   IHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSY 120
             HDNK + +WVMCPTCRQ TD  NIAYADDR DKSCNS + + VQ  EK E S  VQGSY
Sbjct: 1322 -HDNKFQRKWVMCPTCRQHTDFRNIAYADDRNDKSCNSAVLNTVQGYEKCEASLIVQGSY 1380

Query: 121  GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSA 180
            GTKIEA+TRRIL IKS+DP+AK+LVFSSWNDVLDVLEHAF AN IT I+MKG ++ + + 
Sbjct: 1381 GTKIEAITRRILGIKSSDPEAKVLVFSSWNDVLDVLEHAFNANGITYIRMKGGSNTIGN- 1439

Query: 181  NLQHRNALQKE 191
               HR   QKE
Sbjct: 1440 ---HRVHSQKE 1447

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486454|ref|XP_003633446.1| PREDICTED: E3 ubiquitin-protein ligase SHPRH-like [Vitis vinifera]

 Score =  245 bits (626), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 113/174 (64%), Positives = 137/174 (78%), Gaps = 2/174 (1%)

Query: 1    MTEEVVT--ISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQ 58
            +T++  T  IS   + + + + + D+E CP+CQEKL N++MVFQCGH  CC C FAMTE+
Sbjct: 1344 LTQDTATLLISCPVEEKNKCIRETDDEACPVCQEKLSNRRMVFQCGHVICCNCLFAMTEK 1403

Query: 59   RLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQG 118
            RL+H  K +++W+MCPTCRQ TD+GNIAYADDRQ KSC+S   H VQ  EK E S  VQG
Sbjct: 1404 RLVHHGKFQDKWLMCPTCRQHTDVGNIAYADDRQTKSCDSAELHTVQSVEKSEASVIVQG 1463

Query: 119  SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            SYGTKIEAVTRRILWIK T+PKAKILVFSSWNDVL+VLEHA  ANNIT ++MKG
Sbjct: 1464 SYGTKIEAVTRRILWIKCTEPKAKILVFSSWNDVLNVLEHALNANNITYVRMKG 1517

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736470|emb|CBI25341.3| unnamed protein product [Vitis vinifera]

 Score =  245 bits (626), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 113/174 (64%), Positives = 137/174 (78%), Gaps = 2/174 (1%)

Query: 1    MTEEVVT--ISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQ 58
            +T++  T  IS   + + + + + D+E CP+CQEKL N++MVFQCGH  CC C FAMTE+
Sbjct: 1369 LTQDTATLLISCPVEEKNKCIRETDDEACPVCQEKLSNRRMVFQCGHVICCNCLFAMTEK 1428

Query: 59   RLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQG 118
            RL+H  K +++W+MCPTCRQ TD+GNIAYADDRQ KSC+S   H VQ  EK E S  VQG
Sbjct: 1429 RLVHHGKFQDKWLMCPTCRQHTDVGNIAYADDRQTKSCDSAELHTVQSVEKSEASVIVQG 1488

Query: 119  SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            SYGTKIEAVTRRILWIK T+PKAKILVFSSWNDVL+VLEHA  ANNIT ++MKG
Sbjct: 1489 SYGTKIEAVTRRILWIKCTEPKAKILVFSSWNDVLNVLEHALNANNITYVRMKG 1542

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860973|emb|CAN82939.1| hypothetical protein VITISV_013126 [Vitis vinifera]

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 113/174 (64%), Positives = 137/174 (78%), Gaps = 2/174 (1%)

Query: 1    MTEEVVT--ISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQ 58
            +T++  T  IS   + + + + + D+E CP+CQEKL N++MVFQCGH  CC C FAMTE+
Sbjct: 2068 LTQDTATLLISXPVEEKNKCIRETDDEACPVCQEKLSNRRMVFQCGHVICCNCLFAMTEK 2127

Query: 59   RLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQG 118
            RL+H  K +++W+MCPTCRQ TD+GNIAYADDRQ KSC+S   H VQ  EK E S  VQG
Sbjct: 2128 RLVHHGKFQDKWLMCPTCRQHTDVGNIAYADDRQTKSCDSAELHTVQSXEKSEASVIVQG 2187

Query: 119  SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            SYGTKIEAVTRRILWIK T+PKAKILVFSSWNDVL+VLEHA  ANNIT ++MKG
Sbjct: 2188 SYGTKIEAVTRRILWIKCTEPKAKILVFSSWNDVLNVLEHALNANNITYVRMKG 2241

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500801|ref|XP_003519219.1| PREDICTED: E3 ubiquitin-protein ligase SHPRH-like [Glycine max]

 Score =  240 bits (613), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 115/172 (66%), Positives = 134/172 (77%), Gaps = 2/172 (1%)

Query: 1    MTEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRL 60
             T E     NST+ +   LSK+D+ETCPICQEKLG QKMVFQCGH TCCKC FAMTE+RL
Sbjct: 1268 FTRETTATPNSTEEKDALLSKSDDETCPICQEKLGKQKMVFQCGHVTCCKCLFAMTEKRL 1327

Query: 61   IHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSY 120
              ++K+ N WVMCPTCRQ TD GNIAYA D Q +S +  + H +   EK E S +V+GSY
Sbjct: 1328 -QNSKLHN-WVMCPTCRQHTDFGNIAYAVDAQHESSDPSVLHPIDSSEKFEASISVKGSY 1385

Query: 121  GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            GTKIEAVTRRILW+K+ D +AK+LVFSSWNDVLDVLEHAF ANNIT I+MKG
Sbjct: 1386 GTKIEAVTRRILWVKANDHRAKVLVFSSWNDVLDVLEHAFAANNITYIRMKG 1437

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449499151|ref|XP_004160739.1| PREDICTED: LOW QUALITY PROTEIN: E3 ubiquitin-protein ligase SHPRH-like [Cucumis sativus]

 Score =  235 bits (599), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 111/172 (64%), Positives = 136/172 (79%), Gaps = 3/172 (1%)

Query: 1    MTEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRL 60
            +T+E    S +T+ + E+ SKADEE+CP+CQEKL NQKMVFQCGH TCCKC FAMTE+ L
Sbjct: 1350 LTQEPAITSTATEQKNENTSKADEESCPVCQEKLNNQKMVFQCGHITCCKCLFAMTEKTL 1409

Query: 61   IHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSY 120
             H +K++ +WVMCPTCRQ TD GNIAYADD ++++   D    ++   + E S TVQGSY
Sbjct: 1410 -HGSKIQTKWVMCPTCRQHTDFGNIAYADDSKNETL--DPSTSLETSREHEMSITVQGSY 1466

Query: 121  GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            GTKIEAV RRILWIK TD +AK+LVFSSWNDVLDVL +AF+ANNIT I+MKG
Sbjct: 1467 GTKIEAVVRRILWIKYTDSEAKVLVFSSWNDVLDVLHYAFVANNITFIRMKG 1518

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441236|ref|XP_004138388.1| PREDICTED: E3 ubiquitin-protein ligase SHPRH-like [Cucumis sativus]

 Score =  235 bits (599), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 111/172 (64%), Positives = 136/172 (79%), Gaps = 3/172 (1%)

Query: 1    MTEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRL 60
            +T+E    S +T+ + E+ SKADEE+CP+CQEKL NQKMVFQCGH TCCKC FAMTE+ L
Sbjct: 1350 LTQEPAITSTATEQKNENTSKADEESCPVCQEKLNNQKMVFQCGHITCCKCLFAMTEKTL 1409

Query: 61   IHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSY 120
             H +K++ +WVMCPTCRQ TD GNIAYADD ++++   D    ++   + E S TVQGSY
Sbjct: 1410 -HGSKIQTKWVMCPTCRQHTDFGNIAYADDSKNETL--DPSTSLETSREHEMSITVQGSY 1466

Query: 121  GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            GTKIEAV RRILWIK TD +AK+LVFSSWNDVLDVL +AF+ANNIT I+MKG
Sbjct: 1467 GTKIEAVVRRILWIKYTDSEAKVLVFSSWNDVLDVLHYAFVANNITFIRMKG 1518

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297827713|ref|XP_002881739.1| SNF2 domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297327578|gb|EFH57998.1| SNF2 domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  221 bits (563), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 108/169 (63%), Positives = 127/169 (75%), Gaps = 9/169 (5%)

Query: 4    EVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHD 63
            E +  S+  +   E+L K DE  CPICQE L NQKMVFQCGH TCC CFFAMTE++ + +
Sbjct: 1295 ETLEASDPVEQEGENLLKRDE-ACPICQEILRNQKMVFQCGHSTCCNCFFAMTERKSVQE 1353

Query: 64   NKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTK 123
               K  WVMCP CRQ TD+ NIAYADDR++ S +       QD +  E S  VQGSYGTK
Sbjct: 1354 TLQK--WVMCPICRQHTDVRNIAYADDRRNSSSSD------QDHKDNEASLVVQGSYGTK 1405

Query: 124  IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            IEAVTRRILWIKS+DP+AK+LVFSSWNDVLDVL+HAF AN+ITCI+MKG
Sbjct: 1406 IEAVTRRILWIKSSDPQAKVLVFSSWNDVLDVLQHAFAANSITCIRMKG 1454

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|240254615|ref|NP_181609.4| RING-finger, DEAD-like helicase, PHD and SNF2 domain-containing protein [Arabidopsis thaliana] gi|330254782|gb|AEC09876.1| RING-finger, DEAD-like helicase, PHD and SNF2 domain-containing protein [Arabidopsis thaliana]

 Score =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 108/169 (63%), Positives = 125/169 (73%), Gaps = 9/169 (5%)

Query: 4    EVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHD 63
            E V  S+  +   E+L K DE  CPIC E L NQKMVFQCGH TCC CFFAMTE++ + +
Sbjct: 1322 ETVDASDPAEQESENLLKRDE-ACPICHEILRNQKMVFQCGHSTCCNCFFAMTERKSVQE 1380

Query: 64   NKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTK 123
               K  WVMCP CRQ TD+ NIAYADDR++ S +       QD +  E S  VQGSYGTK
Sbjct: 1381 TLQK--WVMCPICRQHTDVRNIAYADDRRNSSSSD------QDHKDSEASLVVQGSYGTK 1432

Query: 124  IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172
            IEAVTRRILWIKS+DP+ K+LVFSSWNDVLDVLEHAF AN+ITCI+MKG
Sbjct: 1433 IEAVTRRILWIKSSDPQTKVLVFSSWNDVLDVLEHAFAANSITCIRMKG 1481

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	210
TAIR|locus:2064786	1664	AT2G40770 [Arabidopsis thalian	0.890	0.112	0.587	1.2e-52
POMBASE|SPAC144.05	1375	SPAC144.05 "ATP-dependent DNA	0.861	0.131	0.264	1.6e-12
UNIPROTKB|E1C5L6	1682	SHPRH "Uncharacterized protein	0.533	0.066	0.335	5.9e-10
UNIPROTKB|E1C615	1682	SHPRH "Uncharacterized protein	0.533	0.066	0.335	5.9e-10
UNIPROTKB|E2R8G0	1685	SHPRH "Uncharacterized protein	0.5	0.062	0.347	9.6e-10
UNIPROTKB|F1S736	1688	SHPRH "Uncharacterized protein	0.5	0.062	0.347	9.6e-10
UNIPROTKB|E1BLB1	1688	SHPRH "Uncharacterized protein	0.5	0.062	0.347	9.6e-10
MGI|MGI:1917581	1674	Shprh "SNF2 histone linker PHD	0.5	0.062	0.330	1.6e-09
RGD|1310342	1701	Shprh "SNF2 histone linker PHD	0.5	0.061	0.330	1.6e-09
UNIPROTKB|Q149N8	1683	SHPRH "E3 ubiquitin-protein li	0.5	0.062	0.338	4e-09

TAIR|locus:2064786 AT2G40770 [Arabidopsis thaliana (taxid:3702)]

 Score = 559 (201.8 bits), Expect = 1.2e-52, P = 1.2e-52
 Identities = 117/199 (58%), Positives = 141/199 (70%)

Query:     4 EVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHD 63
             E V  S+  +   E+L K DE  CPIC E L NQKMVFQCGH TCC CFFAMTE++ + +
Sbjct:  1322 ETVDASDPAEQESENLLKRDE-ACPICHEILRNQKMVFQCGHSTCCNCFFAMTERKSVQE 1380

Query:    64 NKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTK 123
                K  WVMCP CRQ TD+ NIAYADDR++ S +SD     QD +  E S  VQGSYGTK
Sbjct:  1381 TLQK--WVMCPICRQHTDVRNIAYADDRRNSS-SSD-----QDHKDSEASLVVQGSYGTK 1432

Query:   124 IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQ 183
             IEAVTRRILWIKS+DP+ K+LVFSSWNDVLDVLEHAF AN+ITCI+MKG   K  +A  +
Sbjct:  1433 IEAVTRRILWIKSSDPQTKVLVFSSWNDVLDVLEHAFAANSITCIRMKG-GRKSQTAISK 1491

Query:   184 HRNALQKELTRHMPSSQSQ 202
              + + +KE T+   S Q +
Sbjct:  1492 FKGS-EKE-TQKTNSHQKE 1508

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

POMBASE|SPAC144.05 SPAC144.05 "ATP-dependent DNA helicase (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 181 (68.8 bits), Expect = 1.6e-12, P = 1.6e-12
 Identities = 55/208 (26%), Positives = 96/208 (46%)

Query:     8 ISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVK 67
             ++N  +H +  L     + C IC++ +  Q  +  CGH  C  C     E  L H +   
Sbjct:  1075 LTNLYEHIV--LKAESHQICIICRDII-KQGFITTCGHLYCSFCL----EAWLKHSSS-- 1125

Query:    68 NEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEK-----GEESFT------V 116
                  CP C+ + +  N  Y  + +D     +   G    ++      +E++       +
Sbjct:  1126 -----CPMCKTKLNKNNAYYIGESRDIYSRQEFVTGFNKRDERLEILDDEAYRQISNMEL 1180

Query:   117 QGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHK 176
             + S+G+KI+ +++ +L++K  +   K++VFS W DVLDVL  +F AN I  I+  G++  
Sbjct:  1181 KESFGSKIDTISKHLLYLKHNELYPKVVVFSQWLDVLDVLHKSFEANGIVFIRFDGKSKN 1240

Query:   177 LPSANLQHRNALQKELTRHMPSSQSQSL 204
                   +   +LQ  LT H   SQS  L
Sbjct:  1241 TCLKRFKEERSLQV-LTLHA-RSQSSGL 1266

GO:0000790 "nuclear chromatin" evidence=NAS

GO:0003677 "DNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0004842 "ubiquitin-protein ligase activity" evidence=ISM

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0006281 "DNA repair" evidence=ISS

GO:0008094 "DNA-dependent ATPase activity" evidence=ISM

GO:0008270 "zinc ion binding" evidence=ISM

GO:0016567 "protein ubiquitination" evidence=ISM

UNIPROTKB|E1C5L6 SHPRH "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 158 (60.7 bits), Expect = 5.9e-10, P = 5.9e-10
 Identities = 43/128 (33%), Positives = 61/128 (47%)

Query:    47 TCCKCFFAMTEQRLIHDNKV--KNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGV 104
             TC  CF       +I    V  +   + C  CRQ T    I+Y    +  +   D+P   
Sbjct:  1446 TCGHCFCNECIAIIIEQYSVGTRRSSIKCAICRQTTSHKEISYVFTAETANQEDDIP--- 1502

Query:   105 QDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN 164
                        V+GS+ TK+EAV R +  I+  DP AK LVFS+W DVLD++  A   NN
Sbjct:  1503 -----------VKGSHSTKVEAVVRTLKRIQFKDPGAKSLVFSTWQDVLDIIAKALYDNN 1551

Query:   165 ITCIKMKG 172
             +T  ++ G
Sbjct:  1552 MTFSQING 1559

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E1C615 SHPRH "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 158 (60.7 bits), Expect = 5.9e-10, P = 5.9e-10
 Identities = 43/128 (33%), Positives = 61/128 (47%)

Query:    47 TCCKCFFAMTEQRLIHDNKV--KNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGV 104
             TC  CF       +I    V  +   + C  CRQ T    I+Y    +  +   D+P   
Sbjct:  1446 TCGHCFCNECIAIIIEQYSVGTRRSSIKCAICRQTTSHKEISYVFTAETANQEDDIP--- 1502

Query:   105 QDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN 164
                        V+GS+ TK+EAV R +  I+  DP AK LVFS+W DVLD++  A   NN
Sbjct:  1503 -----------VKGSHSTKVEAVVRTLKRIQFKDPGAKSLVFSTWQDVLDIIAKALYDNN 1551

Query:   165 ITCIKMKG 172
             +T  ++ G
Sbjct:  1552 MTFSQING 1559

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2R8G0 SHPRH "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 156 (60.0 bits), Expect = 9.6e-10, P = 9.6e-10
 Identities = 42/121 (34%), Positives = 58/121 (47%)

Query:    47 TCCKCFFAMTEQRLIHDNKVKNEW--VMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGV 104
             TC  CF       +I    V +    + C  CRQ T    I+Y    +  S   D+P   
Sbjct:  1449 TCGHCFCNECISIIIEQYSVGSHRSSIKCAICRQTTSHKEISYVFTSEKASQEEDIP--- 1505

Query:   105 QDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN 164
                        V+GS+ TK+EAV R ++ I+  DP AK LVFS+W DVLD++  A   NN
Sbjct:  1506 -----------VKGSHSTKVEAVVRTLMRIQLRDPGAKALVFSTWQDVLDIISKALTDNN 1554

Query:   165 I 165
             +
Sbjct:  1555 M 1555

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

UNIPROTKB|F1S736 SHPRH "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 156 (60.0 bits), Expect = 9.6e-10, P = 9.6e-10
 Identities = 42/121 (34%), Positives = 58/121 (47%)

Query:    47 TCCKCFFAMTEQRLIHDNKVKNEW--VMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGV 104
             TC  CF       +I    V +    + C  CRQ T    I+Y    +  S   D+P   
Sbjct:  1452 TCGHCFCNECISIIIEQYSVGSHRSSIKCAICRQTTSHKEISYVFTSEKASQEEDIP--- 1508

Query:   105 QDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN 164
                        V+GS+ TK+EAV R ++ I+  DP AK LVFS+W DVLD++  A   NN
Sbjct:  1509 -----------VKGSHSTKVEAVVRTLMRIQLRDPGAKALVFSTWQDVLDIISKALTDNN 1557

Query:   165 I 165
             +
Sbjct:  1558 M 1558

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

UNIPROTKB|E1BLB1 SHPRH "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 156 (60.0 bits), Expect = 9.6e-10, P = 9.6e-10
 Identities = 42/121 (34%), Positives = 58/121 (47%)

Query:    47 TCCKCFFAMTEQRLIHDNKVKNEW--VMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGV 104
             TC  CF       +I    V +    + C  CRQ T    I+Y    +  S   D+P   
Sbjct:  1452 TCGHCFCNECISIIIEQYSVGSHRSSIRCAICRQTTSHKEISYVFTSEKASQEEDIP--- 1508

Query:   105 QDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN 164
                        V+GS+ TK+EAV R ++ I+  DP AK LVFS+W DVLD++  A   NN
Sbjct:  1509 -----------VKGSHSTKVEAVVRTLMRIQLRDPGAKALVFSTWQDVLDIISKALTDNN 1557

Query:   165 I 165
             +
Sbjct:  1558 M 1558

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

MGI|MGI:1917581 Shprh "SNF2 histone linker PHD RING helicase" [Mus musculus (taxid:10090)]

 Score = 154 (59.3 bits), Expect = 1.6e-09, P = 1.6e-09
 Identities = 40/121 (33%), Positives = 58/121 (47%)

Query:    47 TCCKCFFAMTEQRLIHDNKVKNEW--VMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGV 104
             TC  CF       +I    V +    + C  CRQ T    ++Y    +  +   D+P   
Sbjct:  1438 TCGHCFCNECTSIIIEQYSVGSHRSSIKCAICRQTTSHKEVSYVFTSEKANQEDDIP--- 1494

Query:   105 QDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN 164
                        V+GS+ TK+EAV R ++ I+  DP AK LVFS+W DVLD++  A   NN
Sbjct:  1495 -----------VKGSHSTKVEAVVRTLMKIQLRDPGAKALVFSTWQDVLDIISKALTDNN 1543

Query:   165 I 165
             +
Sbjct:  1544 M 1544

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

RGD|1310342 Shprh "SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase" [Rattus norvegicus (taxid:10116)]

 Score = 154 (59.3 bits), Expect = 1.6e-09, P = 1.6e-09
 Identities = 40/121 (33%), Positives = 58/121 (47%)

Query:    47 TCCKCFFAMTEQRLIHDNKVKNEW--VMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGV 104
             TC  CF       +I    V +    + C  CRQ T    ++Y    +  +   D+P   
Sbjct:  1465 TCGHCFCNECTSIIIEQYSVGSHRSSIKCAICRQTTSHKEVSYVFTSEKANQEDDIP--- 1521

Query:   105 QDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN 164
                        V+GS+ TK+EAV R ++ I+  DP AK LVFS+W DVLD++  A   NN
Sbjct:  1522 -----------VKGSHSTKVEAVVRTLMKIQLKDPGAKALVFSTWQDVLDIISKALTDNN 1570

Query:   165 I 165
             +
Sbjct:  1571 M 1571

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q149N8 SHPRH "E3 ubiquitin-protein ligase SHPRH" [Homo sapiens (taxid:9606)]

 Score = 153 (58.9 bits), Expect = 4.0e-09, P = 4.0e-09
 Identities = 41/121 (33%), Positives = 58/121 (47%)

Query:    47 TCCKCFFAMTEQRLIHDNKVKNEW--VMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGV 104
             TC  CF       +I    V +    + C  CRQ T    I+Y    +  +   D+P   
Sbjct:  1447 TCGHCFCNECISIIIEQYSVGSHRSSIKCAICRQTTSHKEISYVFTSEKANQEEDIP--- 1503

Query:   105 QDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN 164
                        V+GS+ TK+EAV R ++ I+  DP AK LVFS+W DVLD++  A   NN
Sbjct:  1504 -----------VKGSHSTKVEAVVRTLMKIQLRDPGAKALVFSTWQDVLDIISKALTDNN 1552

Query:   165 I 165
             +
Sbjct:  1553 M 1553

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

Your Input: CHR953 SW2/SNF2 family-like protein (169 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	210
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-05
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	4e-05
smart00184	40	smart00184, RING, Ring finger	0.002

>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 11/56 (19%)

Query: 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78
          +E  CPIC + L +  ++  CGH  C +C       R +           CP CR 
Sbjct: 1  EELECPICLDLLRDPVVLTPCGHVFCRECI-----LRYLKKKS------KCPICRT 45

Length = 45

>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

 Score = 39.4 bits (92), Expect = 4e-05
 Identities = 14/53 (26%), Positives = 18/53 (33%), Gaps = 10/53 (18%)

Query: 26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78
           CPIC E+     ++  CGH  C  C     +               CP CR 
Sbjct: 1  ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNT----------CPLCRT 43

Length = 45

>gnl|CDD|214546 smart00184, RING, Ring finger

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 14/50 (28%), Positives = 17/50 (34%), Gaps = 10/50 (20%)

Query: 27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC 76
          CPIC E+     ++  CGH  C  C     E               CP C
Sbjct: 1  CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNT----------CPIC 40

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s). Length = 40

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	210
KOG1002	791	consensus Nucleotide excision repair protein RAD16	99.93
KOG1001	674	consensus Helicase-like transcription factor HLTF/	99.6
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.43
KOG0298	1394	consensus DEAD box-containing helicase-like transc	99.24
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.2
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.12
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.07
PHA02929	238	N1R/p28-like protein; Provisional	99.07
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.06
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	99.02
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.01
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.01
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.01
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.98
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.96
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.92
PHA02926	242	zinc finger-like protein; Provisional	98.91
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.89
PF14634	44	zf-RING_5: zinc-RING finger domain	98.85
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.83
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.83
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.79
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.7
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	98.7
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.67
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.62
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.61
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.52
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.52
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.51
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.51
KOG4439	901	consensus RNA polymerase II transcription terminat	98.5
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.5
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.49
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.45
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.45
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.44
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.42
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.39
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.35
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.34
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.18
KOG0383	696	consensus Predicted helicase [General function pre	98.17
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	98.14
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.06
PRK04914	956	ATP-dependent helicase HepA; Validated	98.03
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.98
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.95
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.91
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	97.9
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.88
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	97.85
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	97.85
PRK13766	773	Hef nuclease; Provisional	97.85
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	97.74
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.73
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	97.73
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.68
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.65
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.57
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	97.54
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.53
COG5152	259	Uncharacterized conserved protein, contains RING a	97.49
KOG2660	331	consensus Locus-specific chromosome binding protei	97.39
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.35
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.35
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.35
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.35
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.28
PF04641	260	Rtf2: Rtf2 RING-finger	97.23
KOG4739	233	consensus Uncharacterized protein involved in syna	97.17
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.12
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.12
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	97.11
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	97.11
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	97.1
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	96.96
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.95
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.92
KOG0825	1134	consensus PHD Zn-finger protein [General function	96.9
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.89
PTZ00110	545	helicase; Provisional	96.81
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.81
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.77
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	96.77
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.73
COG5219	1525	Uncharacterized conserved protein, contains RING Z	96.73
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	96.7
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	96.63
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	96.57
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	96.57
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	96.55
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	96.5
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.24
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.24
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	96.2
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.17
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	96.16
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	96.16
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	96.1
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	96.09
PRK05298	652	excinuclease ABC subunit B; Provisional	96.03
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.03
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	96.03
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.98
KOG4445	368	consensus Uncharacterized conserved protein, conta	95.95
KOG0334	997	consensus RNA helicase [RNA processing and modific	95.87
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.85
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	95.77
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.77
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	95.73
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	95.67
PHA02558	501	uvsW UvsW helicase; Provisional	95.6
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.56
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	95.54
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	95.52
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	95.5
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	95.45
KOG3002	299	consensus Zn finger protein [General function pred	95.24
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.21
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	95.18
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	95.16
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	95.01
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	94.98
PTZ00424	401	helicase 45; Provisional	94.84
PHA03096	284	p28-like protein; Provisional	94.76
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	94.67
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	94.64
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	94.6
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	94.49
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	94.35
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	94.25
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	94.19
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	94.17
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	94.15
smart00490	82	HELICc helicase superfamily c-terminal domain.	93.98
PRK12904	830	preprotein translocase subunit SecA; Reviewed	93.95
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	93.89
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	93.87
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	93.8
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	93.68
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	93.58
PRK13107	908	preprotein translocase subunit SecA; Reviewed	93.56
KOG4367	699	consensus Predicted Zn-finger protein [Function un	93.42
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	93.42
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	93.39
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	93.38
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	93.31
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	93.26
KOG0354	746	consensus DEAD-box like helicase [General function	92.93
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	92.87
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	92.86
PRK09200	790	preprotein translocase subunit SecA; Reviewed	92.56
PHA02825	162	LAP/PHD finger-like protein; Provisional	92.48
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	92.47
PF11496	297	HDA2-3: Class II histone deacetylase complex subun	92.39
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	92.06
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	92.04
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	91.9
PHA02862	156	5L protein; Provisional	91.77
KOG0327	397	consensus Translation initiation factor 4F, helica	91.75
KOG2231	669	consensus Predicted E3 ubiquitin ligase [Posttrans	91.48
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	91.37
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	90.9
KOG3113	293	consensus Uncharacterized conserved protein [Funct	90.8
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	90.52
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	90.23
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	90.12
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	89.85
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	89.67
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	89.39
KOG3899	381	consensus Uncharacterized conserved protein [Funct	89.12
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	88.89
KOG3039	303	consensus Uncharacterized conserved protein [Funct	88.43
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	88.12
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	88.11
KOG1940	276	consensus Zn-finger protein [General function pred	88.0
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	87.58
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	87.5
COG5109	396	Uncharacterized conserved protein, contains RING Z	87.43
KOG1123	776	consensus RNA polymerase II transcription initiati	87.41
PRK10689	1147	transcription-repair coupling factor; Provisional	86.33
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	86.28
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	85.82
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	85.03
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	84.73
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	84.1
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	84.05
KOG0343	758	consensus RNA Helicase [RNA processing and modific	83.73
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	83.37
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	83.35
PRK13767	876	ATP-dependent helicase; Provisional	82.74
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	82.64
KOG0347	731	consensus RNA helicase [RNA processing and modific	82.57
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	82.2
cd03028	90	GRX_PICOT_like Glutaredoxin (GRX) family, PKC-inte	81.98
KOG4284	980	consensus DEAD box protein [Transcription]	81.91
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	81.9
PLN02189	1040	cellulose synthase	80.98

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=99.93  E-value=1.6e-26  Score=197.71  Aligned_cols=156  Identities=23%  Similarity=0.381  Sum_probs=122.5

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccCccccCCCCCCCC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPH  102 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~~~~~~~~~~  102 (210)
                      +..+|.+|.++..+ ++.+.|.|.||.-|+.++++..+.      +....||+|...++.+.-.....       ...+.
T Consensus       535 ~~~~C~lc~d~aed-~i~s~ChH~FCrlCi~eyv~~f~~------~~nvtCP~C~i~LsiDlse~ale-------k~~l~  600 (791)
T KOG1002|consen  535 GEVECGLCHDPAED-YIESSCHHKFCRLCIKEYVESFME------NNNVTCPVCHIGLSIDLSEPALE-------KTDLK  600 (791)
T ss_pred             CceeecccCChhhh-hHhhhhhHHHHHHHHHHHHHhhhc------ccCCCCccccccccccccchhhh-------hcchh
Confidence            45689999999887 599999999999999999876542      44589999999887762111110       00111


Q ss_pred             CCCCcccccCCcee-cCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchh
Q 028376          103 GVQDCEKGEESFTV-QGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSAN  181 (210)
Q Consensus       103 ~~~~~~~~~~~~~~-~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~  181 (210)
                      +.+... ....+.+ .+..||||+||++.|..+++.+...|+|||||||+|||+|+..|.+.|+.++.++|+|.      
T Consensus       601 ~Fk~sS-IlnRinm~~~qsSTKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs------  673 (791)
T KOG1002|consen  601 GFKASS-ILNRINMDDWQSSTKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMS------  673 (791)
T ss_pred             hhhhHH-HhhhcchhhhcchhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCC------
Confidence            111100 0111221 56889999999999999999999999999999999999999999999999999999977      


Q ss_pred             hHhhhHHHHHHhhcCCCCC
Q 028376          182 LQHRNALQKELTRHMPSSQ  200 (210)
Q Consensus       182 ~~~R~~~l~~F~~~~p~~~  200 (210)
                      +++|.++|+.|.+ ||++.
T Consensus       674 ~~ardatik~F~n-d~~c~  691 (791)
T KOG1002|consen  674 PAARDATIKYFKN-DIDCR  691 (791)
T ss_pred             hHHHHHHHHHhcc-CCCeE
Confidence            9999999999998 88875

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=99.60  E-value=3.3e-16  Score=142.46  Aligned_cols=146  Identities=21%  Similarity=0.319  Sum_probs=113.3

Q ss_pred             HHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccCcccc
Q 028376           15 RIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDK   94 (210)
Q Consensus        15 ~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~~   94 (210)
                      ++..+...  ..|++|.+ .. ..+++.|||.||.+|+...++.         .....||.||..+...++......+..
T Consensus       447 ~i~~l~~~--~~c~ic~~-~~-~~~it~c~h~~c~~c~~~~i~~---------~~~~~~~~cr~~l~~~~l~s~~~~~~~  513 (674)
T KOG1001|consen  447 LIVDLSVS--HWCHICCD-LD-SFFITRCGHDFCVECLKKSIQQ---------SENAPCPLCRNVLKEKKLLSANPLPSI  513 (674)
T ss_pred             HHHHHhhc--cccccccc-cc-cceeecccchHHHHHHHhcccc---------ccCCCCcHHHHHHHHHHHhhcccccch
Confidence            45555544  89999999 44 4699999999999999998765         223389999998877766533222111


Q ss_pred             CCCCCCCCCCCCcccccCCceecCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCC
Q 028376           95 SCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGEN  174 (210)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m  174 (210)
                      ..+                  .. ..|+||.++++.|........ .|+||||||+.+|++++..|...|+.|.+|+|.|
T Consensus       514 ~~~------------------~~-~~s~ki~~~~~~l~~~~~s~~-~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~  573 (674)
T KOG1001|consen  514 IND------------------LL-PESSKIYAFLKILQAKEMSEQ-PKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEM  573 (674)
T ss_pred             hhh------------------cc-chhhhhHHHHHHHhhccCCCC-CceeeehhHHHHHHHhhhhhhhcccccchhhhhh
Confidence            100                  00 168999999999985554444 6999999999999999999999999999999996


Q ss_pred             CCCcchhhHhhhHHHHHHhhcCCCCC
Q 028376          175 HKLPSANLQHRNALQKELTRHMPSSQ  200 (210)
Q Consensus       175 ~~~~~~~~~~R~~~l~~F~~~~p~~~  200 (210)
                      .      .++|.+++..|.. +|++.
T Consensus       574 ~------~~~r~~s~~~~~~-~~~~~  592 (674)
T KOG1001|consen  574 L------MKIRTKSFTDFPC-DPLVT  592 (674)
T ss_pred             H------HHHHHhhhccccc-CccHH
Confidence            6      9999999999994 87754

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=99.43  E-value=2.6e-13  Score=122.21  Aligned_cols=78  Identities=21%  Similarity=0.376  Sum_probs=71.9

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      --|.|+..|-..|.+++.+  ++|+|||||||.||||++..|...|++|+|+||+.+      ...|+..|++|++    
T Consensus       758 mdSgK~r~L~~LLp~~k~~--G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTq------V~~RQ~lId~Fn~----  825 (941)
T KOG0389|consen  758 MDSGKCRKLKELLPKIKKK--GDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQ------VNDRQDLIDEFNT----  825 (941)
T ss_pred             hhhhhHhHHHHHHHHHhhc--CCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCcc------chHHHHHHHhhcc----
Confidence            4589999999999999865  699999999999999999999999999999999999      9999999999999    


Q ss_pred             CCCccccccccC
Q 028376          199 SQSQSLFKCYYS  210 (210)
Q Consensus       199 ~~~~~~~~~~~~  210 (210)
                        ..|+|.|+.|
T Consensus       826 --d~difVFLLS  835 (941)
T KOG0389|consen  826 --DKDIFVFLLS  835 (941)
T ss_pred             --CCceEEEEEe
Confidence              7778877765

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=99.24  E-value=6.8e-12  Score=117.85  Aligned_cols=124  Identities=30%  Similarity=0.514  Sum_probs=100.6

Q ss_pred             HHHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccCccc
Q 028376           14 HRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQD   93 (210)
Q Consensus        14 ~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~   93 (210)
                      .+...+...+...|.+|.+.+.....+..|||.+|..|...|...           ...||.|.                
T Consensus      1143 ~~~y~~~~~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~-----------~s~~~~~k---------------- 1195 (1394)
T KOG0298|consen 1143 DVRYLMNLSGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYA-----------SSRCPICK---------------- 1195 (1394)
T ss_pred             hHHHHHHhhcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHH-----------hccCcchh----------------
Confidence            344445556667999999999865789999999999999999644           44799886                


Q ss_pred             cCCCCCCCCCCCCcccccCCceecCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376           94 KSCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE  173 (210)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~  173 (210)
                                           ...+.+++||.++...+++++.+++.+|+||||||+..||.++.++..|||.+.+..|+
T Consensus      1196 ---------------------si~~dfg~kI~~v~~~il~iK~k~~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~t 1254 (1394)
T KOG0298|consen 1196 ---------------------SIKGDFGTKIDSVVIAILYIKFKNEQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGET 1254 (1394)
T ss_pred             ---------------------hhhhhhccCchhHHHHHHHHhccCcCceEEEEEehHHHHHHHHHHHHhhhhHhhhccCC
Confidence                                 02356789999999999999999999999999999999999999999999999776654


Q ss_pred             CCCCcchhhHhhhHHHHHHhh
Q 028376          174 NHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       174 m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      -         .-...+..|.+
T Consensus      1255 ~---------d~~dc~~~fk~ 1266 (1394)
T KOG0298|consen 1255 E---------DFDDCIICFKS 1266 (1394)
T ss_pred             c---------chhhhhhhccc
Confidence            2         34455555554

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.20  E-value=1.9e-11  Score=94.46  Aligned_cols=71  Identities=21%  Similarity=0.453  Sum_probs=52.5

Q ss_pred             hcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccc-----cCCCccccccCCcccccCCCeEEcc
Q 028376           18 SLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDN-----KVKNEWVMCPTCRQRTDIGNIAYAD   89 (210)
Q Consensus        18 ~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~-----~~~~~~~~CP~Cr~~~~~~~l~~~~   89 (210)
                      .+...+..+|+||++.+.+ +++++|||.||..|+..|+........     ........||+||..+...+++.+.
T Consensus        12 ~~~~~~~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiy   87 (193)
T PLN03208         12 LVDSGGDFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIY   87 (193)
T ss_pred             eccCCCccCCccCCCcCCC-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEee
Confidence            3455677899999999887 589999999999999999754221100     0023457899999999988887443

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.12  E-value=4.7e-11  Score=93.98  Aligned_cols=59  Identities=22%  Similarity=0.586  Sum_probs=50.8

Q ss_pred             CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376           21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA   88 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~   88 (210)
                      +...++|.||++...+ ++++.|||+||-.|+.+|++-        ......||+|+..+..+.|+-+
T Consensus        44 ~~~~FdCNICLd~akd-PVvTlCGHLFCWpClyqWl~~--------~~~~~~cPVCK~~Vs~~~vvPl  102 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKD-PVVTLCGHLFCWPCLYQWLQT--------RPNSKECPVCKAEVSIDTVVPL  102 (230)
T ss_pred             CCCceeeeeeccccCC-CEEeecccceehHHHHHHHhh--------cCCCeeCCccccccccceEEee
Confidence            5667899999999987 599999999999999999865        3556689999999999988743

>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]

Probab=99.07  E-value=6.6e-11  Score=95.80  Aligned_cols=56  Identities=25%  Similarity=0.644  Sum_probs=47.3

Q ss_pred             CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376           21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA   88 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~   88 (210)
                      ...+..|.+|++...+ +..++|||+||-.|+..|.           +....||.||..+.+++++..
T Consensus       236 ~~a~~kC~LCLe~~~~-pSaTpCGHiFCWsCI~~w~-----------~ek~eCPlCR~~~~pskvi~L  291 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSN-PSATPCGHIFCWSCILEWC-----------SEKAECPLCREKFQPSKVICL  291 (293)
T ss_pred             CCCCCceEEEecCCCC-CCcCcCcchHHHHHHHHHH-----------ccccCCCcccccCCCcceeee
Confidence            3455789999999887 4899999999999999996           445569999999999987643

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.07  E-value=1.1e-10  Score=93.74  Aligned_cols=53  Identities=26%  Similarity=0.649  Sum_probs=41.2

Q ss_pred             hcCCCCccccccccccccCC-------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           18 SLSKADEETCPICQEKLGNQ-------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        18 ~l~~~~~~~C~iC~~~~~~~-------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ......+.+|+||++.+..+       +++++|||.||..|+.+|++           ....||+||.++.
T Consensus       168 ~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-----------~~~tCPlCR~~~~  227 (238)
T PHA02929        168 LYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-----------EKNTCPVCRTPFI  227 (238)
T ss_pred             hhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-----------cCCCCCCCCCEee
Confidence            33445678999999986542       25679999999999999963           3458999999764

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.06  E-value=6.5e-11  Score=89.46  Aligned_cols=57  Identities=28%  Similarity=0.694  Sum_probs=45.4

Q ss_pred             cCCCCccccccccccccCCC-eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           19 LSKADEETCPICQEKLGNQK-MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        19 l~~~~~~~C~iC~~~~~~~~-~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .+.+....||||++.+.... +-+.|||+||..|++..+           ....+||+|++.+...+++
T Consensus       126 ~~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~al-----------k~~~~CP~C~kkIt~k~~~  183 (187)
T KOG0320|consen  126 LRKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDAL-----------KNTNKCPTCRKKITHKQFH  183 (187)
T ss_pred             cccccccCCCceecchhhccccccccchhHHHHHHHHHH-----------HhCCCCCCcccccchhhhe
Confidence            34455678999999887653 459999999999999986           3456899999988777654

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=99.02  E-value=5.6e-10  Score=100.94  Aligned_cols=72  Identities=18%  Similarity=0.333  Sum_probs=64.2

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      ..|.|+.-|=+.|..+.++  +.|++||||||.||||++..+.-.|+.|.|+||+++      ...|.++|+.|+. +|+
T Consensus       468 ~nSGKm~vLDkLL~~Lk~~--GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~------~eeR~~aI~~fn~-~~s  538 (971)
T KOG0385|consen  468 TNSGKMLVLDKLLPKLKEQ--GHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTS------HEEREDAIEAFNA-PPS  538 (971)
T ss_pred             hcCcceehHHHHHHHHHhC--CCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCC------cHHHHHHHHhcCC-CCc
Confidence            3478988888888887754  899999999999999999999999999999999988      9999999999998 554


Q ss_pred             C
Q 028376          199 S  199 (210)
Q Consensus       199 ~  199 (210)
                      .
T Consensus       539 ~  539 (971)
T KOG0385|consen  539 E  539 (971)
T ss_pred             c
Confidence            3

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A

Probab=99.01  E-value=1e-10  Score=69.95  Aligned_cols=42  Identities=31%  Similarity=0.796  Sum_probs=33.3

Q ss_pred             ccccccccccc--CCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376           25 ETCPICQEKLG--NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR   77 (210)
Q Consensus        25 ~~C~iC~~~~~--~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr   77 (210)
                      .+|+||++.+.  ...+.++|||.||.+|+.+|++.           ...||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~-----------~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR-----------NNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH-----------SSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh-----------CCcCCccC
Confidence            37999999884  34577899999999999999854           24999997

...

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A

Probab=99.01  E-value=1.3e-10  Score=67.62  Aligned_cols=39  Identities=38%  Similarity=0.917  Sum_probs=31.7

Q ss_pred             cccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        27 C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      |+||.+.+.++.++++|||.||.+|+.+|++.           ...||.|
T Consensus         1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~-----------~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEK-----------NPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHC-----------TSB-TTT
T ss_pred             CCCCCCcccCcCEECCCCCchhHHHHHHHHHC-----------cCCCcCC
Confidence            89999999885478999999999999999743           3689987

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A

Probab=99.01  E-value=1.5e-10  Score=68.31  Aligned_cols=42  Identities=29%  Similarity=0.819  Sum_probs=29.4

Q ss_pred             cccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        27 C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      |+||++.+.+ ++.++|||.||..|+..+.+..       ......||.|
T Consensus         1 CpiC~~~~~~-Pv~l~CGH~FC~~Cl~~~~~~~-------~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD-PVSLPCGHSFCRSCLERLWKEP-------SGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS-EEE-SSSSEEEHHHHHHHHCCS-------SSST---SSS
T ss_pred             CCccchhhCC-ccccCCcCHHHHHHHHHHHHcc-------CCcCCCCcCC
Confidence            8999999998 5999999999999999995321       1222689987

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=98.98  E-value=1.9e-10  Score=70.64  Aligned_cols=46  Identities=35%  Similarity=0.858  Sum_probs=37.7

Q ss_pred             ccccccccccccCCCeecCCCCc-chHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           24 EETCPICQEKLGNQKMVFQCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      +..|.||.+...+ .++++|||. ||..|+.+|..           ....||.||+++.
T Consensus         2 ~~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~-----------~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD-VVLLPCGHLCFCEECAERLLK-----------RKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHH-----------TTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc-eEEeCCCChHHHHHHhHHhcc-----------cCCCCCcCChhhc
Confidence            5689999998876 588999999 99999999963           3468999999874

...

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.96  E-value=2.2e-09  Score=102.16  Aligned_cols=68  Identities=18%  Similarity=0.336  Sum_probs=62.5

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      .|.|+..|.+.|..+..  .+.|+||||||+.+|++|+..|...|++|++++|+++      ..+|.++|+.|+.+
T Consensus       469 ~SgKl~lLdkLL~~Lk~--~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts------~~eRq~~Id~Fn~~  536 (1033)
T PLN03142        469 NSGKMVLLDKLLPKLKE--RDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTG------GEDRDASIDAFNKP  536 (1033)
T ss_pred             hhhHHHHHHHHHHHHHh--cCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCC------HHHHHHHHHHhccc
Confidence            47899998888888764  5899999999999999999999999999999999987      99999999999873

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.92  E-value=8.2e-10  Score=64.90  Aligned_cols=41  Identities=37%  Similarity=0.914  Sum_probs=34.7

Q ss_pred             cccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        27 C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      |+||.+.+..+..+++|||.||..|+.+|++.         .....||.|
T Consensus         1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~---------~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLEN---------SGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHH---------TSSSBTTTT
T ss_pred             CCcCCccccCCCEEecCCCcchHHHHHHHHHh---------cCCccCCcC
Confidence            89999998875448999999999999999864         345679987

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. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....

>PHA02926 zinc finger-like protein; Provisional

Probab=98.91  E-value=1.3e-09  Score=85.45  Aligned_cols=61  Identities=25%  Similarity=0.511  Sum_probs=44.9

Q ss_pred             HHhcCCCCccccccccccccC--------CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           16 IESLSKADEETCPICQEKLGN--------QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        16 ~~~l~~~~~~~C~iC~~~~~~--------~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      -.+.+.+.+.+|+||++..-.        .+++.+|+|.||..|+..|.+...  .   .+....||.||..+.
T Consensus       162 e~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~--~---~~~~rsCPiCR~~f~  230 (242)
T PHA02926        162 EDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR--E---TGASDNCPICRTRFR  230 (242)
T ss_pred             HHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc--c---cCcCCcCCCCcceee
Confidence            345556777999999987522        157889999999999999965321  1   245668999999764

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.89  E-value=1.5e-09  Score=94.19  Aligned_cols=69  Identities=20%  Similarity=0.464  Sum_probs=53.7

Q ss_pred             HHHHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEcc
Q 028376           13 KHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYAD   89 (210)
Q Consensus        13 ~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~   89 (210)
                      +++...+... +..||||++++.. +..+.|||+||..|+-+++....      ......||+|+..+...+|..+.
T Consensus       176 e~i~qv~~~t-~~~CPICL~~~~~-p~~t~CGHiFC~~CiLqy~~~s~------~~~~~~CPiC~s~I~~kdl~pv~  244 (513)
T KOG2164|consen  176 EDIFQVYGST-DMQCPICLEPPSV-PVRTNCGHIFCGPCILQYWNYSA------IKGPCSCPICRSTITLKDLLPVF  244 (513)
T ss_pred             HHhhhhhcCc-CCcCCcccCCCCc-ccccccCceeeHHHHHHHHhhhc------ccCCccCCchhhhccccceeeee
Confidence            3444444444 7899999999887 48888999999999999976531      46778999999999998886443

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.85  E-value=2.4e-09  Score=63.95  Aligned_cols=42  Identities=38%  Similarity=0.891  Sum_probs=34.3

Q ss_pred             ccccccccc--cCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376           26 TCPICQEKL--GNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ   78 (210)
Q Consensus        26 ~C~iC~~~~--~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~   78 (210)
                      .|++|.+.+  ..++.+++|||+||..|+..+.           .....||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-----------~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-----------GKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-----------CCCCCCcCCCC
Confidence            489998887  3346899999999999999883           34578999985

>smart00504 Ubox Modified RING finger domain

Probab=98.83  E-value=3.4e-09  Score=68.11  Aligned_cols=51  Identities=14%  Similarity=0.123  Sum_probs=43.0

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEE
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAY   87 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~   87 (210)
                      ..|+||.+.+.+ +++++|||+||..|+.+|+..           ...||.|+.++...++..
T Consensus         2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~-----------~~~cP~~~~~~~~~~l~~   52 (63)
T smart00504        2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLS-----------HGTDPVTGQPLTHEDLIP   52 (63)
T ss_pred             cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHH-----------CCCCCCCcCCCChhhcee
Confidence            479999999988 589999999999999999743           348999999987776553

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.83  E-value=9.5e-09  Score=93.37  Aligned_cols=68  Identities=21%  Similarity=0.336  Sum_probs=64.2

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHH-hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFI-ANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~-~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..|-|++.|.++|..|.++  ++|+++|||-..||++|+..|. .+|+.|+|+||+.+      .+.|...|++|+.
T Consensus       527 k~sGKm~vl~~ll~~W~kq--g~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~------~~~R~~lVd~Fne  595 (923)
T KOG0387|consen  527 KRSGKMKVLAKLLKDWKKQ--GDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTP------AALRQKLVDRFNE  595 (923)
T ss_pred             hhcchHHHHHHHHHHHhhC--CCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCc------cchhhHHHHhhcC
Confidence            4589999999999999966  6799999999999999999999 79999999999998      9999999999998

>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Probab=98.79  E-value=4.2e-09  Score=62.40  Aligned_cols=44  Identities=32%  Similarity=0.810  Sum_probs=35.1

Q ss_pred             ccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376           26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR   79 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~   79 (210)
                      .|+||.+.+.....+.+|||.||..|+..|++.          ....||.|+..
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~----------~~~~Cp~C~~~   44 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKS----------GKNTCPLCRTP   44 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHh----------CcCCCCCCCCc
Confidence            599999988654455669999999999999643          34579999875

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A

Probab=98.70  E-value=9.5e-09  Score=60.73  Aligned_cols=40  Identities=35%  Similarity=0.980  Sum_probs=22.2

Q ss_pred             cccccccccC---CCeecCCCCcchHhhHHHHHHHhhhccccCCCcccccc
Q 028376           27 CPICQEKLGN---QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCP   74 (210)
Q Consensus        27 C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP   74 (210)
                      |+||.+ +.+   ++++++|||+||.+|+.++....       .....+||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~-------~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKS-------DRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH--------S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcC-------CCCeeeCc
Confidence            899988 543   35889999999999999997642       13566776

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=98.70  E-value=4.3e-08  Score=92.29  Aligned_cols=68  Identities=21%  Similarity=0.378  Sum_probs=62.2

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      .-.-|+++|.=+|+.+...  +.+++||+|-+.|||+++.+|.-+|..|+|+||+..      ..+|+..+++||.
T Consensus      1257 yDcGKLQtLAiLLqQLk~e--ghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~------vEqRQaLmerFNa 1324 (1958)
T KOG0391|consen 1257 YDCGKLQTLAILLQQLKSE--GHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTS------VEQRQALMERFNA 1324 (1958)
T ss_pred             cccchHHHHHHHHHHHHhc--CceEEehhHHHHHHHHHHHHHhhcceEEEEecCCcc------HHHHHHHHHHhcC
Confidence            3478999988888877754  899999999999999999999999999999999977      9999999999998

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.67  E-value=3.6e-08  Score=93.08  Aligned_cols=68  Identities=15%  Similarity=0.231  Sum_probs=56.5

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      |-|+=-|=++|-+++  ..+.|||||||-+.|||||+..|...|++|-|+||+++      ...|.++|++|+.++
T Consensus       682 SGKlVLLDKLL~rLk--~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvr------gelRq~AIDhFnap~  749 (1373)
T KOG0384|consen  682 SGKLVLLDKLLPRLK--EGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVR------GELRQQAIDHFNAPD  749 (1373)
T ss_pred             cCcEEeHHHHHHHHh--cCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcc------hHHHHHHHHhccCCC
Confidence            455433333444444  45899999999999999999999999999999999988      999999999999744

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.62  E-value=3.2e-08  Score=65.58  Aligned_cols=44  Identities=30%  Similarity=0.706  Sum_probs=33.2

Q ss_pred             CccccccccccccCC------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376           23 DEETCPICQEKLGNQ------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR   77 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr   77 (210)
                      .+..|+||++++.++            ....+|||.|+..|+.+|++           ....||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~-----------~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLK-----------QNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHT-----------TSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHh-----------cCCcCCCCC
Confidence            345699999988332            25568999999999999973           334999997

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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.61  E-value=2.6e-08  Score=85.76  Aligned_cols=51  Identities=22%  Similarity=0.563  Sum_probs=41.9

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ....|+||.+.+..+ ++++|||.||..|+..++..           ...||.|+..+....+
T Consensus        25 ~~l~C~IC~d~~~~P-vitpCgH~FCs~CI~~~l~~-----------~~~CP~Cr~~~~~~~L   75 (397)
T TIGR00599        25 TSLRCHICKDFFDVP-VLTSCSHTFCSLCIRRCLSN-----------QPKCPLCRAEDQESKL   75 (397)
T ss_pred             cccCCCcCchhhhCc-cCCCCCCchhHHHHHHHHhC-----------CCCCCCCCCccccccC
Confidence            457999999999874 78999999999999999632           3479999998765544

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

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]

Probab=98.52  E-value=3e-08  Score=89.96  Aligned_cols=54  Identities=20%  Similarity=0.599  Sum_probs=45.8

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEE
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAY   87 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~   87 (210)
                      +...|+.|...+.+ .+++.|||+||..|+...++.          ...+||.|..+|..+|+..
T Consensus       642 ~~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~et----------RqRKCP~Cn~aFganDv~~  695 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYET----------RQRKCPKCNAAFGANDVHR  695 (698)
T ss_pred             hceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHH----------hcCCCCCCCCCCCcccccc
Confidence            34579999988877 599999999999999998754          4568999999999998753

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.52  E-value=8.2e-08  Score=79.60  Aligned_cols=53  Identities=28%  Similarity=0.582  Sum_probs=39.5

Q ss_pred             Ccccccccccc--ccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           23 DEETCPICQEK--LGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        23 ~~~~C~iC~~~--~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ++..||+|...  +...  ..+.+|||.||..|+..++          ..+...||.|+.++...++
T Consensus         2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~----------~~~~~~CP~C~~~lrk~~f   58 (309)
T TIGR00570         2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLF----------VRGSGSCPECDTPLRKNNF   58 (309)
T ss_pred             CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHh----------cCCCCCCCCCCCccchhhc
Confidence            45789999773  3322  1334899999999999985          2345689999999988764

All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>smart00184 RING Ring finger

Probab=98.51  E-value=8.3e-08  Score=54.75  Aligned_cols=39  Identities=38%  Similarity=0.931  Sum_probs=31.6

Q ss_pred             cccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        27 C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      |+||.+.... .++++|||.||..|+..|++.          ....||.|
T Consensus         1 C~iC~~~~~~-~~~~~C~H~~c~~C~~~~~~~----------~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKD-PVVLPCGHTFCRSCIRKWLKS----------GNNTCPIC   39 (39)
T ss_pred             CCcCccCCCC-cEEecCCChHHHHHHHHHHHh----------CcCCCCCC
Confidence            7899988654 588999999999999999741          33579987

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

Probab=98.51  E-value=8.4e-08  Score=80.35  Aligned_cols=51  Identities=25%  Similarity=0.644  Sum_probs=41.5

Q ss_pred             CCCccccccccccccCC------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           21 KADEETCPICQEKLGNQ------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ..++..|.||++.+..+            +..++|||+++..|++.|+|++           .+||.||.++-.
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-----------QTCPICr~p~if  346 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-----------QTCPICRRPVIF  346 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-----------cCCCcccCcccc
Confidence            56788999999985432            3678999999999999998763           489999998543

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=98.50  E-value=3e-07  Score=82.97  Aligned_cols=70  Identities=20%  Similarity=0.349  Sum_probs=65.4

Q ss_pred             CCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          118 GSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       118 ~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..+|+|+..+++.+..+ .....+|+||-|||+++|+++...|+..|+.|..++|...      .++|+.+++.|+.
T Consensus       725 ~r~S~Ki~~~l~~le~i-~~~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~------vK~Rq~iv~~FN~  794 (901)
T KOG4439|consen  725 DRPSCKIAMVLEILETI-LTSSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVL------VKDRQEIVDEFNQ  794 (901)
T ss_pred             ccchhHHHHHHHHHHHH-hhcccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccc------hhHHHHHHHHHHh
Confidence            36899999999999998 5677899999999999999999999999999999999966      9999999999996

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.50  E-value=5.3e-08  Score=78.20  Aligned_cols=53  Identities=25%  Similarity=0.662  Sum_probs=42.9

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHH-HHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFA-MTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~-~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ..+..|++|.+.+.. +..++|||+||..|+.. |..          .....||.||+...+.++
T Consensus       213 ~~d~kC~lC~e~~~~-ps~t~CgHlFC~~Cl~~~~t~----------~k~~~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEV-PSCTPCGHLFCLSCLLISWTK----------KKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCC-cccccccchhhHHHHHHHHHh----------hccccCchhhhhccchhh
Confidence            446789999999987 58999999999999998 632          233459999998877765

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]

Probab=98.49  E-value=3.7e-08  Score=81.51  Aligned_cols=50  Identities=26%  Similarity=0.524  Sum_probs=43.4

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ...|.||.+.+.. +++++|+|.||.-||..++           ...+.||.|+.++...++
T Consensus        23 lLRC~IC~eyf~i-p~itpCsHtfCSlCIR~~L-----------~~~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   23 LLRCGICFEYFNI-PMITPCSHTFCSLCIRKFL-----------SYKPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHHhHHHHHhcC-ceeccccchHHHHHHHHHh-----------ccCCCCCceecccchhhh
Confidence            3589999999987 5999999999999999995           567899999998876654

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

Probab=98.45  E-value=7.4e-08  Score=78.23  Aligned_cols=49  Identities=24%  Similarity=0.552  Sum_probs=41.8

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ....|.||.+.+.. +.+++|||.||.-||..++           +..+.||+||......
T Consensus        24 s~lrC~IC~~~i~i-p~~TtCgHtFCslCIR~hL-----------~~qp~CP~Cr~~~~es   72 (391)
T COG5432          24 SMLRCRICDCRISI-PCETTCGHTFCSLCIRRHL-----------GTQPFCPVCREDPCES   72 (391)
T ss_pred             hHHHhhhhhheeec-ceecccccchhHHHHHHHh-----------cCCCCCccccccHHhh
Confidence            34679999999987 4999999999999999995           6678999999976544

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger

Probab=98.45  E-value=1.6e-07  Score=63.16  Aligned_cols=53  Identities=21%  Similarity=0.495  Sum_probs=39.0

Q ss_pred             CccccccccccccC------------CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGN------------QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~------------~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ++..|+||...+..            +.+.-.|+|.|+..||.+|++..        .....||+||++....
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~--------~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQ--------SSKGQCPMCRQPWKFK   84 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccc--------cCCCCCCCcCCeeeeC
Confidence            36778888766542            12556899999999999998652        3356999999986543

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.44  E-value=5.9e-07  Score=85.17  Aligned_cols=74  Identities=16%  Similarity=0.321  Sum_probs=61.3

Q ss_pred             CCCchHHHHHHHHHHHHhc------------CCCCcEEEEcchHHHHHHHHHHHHhC---CceEEEeeCCCCCCcchhhH
Q 028376          119 SYGTKIEAVTRRILWIKST------------DPKAKILVFSSWNDVLDVLEHAFIAN---NITCIKMKGENHKLPSANLQ  183 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~------------~~~~K~iVFSQf~~~L~li~~~L~~~---gi~~~~~~G~m~~~~~~~~~  183 (210)
                      ..+.|+.||.+.|.+=--.            -.+.+++||.||.+|||+++..|-+.   .+.|.|+||+.+      +.
T Consensus      1307 ~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVp------p~ 1380 (1549)
T KOG0392|consen 1307 QHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVP------PG 1380 (1549)
T ss_pred             hhchhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCC------cH
Confidence            3578999998888643221            13579999999999999999999864   567889999999      99


Q ss_pred             hhhHHHHHHhhcCCCC
Q 028376          184 HRNALQKELTRHMPSS  199 (210)
Q Consensus       184 ~R~~~l~~F~~~~p~~  199 (210)
                      +|.+++++||+ ||+.
T Consensus      1381 ~R~kiV~~FN~-DptI 1395 (1549)
T KOG0392|consen 1381 DRQKIVERFNE-DPTI 1395 (1549)
T ss_pred             HHHHHHHHhcC-CCce
Confidence            99999999999 8864

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=98.42  E-value=5.5e-08  Score=61.61  Aligned_cols=49  Identities=27%  Similarity=0.584  Sum_probs=24.8

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      ..|++|.+.+..+..+..|.|+||..|+...+           +  ..||+|+.|....|+.
T Consensus         8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~-----------~--~~CPvC~~Paw~qD~~   56 (65)
T PF14835_consen    8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCI-----------G--SECPVCHTPAWIQDIQ   56 (65)
T ss_dssp             TS-SSS-S--SS-B---SSS--B-TTTGGGGT-----------T--TB-SSS--B-S-SS--
T ss_pred             cCCcHHHHHhcCCceeccCccHHHHHHhHHhc-----------C--CCCCCcCChHHHHHHH
Confidence            57999999998876689999999999997653           1  2599999988777654

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis

Probab=98.39  E-value=2.6e-07  Score=61.26  Aligned_cols=53  Identities=23%  Similarity=0.259  Sum_probs=40.3

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +.+.|+|+.+.+.+ ++++++||.|++.|+..|++          .....||.|+.++...+++
T Consensus         3 ~~f~CpIt~~lM~d-PVi~~~G~tyer~~I~~~l~----------~~~~~~P~t~~~l~~~~l~   55 (73)
T PF04564_consen    3 DEFLCPITGELMRD-PVILPSGHTYERSAIERWLE----------QNGGTDPFTRQPLSESDLI   55 (73)
T ss_dssp             GGGB-TTTSSB-SS-EEEETTSEEEEHHHHHHHHC----------TTSSB-TTT-SB-SGGGSE
T ss_pred             cccCCcCcCcHhhC-ceeCCcCCEEcHHHHHHHHH----------cCCCCCCCCCCcCCcccce
Confidence            45789999999998 49999999999999999973          3467899999998877664

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.35  E-value=2.1e-07  Score=76.07  Aligned_cols=49  Identities=22%  Similarity=0.400  Sum_probs=40.0

Q ss_pred             ccccccccccccC--CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           24 EETCPICQEKLGN--QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        24 ~~~C~iC~~~~~~--~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ..+|.||+..+..  ..+++||.|.|+..|+++|+-          +....||+||.++.+
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~----------~y~~~CPvCrt~iPP  373 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL----------GYSNKCPVCRTAIPP  373 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHh----------hhcccCCccCCCCCC
Confidence            4789999988753  357899999999999999972          456789999998753

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=98.34  E-value=1.8e-06  Score=81.72  Aligned_cols=69  Identities=23%  Similarity=0.387  Sum_probs=61.1

Q ss_pred             CCC-chHHHHHHHH-HHHHhcCCCC--cEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          119 SYG-TKIEAVTRRI-LWIKSTDPKA--KILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       119 ~~S-sKi~al~~~L-~~~~~~~~~~--K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..| .|+..+.+.| ..+..+  +.  |+||||||+.+|++++..|...++.|++++|+++      .++|...|++|+.
T Consensus       688 ~~s~~k~~~l~~ll~~~~~~~--~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~------~~~r~~~i~~f~~  759 (866)
T COG0553         688 QLSKGKLQALDELLLDKLLEE--GHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTP------AKRRQELIDRFNA  759 (866)
T ss_pred             hccchHHHHHHHHHHHHHHhh--cccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCC------hhhHHHHHHHhhc
Confidence            345 8999999888 555544  45  9999999999999999999999999999999987      9999999999998


Q ss_pred             c
Q 028376          195 H  195 (210)
Q Consensus       195 ~  195 (210)
                      +
T Consensus       760 ~  760 (866)
T COG0553         760 D  760 (866)
T ss_pred             C
Confidence            4

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.26  E-value=6.1e-07  Score=75.62  Aligned_cols=48  Identities=25%  Similarity=0.597  Sum_probs=39.0

Q ss_pred             ccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           26 TCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        26 ~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .|.||++.+...  ..++||.|.|+..|++.|+.+          .+..||+|+..+...
T Consensus       231 ~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~----------~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  231 TCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQ----------TRTFCPVCKRDIRTD  280 (348)
T ss_pred             eEEEeecccccCCeeeEecCCCchhhccchhhHhh----------cCccCCCCCCcCCCC
Confidence            899999988653  467999999999999999854          345699999966543

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.22  E-value=2.4e-07  Score=56.36  Aligned_cols=47  Identities=30%  Similarity=0.781  Sum_probs=37.7

Q ss_pred             ccccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           24 EETCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      +.+|.||.+.+.+ .++..||| ..|.+|-.+..          ......||.||+++.
T Consensus         7 ~dECTICye~pvd-sVlYtCGHMCmCy~Cg~rl~----------~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVD-SVLYTCGHMCMCYACGLRLK----------KALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcch-HHHHHcchHHhHHHHHHHHH----------HccCCcCcchhhHHH
Confidence            4899999998887 48899999 57889987763          235568999999864

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.18  E-value=5.3e-06  Score=76.69  Aligned_cols=71  Identities=17%  Similarity=0.298  Sum_probs=63.2

Q ss_pred             cCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          117 QGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       117 ~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      .+..|.|+..|+..+..++ +...+|+++-|.++.+|++++..++..|..++|+||+|+      .++|++++++|+.
T Consensus       573 ~~~ks~kl~~L~~ll~~~~-ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~------~~qRq~~vd~FN~  643 (776)
T KOG0390|consen  573 DGSKSGKLLVLVFLLEVIR-EKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTS------IKQRQKLVDTFND  643 (776)
T ss_pred             cchhhhHHHHHHHHHHHHh-hhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCc------hHHHHHHHHhccC
Confidence            4556889999998875554 457899999999999999999999999999999999987      9999999999997

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=98.17  E-value=8.6e-07  Score=81.02  Aligned_cols=66  Identities=20%  Similarity=0.271  Sum_probs=59.6

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      .+.|..-|...+++++.  .+++++||||++.+|||++..+...| .|.|+||+..      -..|+++|++|+-
T Consensus       613 ~~~k~~~l~~~~~~l~~--~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~------~~~rq~ai~~~n~  678 (696)
T KOG0383|consen  613 ASGKLTLLLKMLKKLKS--SGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPIT------GPERQAAIDRFNA  678 (696)
T ss_pred             HHHHHHHHHHHHHHHHh--cchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCcc------chhhhhhccccCC
Confidence            36778888888888874  48999999999999999999999999 9999999966      8999999999996

>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.14  E-value=1.5e-06  Score=70.31  Aligned_cols=51  Identities=24%  Similarity=0.665  Sum_probs=41.4

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ..+.+|++|.+.+..|-++.+|||+||..|+...+..         .....||.|+.+..
T Consensus       237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~---------~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLW---------DASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCCCeeeccccceeehhhhhhhhcc---------hhhcccCccCCCCc
Confidence            4668999999999887666779999999999987532         44579999988654

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.06  E-value=2.1e-06  Score=77.68  Aligned_cols=52  Identities=31%  Similarity=0.546  Sum_probs=42.4

Q ss_pred             CCccccccccccccCC----CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           22 ADEETCPICQEKLGNQ----KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~----~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      ..+..|+||.+.+...    +..++|||+||..|+..|+++.           ..||.||..+....
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-----------qtCP~CR~~~~~~~  344 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-----------QTCPTCRTVLYDYV  344 (543)
T ss_pred             hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-----------CcCCcchhhhhccc
Confidence            3467899999998774    5889999999999999998763           48999999554443

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.03  E-value=2e-05  Score=75.30  Aligned_cols=67  Identities=13%  Similarity=0.132  Sum_probs=59.4

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHH-HhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAF-IANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L-~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      ....|++.|++.|...    .+.|+|||+++..+.+.|...| ...||+...|+|+|+      ..+|.++++.|+.+
T Consensus       476 ~~d~Ki~~L~~~L~~~----~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s------~~eR~~~~~~F~~~  543 (956)
T PRK04914        476 NFDPRVEWLIDFLKSH----RSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMS------IIERDRAAAYFADE  543 (956)
T ss_pred             ccCHHHHHHHHHHHhc----CCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCC------HHHHHHHHHHHhcC
Confidence            4568999999888653    4789999999999999999999 578999999999977      99999999999973

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.98  E-value=3.1e-06  Score=70.06  Aligned_cols=45  Identities=38%  Similarity=0.844  Sum_probs=38.5

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ   78 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~   78 (210)
                      .+...|+||++.+..+ .+++|||.||..|+..+..           ....||.||.
T Consensus        11 ~~~~~C~iC~~~~~~p-~~l~C~H~~c~~C~~~~~~-----------~~~~Cp~cr~   55 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP-VLLPCGHNFCRACLTRSWE-----------GPLSCPVCRP   55 (386)
T ss_pred             cccccChhhHHHhhcC-ccccccchHhHHHHHHhcC-----------CCcCCcccCC
Confidence            4667999999999986 8999999999999999842           3468999993

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.95  E-value=3.6e-06  Score=68.95  Aligned_cols=50  Identities=26%  Similarity=0.482  Sum_probs=41.8

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      -..+|+||+....-+ +.+.|+|.||..|++-..          ......|++||.++..+
T Consensus         6 ~~~eC~IC~nt~n~P-v~l~C~HkFCyiCiKGsy----------~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    6 KKKECLICYNTGNCP-VNLYCFHKFCYICIKGSY----------KNDKKTCAVCRFPIDST   55 (324)
T ss_pred             cCCcceeeeccCCcC-ccccccchhhhhhhcchh----------hcCCCCCceecCCCCcc
Confidence            356899999988764 899999999999999764          35566899999999765

>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.91  E-value=5.5e-06  Score=69.49  Aligned_cols=49  Identities=27%  Similarity=0.644  Sum_probs=40.1

Q ss_pred             CCccccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      +...+|.||+....+ .+++||.| ..|.+|.+.+.           -....||+||.++..
T Consensus       288 ~~gkeCVIClse~rd-t~vLPCRHLCLCs~Ca~~Lr-----------~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRD-TVVLPCRHLCLCSGCAKSLR-----------YQTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcc-eEEecchhhehhHhHHHHHH-----------HhhcCCCccccchHh
Confidence            345789999999987 59999999 67999999872           344589999998754

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=97.90  E-value=3.8e-05  Score=67.38  Aligned_cols=69  Identities=25%  Similarity=0.303  Sum_probs=62.4

Q ss_pred             CCchHHHHHHHHHH--HHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          120 YGTKIEAVTRRILW--IKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       120 ~SsKi~al~~~L~~--~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      -..|+.++.+.|..  +.-..++.|.|||-....+||-|+..+.+.|++++|+||+.+      ...|...++.|+.
T Consensus       470 giaK~~av~eyi~~~~~l~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~------s~~R~ll~qsFQ~  540 (689)
T KOG1000|consen  470 GIAKAAAVCEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTP------SHRRTLLCQSFQT  540 (689)
T ss_pred             cccccHHHHHHHHhCcccccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCC------chhHHHHHHHhcc
Confidence            46899999999986  122467899999999999999999999999999999999988      9999999999998

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.88  E-value=6.3e-06  Score=71.16  Aligned_cols=66  Identities=23%  Similarity=0.385  Sum_probs=47.7

Q ss_pred             hhhccCchHHHHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376            5 VVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus         5 ~~~~~~~~~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ++..+..............+++|.+|...+.. ++.++|||.||..|+.+.+           .....||.||..+..
T Consensus        65 ~~~~~~~~~~~s~~~~~~sef~c~vc~~~l~~-pv~tpcghs~c~~Cl~r~l-----------d~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   65 TMADSTPKALLSGPEEIRSEFECCVCSRALYP-PVVTPCGHSFCLECLDRSL-----------DQETECPLCRDELVE  130 (398)
T ss_pred             hhhhhhhhhhhccCccccchhhhhhhHhhcCC-CccccccccccHHHHHHHh-----------ccCCCCccccccccc
Confidence            33333333333333334677899999998887 5889999999999988853           466789999998763

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]

Probab=97.85  E-value=7.6e-05  Score=65.59  Aligned_cols=82  Identities=10%  Similarity=0.179  Sum_probs=70.0

Q ss_pred             CCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEE-EeeCC--CCCCcchhhHhhhHHHHHHhh
Q 028376          118 GSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCI-KMKGE--NHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       118 ~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~-~~~G~--m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      +....|++.|.+.|.+..+..++.++|||++|.+..+.|-..|...|+.-. +|-|.  ......|+.++...+|+.|++
T Consensus       344 ~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~  423 (542)
T COG1111         344 GVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRK  423 (542)
T ss_pred             cCCCccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhc
Confidence            445689999999999999888899999999999999999999999999876 88773  223366889999999999998


Q ss_pred             cCCCC
Q 028376          195 HMPSS  199 (210)
Q Consensus       195 ~~p~~  199 (210)
                      ++=++
T Consensus       424 Ge~nV  428 (542)
T COG1111         424 GEYNV  428 (542)
T ss_pred             CCceE
Confidence            65443

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=97.85  E-value=3.2e-05  Score=72.35  Aligned_cols=68  Identities=19%  Similarity=0.212  Sum_probs=59.0

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh----------------------CCceEEEeeCCCCC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA----------------------NNITCIKMKGENHK  176 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~----------------------~gi~~~~~~G~m~~  176 (210)
                      ..|.|+--|++.|..--  +=++|.|||||-...|++|+.+|..                      .|..|.|+||+.. 
T Consensus      1123 ~~SgKmiLLleIL~mce--eIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~- 1199 (1567)
T KOG1015|consen 1123 EHSGKMILLLEILRMCE--EIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTT- 1199 (1567)
T ss_pred             hcCcceehHHHHHHHHH--HhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCccc-
Confidence            35889988888887543  4589999999999999999999974                      3778999999987 


Q ss_pred             CcchhhHhhhHHHHHHhh
Q 028376          177 LPSANLQHRNALQKELTR  194 (210)
Q Consensus       177 ~~~~~~~~R~~~l~~F~~  194 (210)
                           ..+|.+..++|+.
T Consensus      1200 -----s~~R~k~~~~FNd 1212 (1567)
T KOG1015|consen 1200 -----SQSRKKWAEEFND 1212 (1567)
T ss_pred             -----HHHHHHHHHHhcC
Confidence                 9999999999986

>PRK13766 Hef nuclease; Provisional

Probab=97.85  E-value=9.2e-05  Score=69.81  Aligned_cols=79  Identities=13%  Similarity=0.220  Sum_probs=66.4

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCC--cchhhHhhhHHHHHHhhcC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKL--PSANLQHRNALQKELTRHM  196 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~--~~~~~~~R~~~l~~F~~~~  196 (210)
                      ....|++.|.+.|.++....++.|+|||+++..+.+.|...|...|+++.++.|..+..  ..|+..+|.+++++|+++.
T Consensus       344 ~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~  423 (773)
T PRK13766        344 IEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGE  423 (773)
T ss_pred             cCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCC
Confidence            44689999999999888777899999999999999999999999999999999972110  1244899999999999854


Q ss_pred             C
Q 028376          197 P  197 (210)
Q Consensus       197 p  197 (210)
                      .
T Consensus       424 ~  424 (773)
T PRK13766        424 F  424 (773)
T ss_pred             C
Confidence            3

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=97.74  E-value=4.8e-05  Score=69.34  Aligned_cols=68  Identities=12%  Similarity=0.316  Sum_probs=61.8

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      .-|.|+..|=+.|.+++..  +.++++|-|-|.|+++++..|.-.|..|+|+||+-.      ...|..++..|+.
T Consensus      1025 tdSgKL~~LDeLL~kLkae--gHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk------~~dRrd~vrDwQ~ 1092 (1185)
T KOG0388|consen 1025 TDSGKLVVLDELLPKLKAE--GHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSK------ASDRRDVVRDWQA 1092 (1185)
T ss_pred             ccccceeeHHHHHHHhhcC--CceEEehhHHHHHHHHHHHHHHhhccceEEecCcch------hhHHHHHHhhccC
Confidence            4578888888888888754  899999999999999999999999999999999966      9999999999997

>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.73  E-value=1.3e-05  Score=69.77  Aligned_cols=49  Identities=22%  Similarity=0.575  Sum_probs=38.1

Q ss_pred             CccccccccccccCC----------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           23 DEETCPICQEKLGNQ----------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~----------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ....|+||+.++.-.                .+++||.|+|+..|+.+|.+.          ..-.||+||.++.
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~----------ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT----------YKLICPVCRCPLP  634 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh----------hcccCCccCCCCC
Confidence            346899998876421                367899999999999999642          3347999999875

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=97.73  E-value=5.3e-05  Score=71.10  Aligned_cols=70  Identities=20%  Similarity=0.370  Sum_probs=63.0

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      -+-|.+-|-+.|-++++.  +.+++.|+|-|.++++++..|.-.++.|+|+||+..      ..+|...|+.|+.+|.
T Consensus       708 ~sGKfELLDRiLPKLkat--gHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK------~~eRg~ll~~FN~Pds  777 (1157)
T KOG0386|consen  708 VSGKFELLDRILPKLKAT--GHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTK------VEERGDLLEIFNAPDS  777 (1157)
T ss_pred             hccHHHHHHhhhHHHHhc--CcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcc------hhhHHHHHHHhcCCCC
Confidence            367888888888888765  899999999999999999999999999999999988      9999999999997553

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.68  E-value=1.8e-05  Score=48.58  Aligned_cols=49  Identities=27%  Similarity=0.636  Sum_probs=37.5

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ....|..|...-.. .++++|||++|..|+.-.             .-..||.|.+++...++
T Consensus         6 ~~~~~~~~~~~~~~-~~~~pCgH~I~~~~f~~~-------------rYngCPfC~~~~~~~~~   54 (55)
T PF14447_consen    6 PEQPCVFCGFVGTK-GTVLPCGHLICDNCFPGE-------------RYNGCPFCGTPFEFDDP   54 (55)
T ss_pred             cceeEEEccccccc-cccccccceeeccccChh-------------hccCCCCCCCcccCCCC
Confidence            44578888776555 589999999999998743             33479999999887653

>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.65  E-value=5.7e-06  Score=69.15  Aligned_cols=51  Identities=27%  Similarity=0.568  Sum_probs=40.2

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ....|+||++.+......-.|+|.||.+||...+.          .+...||.||+.+...
T Consensus        42 ~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r----------~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   42 IQVICPICLSLLKKTMTTKECLHRFCFDCIWKALR----------SGNNECPTCRKKLVSK   92 (381)
T ss_pred             hhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHH----------hcCCCCchHHhhcccc
Confidence            45689999998876545569999999999988753          4556899999976543

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]

Probab=97.57  E-value=0.0001  Score=62.69  Aligned_cols=53  Identities=30%  Similarity=0.610  Sum_probs=41.5

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      ...|-||.+.-.+ ..+-+|||+.|..|+..|-+.         .....||.||..+.-.+-+
T Consensus       369 FeLCKICaendKd-vkIEPCGHLlCt~CLa~WQ~s---------d~gq~CPFCRcEIKGte~v  421 (563)
T KOG1785|consen  369 FELCKICAENDKD-VKIEPCGHLLCTSCLAAWQDS---------DEGQTCPFCRCEIKGTEPV  421 (563)
T ss_pred             HHHHHHhhccCCC-cccccccchHHHHHHHhhccc---------CCCCCCCceeeEeccccce
Confidence            3579999886555 577899999999999999422         3366899999998776543

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Probab=97.54  E-value=0.00071  Score=48.69  Aligned_cols=67  Identities=19%  Similarity=0.288  Sum_probs=59.9

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      .|++.+.+.+.....  ++.|+|||......++.+...|...++++..+.|+++      ...|..+++.|++++
T Consensus        12 ~k~~~i~~~i~~~~~--~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~------~~~~~~~~~~f~~~~   78 (131)
T cd00079          12 EKLEALLELLKEHLK--KGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGS------QEEREEVLKDFREGE   78 (131)
T ss_pred             HHHHHHHHHHHhccc--CCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCC------HHHHHHHHHHHHcCC
Confidence            688888888877543  5789999999999999999999999999999999977      999999999999855

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C

Probab=97.53  E-value=3.8e-05  Score=48.20  Aligned_cols=45  Identities=20%  Similarity=0.380  Sum_probs=30.4

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccC
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPT   75 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~   75 (210)
                      .-...|||...++.+|..-..|||+|..+.+.+++.         ......||+
T Consensus         9 ~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~---------~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQ---------RNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCT---------TTS-EE-SC
T ss_pred             EeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHH---------hcCCCCCCC
Confidence            345789999999998655579999999999999972         256778998

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=97.49  E-value=3.8e-05  Score=59.43  Aligned_cols=45  Identities=27%  Similarity=0.583  Sum_probs=37.1

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      .+.|.||...... ++++.|||.||..|...-.           .....|.+|.+..
T Consensus       196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y-----------~kg~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKY-----------QKGDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccc-hhhhhcchhHHHHHHHHHh-----------ccCCcceecchhh
Confidence            4689999999887 5999999999999987653           4456899998754

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]

Probab=97.39  E-value=5.9e-05  Score=62.73  Aligned_cols=51  Identities=25%  Similarity=0.508  Sum_probs=43.3

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .....|.+|...+.++..++-|-|.||..|+..+++.           ...||.|...+...
T Consensus        13 n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~-----------~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEE-----------SKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhccceeecchhHHHHHHHHHHHHHHHHHHH-----------hccCCccceeccCc
Confidence            4557899999999987788999999999999999854           45899999877654

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A

Probab=97.35  E-value=0.00012  Score=47.98  Aligned_cols=59  Identities=19%  Similarity=0.244  Sum_probs=26.5

Q ss_pred             cccccccccccc-CC--C-ee---cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           24 EETCPICQEKLG-NQ--K-MV---FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        24 ~~~C~iC~~~~~-~~--~-~~---~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ..+|+||..... ..  + .+   ..|++.|+..|+.+|+.........-.-....||.|+.++..
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            468999987643 21  1 11   389999999999999976432211001223469999998754

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.35  E-value=0.00013  Score=61.87  Aligned_cols=60  Identities=25%  Similarity=0.587  Sum_probs=42.7

Q ss_pred             hcCCCCccccccccccccCC-------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           18 SLSKADEETCPICQEKLGNQ-------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        18 ~l~~~~~~~C~iC~~~~~~~-------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      .++...+..|.||++.+...       +++.+|.|.||..|+..|-..  .+..  ......||.||....
T Consensus       155 a~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~--~q~~--~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  155 ALQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQA--TQFE--SKTSKSCPFCRVPSS  221 (344)
T ss_pred             CcCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhh--hccc--cccccCCCcccCccc
Confidence            45557788999999877543       244789999999999999422  1110  233678999999754

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.35  E-value=0.00023  Score=56.92  Aligned_cols=65  Identities=14%  Similarity=0.262  Sum_probs=51.2

Q ss_pred             HhcCCCCccccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccCcc
Q 028376           17 ESLSKADEETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQ   92 (210)
Q Consensus        17 ~~l~~~~~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~   92 (210)
                      ..+..+....||+|.+.+.+.   .++.+|||++|.+|++.++.           .-..||+|..++...+|+......
T Consensus       214 ~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-----------~D~v~pv~d~plkdrdiI~LqrGG  281 (303)
T KOG3039|consen  214 KLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-----------KDMVDPVTDKPLKDRDIIGLQRGG  281 (303)
T ss_pred             hhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-----------ccccccCCCCcCcccceEeeeccc
Confidence            334455678899999988763   36779999999999999963           334799999999999998776543

>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B

Probab=97.35  E-value=0.00013  Score=43.83  Aligned_cols=44  Identities=36%  Similarity=0.878  Sum_probs=21.6

Q ss_pred             cccccccccCCC-ee--cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           27 CPICQEKLGNQK-MV--FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        27 C~iC~~~~~~~~-~~--~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      ||+|.+.+.... -+  =+||+-+|..|+....+          .....||.||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~----------~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE----------NEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTT----------SS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHh----------ccCCCCCCCCCCC
Confidence            789988874321 22  37899999999998842          3466899999875

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.28  E-value=8.4e-05  Score=60.90  Aligned_cols=45  Identities=29%  Similarity=0.620  Sum_probs=37.3

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      +.|.||..++.. ++++.|||.||..|....+           ....+|++|.+.+.
T Consensus       242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~-----------qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPY-----------QKGEKCYVCSQQTH  286 (313)
T ss_pred             cccccccccccc-chhhcCCceeehhhhcccc-----------ccCCcceecccccc
Confidence            469999999988 5999999999999987763           34468999988654

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.23  E-value=0.00042  Score=57.10  Aligned_cols=57  Identities=18%  Similarity=0.364  Sum_probs=44.3

Q ss_pred             CCccccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccC
Q 028376           22 ADEETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADD   90 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~   90 (210)
                      ...+.|||....+...   ..+.+|||+|+..++.++           . ....||+|..++...+|+.+.+
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-----------k-~~~~Cp~c~~~f~~~DiI~Lnp  170 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-----------K-KSKKCPVCGKPFTEEDIIPLNP  170 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-----------c-ccccccccCCccccCCEEEecC
Confidence            3457899998887532   355699999999999987           1 2336999999999999886654

>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=97.17  E-value=0.00017  Score=57.71  Aligned_cols=48  Identities=23%  Similarity=0.497  Sum_probs=34.7

Q ss_pred             cccccccccc-cCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           25 ETCPICQEKL-GNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        25 ~~C~iC~~~~-~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .-|..|..-. .++..+|.|+|+||..|....             ....||.|++++...++
T Consensus         4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~-------------~~~~C~lCkk~ir~i~l   52 (233)
T KOG4739|consen    4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS-------------SPDVCPLCKKSIRIIQL   52 (233)
T ss_pred             EEeccccccCCCCceeeeechhhhhhhhcccC-------------Cccccccccceeeeeec
Confidence            4577785443 344578999999999998743             22389999999766544

>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins

Probab=97.12  E-value=0.0006  Score=41.40  Aligned_cols=43  Identities=19%  Similarity=0.557  Sum_probs=31.4

Q ss_pred             ccccccccc-cCCCeecCCC-----CcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376           26 TCPICQEKL-GNQKMVFQCG-----HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR   77 (210)
Q Consensus        26 ~C~iC~~~~-~~~~~~~~Cg-----H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr   77 (210)
                      .|.||++.. ...+.+.||.     |.++..|+.+|+..         .....||+|+
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~---------~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINE---------SGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHH---------cCCCcCCCCC
Confidence            488998721 1224778995     89999999999865         3345899985

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=97.12  E-value=0.00023  Score=61.44  Aligned_cols=49  Identities=27%  Similarity=0.702  Sum_probs=37.7

Q ss_pred             CCCCccccccccccccCCC---eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           20 SKADEETCPICQEKLGNQK---MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        20 ~~~~~~~C~iC~~~~~~~~---~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      .-.+...||+|++.+....   +.+.|.|.|...|+..|-             ...||+||-...
T Consensus       171 ~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~-------------~~scpvcR~~q~  222 (493)
T KOG0804|consen  171 GLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW-------------DSSCPVCRYCQS  222 (493)
T ss_pred             CcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc-------------cCcChhhhhhcC
Confidence            3456678999998876532   446999999999999992             247999988655

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.11  E-value=0.002  Score=57.61  Aligned_cols=69  Identities=14%  Similarity=0.261  Sum_probs=62.0

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      ...|...|.+.|..+. .++..|+|||..-...-+-++..|...||+..-|+|.++      ..+|..+|+.|.++
T Consensus       322 ~~~K~~~l~~lL~~~~-~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~s------Q~eR~~~L~~FreG  390 (519)
T KOG0331|consen  322 ETAKLRKLGKLLEDIS-SDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKS------QSERDWVLKGFREG  390 (519)
T ss_pred             HHHHHHHHHHHHHHHh-ccCCCcEEEEecchhhHHHHHHHHHhcCcceeeeccccc------HHHHHHHHHhcccC
Confidence            5677778888887776 677899999999999999999999999999999999976      99999999999873

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=97.11  E-value=0.0024  Score=56.78  Aligned_cols=66  Identities=11%  Similarity=0.112  Sum_probs=59.3

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      -++|..+|++.|...    -+.-+|||.....-.+.|...|++.||..++|+|+..      ..||+.+|+.|+++
T Consensus       501 ed~k~kkL~eil~~~----~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~------qeQRe~aL~~fr~~  566 (673)
T KOG0333|consen  501 EDEKRKKLIEILESN----FDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKS------QEQRENALADFREG  566 (673)
T ss_pred             chHHHHHHHHHHHhC----CCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCcc------HHHHHHHHHHHHhc
Confidence            467888888888753    4678999999999999999999999999999999987      99999999999984

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.10  E-value=0.0001  Score=48.19  Aligned_cols=52  Identities=25%  Similarity=0.478  Sum_probs=36.8

Q ss_pred             CccccccccccccC------------CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           23 DEETCPICQEKLGN------------QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        23 ~~~~C~iC~~~~~~------------~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      .++.|.||.-++..            +.+.-.|.|.|..-|+.+|+..        ......||+||.....
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~--------~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNT--------PTSQGQCPMCRQTWQF   82 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcC--------ccccccCCcchheeEe
Confidence            34477777766542            1244589999999999999754        2445689999987643

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.96  E-value=0.00018  Score=58.32  Aligned_cols=55  Identities=16%  Similarity=0.517  Sum_probs=42.0

Q ss_pred             CCccccccccccccCC---------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           22 ADEETCPICQEKLGNQ---------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~---------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .++..|.+|...+...         ...++|+|+|+..|+.-|.-         -+....||.|...+..+..
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWci---------vGKkqtCPYCKekVdl~rm  285 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCI---------VGKKQTCPYCKEKVDLKRM  285 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhhee---------ecCCCCCchHHHHhhHhhh
Confidence            4667899997765432         24589999999999999952         3677899999988766643

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]

Probab=96.95  E-value=0.0004  Score=60.49  Aligned_cols=51  Identities=29%  Similarity=0.712  Sum_probs=41.2

Q ss_pred             CccccccccccccCCCee-cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           23 DEETCPICQEKLGNQKMV-FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~-~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .+..|++|...+.++ +. +.|||.||..|+..|.           .....||.|+..+...+.
T Consensus        20 ~~l~C~~C~~vl~~p-~~~~~cgh~fC~~C~~~~~-----------~~~~~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   20 ENLLCPICMSVLRDP-VQTTTCGHRFCAGCLLESL-----------SNHQKCPVCRQELTQAEE   71 (391)
T ss_pred             ccccCccccccccCC-CCCCCCCCcccccccchhh-----------ccCcCCcccccccchhhc
Confidence            457899999999885 66 5999999999999995           336799999887765543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.92  E-value=0.00052  Score=57.39  Aligned_cols=58  Identities=28%  Similarity=0.658  Sum_probs=43.8

Q ss_pred             CccccccccccccCCC---eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccC
Q 028376           23 DEETCPICQEKLGNQK---MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADD   90 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~---~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~   90 (210)
                      ++..||.|.+++....   .--+||-.+|.-|+..+-+.          -..+||.||+.....++.|++.
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~----------lngrcpacrr~y~denv~~~~~   73 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQN----------LNGRCPACRRKYDDENVRYVTL   73 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhh----------ccCCChHhhhhccccceeEEec
Confidence            3445999999876432   23489999999999987432          3458999999999999887653

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]

Probab=96.90  E-value=0.00019  Score=65.79  Aligned_cols=51  Identities=22%  Similarity=0.369  Sum_probs=37.7

Q ss_pred             CccccccccccccCCC--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           23 DEETCPICQEKLGNQK--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      ....|++|+..+.+..  .-.+|+|.||..|+..|.           ....+||+||..|..-.
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWs-----------R~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWS-----------RCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhh-----------hhcccCchhhhhhheee
Confidence            4456888876655432  335899999999999994           45568999999876543

>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.89  E-value=0.00049  Score=57.84  Aligned_cols=50  Identities=22%  Similarity=0.523  Sum_probs=39.7

Q ss_pred             CCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           20 SKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        20 ~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      -+.++..|+||...+.+ .+..||+|.-|..|+.+++-           ....|-.|...+.
T Consensus       418 p~sEd~lCpICyA~pi~-Avf~PC~H~SC~~CI~qHlm-----------N~k~CFfCktTv~  467 (489)
T KOG4692|consen  418 PDSEDNLCPICYAGPIN-AVFAPCSHRSCYGCITQHLM-----------NCKRCFFCKTTVI  467 (489)
T ss_pred             CCcccccCcceecccch-hhccCCCCchHHHHHHHHHh-----------cCCeeeEecceee
Confidence            35677889999887776 58999999999999999852           3447888877543

>PTZ00110 helicase; Provisional

Probab=96.81  E-value=0.0063  Score=55.35  Aligned_cols=68  Identities=16%  Similarity=0.191  Sum_probs=59.3

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..|...|.+.|..+..  +..|+|||..-....+.|...|...|++...++|.|+      ..+|..+++.|+++.
T Consensus       360 ~~k~~~L~~ll~~~~~--~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~------~~eR~~il~~F~~G~  427 (545)
T PTZ00110        360 HEKRGKLKMLLQRIMR--DGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKK------QEERTWVLNEFKTGK  427 (545)
T ss_pred             hhHHHHHHHHHHHhcc--cCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCc------HHHHHHHHHHHhcCC
Confidence            4677888877776553  5789999999999999999999999999999999977      999999999999743

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.81  E-value=0.00062  Score=57.85  Aligned_cols=47  Identities=26%  Similarity=0.470  Sum_probs=34.0

Q ss_pred             ccccccccccccC---CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376           24 EETCPICQEKLGN---QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ   78 (210)
Q Consensus        24 ~~~C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~   78 (210)
                      ...|.||.+....   -..+..|||+|+..|+..|++...        ....||.|+.
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~P--------s~R~cpic~i   53 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDP--------SNRGCPICQI   53 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCC--------ccCCCCceee
Confidence            3589999654432   134567999999999999986522        2268999984

>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.77  E-value=0.00021  Score=58.52  Aligned_cols=42  Identities=38%  Similarity=0.834  Sum_probs=34.3

Q ss_pred             ccccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           24 EETCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ...|.||++.+.+ -++++||| +-|..|-.++               ..||+||+.+.
T Consensus       300 ~~LC~ICmDaP~D-CvfLeCGHmVtCt~CGkrm---------------~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRD-CVFLECGHMVTCTKCGKRM---------------NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcc-eEEeecCcEEeehhhcccc---------------ccCchHHHHHH
Confidence            4579999999987 59999999 5688886655               38999998653

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.77  E-value=0.00092  Score=54.80  Aligned_cols=50  Identities=28%  Similarity=0.574  Sum_probs=37.3

Q ss_pred             cccccccc-ccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           26 TCPICQEK-LGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        26 ~C~iC~~~-~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .||+|... ..++   ..+-+|||..|.+|+..++.          .+...||.|...+....+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~----------~g~~~CpeC~~iLRk~nf   55 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS----------LGPAQCPECMVILRKNNF   55 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHh----------cCCCCCCcccchhhhccc
Confidence            59999543 2222   23459999999999999973          456689999998887654

>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.73  E-value=0.00062  Score=57.44  Aligned_cols=44  Identities=30%  Similarity=0.864  Sum_probs=33.5

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ...|.||.+.+.+ .+..+|||..|  |..-.            ...+.||+||..+..
T Consensus       305 p~lcVVcl~e~~~-~~fvpcGh~cc--ct~cs------------~~l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  305 PDLCVVCLDEPKS-AVFVPCGHVCC--CTLCS------------KHLPQCPVCRQRIRL  348 (355)
T ss_pred             CCceEEecCCccc-eeeecCCcEEE--chHHH------------hhCCCCchhHHHHHH
Confidence            3579999999887 58899999876  65543            234569999998754

>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=96.73  E-value=0.00075  Score=63.24  Aligned_cols=68  Identities=21%  Similarity=0.429  Sum_probs=47.7

Q ss_pred             hhhccCchHHHHHhcCC------CCcccccccccccc------CCCeecCCCCcchHhhHHHHHHHhhhccccCCCcccc
Q 028376            5 VVTISNSTKHRIESLSK------ADEETCPICQEKLG------NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVM   72 (210)
Q Consensus         5 ~~~~~~~~~~~~~~l~~------~~~~~C~iC~~~~~------~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~   72 (210)
                      +..+-.++-+.+.+.+.      ++..+|+||...+.      +.-....|.|-|+..|+-+|+..         ++...
T Consensus      1444 ~~~~ngs~~D~l~l~kkNi~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~S---------s~~s~ 1514 (1525)
T COG5219        1444 MIKKNGSFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFAS---------SARSN 1514 (1525)
T ss_pred             HHhccchHHHHHHHHHhhhhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHh---------cCCCC
Confidence            33444556666665543      46689999965543      11255689999999999999864         56679


Q ss_pred             ccCCccccc
Q 028376           73 CPTCRQRTD   81 (210)
Q Consensus        73 CP~Cr~~~~   81 (210)
                      ||.||..+.
T Consensus      1515 CPlCRseit 1523 (1525)
T COG5219        1515 CPLCRSEIT 1523 (1525)
T ss_pred             CCccccccc
Confidence            999997654

>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

Probab=96.70  E-value=0.001  Score=43.91  Aligned_cols=33  Identities=21%  Similarity=0.326  Sum_probs=26.7

Q ss_pred             eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           39 MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        39 ~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      +.-.|.|.|..-|+.+|+.           ....||++|+....
T Consensus        50 ~wG~CnHaFH~HCI~rWL~-----------Tk~~CPld~q~w~~   82 (88)
T COG5194          50 VWGVCNHAFHDHCIYRWLD-----------TKGVCPLDRQTWVL   82 (88)
T ss_pred             EEEecchHHHHHHHHHHHh-----------hCCCCCCCCceeEE
Confidence            4568999999999999973           35589999987643

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=96.63  E-value=0.0026  Score=58.97  Aligned_cols=70  Identities=24%  Similarity=0.314  Sum_probs=53.1

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC------------------CceEEEeeCCCCCCcchhh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN------------------NITCIKMKGENHKLPSANL  182 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~------------------gi~~~~~~G~m~~~~~~~~  182 (210)
                      +-|+-.+++.+.+-  ..-++|+|||||-...|++|+..|...                  ++.|+|+||+..      .
T Consensus       702 ~pk~V~~~~~~des--~~~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~------a  773 (1387)
T KOG1016|consen  702 GPKIVISLEILDES--TQIGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTS------A  773 (1387)
T ss_pred             CCceEEEEeeeccc--cccCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcc------c
Confidence            34444444444332  234799999999999999999999864                  357899999977      9


Q ss_pred             HhhhHHHHHHhhcCCCC
Q 028376          183 QHRNALQKELTRHMPSS  199 (210)
Q Consensus       183 ~~R~~~l~~F~~~~p~~  199 (210)
                      +.|.+.|++|+. .|+.
T Consensus       774 ~~rekLinqfN~-e~~l  789 (1387)
T KOG1016|consen  774 ADREKLINQFNS-EPGL  789 (1387)
T ss_pred             chHHHHHHhccC-CCCc
Confidence            999999999997 5543

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.57  E-value=0.0011  Score=56.80  Aligned_cols=54  Identities=26%  Similarity=0.618  Sum_probs=41.5

Q ss_pred             ccccccccccccCC----CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           24 EETCPICQEKLGNQ----KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        24 ~~~C~iC~~~~~~~----~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      ...||||++....+    .+.+.|||.|-.+|++.|+.+         .....||.|...-...+|.
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k---------~~~~~cp~c~~katkr~i~   61 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGK---------KTKMQCPLCSGKATKRQIR   61 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhh---------hhhhhCcccCChhHHHHHH
Confidence            46899999887643    266899999999999999853         3456899998766555543

>TIGR00603 rad25 DNA repair helicase rad25

Probab=96.57  E-value=0.0094  Score=55.69  Aligned_cols=61  Identities=20%  Similarity=0.181  Sum_probs=49.0

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..|+.++...|.+..  .++.|+|||++....++.+...|   |.++  ++|.++      ..+|.++++.|+.
T Consensus       479 p~K~~~~~~Li~~he--~~g~kiLVF~~~~~~l~~~a~~L---~~~~--I~G~ts------~~ER~~il~~Fr~  539 (732)
T TIGR00603       479 PNKFRACQFLIRFHE--QRGDKIIVFSDNVFALKEYAIKL---GKPF--IYGPTS------QQERMQILQNFQH  539 (732)
T ss_pred             hHHHHHHHHHHHHHh--hcCCeEEEEeCCHHHHHHHHHHc---CCce--EECCCC------HHHHHHHHHHHHh
Confidence            467777776665432  46899999999999988888877   4554  789977      9999999999985

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=96.55  E-value=0.012  Score=51.66  Aligned_cols=67  Identities=13%  Similarity=0.131  Sum_probs=56.3

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+..|.+.+.    .....|+|||..-....+.+...|...|+....+.|.|+      .++|..+++.|+++..
T Consensus       240 ~~k~~~l~~ll~----~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~------~~~R~~~l~~F~~g~~  306 (423)
T PRK04837        240 EEKMRLLQTLIE----EEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVA------QKKRLRILEEFTRGDL  306 (423)
T ss_pred             HHHHHHHHHHHH----hcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCC------hhHHHHHHHHHHcCCC
Confidence            356666655543    345689999999999999999999999999999999977      9999999999998554

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=96.50  E-value=0.017  Score=50.89  Aligned_cols=57  Identities=21%  Similarity=0.233  Sum_probs=51.0

Q ss_pred             hcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          136 STDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       136 ~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      ......++|||..-....+.+...|...|+....++|.|+      ..+|..+++.|+.+..+
T Consensus       241 ~~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~------~~~R~~~l~~f~~G~~~  297 (434)
T PRK11192        241 KQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMV------QAKRNEAIKRLTDGRVN  297 (434)
T ss_pred             hcCCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCC------HHHHHHHHHHHhCCCCc
Confidence            3445789999999999999999999999999999999977      99999999999985544

>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.24  E-value=0.0037  Score=52.33  Aligned_cols=47  Identities=34%  Similarity=0.832  Sum_probs=38.0

Q ss_pred             ccccccccccccCC-----CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           24 EETCPICQEKLGNQ-----KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        24 ~~~C~iC~~~~~~~-----~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      ...|-||.+.+...     +.++.|||.+|..|+..++          ......||.||.+.
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~----------~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLL----------GNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHh----------cCceeeccCCCCcc
Confidence            46799998776532     5778899999999999986          35667889999985

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=96.24  E-value=0.0034  Score=52.82  Aligned_cols=51  Identities=25%  Similarity=0.615  Sum_probs=39.9

Q ss_pred             CCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           20 SKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        20 ~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      .+++...|.||.+.+.- ..++||+|..|.-|..+.-.         ......||.||...
T Consensus        57 tDEen~~C~ICA~~~TY-s~~~PC~H~~CH~Ca~RlRA---------LY~~K~C~~CrTE~  107 (493)
T COG5236          57 TDEENMNCQICAGSTTY-SARYPCGHQICHACAVRLRA---------LYMQKGCPLCRTET  107 (493)
T ss_pred             cccccceeEEecCCceE-EEeccCCchHHHHHHHHHHH---------HHhccCCCcccccc
Confidence            35667889999998876 48899999999999887621         24556899999853

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=96.20  E-value=0.025  Score=50.23  Aligned_cols=66  Identities=14%  Similarity=0.273  Sum_probs=56.7

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..|+++|.+.|..    .+..++|||..-....+.+...|...|+....|+|.|+      ..+|..+++.|.++.
T Consensus       227 ~~k~~~l~~ll~~----~~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~------~~eR~~~l~~F~~g~  292 (460)
T PRK11776        227 DERLPALQRLLLH----HQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLE------QRDRDQVLVRFANRS  292 (460)
T ss_pred             HHHHHHHHHHHHh----cCCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCC------HHHHHHHHHHHHcCC
Confidence            3477777766643    34678999999999999999999999999999999977      999999999999743

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=96.17  E-value=0.0028  Score=52.28  Aligned_cols=43  Identities=33%  Similarity=0.719  Sum_probs=35.4

Q ss_pred             cccccccccccCCCeec-CCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376           25 ETCPICQEKLGNQKMVF-QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ   78 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~-~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~   78 (210)
                      ..|+.|...+.++ +.+ .|+|.||.+|+...+          ......||.|..
T Consensus       275 LkCplc~~Llrnp-~kT~cC~~~fc~eci~~al----------~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP-MKTPCCGHTFCDECIGTAL----------LDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCc-ccCccccchHHHHHHhhhh----------hhccccCCCccc
Confidence            6799999988885 666 789999999999765          345678999976

>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

Probab=96.16  E-value=0.029  Score=50.71  Aligned_cols=65  Identities=11%  Similarity=0.240  Sum_probs=55.9

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      .|++.|...|..    ....++|||..=....+.+...|...|+....+.|.|+      ..+|.++++.|+++.
T Consensus       259 ~k~~~L~~ll~~----~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~------q~~R~~~l~~F~~g~  323 (513)
T COG0513         259 EKLELLLKLLKD----EDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLP------QEERDRALEKFKDGE  323 (513)
T ss_pred             HHHHHHHHHHhc----CCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCC------HHHHHHHHHHHHcCC
Confidence            477777766653    33448999999999999999999999999999999977      999999999999643

>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans

Probab=96.16  E-value=0.0066  Score=51.96  Aligned_cols=66  Identities=26%  Similarity=0.453  Sum_probs=43.1

Q ss_pred             CCccccccccccccCCCeec----------------CCCCcc-----hHhhHHHHHHHhhhccc--cCCCccccccCCcc
Q 028376           22 ADEETCPICQEKLGNQKMVF----------------QCGHFT-----CCKCFFAMTEQRLIHDN--KVKNEWVMCPTCRQ   78 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~----------------~CgH~f-----C~~C~~~~~~~~~~~~~--~~~~~~~~CP~Cr~   78 (210)
                      .+.+.|..|+....+--+.-                +|+..+     |.+|+.+|+.....+..  .+..++..||+||+
T Consensus       269 ~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa  348 (358)
T PF10272_consen  269 QELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRA  348 (358)
T ss_pred             cccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcc
Confidence            56678999987544311222                333333     78999999864332211  23577889999999


Q ss_pred             cccCCCeEE
Q 028376           79 RTDIGNIAY   87 (210)
Q Consensus        79 ~~~~~~l~~   87 (210)
                      .+...||.+
T Consensus       349 ~FCilDV~~  357 (358)
T PF10272_consen  349 KFCILDVCY  357 (358)
T ss_pred             cceeeeeec
Confidence            999888754

They are purported to be transmembrane protein-precursors but their function is unknown.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=96.10  E-value=0.029  Score=51.41  Aligned_cols=67  Identities=10%  Similarity=0.146  Sum_probs=56.1

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+..|+..|.    .....|+|||..-....+.|...|...|+....|+|.|+      ..+|..+++.|.++..
T Consensus       242 ~~k~~~L~~ll~----~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~------~~eR~~il~~Fr~G~~  308 (572)
T PRK04537        242 EEKQTLLLGLLS----RSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVP------QKKRESLLNRFQKGQL  308 (572)
T ss_pred             HHHHHHHHHHHh----cccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCC------HHHHHHHHHHHHcCCC
Confidence            345665555443    345789999999999999999999999999999999977      9999999999997543

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=96.09  E-value=0.0012  Score=52.81  Aligned_cols=54  Identities=20%  Similarity=0.502  Sum_probs=37.4

Q ss_pred             CCCccccccccccc-cCCC---eecC-CCCcchHhhHHHHHHHhhhccccCCCcccccc--CCcccccCCC
Q 028376           21 KADEETCPICQEKL-GNQK---MVFQ-CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCP--TCRQRTDIGN   84 (210)
Q Consensus        21 ~~~~~~C~iC~~~~-~~~~---~~~~-CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP--~Cr~~~~~~~   84 (210)
                      +..+..||+|.... -+|.   .+-| |.|..|.+|+.+++.          .+...||  .|.+-++...
T Consensus         7 ~~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs----------~GpAqCP~~gC~kILRK~k   67 (314)
T COG5220           7 EMEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS----------RGPAQCPYKGCGKILRKIK   67 (314)
T ss_pred             hhhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc----------CCCCCCCCccHHHHHHHhc
Confidence            34557899996432 2222   2235 999999999999973          4567898  7988766543

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.03  E-value=0.039  Score=51.34  Aligned_cols=69  Identities=10%  Similarity=0.062  Sum_probs=61.8

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      +..+++.|++.|..+..  .+.++|||+.-....+.+...|..+|++...++|.|+      ..+|..+++.|..+.
T Consensus       428 ~~~q~~~L~~~L~~~~~--~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~------~~~R~~~l~~f~~g~  496 (652)
T PRK05298        428 TKGQVDDLLSEIRKRVA--KGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDID------TLERVEIIRDLRLGE  496 (652)
T ss_pred             ccccHHHHHHHHHHHHh--CCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCC------HHHHHHHHHHHHcCC
Confidence            45678999999998874  4789999999999999999999999999999999977      999999999998744

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=96.03  E-value=0.0026  Score=54.24  Aligned_cols=48  Identities=29%  Similarity=0.670  Sum_probs=37.3

Q ss_pred             ccccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           24 EETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        24 ~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      ...|..|.+.+.-.   .--+||.|+|+..|+.+++++         +....||.||+-.
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---------n~~rsCP~Crklr  415 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---------NGTRSCPNCRKLR  415 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---------CCCCCCccHHHHH
Confidence            35699998766432   245899999999999999865         5677999999643

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=96.03  E-value=0.036  Score=49.49  Aligned_cols=66  Identities=14%  Similarity=0.296  Sum_probs=55.1

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      +.|...|.+.+.    ..+..|+|||..-....+.+...|...|+....+.|.|+      ..+|..+++.|+++.
T Consensus       320 ~~k~~~l~~ll~----~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~------~~~R~~~~~~Fr~G~  385 (475)
T PRK01297        320 SDKYKLLYNLVT----QNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVP------QHKRIKTLEGFREGK  385 (475)
T ss_pred             hhHHHHHHHHHH----hcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCC------HHHHHHHHHHHhCCC
Confidence            456655554443    345679999999999999999999999999999999977      999999999998744

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.98  E-value=0.0032  Score=58.53  Aligned_cols=41  Identities=27%  Similarity=0.597  Sum_probs=35.0

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR   79 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~   79 (210)
                      ..|..|...+.-|.+...|||.|+..|+..              ....||.|+..
T Consensus       841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e~--------------~~~~CP~C~~e  881 (933)
T KOG2114|consen  841 SKCSACEGTLDLPFVHFLCGHSYHQHCLED--------------KEDKCPKCLPE  881 (933)
T ss_pred             eeecccCCccccceeeeecccHHHHHhhcc--------------CcccCCccchh
Confidence            579999999988888899999999999972              34589999873

>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]

Probab=95.95  E-value=0.0031  Score=51.98  Aligned_cols=73  Identities=23%  Similarity=0.453  Sum_probs=47.8

Q ss_pred             chHHHHHhcCCCC--ccccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccc---c---------CCCcccccc
Q 028376           11 STKHRIESLSKAD--EETCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDN---K---------VKNEWVMCP   74 (210)
Q Consensus        11 ~~~~~~~~l~~~~--~~~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~---~---------~~~~~~~CP   74 (210)
                      +.+..-+.|.+.+  ...|.||+.-+...  .++|.|.|.|+..|+.+++........   .         .......||
T Consensus       100 lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcp  179 (368)
T KOG4445|consen  100 LIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCP  179 (368)
T ss_pred             HHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Confidence            3344444455543  46899998877654  367899999999999999865432110   0         023344599


Q ss_pred             CCcccccCC
Q 028376           75 TCRQRTDIG   83 (210)
Q Consensus        75 ~Cr~~~~~~   83 (210)
                      +||.++...
T Consensus       180 Vcre~i~~e  188 (368)
T KOG4445|consen  180 VCRERIKIE  188 (368)
T ss_pred             Hhhhhcccc
Confidence            999987654

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=95.87  E-value=0.02  Score=54.57  Aligned_cols=66  Identities=12%  Similarity=0.159  Sum_probs=61.7

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      -..|+..|+++|..+..   +.|+|||++=..-++.+-..|.+.|+.+..+.|..+      ...|...|+.|++
T Consensus       596 e~eKf~kL~eLl~e~~e---~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~------q~dR~sti~dfK~  661 (997)
T KOG0334|consen  596 ENEKFLKLLELLGERYE---DGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVD------QHDRSSTIEDFKN  661 (997)
T ss_pred             chHHHHHHHHHHHHHhh---cCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCc------hHHHHhHHHHHhc
Confidence            57999999999987764   789999999999999999999999999999999977      9999999999998

>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.85  E-value=0.0067  Score=52.13  Aligned_cols=52  Identities=19%  Similarity=0.406  Sum_probs=36.0

Q ss_pred             CccccccccccccC--CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376           23 DEETCPICQEKLGN--QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR   77 (210)
Q Consensus        23 ~~~~C~iC~~~~~~--~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr   77 (210)
                      ....|.||.+....  ....+||+|+||..|+..+++-... .|  ......||.+.
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~-eg--~v~~l~Cp~~~  236 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQ-EG--QVSCLKCPDPK  236 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhh-cc--eeeeecCCCCC
Confidence            34679999876542  2366899999999999999865432 22  34556787543

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=95.77  E-value=0.053  Score=50.44  Aligned_cols=70  Identities=11%  Similarity=0.088  Sum_probs=62.2

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      .+..+++.|++.|..+..  .+.++|||+.-....+.+...|...||+...++|.|+      ..+|.++++.|..+.
T Consensus       423 ~~~~qi~~Ll~eI~~~~~--~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~------~~eR~~~l~~fr~G~  492 (655)
T TIGR00631       423 PTDGQVDDLLSEIRQRVA--RNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEID------TLERVEIIRDLRLGE  492 (655)
T ss_pred             eccchHHHHHHHHHHHHc--CCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCC------HHHHHHHHHHHhcCC
Confidence            346789999999998774  4789999999999999999999999999999999977      999999999998744

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

>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.77  E-value=0.012  Score=46.67  Aligned_cols=67  Identities=19%  Similarity=0.381  Sum_probs=48.5

Q ss_pred             hHHHHHhcCCCCc-cccccccccccCC-CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           12 TKHRIESLSKADE-ETCPICQEKLGNQ-KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        12 ~~~~~~~l~~~~~-~~C~iC~~~~~~~-~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ++++++=+++.+- ..|..|..++... .+.+.|.|+|+-.|+.++..+-.++.   .-....||.|...+-
T Consensus        37 VQSYLqWL~DsDY~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanT---APaGyqCP~Cs~eiF  105 (299)
T KOG3970|consen   37 VQSYLQWLQDSDYNPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANT---APAGYQCPCCSQEIF  105 (299)
T ss_pred             HHHHHHHHhhcCCCCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcC---CCCcccCCCCCCccC
Confidence            4566777888764 6899999888653 36689999999999999854432221   233457999998653

>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]

Probab=95.73  E-value=0.0048  Score=51.15  Aligned_cols=42  Identities=24%  Similarity=0.617  Sum_probs=31.9

Q ss_pred             ccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      -|..|.-++..=..+.+|.|+||.+|...             .....||.|..++
T Consensus        92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~-------------~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   92 FCDRCDFPIAIYGRMIPCKHVFCLECARS-------------DSDKICPLCDDRV  133 (389)
T ss_pred             eecccCCcceeeecccccchhhhhhhhhc-------------CccccCcCcccHH
Confidence            48889877665457899999999999763             2345799997754

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=95.67  E-value=0.058  Score=49.80  Aligned_cols=65  Identities=8%  Similarity=0.114  Sum_probs=54.5

Q ss_pred             hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      +++.++..+.    ..++.++|||..-....+.+...|...|++...|+|+|+      .++|..+++.|..+..
T Consensus       223 ~~~~l~~~l~----~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~------~~~R~~i~~~F~~g~~  287 (607)
T PRK11057        223 PLDQLMRYVQ----EQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD------NDVRADVQEAFQRDDL  287 (607)
T ss_pred             hHHHHHHHHH----hcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCC------HHHHHHHHHHHHCCCC
Confidence            4555554443    346789999999999999999999999999999999977      9999999999997543

>PHA02558 uvsW UvsW helicase; Provisional

Probab=95.60  E-value=0.06  Score=48.48  Aligned_cols=67  Identities=12%  Similarity=0.050  Sum_probs=53.9

Q ss_pred             hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      +...+.+.+..+.  ..+.+++||...+.+.+.+...|...|++...++|.|+      ..+|.++++.|+++..
T Consensus       329 Rn~~I~~~~~~~~--~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~------~~eR~~i~~~~~~~~~  395 (501)
T PHA02558        329 RNKWIANLALKLA--KKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVD------TEDRNEMKKIAEGGKG  395 (501)
T ss_pred             HHHHHHHHHHHHH--hcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCC------HHHHHHHHHHHhCCCC
Confidence            3344454555544  34678999999999999999999999999999999977      9999999999987443

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length

Probab=95.56  E-value=0.0083  Score=43.98  Aligned_cols=36  Identities=19%  Similarity=0.422  Sum_probs=28.8

Q ss_pred             CCCccccccccccccC--CCeecCCC------CcchHhhHHHHH
Q 028376           21 KADEETCPICQEKLGN--QKMVFQCG------HFTCCKCFFAMT   56 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~--~~~~~~Cg------H~fC~~C~~~~~   56 (210)
                      ..-..+|.||.+.+..  +.+..+||      |.||.+|+.+|-
T Consensus        23 ~~~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   23 PRCTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             cccCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence            3447899999998876  44556777      899999999993

The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=95.54  E-value=0.079  Score=47.28  Aligned_cols=67  Identities=9%  Similarity=0.066  Sum_probs=54.6

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      .+++.+++.|..   ..++.++|||..-....+.+...|...|++...|.|+|+      ..+|..+++.|..+..
T Consensus       211 ~~~~~l~~~l~~---~~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~------~~eR~~i~~~F~~g~~  277 (470)
T TIGR00614       211 KILEDLLRFIRK---EFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLE------ISARDDVHHKFQRDEI  277 (470)
T ss_pred             cHHHHHHHHHHH---hcCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCC------HHHHHHHHHHHHcCCC
Confidence            345555555442   345667799999999999999999999999999999977      9999999999997543

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

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=95.52  E-value=0.079  Score=47.10  Aligned_cols=55  Identities=13%  Similarity=0.168  Sum_probs=49.2

Q ss_pred             hcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          136 STDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       136 ~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ......++|||..-....+.+...|...|+....|+|.|+      ..+|.++++.|.++.
T Consensus       241 ~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~------~~~R~~~l~~F~~g~  295 (456)
T PRK10590        241 GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKS------QGARTRALADFKSGD  295 (456)
T ss_pred             HcCCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCC------HHHHHHHHHHHHcCC
Confidence            3455679999999999999999999999999999999977      999999999999743

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=95.50  E-value=0.074  Score=48.88  Aligned_cols=68  Identities=9%  Similarity=0.066  Sum_probs=56.8

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      ..|...+++.|..    ..+.+.|||..-....+.+...|...|++...|+|+|+      ..+|..+++.|..+..+
T Consensus       209 ~~~~~~l~~~l~~----~~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~------~~~R~~i~~~F~~g~~~  276 (591)
T TIGR01389       209 NNKQKFLLDYLKK----HRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLS------NKVRAENQEDFLYDDVK  276 (591)
T ss_pred             CCHHHHHHHHHHh----cCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCC------HHHHHHHHHHHHcCCCc
Confidence            3456666666553    33679999999999999999999999999999999977      99999999999986544

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0

Probab=95.45  E-value=0.017  Score=42.09  Aligned_cols=63  Identities=19%  Similarity=0.509  Sum_probs=45.5

Q ss_pred             HHHHhcCCCCccccccccccccCCCee---cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           14 HRIESLSKADEETCPICQEKLGNQKMV---FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        14 ~~~~~l~~~~~~~C~iC~~~~~~~~~~---~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      .++.+..+....+|-||.+...+...+   --||-.+|.-|...+-+.        ..-.+.||+|+..+....
T Consensus        70 qvmnvF~d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~--------~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   70 QVMNVFLDPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKF--------CNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             HHheeecCCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHH--------cccCCCCCcccccccccc
Confidence            344444466667999999887665343   369999999999887433        356789999999886653

>KOG3002 consensus Zn finger protein [General function prediction only]

Probab=95.24  E-value=0.015  Score=48.81  Aligned_cols=45  Identities=38%  Similarity=0.885  Sum_probs=36.1

Q ss_pred             CCCccccccccccccCCCeecCC--CCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           21 KADEETCPICQEKLGNQKMVFQC--GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~~~~~~C--gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ..+..+||+|.+.+..+  +.+|  ||+.|..|-.+.              ...||.||.++.
T Consensus        45 ~~~lleCPvC~~~l~~P--i~QC~nGHlaCssC~~~~--------------~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPP--IFQCDNGHLACSSCRTKV--------------SNKCPTCRLPIG   91 (299)
T ss_pred             chhhccCchhhccCccc--ceecCCCcEehhhhhhhh--------------cccCCccccccc
Confidence            44567999999999864  5666  899999998654              348999999886

>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]

Probab=95.21  E-value=0.0092  Score=49.86  Aligned_cols=54  Identities=24%  Similarity=0.608  Sum_probs=42.8

Q ss_pred             CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ..+...||+|.....++.++..-|-+||..|+-.++.           ....||+=..+....++
T Consensus       297 ~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~-----------~~~~CPVT~~p~~v~~l  350 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVV-----------NYGHCPVTGYPASVDHL  350 (357)
T ss_pred             CCccccChhHHhccCCCceEEecceEEeHHHHHHHHH-----------hcCCCCccCCcchHHHH
Confidence            3466789999988888778888899999999999973           34589987777655443

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=95.18  E-value=0.12  Score=47.97  Aligned_cols=67  Identities=15%  Similarity=0.105  Sum_probs=57.3

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|.++|.+.|..    ....++|||..-....+.+...|...|+....++|.|+      ..+|.++++.|..+..
T Consensus       230 ~~k~~~L~~~L~~----~~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~------q~~R~~il~~Fr~G~~  296 (629)
T PRK11634        230 MRKNEALVRFLEA----EDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMN------QALREQTLERLKDGRL  296 (629)
T ss_pred             hhHHHHHHHHHHh----cCCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCC------HHHHHHHHHHHhCCCC
Confidence            4678888777653    34579999999999999999999999999999999977      9999999999998544

>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.16  E-value=0.016  Score=49.61  Aligned_cols=49  Identities=22%  Similarity=0.530  Sum_probs=35.7

Q ss_pred             ccccccccccc--cCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           24 EETCPICQEKL--GNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        24 ~~~C~iC~~~~--~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      .+.|||=.+.-  ++||+.+.|||++|.+-+.++...        +....+||.|-...
T Consensus       334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~n--------g~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKN--------GSQSFKCPYCPVEQ  384 (394)
T ss_pred             eeecccchhhccCCCCCeeeeccceecHHHHHHHhhC--------CCeeeeCCCCCccc
Confidence            45688754332  456899999999999999998532        34468999995543

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=95.01  E-value=0.051  Score=46.88  Aligned_cols=66  Identities=11%  Similarity=0.048  Sum_probs=55.2

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      -|-..|+..|.+    ..+.-+|||+.-...-+.+...|...|+....+.|.|+      ..+|.-+++.|+.+..
T Consensus       286 ~K~~yLV~ll~e----~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqms------q~~Rlg~l~~Fk~~~r  351 (476)
T KOG0330|consen  286 DKDTYLVYLLNE----LAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMS------QSKRLGALNKFKAGAR  351 (476)
T ss_pred             ccchhHHHHHHh----hcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhh------HHHHHHHHHHHhccCC
Confidence            345556655553    45678999999999999999999999999999999966      9999999999998543

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=94.98  E-value=0.0093  Score=41.93  Aligned_cols=32  Identities=34%  Similarity=0.895  Sum_probs=25.7

Q ss_pred             CCccccccccccccCCC-eecCCCCcchHhhHH
Q 028376           22 ADEETCPICQEKLGNQK-MVFQCGHFTCCKCFF   53 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~-~~~~CgH~fC~~C~~   53 (210)
                      .+...|++|...+.... ++.||||+++..|+.
T Consensus        76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            35577999999887643 558999999999975

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

>PTZ00424 helicase 45; Provisional

Probab=94.84  E-value=0.18  Score=43.73  Aligned_cols=55  Identities=15%  Similarity=0.247  Sum_probs=49.0

Q ss_pred             hcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          136 STDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       136 ~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ...+..++|||..-....+.+...|...|+....++|.|+      ..+|..+++.|+++.
T Consensus       263 ~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~------~~~R~~i~~~f~~g~  317 (401)
T PTZ00424        263 ETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMD------QKDRDLIMREFRSGS  317 (401)
T ss_pred             HhcCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCC------HHHHHHHHHHHHcCC
Confidence            3445679999999999999999999999999999999977      999999999999744

>PHA03096 p28-like protein; Provisional

Probab=94.76  E-value=0.018  Score=47.95  Aligned_cols=34  Identities=18%  Similarity=0.332  Sum_probs=27.5

Q ss_pred             cccccccccccCC-------CeecCCCCcchHhhHHHHHHH
Q 028376           25 ETCPICQEKLGNQ-------KMVFQCGHFTCCKCFFAMTEQ   58 (210)
Q Consensus        25 ~~C~iC~~~~~~~-------~~~~~CgH~fC~~C~~~~~~~   58 (210)
                      -.|.||++.....       +++..|-|.||..|+..|...
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~  219 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE  219 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence            7899998865422       477899999999999999644

>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.67  E-value=0.016  Score=54.25  Aligned_cols=36  Identities=25%  Similarity=0.515  Sum_probs=29.1

Q ss_pred             CccccccccccccC-CCeecCCCCcchHhhHHHHHHH
Q 028376           23 DEETCPICQEKLGN-QKMVFQCGHFTCCKCFFAMTEQ   58 (210)
Q Consensus        23 ~~~~C~iC~~~~~~-~~~~~~CgH~fC~~C~~~~~~~   58 (210)
                      ....|.+|..++.. +.++.+|||.|+.+|+.+.+..
T Consensus       816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~  852 (911)
T KOG2034|consen  816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLS  852 (911)
T ss_pred             CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHc
Confidence            45679999887654 4577899999999999988654

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]

Probab=94.64  E-value=0.0095  Score=41.39  Aligned_cols=29  Identities=17%  Similarity=0.290  Sum_probs=24.0

Q ss_pred             ecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376           40 VFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR   79 (210)
Q Consensus        40 ~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~   79 (210)
                      --.|.|.|+.-|+.+|+.           .+..||+|.+.
T Consensus        78 WG~CNHaFH~hCisrWlk-----------tr~vCPLdn~e  106 (114)
T KOG2930|consen   78 WGVCNHAFHFHCISRWLK-----------TRNVCPLDNKE  106 (114)
T ss_pred             eeecchHHHHHHHHHHHh-----------hcCcCCCcCcc
Confidence            358999999999999974           34589999774

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=94.60  E-value=0.18  Score=45.67  Aligned_cols=69  Identities=17%  Similarity=0.189  Sum_probs=55.7

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh-CCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA-NNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~-~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|...|.+.|....  ....++|||..-....+.+...|.. .|+....|.|.|+      ..+|..+++.|..+.-
T Consensus       350 ~~k~~~l~~~l~~~~--~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~------~~eR~~il~~Fr~G~~  419 (518)
T PLN00206        350 KQKKQKLFDILKSKQ--HFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKS------MKERREVMKSFLVGEV  419 (518)
T ss_pred             hhHHHHHHHHHHhhc--ccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCC------HHHHHHHHHHHHCCCC
Confidence            346667776665433  2245899999999999999999975 7999999999977      9999999999998543

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=94.49  E-value=0.17  Score=43.57  Aligned_cols=67  Identities=12%  Similarity=0.126  Sum_probs=57.0

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      -.|.++|.+...-+    .-..+|||.+=.....++...|.+.|.....+.|.|.      ..+|.+++++|+.+.-
T Consensus       315 ~~K~~~l~~lyg~~----tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~------~~~R~~ii~~Fr~g~~  381 (477)
T KOG0332|consen  315 DDKYQALVNLYGLL----TIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLT------VEQRAAIIDRFREGKE  381 (477)
T ss_pred             hhHHHHHHHHHhhh----hhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccch------hHHHHHHHHHHhcCcc
Confidence            57888888744322    2468999999999999999999999999999999976      9999999999998543

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=94.35  E-value=0.085  Score=46.79  Aligned_cols=69  Identities=14%  Similarity=0.076  Sum_probs=59.3

Q ss_pred             CCchHHHHHHHHHHHHhcCC-----CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          120 YGTKIEAVTRRILWIKSTDP-----KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~-----~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      -..|...|+++|........     .+|++||.-=..+.+-++..|..+|+++..+.|...      ..+|.++|+.|..
T Consensus       312 ~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~t------q~er~~al~~Fr~  385 (482)
T KOG0335|consen  312 EMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRT------QIEREQALNDFRN  385 (482)
T ss_pred             chhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhh------hhHHHHHHHHhhc
Confidence            36888999988876542212     349999999999999999999999999999999955      9999999999997

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=94.25  E-value=0.2  Score=48.27  Aligned_cols=64  Identities=16%  Similarity=0.132  Sum_probs=58.0

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..|..+|++.|.+...  .+..+|||+......+.|...|...||++..+.+.        ..+|++.|..|..
T Consensus       581 ~eK~~Ali~~I~~~~~--~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLnak--------q~~REa~Iia~AG  644 (1025)
T PRK12900        581 REKYNAIVLKVEELQK--KGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNAK--------QHDREAEIVAEAG  644 (1025)
T ss_pred             HHHHHHHHHHHHHHhh--CCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecCC--------HHHhHHHHHHhcC
Confidence            4689999999987764  37899999999999999999999999999999986        8899999999997

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=94.19  E-value=0.21  Score=42.75  Aligned_cols=65  Identities=8%  Similarity=0.108  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          124 IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       124 i~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      =..|+..|.....+ +..-++||.|=+..-.++...|+..+++...+.+-|+      .++|.++|.+|+.+
T Consensus       239 daYLv~~Lr~~~~~-~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~------Q~eR~~aLsrFrs~  303 (442)
T KOG0340|consen  239 DAYLVHLLRDFENK-ENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMP------QKERLAALSRFRSN  303 (442)
T ss_pred             HHHHHHHHhhhhhc-cCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcch------HHHHHHHHHHHhhc
Confidence            34566666665543 6788899999999999999999999999999999988      99999999999973

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]

Probab=94.17  E-value=0.15  Score=42.34  Aligned_cols=63  Identities=14%  Similarity=0.242  Sum_probs=55.5

Q ss_pred             hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      |.++|.+....+.    -.+.|||..-..-.|++..-++..++....+.|.|+      .++|.+++..|+.+
T Consensus       253 KfdtLcdLYd~Lt----ItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~------qkERd~im~dFRsg  315 (400)
T KOG0328|consen  253 KFDTLCDLYDTLT----ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDME------QKERDKIMNDFRSG  315 (400)
T ss_pred             hHhHHHHHhhhhe----hheEEEEecccchhhHHHHHHHhhCceeeeccCCcc------hhHHHHHHHHhhcC
Confidence            6777776665443    468999999999999999999999999999999998      99999999999973

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=94.15  E-value=0.21  Score=47.03  Aligned_cols=65  Identities=8%  Similarity=0.124  Sum_probs=52.6

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHH
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKEL  192 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F  192 (210)
                      ...|..++++.+.....  .+..+|||.......+.+...|..+||++..+.|.|.      ..+|..+.+.|
T Consensus       406 ~~~K~~ai~~~i~~~~~--~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~------~~E~~ii~~ag  470 (762)
T TIGR03714       406 LPEKLMATLEDVKEYHE--TGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNA------AKEAQIIAEAG  470 (762)
T ss_pred             HHHHHHHHHHHHHHHhh--CCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCCh------HHHHHHHHHcC
Confidence            35689999999987653  3678999999999999999999999999999999965      55554444433

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=93.98  E-value=0.13  Score=33.21  Aligned_cols=37  Identities=11%  Similarity=0.161  Sum_probs=32.2

Q ss_pred             HHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          155 VLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       155 li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      .+...|...++++..++|.|+      ..+|..+++.|+.++.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~------~~~r~~~~~~f~~~~~   38 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLS------QEEREEILEKFNNGKI   38 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCC------HHHHHHHHHHHHcCCC
Confidence            467788889999999999977      9999999999998543

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=93.95  E-value=0.27  Score=46.77  Aligned_cols=66  Identities=15%  Similarity=0.057  Sum_probs=58.2

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..|..++++.+.+...  .+..+|||+......+.+...|...||++..+.|.        ..+|.+.|..|....
T Consensus       413 ~~K~~aI~~~I~~~~~--~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--------q~eREa~Iia~Ag~~  478 (830)
T PRK12904        413 KEKFDAVVEDIKERHK--KGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--------NHEREAEIIAQAGRP  478 (830)
T ss_pred             HHHHHHHHHHHHHHHh--cCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--------hHHHHHHHHHhcCCC
Confidence            4689999999987653  36789999999999999999999999999999997        779999999999733

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=93.89  E-value=0.34  Score=45.03  Aligned_cols=64  Identities=13%  Similarity=0.061  Sum_probs=54.3

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..|..+|++.+..+...  +..+|||..-....+.+...|..+||++..+.|.        ..+|++.+..|..
T Consensus       456 ~~K~~aL~~~i~~~~~~--~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~--------~~~rE~~ii~~ag  519 (656)
T PRK12898        456 AAKWAAVAARVRELHAQ--GRPVLVGTRSVAASERLSALLREAGLPHQVLNAK--------QDAEEAAIVARAG  519 (656)
T ss_pred             HHHHHHHHHHHHHHHhc--CCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCC--------cHHHHHHHHHHcC
Confidence            46899999988876532  3569999999999999999999999999999998        4478888888875

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=93.87  E-value=0.13  Score=46.04  Aligned_cols=68  Identities=15%  Similarity=0.271  Sum_probs=60.2

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      +.-.|+..|+++|.....   ..|+|||..=..-.+-|...|+.+||....+.|.|.      .+.|+.+|..|++.
T Consensus       450 s~~~Kl~wl~~~L~~f~S---~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkd------qa~rn~~ls~fKkk  517 (731)
T KOG0339|consen  450 SEEKKLNWLLRHLVEFSS---EGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKD------QAERNEVLSKFKKK  517 (731)
T ss_pred             CcHHHHHHHHHHhhhhcc---CCcEEEEEeccCCHHHHHHHhccccceeeeecCchh------hHHHHHHHHHHhhc
Confidence            456899999999987653   469999999888899999999999999999999966      99999999999984

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=93.80  E-value=0.34  Score=45.59  Aligned_cols=65  Identities=15%  Similarity=0.079  Sum_probs=57.9

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      -.|..++++.+.+...  .+..+|||.....-.+.+...|.++||++..+.|.        ...|++.|..|...
T Consensus       388 ~~k~~ai~~~i~~~~~--~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--------q~~rEa~ii~~ag~  452 (745)
T TIGR00963       388 EEKWKAVVDEIKERHA--KGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--------NHEREAEIIAQAGR  452 (745)
T ss_pred             HHHHHHHHHHHHHHHh--cCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--------hHHHHHHHHHhcCC
Confidence            3588899999887764  47889999999999999999999999999999998        77999999999873

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=93.68  E-value=0.073  Score=47.26  Aligned_cols=63  Identities=21%  Similarity=0.528  Sum_probs=44.3

Q ss_pred             CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCcccccc--CCcccccCCCeE
Q 028376           21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCP--TCRQRTDIGNIA   86 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP--~Cr~~~~~~~l~   86 (210)
                      ......|.||.+......+...|||.||..|+..++........   ....+||  .|+..+....+.
T Consensus        67 ~~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~---~~~i~cp~~~C~a~v~~~~i~  131 (444)
T KOG1815|consen   67 KKGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGTKIHEGE---EAKIKCPAHGCPALVGEDTVE  131 (444)
T ss_pred             CCccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhheeeccc---cccccCCCCCccccCCCceee
Confidence            34568899998877543466799999999999999877553221   2225676  587777666554

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

Probab=93.58  E-value=0.3  Score=43.36  Aligned_cols=67  Identities=24%  Similarity=0.232  Sum_probs=55.7

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+.++...+....   .+.+++||.+.......+...|...|+ ...++|..+      ...|.+++++|..++.
T Consensus       267 ~~~~~~~~~~~~~~~---~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~------~~eR~~il~~fr~g~~  333 (442)
T COG1061         267 ERKIAAVRGLLLKHA---RGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETP------KEEREAILERFRTGGI  333 (442)
T ss_pred             HHHHHHHHHHHHHhc---CCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCC------HHHHHHHHHHHHcCCC
Confidence            455556665555432   478999999999999999999999999 788899987      9999999999998553

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=93.56  E-value=0.27  Score=47.02  Aligned_cols=67  Identities=12%  Similarity=0.115  Sum_probs=60.4

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      -.|..|+++.+.++.+.  +-.+|||+.....-+++...|..+||++..+.|.+.      ..+|..+.+.|+.+
T Consensus       432 ~~K~~Aii~ei~~~~~~--GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~------~~Ea~ii~~Ag~~G  498 (908)
T PRK13107        432 DEKYQAIIKDIKDCRER--GQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFH------EREAEIVAQAGRTG  498 (908)
T ss_pred             HHHHHHHHHHHHHHHHc--CCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCccc------HHHHHHHHhCCCCC
Confidence            57889999999988754  788999999999999999999999999999999966      89999999998863

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]

Probab=93.42  E-value=0.042  Score=47.75  Aligned_cols=35  Identities=26%  Similarity=0.665  Sum_probs=29.6

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHH
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQ   58 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~   58 (210)
                      +...|++|..-+.+ +++++|+|.+|..|....+.+
T Consensus         3 eelkc~vc~~f~~e-piil~c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    3 EELKCPVCGSFYRE-PIILPCSHNLCQACARNILVQ   37 (699)
T ss_pred             ccccCceehhhccC-ceEeecccHHHHHHHHhhccc
Confidence            45689999988887 599999999999999876543

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=93.42  E-value=0.31  Score=43.91  Aligned_cols=68  Identities=18%  Similarity=0.291  Sum_probs=52.2

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh----------------------CCceEEEeeCCCCCCc
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA----------------------NNITCIKMKGENHKLP  178 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~----------------------~gi~~~~~~G~m~~~~  178 (210)
                      ...+=+|...|+..-+..+..|.|||-+-+++.+.--.+|..                      .+.+|+|+.|+|.   
T Consensus       406 KLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~---  482 (708)
T KOG0348|consen  406 KLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSME---  482 (708)
T ss_pred             chhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchh---
Confidence            345567888888877777788999998877776554444432                      2457999999976   


Q ss_pred             chhhHhhhHHHHHHhh
Q 028376          179 SANLQHRNALQKELTR  194 (210)
Q Consensus       179 ~~~~~~R~~~l~~F~~  194 (210)
                         ...|..++..|..
T Consensus       483 ---QeeRts~f~~Fs~  495 (708)
T KOG0348|consen  483 ---QEERTSVFQEFSH  495 (708)
T ss_pred             ---HHHHHHHHHhhcc
Confidence               9999999999997

>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]

Probab=93.39  E-value=0.068  Score=52.94  Aligned_cols=62  Identities=19%  Similarity=0.583  Sum_probs=43.8

Q ss_pred             CCCCcccccccccc-cc-CCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           20 SKADEETCPICQEK-LG-NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        20 ~~~~~~~C~iC~~~-~~-~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ++..+..|.||... +. .+.+.+.|+|+|+..|....+++.+.... -.-+-..||.|..++..
T Consensus      3482 kQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPR-ItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPR-ITFGFISCPICKNKINH 3545 (3738)
T ss_pred             hcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCe-eEEeeeecccccchhhh
Confidence            45567789999654 33 23577999999999999999998763210 01233469999988753

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=93.38  E-value=0.13  Score=33.52  Aligned_cols=34  Identities=12%  Similarity=0.171  Sum_probs=30.2

Q ss_pred             HHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          158 HAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       158 ~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+..|+.+..++|.|+      ..+|..+++.|+.+..
T Consensus         1 ~~L~~~~~~~~~i~~~~~------~~~r~~~~~~f~~~~~   34 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMS------QKERQEILKKFNSGEI   34 (78)
T ss_dssp             HHHHHTTSSEEEESTTSH------HHHHHHHHHHHHTTSS
T ss_pred             CChHHCCCcEEEEECCCC------HHHHHHHHHHhhccCc
Confidence            368899999999999966      9999999999998555

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional

Probab=93.31  E-value=0.4  Score=47.14  Aligned_cols=54  Identities=7%  Similarity=0.007  Sum_probs=48.8

Q ss_pred             cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          137 TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ...+...|||.....-.+.+...|...|+....|.|+|+      ..+|..+++.|..+.
T Consensus       677 ~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs------~eeR~~vqe~F~~Ge  730 (1195)
T PLN03137        677 NHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMD------PAQRAFVQKQWSKDE  730 (1195)
T ss_pred             cccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCC------HHHHHHHHHHHhcCC
Confidence            344678999999999999999999999999999999977      999999999999854

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=93.26  E-value=0.36  Score=46.20  Aligned_cols=67  Identities=13%  Similarity=0.105  Sum_probs=60.2

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      -.|..|+++.+.+...  .+-=+|||+....--+.+...|.+.||++..+.|.+.      ..+|..+.+.|+.+
T Consensus       427 ~~k~~av~~~i~~~~~--~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~------q~Ea~iia~Ag~~G  493 (896)
T PRK13104        427 ADKFQAIIEDVRECGV--RKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFH------EKEAQIIAEAGRPG  493 (896)
T ss_pred             HHHHHHHHHHHHHHHh--CCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCC------hHHHHHHHhCCCCC
Confidence            4688899999988764  4778999999999999999999999999999999976      99999999999874

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=92.93  E-value=0.57  Score=43.87  Aligned_cols=78  Identities=9%  Similarity=0.143  Sum_probs=63.1

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHH---hCCceEEEeeC--CCCCCcchhhHhhhHHHHHHhh
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFI---ANNITCIKMKG--ENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~---~~gi~~~~~~G--~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      -..|++.|.+.|.+....+++.++|||+-+......|-.+|.   ..||+-.-|-|  ......+|+.++...+|+.|+.
T Consensus       393 ~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~  472 (746)
T KOG0354|consen  393 ENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRD  472 (746)
T ss_pred             cChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhC
Confidence            368999999999999999999999999999888777777777   45666555544  4445578999999999999998


Q ss_pred             cCC
Q 028376          195 HMP  197 (210)
Q Consensus       195 ~~p  197 (210)
                      ++=
T Consensus       473 G~~  475 (746)
T KOG0354|consen  473 GEI  475 (746)
T ss_pred             CCc
Confidence            543

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=92.87  E-value=0.06  Score=46.87  Aligned_cols=59  Identities=29%  Similarity=0.624  Sum_probs=39.7

Q ss_pred             CCcccccccc-ccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCcccccc--CCcccccCCCe
Q 028376           22 ADEETCPICQ-EKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCP--TCRQRTDIGNI   85 (210)
Q Consensus        22 ~~~~~C~iC~-~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP--~Cr~~~~~~~l   85 (210)
                      ....+|.||. +.+...  ..+..|+|.||.+|+.++++-...     .+..+.||  .|...+...+.
T Consensus       144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~-----~~~~~~C~~~~C~~~l~~~~c  207 (384)
T KOG1812|consen  144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLL-----SGTVIRCPHDGCESRLTLESC  207 (384)
T ss_pred             cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhc-----cCCCccCCCCCCCccCCHHHH
Confidence            3467899998 433321  235689999999999999875411     35677887  46666655443

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=92.86  E-value=0.08  Score=42.10  Aligned_cols=40  Identities=28%  Similarity=0.719  Sum_probs=29.9

Q ss_pred             cccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           27 CPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        27 C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      |-.|.+.-.. ..++||.| .+|..|-..               ...||+|+.+...
T Consensus       161 Cr~C~~~~~~-VlllPCrHl~lC~~C~~~---------------~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGEREAT-VLLLPCRHLCLCGICDES---------------LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcCCce-EEeecccceEeccccccc---------------CccCCCCcChhhc
Confidence            9999886654 57789998 678888432               4579999886543

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=92.56  E-value=0.56  Score=44.55  Aligned_cols=65  Identities=9%  Similarity=0.057  Sum_probs=53.0

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELT  193 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~  193 (210)
                      ..|..+|++.+.....  .+.++|||.......+.+...|...||++..+.|.|.      ..+|..+...|.
T Consensus       411 ~~K~~al~~~i~~~~~--~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~------~~e~~~i~~ag~  475 (790)
T PRK09200        411 DEKYKAVIEEVKERHE--TGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNA------AKEAQIIAEAGQ  475 (790)
T ss_pred             HHHHHHHHHHHHHHHh--cCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCcc------HHHHHHHHHcCC
Confidence            5789999999987543  4789999999999999999999999999999999965      555554444443

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=92.48  E-value=0.15  Score=38.52  Aligned_cols=50  Identities=16%  Similarity=0.394  Sum_probs=37.5

Q ss_pred             CccccccccccccCCCeecCCCC-----cchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGH-----FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH-----~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ....|-||.+....  ...||.-     ..+.+|+.+|+..         ++...|+.|+.++...
T Consensus         7 ~~~~CRIC~~~~~~--~~~PC~CkGs~k~VH~sCL~rWi~~---------s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          7 MDKCCWICKDEYDV--VTNYCNCKNENKIVHKECLEEWINT---------SKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCeeEecCCCCCC--ccCCcccCCCchHHHHHHHHHHHhc---------CCCCcccccCCeEEEE
Confidence            45689999887543  3467765     4489999999854         4667899999987655

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=92.47  E-value=0.016  Score=37.59  Aligned_cols=40  Identities=38%  Similarity=0.846  Sum_probs=24.5

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ..||.|..++....     ||..|..|-..+            .....||.|..++.
T Consensus         2 ~~CP~C~~~L~~~~-----~~~~C~~C~~~~------------~~~a~CPdC~~~Le   41 (70)
T PF07191_consen    2 NTCPKCQQELEWQG-----GHYHCEACQKDY------------KKEAFCPDCGQPLE   41 (70)
T ss_dssp             -B-SSS-SBEEEET-----TEEEETTT--EE------------EEEEE-TTT-SB-E
T ss_pred             CcCCCCCCccEEeC-----CEEECccccccc------------eecccCCCcccHHH
Confidence            47999998875432     899999998876            45668999998764

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>PF11496 HDA2-3: Class II histone deacetylase complex subunits 2 and 3; InterPro: IPR021006 This entry contains the class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi

Probab=92.39  E-value=0.24  Score=41.69  Aligned_cols=57  Identities=19%  Similarity=0.229  Sum_probs=44.6

Q ss_pred             CCCchHHHHHHHHHHHHh---cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376          119 SYGTKIEAVTRRILWIKS---TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH  175 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~---~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~  175 (210)
                      ..|+|...|-+.|..+..   .+.+.++||.++-...+|+||..|...++.|.|++|.+-
T Consensus        93 ~tS~KF~~L~~Li~~li~~~~~~~~~~ilIv~~~~k~ldllE~~llGk~~~~kr~sg~~l  152 (297)
T PF11496_consen   93 YTSGKFQFLNDLIDSLIDRDRREYPLHILIVSRSGKELDLLEGLLLGKKLNYKRYSGESL  152 (297)
T ss_dssp             HT-HHHHHHHHHHHHH-----TTSSEEEEEEE-STHHHHHHHHHHTTSSSEEEESSS--S
T ss_pred             HcCchHHHHHHHHHHHHhhhcccCCceEEEEecCccHHHHHHHHHccCCeeEEecCCCCC
Confidence            458999887777766622   455789999999999999999999999999999999864

The member from Schizosaccharomyces pombe (Fission yeast) is referred to as Ccq1 in Q10432 from SWISSPROT. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C terminus []. ; PDB: 3HGQ_C 3HGT_B.

>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A

Probab=92.06  E-value=0.15  Score=30.45  Aligned_cols=41  Identities=20%  Similarity=0.512  Sum_probs=25.3

Q ss_pred             cccccccccCC-CeecCCCC-----cchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           27 CPICQEKLGNQ-KMVFQCGH-----FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        27 C~iC~~~~~~~-~~~~~CgH-----~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      |-||.+.-... +.+.||+-     ..+..|+.+|+..         .+...|++|
T Consensus         1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~---------~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE---------SGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH---------HT-SB-TTT
T ss_pred             CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh---------cCCCcCCCC
Confidence            67887765543 47788852     5688999999875         234468877

>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]

Probab=92.04  E-value=0.17  Score=47.56  Aligned_cols=56  Identities=18%  Similarity=0.373  Sum_probs=40.1

Q ss_pred             CCCccccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           21 KADEETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      ..+..+|.||.+.+...   +.-..|.|+|...||..|...... .   ....-.||.|+...
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek-~---~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEK-T---GQDGWRCPACQSVS  246 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhh-c---cCccccCCcccchh
Confidence            45678999999987643   233578999999999999766221 1   23555799998543

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype

Probab=91.90  E-value=0.92  Score=43.39  Aligned_cols=64  Identities=11%  Similarity=0.133  Sum_probs=52.2

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhh-----HHHHHHhh
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRN-----ALQKELTR  194 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~-----~~l~~F~~  194 (210)
                      .|+..++..|..+.. ..+.++|||..-....+.+...|...|+  ..+.|.|.      ..+|.     +++++|..
T Consensus       255 ~Kl~~lv~~L~~ll~-e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~------q~dR~~~~~~~il~~Fk~  323 (844)
T TIGR02621       255 KFLSTMVKELNLLMK-DSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLR------GAERDDLVKKEIFNRFLP  323 (844)
T ss_pred             HHHHHHHHHHHHHHh-hCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCC------HHHHhhHHHHHHHHHHhc
Confidence            356666666655443 3467899999999999999999999998  78999977      99999     88999986

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>PHA02862 5L protein; Provisional

Probab=91.77  E-value=0.17  Score=37.59  Aligned_cols=50  Identities=20%  Similarity=0.451  Sum_probs=37.3

Q ss_pred             ccccccccccccCCCeecCCC-----CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           24 EETCPICQEKLGNQKMVFQCG-----HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~Cg-----H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      ...|-||.+.-.+  ...||.     ...+.+|+.+|+..         .+...|+.|+.++....
T Consensus         2 ~diCWIC~~~~~e--~~~PC~C~GS~K~VHq~CL~~WIn~---------S~k~~CeLCkteY~Ik~   56 (156)
T PHA02862          2 SDICWICNDVCDE--RNNFCGCNEEYKVVHIKCMQLWINY---------SKKKECNLCKTKYNIKK   56 (156)
T ss_pred             CCEEEEecCcCCC--CcccccccCcchhHHHHHHHHHHhc---------CCCcCccCCCCeEEEEE
Confidence            3579999887543  256775     36789999999843         56779999999876543

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=91.75  E-value=0.66  Score=39.99  Aligned_cols=76  Identities=18%  Similarity=0.271  Sum_probs=62.3

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC---
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP---  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p---  197 (210)
                      ..|+..|.....      .-..++||-.-..-++.+...|..+|+...-+.|-|.      ..+|..++++|+.+.-   
T Consensus       250 ~~k~~~l~dl~~------~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~------q~~R~~~~~ef~~gssrvl  317 (397)
T KOG0327|consen  250 EEKLDTLCDLYR------RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDME------QNERDTLMREFRSGSSRVL  317 (397)
T ss_pred             cccccHHHHHHH------hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccc------hhhhhHHHHHhhcCCceEE
Confidence            347777776665      2458899999999999999999999999999999987      9999999999998443   


Q ss_pred             ----------CCCCccccccc
Q 028376          198 ----------SSQSQSLFKCY  208 (210)
Q Consensus       198 ----------~~~~~~~~~~~  208 (210)
                                +++..|+..||
T Consensus       318 Ittdl~argidv~~~slviny  338 (397)
T KOG0327|consen  318 ITTDLLARGIDVQQVSLVVNY  338 (397)
T ss_pred             eeccccccccchhhcceeeee
Confidence                      34556666665

>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=91.48  E-value=1.3  Score=41.06  Aligned_cols=163  Identities=18%  Similarity=0.204  Sum_probs=88.8

Q ss_pred             ccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE-EccCccccCCCCCCCCC
Q 028376           26 TCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA-YADDRQDKSCNSDMPHG  103 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~-~~~~~~~~~~~~~~~~~  103 (210)
                      .|+||...+.- ...-.||| ..|..|+.++.....     +......||+||..+....+. +........ +. ....
T Consensus         2 ~c~ic~~s~~~-~~~~s~~h~~v~~~~~~R~~~~~~-----~~~~~~~~~vcr~~~~~~s~~~~~~~~~t~~-~~-~~~~   73 (669)
T KOG2231|consen    2 SCAICAFSPDF-VGRGSCGHNEVCATCVVRLRFELN-----NRKCSNECPVCRREVETKSNGDSSDAVGTFP-EG-RKCD   73 (669)
T ss_pred             CcceeecCccc-cccccccccccchhhhhhhhhhcc-----cccccccCcccccceeeeccccccccccccc-cc-cccc
Confidence            59999887764 47789999 999999998843311     123455679998865433221 111000000 00 0000


Q ss_pred             CCCcccccCCce-ecCCCCchHHHHHHHHHH-----HHhcCCCCcEEEEcchHHHHHHHHHHHHhC----------CceE
Q 028376          104 VQDCEKGEESFT-VQGSYGTKIEAVTRRILW-----IKSTDPKAKILVFSSWNDVLDVLEHAFIAN----------NITC  167 (210)
Q Consensus       104 ~~~~~~~~~~~~-~~~~~SsKi~al~~~L~~-----~~~~~~~~K~iVFSQf~~~L~li~~~L~~~----------gi~~  167 (210)
                      ....+.. ..+. .....-+|++++...-=.     .....++.-...+.-|..+..|=.++-..+          +-.+
T Consensus        74 ~~~~e~~-~~if~~d~~~y~~~~~~~~~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~ki  152 (669)
T KOG2231|consen   74 FDEHEDT-CVIFFADKLTYTKLEACLHHSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKLHLCSLCLQNLKI  152 (669)
T ss_pred             cccccce-eeeeeccccHHHHHHHHHhhhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhhhcccccccccee
Confidence            0001100 1111 223445777777764311     111122223345566777777766664444          4444


Q ss_pred             EEeeCCCCCCcchhhHhhhHHHHHHhhcCCCCCCcccc
Q 028376          168 IKMKGENHKLPSANLQHRNALQKELTRHMPSSQSQSLF  205 (210)
Q Consensus       168 ~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~~~~~~~  205 (210)
                      ..+.++        ...|..+...-+.+||+.++-+-+
T Consensus       153 f~~e~k--------~Yt~~el~~h~~~gd~d~~s~rGh  182 (669)
T KOG2231|consen  153 FINERK--------LYTRAELNLHLMFGDPDDESCRGH  182 (669)
T ss_pred             eeeeee--------hehHHHHHHHHhcCCCccccccCC
Confidence            555566        778888888888889987776654

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function

Probab=91.37  E-value=0.28  Score=36.99  Aligned_cols=62  Identities=21%  Similarity=0.499  Sum_probs=36.0

Q ss_pred             CccccccccccccCCCeecCCC-------Ccc------hHhhHHHHHHHhhhccc--------------------cCCCc
Q 028376           23 DEETCPICQEKLGNQKMVFQCG-------HFT------CCKCFFAMTEQRLIHDN--------------------KVKNE   69 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~Cg-------H~f------C~~C~~~~~~~~~~~~~--------------------~~~~~   69 (210)
                      ++..||||++.+=+. +++.|.       -.+      ...|++++.........                    .....
T Consensus         1 ed~~CpICme~PHNA-VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (162)
T PF07800_consen    1 EDVTCPICMEHPHNA-VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQP   79 (162)
T ss_pred             CCccCceeccCCCce-EEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccc
Confidence            457899999988774 666542       222      35788887543221110                    00123


Q ss_pred             cccccCCcccccCCCe
Q 028376           70 WVMCPTCRQRTDIGNI   85 (210)
Q Consensus        70 ~~~CP~Cr~~~~~~~l   85 (210)
                      ...||+||..+.--.+
T Consensus        80 ~L~CPLCRG~V~GWtv   95 (162)
T PF07800_consen   80 ELACPLCRGEVKGWTV   95 (162)
T ss_pred             cccCccccCceeceEE
Confidence            5579999987655433

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A

Probab=90.90  E-value=0.24  Score=32.74  Aligned_cols=55  Identities=24%  Similarity=0.616  Sum_probs=21.8

Q ss_pred             cCCCCccccccccccccCC----Ce--ecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           19 LSKADEETCPICQEKLGNQ----KM--VFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        19 l~~~~~~~C~iC~~~~~~~----~~--~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ++..+...|.||.+.+...    ++  .--|+-..|+.|++--  .        ..+...||.|+.++...
T Consensus         4 ~k~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE--r--------keg~q~CpqCkt~ykr~   64 (80)
T PF14569_consen    4 LKNLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE--R--------KEGNQVCPQCKTRYKRH   64 (80)
T ss_dssp             -S--SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH--H--------HTS-SB-TTT--B----
T ss_pred             hhhcCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHH--h--------hcCcccccccCCCcccc
Confidence            4556778999998876421    12  2478889999999843  2        35677899999876543

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.80  E-value=0.23  Score=40.26  Aligned_cols=52  Identities=12%  Similarity=0.307  Sum_probs=40.0

Q ss_pred             cccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEcc
Q 028376           25 ETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYAD   89 (210)
Q Consensus        25 ~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~   89 (210)
                      +.|||-.-++...   ..+.+|||+|-..-+.++             ....|++|...+...+++.+.
T Consensus       112 fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei-------------kas~C~~C~a~y~~~dvIvlN  166 (293)
T KOG3113|consen  112 FICPVTGLEMNGKYRFCALRCCGCVFSERALKEI-------------KASVCHVCGAAYQEDDVIVLN  166 (293)
T ss_pred             eecccccceecceEEEEEEeccceeccHHHHHHh-------------hhccccccCCcccccCeEeeC
Confidence            5699887666542   255799999999888876             245899999999999987544

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=90.52  E-value=0.93  Score=40.30  Aligned_cols=66  Identities=11%  Similarity=0.169  Sum_probs=48.9

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHH--hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFI--ANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~--~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      .+--|+..|++.|..    ....|+|||=.--...+.....|.  ..++..+.++|+|.      ..+|+++++.|..
T Consensus       238 ~a~eK~~~lv~~L~~----~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~------q~~R~k~~~~F~~  305 (567)
T KOG0345|consen  238 EADEKLSQLVHLLNN----NKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMS------QKARAKVLEAFRK  305 (567)
T ss_pred             cHHHHHHHHHHHHhc----cccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhc------chhHHHHHHHHHh
Confidence            345678888877775    446899998554444444444444  46888999999976      9999999999997

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=90.23  E-value=0.22  Score=30.21  Aligned_cols=48  Identities=19%  Similarity=0.438  Sum_probs=23.7

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR   79 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~   79 (210)
                      ..||+....+..+..-..|.|.-|-+ ++.+++....      ...-.||.|+++
T Consensus         3 L~CPls~~~i~~P~Rg~~C~H~~CFD-l~~fl~~~~~------~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIPVRGKNCKHLQCFD-LESFLESNQR------TPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSEEEETT--SS--EE-HHHHHHHHHH------S---B-TTT---
T ss_pred             eeCCCCCCEEEeCccCCcCcccceEC-HHHHHHHhhc------cCCeECcCCcCc
Confidence            46999988888876678999998754 3445544331      334689999864

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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=90.12  E-value=0.74  Score=41.02  Aligned_cols=65  Identities=12%  Similarity=0.135  Sum_probs=56.5

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..++..|...|++...   .-|+|||-.--.+.+.+...|..-.++.+.+.|+++      ..+|..+..+|.+
T Consensus       314 ~~~f~ll~~~LKk~~~---~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~------Q~kRT~~~~~F~k  378 (543)
T KOG0342|consen  314 DSRFSLLYTFLKKNIK---RYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQK------QNKRTSTFFEFCK  378 (543)
T ss_pred             cchHHHHHHHHHHhcC---CceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCc------ccccchHHHHHhh
Confidence            4556777777775443   389999999999999999999999999999999988      9999999999998

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=89.85  E-value=1.3  Score=42.19  Aligned_cols=64  Identities=19%  Similarity=0.127  Sum_probs=53.2

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..|..+|++.+....  ..+..+|||.....-.+.+...|.++||++..+.|.+.        +|++.+-.+..
T Consensus       423 ~~K~~al~~~i~~~~--~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~--------~~Ea~ii~~ag  486 (796)
T PRK12906        423 DSKFNAVVKEIKERH--AKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNH--------AKEAEIIMNAG  486 (796)
T ss_pred             HHHHHHHHHHHHHHH--hCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcH--------HHHHHHHHhcC
Confidence            458889999998765  34789999999999999999999999999999999943        66666655554

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=89.67  E-value=1.7  Score=37.38  Aligned_cols=57  Identities=9%  Similarity=0.024  Sum_probs=43.3

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCC--ceEEEeeCCCCCCcchhhHhhhHHH
Q 028376          127 VTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN--ITCIKMKGENHKLPSANLQHRNALQ  189 (210)
Q Consensus       127 l~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~g--i~~~~~~G~m~~~~~~~~~~R~~~l  189 (210)
                      +++.+.+..+..++.|+|||..-....+.+...|+.+|  +.+..+.|.|+      ..+|.+++
T Consensus       259 l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~------~~~R~~~~  317 (357)
T TIGR03158       259 LAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAP------KKDRERAM  317 (357)
T ss_pred             HHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCC------HHHHHHhc
Confidence            34444433334567899999999999999999999875  57788999977      88887654

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=89.39  E-value=2.1  Score=36.43  Aligned_cols=66  Identities=15%  Similarity=0.191  Sum_probs=49.9

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCc--eEEEeeCCCCCCcchhhHhhhH----HHHHHhhc
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNI--TCIKMKGENHKLPSANLQHRNA----LQKELTRH  195 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi--~~~~~~G~m~~~~~~~~~~R~~----~l~~F~~~  195 (210)
                      .|.+.+.+.+..+   ..+.|+|||..-....+.+...|.+++.  ....+.|.|+      ..+|.+    +++.|.++
T Consensus       207 ~~~~~l~~l~~~~---~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~------~~~r~~~~~~~~~~f~~~  277 (358)
T TIGR01587       207 GEISSLERLLEFI---KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFT------EKDRAKKEAELLEEMKKN  277 (358)
T ss_pred             cCHHHHHHHHHHh---hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCC------HHHHHHHHHHHHHHhcCC
Confidence            4555555444332   2367999999999999999999998877  4888999976      888866    48889874


Q ss_pred             C
Q 028376          196 M  196 (210)
Q Consensus       196 ~  196 (210)
                      .
T Consensus       278 ~  278 (358)
T TIGR01587       278 E  278 (358)
T ss_pred             C
Confidence            4

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.12  E-value=0.17  Score=41.84  Aligned_cols=47  Identities=23%  Similarity=0.448  Sum_probs=32.0

Q ss_pred             CCCcchHhhHHHHHHHhhhccc--cCCCccccccCCcccccCCCeEEcc
Q 028376           43 CGHFTCCKCFFAMTEQRLIHDN--KVKNEWVMCPTCRQRTDIGNIAYAD   89 (210)
Q Consensus        43 CgH~fC~~C~~~~~~~~~~~~~--~~~~~~~~CP~Cr~~~~~~~l~~~~   89 (210)
                      |...-|.+|+.+|+.....+-.  ....+...||+||+.+...++.++.
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv~~v~  373 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDVHCVD  373 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeeeeEEE
Confidence            3455678999999743211100  1246788999999999999887664

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.89  E-value=0.22  Score=29.67  Aligned_cols=32  Identities=25%  Similarity=0.699  Sum_probs=21.9

Q ss_pred             eecCC-CCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           39 MVFQC-GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        39 ~~~~C-gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      -+..| .|..|..|+..++           .....||+|..++.
T Consensus        14 ~Li~C~dHYLCl~CLt~ml-----------~~s~~C~iC~~~LP   46 (50)
T PF03854_consen   14 GLIKCSDHYLCLNCLTLML-----------SRSDRCPICGKPLP   46 (50)
T ss_dssp             SEEE-SS-EEEHHHHHHT------------SSSSEETTTTEE--
T ss_pred             CeeeecchhHHHHHHHHHh-----------ccccCCCcccCcCc
Confidence            34556 5999999999884           56678999998764

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. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.43  E-value=0.3  Score=39.47  Aligned_cols=33  Identities=6%  Similarity=0.125  Sum_probs=28.7

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHH
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMT   56 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~   56 (210)
                      +..-|..|+.+..+ +++++=||+||.+||.+++
T Consensus        42 ~FdcCsLtLqPc~d-Pvit~~GylfdrEaILe~i   74 (303)
T KOG3039|consen   42 PFDCCSLTLQPCRD-PVITPDGYLFDREAILEYI   74 (303)
T ss_pred             CcceeeeecccccC-CccCCCCeeeeHHHHHHHH
Confidence            34568999999988 5999999999999998875

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=88.12  E-value=0.63  Score=40.77  Aligned_cols=66  Identities=18%  Similarity=0.282  Sum_probs=54.3

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      +.|.+.+-..+..   ..+++|+|||..-.-+.|.+..-|...||..-.+.|...      ...|+.+|+.|+.+
T Consensus       449 ~~k~~~~~~f~~~---ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~------Q~DrE~al~~~ksG  514 (629)
T KOG0336|consen  449 SEKLEIVQFFVAN---MSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNRE------QSDREMALEDFKSG  514 (629)
T ss_pred             HHHHHHHHHHHHh---cCCCceEEEEEechhhhhhccchhhhcccchhhccCChh------hhhHHHHHHhhhcC
Confidence            4455433333333   356899999999999999999999999999999999976      88999999999973

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]

Probab=88.11  E-value=0.12  Score=47.70  Aligned_cols=52  Identities=23%  Similarity=0.514  Sum_probs=41.1

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      ..+|+||......+ +.+.|.|.||..|+...+..        ......||+|+..+....
T Consensus        21 ~lEc~ic~~~~~~p-~~~kc~~~~l~~~~n~~f~~--------~~~~~~~~lc~~~~eK~s   72 (684)
T KOG4362|consen   21 ILECPICLEHVKEP-SLLKCDHIFLKFCLNKLFES--------KKGPKQCALCKSDIEKRS   72 (684)
T ss_pred             hccCCceeEEeecc-chhhhhHHHHhhhhhceeec--------cCccccchhhhhhhhhhh
Confidence            46899999988774 89999999999999987654        234668999997665443

>KOG1940 consensus Zn-finger protein [General function prediction only]

Probab=88.00  E-value=0.34  Score=40.10  Aligned_cols=45  Identities=38%  Similarity=0.868  Sum_probs=34.8

Q ss_pred             Ccccccccccccc---CCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376           23 DEETCPICQEKLG---NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ   78 (210)
Q Consensus        23 ~~~~C~iC~~~~~---~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~   78 (210)
                      ....||+|.+.+.   ..+..++|||.....|+..+.          ..+ -+||.|.+
T Consensus       157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~----------~~~-y~CP~C~~  204 (276)
T KOG1940|consen  157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMI----------CEG-YTCPICSK  204 (276)
T ss_pred             ccCCCchhHHHhccccccCCccCcccchHHHHHHHHh----------ccC-CCCCcccc
Confidence            3456999977653   235778999999999999885          234 89999988

>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO)

Probab=87.58  E-value=0.39  Score=28.13  Aligned_cols=40  Identities=23%  Similarity=0.504  Sum_probs=21.2

Q ss_pred             cccccccccCCCee-c--CCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           27 CPICQEKLGNQKMV-F--QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        27 C~iC~~~~~~~~~~-~--~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      |.+|.+.+... +. .  .|+=.++..|+..++..         .....||.|
T Consensus         1 C~~C~~iv~~G-~~C~~~~C~~r~H~~C~~~y~r~---------~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQG-QRCSNRDCNVRLHDDCFKKYFRH---------RSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSS-EE-SS--S--EE-HHHHHHHTTT----------SS-B-TTT
T ss_pred             CcccchhHeee-ccCCCCccCchHHHHHHHHHHhc---------CCCCCCcCC
Confidence            67788777654 43 3  48888999999999643         223379987

; PDB: 3NW0_A 2CT0_A.

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=87.50  E-value=2  Score=37.56  Aligned_cols=67  Identities=10%  Similarity=0.212  Sum_probs=54.7

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS  199 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~  199 (210)
                      +|+-.|++-|.     .-.-+++||.-=..-.|-|...|-..|+.-+.+.|+..      ...|..+|+.|+.+.-|+
T Consensus       408 aKiVylLeCLQ-----KT~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKD------QedR~~ai~afr~gkKDV  474 (610)
T KOG0341|consen  408 AKIVYLLECLQ-----KTSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKD------QEDRHYAIEAFRAGKKDV  474 (610)
T ss_pred             hhhhhHHHHhc-----cCCCceEEEeccccChHHHHHHHHHccceeEEeecCcc------hhHHHHHHHHHhcCCCce
Confidence            45555555544     23568999999888899999999999999999999977      999999999999865554

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=87.43  E-value=0.39  Score=40.25  Aligned_cols=50  Identities=20%  Similarity=0.493  Sum_probs=35.6

Q ss_pred             cccccccccc--cCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           25 ETCPICQEKL--GNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        25 ~~C~iC~~~~--~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      +.||+=.+.-  +++++.+.|||++-.+-+..+-++        +....+||.|-.....
T Consensus       337 FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~n--------G~~~FKCPYCP~~~~~  388 (396)
T COG5109         337 FICPVLKELCTDENPPVMLECGHVISKEALSVLSQN--------GVLSFKCPYCPEMSKY  388 (396)
T ss_pred             eeccccHhhhcccCCCeeeeccceeeHHHHHHHhhc--------CcEEeeCCCCCcchhh
Confidence            5688643322  456799999999999998887433        4668899999654333

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=87.41  E-value=2.9  Score=37.81  Aligned_cols=62  Identities=21%  Similarity=0.161  Sum_probs=42.5

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..+|..+.-=+|+...  ..++|+||||--.-.|.  +.+++ .|=+|  +.|..+      ..+|.++|+.|+.
T Consensus       525 NP~KFraCqfLI~~HE--~RgDKiIVFsDnvfALk--~YAik-l~Kpf--IYG~Ts------q~ERm~ILqnFq~  586 (776)
T KOG1123|consen  525 NPNKFRACQFLIKFHE--RRGDKIIVFSDNVFALK--EYAIK-LGKPF--IYGPTS------QNERMKILQNFQT  586 (776)
T ss_pred             CcchhHHHHHHHHHHH--hcCCeEEEEeccHHHHH--HHHHH-cCCce--EECCCc------hhHHHHHHHhccc
Confidence            3567776655555443  36999999998654433  33443 34454  568766      9999999999998

>PRK10689 transcription-repair coupling factor; Provisional

Probab=86.33  E-value=3.3  Score=41.26  Aligned_cols=54  Identities=2%  Similarity=-0.029  Sum_probs=46.3

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376          140 KAKILVFSSWNDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS  199 (210)
Q Consensus       140 ~~K~iVFSQf~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~  199 (210)
                      +.+++||..-...++.+...|.+.  +++...++|.|+      ..+|.+++..|.++..++
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~------q~eRe~im~~Fr~Gk~~V  864 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMR------ERELERVMNDFHHQRFNV  864 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCC------HHHHHHHHHHHHhcCCCE
Confidence            568999988888888888899886  888889999977      999999999999865443

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=86.28  E-value=0.23  Score=45.32  Aligned_cols=33  Identities=27%  Similarity=0.602  Sum_probs=25.3

Q ss_pred             ccccccccccccC---CCeecCCCCcchHhhHHHHH
Q 028376           24 EETCPICQEKLGN---QKMVFQCGHFTCCKCFFAMT   56 (210)
Q Consensus        24 ~~~C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~   56 (210)
                      ...|+||...+..   .++.+.|||..|..|+....
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly   46 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY   46 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh
Confidence            3579999655432   24778999999999999874

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=85.82  E-value=4.1  Score=39.71  Aligned_cols=52  Identities=6%  Similarity=0.024  Sum_probs=46.2

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          140 KAKILVFSSWNDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       140 ~~K~iVFSQf~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      +.+++||..-....+.+...|+..  +++...++|.|+      ..+|.++++.|.++.-
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~------~~eRe~im~~F~~Gk~  713 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMT------ENELEEVMLEFYKGEF  713 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCC------HHHHHHHHHHHHcCCC
Confidence            579999999999999999999884  899999999977      9999999999998543

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]

Probab=85.03  E-value=4.8  Score=37.10  Aligned_cols=54  Identities=9%  Similarity=0.082  Sum_probs=47.7

Q ss_pred             cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          137 TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..++.-.|||..-...-+-+...|..+|+.-..|+|+|.      ...|..+-++|.+++
T Consensus       227 ~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~------~~eR~~~q~~f~~~~  280 (590)
T COG0514         227 PQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLS------NEERERVQQAFLNDE  280 (590)
T ss_pred             cccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCC------HHHHHHHHHHHhcCC
Confidence            344555799999999999999999999999999999976      999999999999844

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase

Probab=84.73  E-value=3.7  Score=39.03  Aligned_cols=52  Identities=12%  Similarity=0.049  Sum_probs=43.7

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHhC--------CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          140 KAKILVFSSWNDVLDVLEHAFIAN--------NITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       140 ~~K~iVFSQf~~~L~li~~~L~~~--------gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      +.|+|||..-....+.+...|...        +.+...|.|+|.      ..+|.++++.|.++.-
T Consensus       271 ~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~------~~eR~~ie~~f~~G~i  330 (742)
T TIGR03817       271 GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYL------PEDRRELERALRDGEL  330 (742)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCC------HHHHHHHHHHHHcCCc
Confidence            679999999999999998887653        566677899966      9999999999998543

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=84.10  E-value=1.9  Score=41.89  Aligned_cols=66  Identities=9%  Similarity=0.043  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          125 EAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       125 ~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      +++...+..+....++.-+|||.......+.|+..|...|+...-|..+|+      ..+|..+.+.|..+.
T Consensus       470 ~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~------~~~R~~Vq~~w~~~~  535 (941)
T KOG0351|consen  470 DALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLP------PKERETVQKAWMSDK  535 (941)
T ss_pred             cchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCC------HHHHHHHHHHHhcCC
Confidence            556666777777788999999999999999999999999999999999977      999999999999844

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=84.05  E-value=2.1  Score=38.59  Aligned_cols=51  Identities=10%  Similarity=0.120  Sum_probs=47.3

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          140 KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       140 ~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..++|||.+-......+...|...|+..-.+.|+      |+..||-.+|+.|.+..
T Consensus       426 ~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGs------LtQ~QRlesL~kFk~~e  476 (691)
T KOG0338|consen  426 QDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGS------LTQEQRLESLEKFKKEE  476 (691)
T ss_pred             ccceEEEEehHHHHHHHHHHHHHhhchhhhhccc------ccHHHHHHHHHHHHhcc
Confidence            5799999999999999999999999999999999      56999999999999844

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=83.73  E-value=5.6  Score=36.38  Aligned_cols=65  Identities=25%  Similarity=0.252  Sum_probs=53.0

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh--CCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA--NNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~--~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..-||+.|-.-|..    .+..|+|||-+--.=...+-.+|.+  -||+..-+.|+|+      ..+|..+.+.|..
T Consensus       297 l~~Ki~~L~sFI~s----hlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~------Q~~R~ev~~~F~~  363 (758)
T KOG0343|consen  297 LEDKIDMLWSFIKS----HLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMS------QKKRIEVYKKFVR  363 (758)
T ss_pred             hhhHHHHHHHHHHh----ccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchh------HHHHHHHHHHHHH
Confidence            35788877777764    5678999987777766777777764  6999999999977      9999999999987

>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair

Probab=83.37  E-value=0.92  Score=27.62  Aligned_cols=40  Identities=23%  Similarity=0.562  Sum_probs=22.4

Q ss_pred             cccccccccCC---------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376           27 CPICQEKLGNQ---------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR   77 (210)
Q Consensus        27 C~iC~~~~~~~---------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr   77 (210)
                      |..|..++...         ..-..|++.||.+|=.=+           ...-..||.|.
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi-----------HE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFI-----------HETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTT-----------TTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhh-----------hccccCCcCCC
Confidence            66777776653         122589999999996533           35566899884

It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.

>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=83.35  E-value=1.2  Score=34.34  Aligned_cols=59  Identities=19%  Similarity=0.304  Sum_probs=35.4

Q ss_pred             CccccccccccccCC------CeecCCCCcchHhhHHHHHHHhhhccccC-CCccccccCCcccccC
Q 028376           23 DEETCPICQEKLGNQ------KMVFQCGHFTCCKCFFAMTEQRLIHDNKV-KNEWVMCPTCRQRTDI   82 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~-~~~~~~CP~Cr~~~~~   82 (210)
                      +...|.||...--+.      .-..+||..|+.-|+..|++.-. +.... .---..||.|..++..
T Consensus       164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgil-TsRQSFdiiFGeCPYCS~Pial  229 (234)
T KOG3268|consen  164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGIL-TSRQSFDIIFGECPYCSDPIAL  229 (234)
T ss_pred             hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHh-hccceeeeeeccCCCCCCccee
Confidence            345677775432111      13469999999999999986422 21100 1112369999888754

>PRK13767 ATP-dependent helicase; Provisional

Probab=82.74  E-value=7.4  Score=37.75  Aligned_cols=64  Identities=11%  Similarity=0.052  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh------CCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          125 EAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA------NNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       125 ~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~------~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..+.+.|.++...  ..++|||..-....+.+...|..      .+.....+.|+|+      ..+|..+++.|+++.
T Consensus       271 ~~l~~~L~~~i~~--~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls------~~~R~~ve~~fk~G~  340 (876)
T PRK13767        271 EALYETLHELIKE--HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLS------REVRLEVEEKLKRGE  340 (876)
T ss_pred             HHHHHHHHHHHhc--CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCC------HHHHHHHHHHHHcCC
Confidence            4455555554432  56899999999888888888876      3466777899966      999999999999854

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

Probab=82.64  E-value=0.67  Score=24.03  Aligned_cols=22  Identities=27%  Similarity=0.558  Sum_probs=10.5

Q ss_pred             ccccccccccCCCee-cCCCCcc
Q 028376           26 TCPICQEKLGNQKMV-FQCGHFT   47 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~-~~CgH~f   47 (210)
                      .||.|...+...... ..|||.|
T Consensus         2 ~CP~C~~~V~~~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPESAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhhcCcCCCCCCCC
Confidence            466666554432222 2366654

Several members are annotated as putative helicases.

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=82.57  E-value=1.8  Score=39.36  Aligned_cols=49  Identities=14%  Similarity=0.150  Sum_probs=46.1

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          140 KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       140 ~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      +.+.|||..-.+....|...|..-+|+-+-+...|.      .++|.+.|++|..
T Consensus       463 PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~------QKqRLknLEkF~~  511 (731)
T KOG0347|consen  463 PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMI------QKQRLKNLEKFKQ  511 (731)
T ss_pred             CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHH------HHHHHHhHHHHhc
Confidence            358999999999999999999999999999999965      9999999999998

>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=82.20  E-value=0.92  Score=42.72  Aligned_cols=57  Identities=18%  Similarity=0.511  Sum_probs=42.0

Q ss_pred             CCCcccccccccc-ccCCCeecCCCC-----cchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           21 KADEETCPICQEK-LGNQKMVFQCGH-----FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        21 ~~~~~~C~iC~~~-~~~~~~~~~CgH-----~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      ..++..|.||... ..+.+..-||..     ..+.+|+.+|++.         ++..+|-.|..++...++.
T Consensus         9 N~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~---------s~~~kCdiChy~~~Fk~IY   71 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMEC---------SGTKKCDICHYEYKFKDIY   71 (1175)
T ss_pred             CccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhc---------CCCcceeeecceeeeeeec
Confidence            3466899999654 334345567753     4688999999863         6678999999999888774

>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins

Probab=81.98  E-value=5.7  Score=26.80  Aligned_cols=34  Identities=3%  Similarity=-0.048  Sum_probs=30.1

Q ss_pred             CCcEEEEcc------hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376          140 KAKILVFSS------WNDVLDVLEHAFIANNITCIKMKGE  173 (210)
Q Consensus       140 ~~K~iVFSQ------f~~~L~li~~~L~~~gi~~~~~~G~  173 (210)
                      ..+++|||.      |-.+-..+...|+..||.|..++=.
T Consensus         7 ~~~vvvf~k~~~~~~~Cp~C~~ak~~L~~~~i~y~~idv~   46 (90)
T cd03028           7 ENPVVLFMKGTPEEPRCGFSRKVVQILNQLGVDFGTFDIL   46 (90)
T ss_pred             cCCEEEEEcCCCCCCCCcHHHHHHHHHHHcCCCeEEEEcC
Confidence            569999987      8888899999999999999998754

The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein

>KOG4284 consensus DEAD box protein [Transcription]

Probab=81.91  E-value=2.2  Score=39.63  Aligned_cols=62  Identities=11%  Similarity=0.146  Sum_probs=52.8

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          127 VTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       127 l~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      -++.|..+...-|-..+|||+.-.+=.+-+...|...||...-+.|.|+      ..+|..+++..+.
T Consensus       259 klq~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~------Q~~Rl~a~~~lr~  320 (980)
T KOG4284|consen  259 KLQKLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMS------QKDRLLAVDQLRA  320 (980)
T ss_pred             HHHHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccc------hhHHHHHHHHhhh
Confidence            3445555555667889999999999999999999999999999999977      9999999888765

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=81.90  E-value=1.5  Score=37.23  Aligned_cols=66  Identities=11%  Similarity=0.247  Sum_probs=57.5

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      .+-|+..|--.+.+++    -..+|||...+.-.+++..-..+.|..+..+..+|-      ...|+++...|.++
T Consensus       306 e~qKvhCLntLfskLq----INQsIIFCNS~~rVELLAkKITelGyscyyiHakM~------Q~hRNrVFHdFr~G  371 (459)
T KOG0326|consen  306 ERQKVHCLNTLFSKLQ----INQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMA------QEHRNRVFHDFRNG  371 (459)
T ss_pred             hhhhhhhHHHHHHHhc----ccceEEEeccchHhHHHHHHHHhccchhhHHHHHHH------Hhhhhhhhhhhhcc
Confidence            4678877777777666    458999999999999999999999999999999966      99999999999873

>PLN02189 cellulose synthase

Probab=80.98  E-value=1.5  Score=42.59  Aligned_cols=54  Identities=26%  Similarity=0.633  Sum_probs=37.7

Q ss_pred             CCCCccccccccccccCC----C--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           20 SKADEETCPICQEKLGNQ----K--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        20 ~~~~~~~C~iC~~~~~~~----~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      +......|.||.+.+...    +  ..-.|+--.|..|.+ + ++        .++...||.|+.++...
T Consensus        30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye-y-er--------~eg~q~CpqCkt~Y~r~   89 (1040)
T PLN02189         30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE-Y-ER--------REGTQNCPQCKTRYKRL   89 (1040)
T ss_pred             ccccCccccccccccCcCCCCCEEEeeccCCCccccchhh-h-hh--------hcCCccCcccCCchhhc
Confidence            344556899999886521    1  223578889999995 3 22        46778999999988743

---

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	210
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	3e-05
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	8e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	4e-04
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	7e-04
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	7e-04

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 11/67 (16%)

Query: 23 DEETCPICQEKLGNQK---MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79
          +   CPIC E    ++    +  CGH  C +C      ++L+  +      V CP C + 
Sbjct: 14 EVLECPICMESFTEEQLRPKLLHCGHTICRQCL-----EKLLASSING---VRCPFCSKI 65

Query: 80 TDIGNIA 86
          T I ++ 
Sbjct: 66 TRITSLT 72

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Length = 78

 Score = 40.1 bits (93), Expect = 3e-05
 Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 13/78 (16%)

Query: 20 SKADEETCPICQEKLGNQKMVF---QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC 76
          +K D   CP+C E L    + F    CG+  C  C+               +E  +CP C
Sbjct: 7  AKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCW----------HRIRTDENGLCPAC 56

Query: 77 RQRTDIGNIAYADDRQDK 94
          R+        Y    Q++
Sbjct: 57 RKPYPEDPAVYKPLSQEE 74

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114

 Score = 39.8 bits (92), Expect = 8e-05
 Identities = 21/82 (25%), Positives = 28/82 (34%), Gaps = 23/82 (28%)

Query: 13 KHRIESLSKADEETCPICQEKLGNQ-----------------KMVFQCGHFTCCKCFFAM 55
          +   E L  A EE C IC EKL                      + +C H     C  AM
Sbjct: 14 RKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAM 73

Query: 56 TEQRLIHDNKVKNEWVMCPTCR 77
                  N  K+  + CP+C+
Sbjct: 74 YC------NGNKDGSLQCPSCK 89

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 9/57 (15%)

Query: 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79
          DE  C IC++ + +  ++  CG+  C +C         I    ++++   CPTC Q 
Sbjct: 14 DELLCLICKDIMTDAVVIPCCGNSYCDEC---------IRTALLESDEHTCPTCHQN 61

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99

 Score = 36.7 bits (85), Expect = 7e-04
 Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 12/81 (14%)

Query: 6  VTISNSTKHRIESLSKADEE-TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDN 64
              +     +  +   D+   C IC E      ++ QC H  C  C      + L +  
Sbjct: 3  SLAESRWPPGLAVMKTIDDLLRCGICFEYFNIAMIIPQCSHNYCSLCI----RKFLSYKT 58

Query: 65 KVKNEWVMCPTCRQRTDIGNI 85
          +       CPTC       ++
Sbjct: 59 Q-------CPTCCVTVTEPDL 72

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72

 Score = 35.9 bits (83), Expect = 7e-04
 Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 13/70 (18%)

Query: 9  SNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKN 68
          S+ +   +  L+      C IC+  L +   + +C H  C  C       R  + +    
Sbjct: 2  SSGSSGNLSELT--PYILCSICKGYLIDATTITECLHTFCKSCIV-----RHFYYSNR-- 52

Query: 69 EWVMCPTCRQ 78
              CP C  
Sbjct: 53 ----CPKCNI 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	210
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.29
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.26
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.25
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.23
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.23
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.23
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.22
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.21
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.21
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.19
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.18
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.18
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.18
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.16
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.16
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.15
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.15
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.15
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.14
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.14
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.13
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.13
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.13
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.13
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.11
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.1
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.09
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.09
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.08
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.06
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.05
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.04
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.04
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.03
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.03
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.03
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.02
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.01
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.01
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.0
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.98
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.98
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.96
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.96
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.96
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.93
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.91
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.9
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.89
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.89
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.88
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.88
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.87
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.84
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.84
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.82
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.82
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.8
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.79
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.79
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.77
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.74
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.73
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.72
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.72
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.65
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.5
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.48
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.42
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.42
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.38
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	98.33
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.25
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	98.21
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	98.18
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	98.17
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.16
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	98.08
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	98.06
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	97.99
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	97.94
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	97.93
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	97.92
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	97.78
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	97.77
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	97.76
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	97.71
4gl2_A	699	Interferon-induced helicase C domain-containing P;	97.58
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	96.7
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	97.44
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	97.4
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	97.23
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	97.08
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	97.04
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	96.97
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	96.9
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	96.89
3nw0_A	238	Non-structural maintenance of chromosomes element	96.82
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	96.77
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	96.68
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	96.64
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	96.59
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	96.36
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	96.35
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	96.26
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	96.2
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	96.09
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	96.06
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.02
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.77
3h1t_A	590	Type I site-specific restriction-modification syst	95.28
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	95.09
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	93.73
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	93.0
3jux_A	822	Protein translocase subunit SECA; protein transloc	92.98
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	92.82
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	92.65
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	92.08
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	92.04
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	91.95
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	91.43
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	90.33
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	89.53
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	88.94
2l82_A	162	Designed protein OR32; structural genomics, northe	88.85
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	87.59
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	82.71
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	82.48
3ipz_A	109	Monothiol glutaredoxin-S14, chloroplastic; electro	82.19
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	81.73
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	80.78
1z60_A	59	TFIIH basal transcription factor complex P44 subun	80.39
2lqo_A	92	Putative glutaredoxin RV3198.1/MT3292; TRX fold, o	80.18

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.29  E-value=2e-12  Score=83.17  Aligned_cols=53  Identities=23%  Similarity=0.514  Sum_probs=44.3

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .+...|+||.+.+.++ +.++|||.||..|+..|+.          .....||.||.++...++
T Consensus        13 ~~~~~C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~----------~~~~~CP~Cr~~~~~~~i   65 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP-KQTECGHRFCESCMAALLS----------SSSPKCTACQESIVKDKV   65 (66)
T ss_dssp             CCCEECTTTCCEESSC-CCCSSSCCCCHHHHHHHHT----------TSSCCCTTTCCCCCTTTC
T ss_pred             CcCCCCCCCChHhcCe-eECCCCCHHHHHHHHHHHH----------hCcCCCCCCCcCCChhhc
Confidence            3567899999999874 7799999999999999962          345689999999887765

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=2.1e-12  Score=84.61  Aligned_cols=55  Identities=31%  Similarity=0.753  Sum_probs=44.6

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .+...|+||++.+.+ ++.++|||.||..|+..|++.        ......||.||.++...++
T Consensus        18 ~~~~~C~IC~~~~~~-~~~~~CgH~fC~~Ci~~~~~~--------~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           18 QEEVICPICLDILQK-PVTIDCGHNFCLKCITQIGET--------SCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCCBCTTTCSBCSS-EEECTTCCEEEHHHHHHHCSS--------SCSCCCCSSSCCCCCCCCC
T ss_pred             ccCCEeccCCcccCC-eEEcCCCChhhHHHHHHHHHc--------CCCCCCCCCCCCcCCcccC
Confidence            356789999999887 488899999999999999531        1356789999999877654

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=2.6e-12  Score=84.13  Aligned_cols=53  Identities=21%  Similarity=0.350  Sum_probs=43.6

Q ss_pred             CCccccccccccccCCCee-cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           22 ADEETCPICQEKLGNQKMV-FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~-~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .+...|+||++.+.++ +. ++|||.||..|+..|+..           ...||+||.++...++.
T Consensus        13 ~~~~~C~IC~~~~~~p-~~~~~CgH~fC~~Ci~~~~~~-----------~~~CP~Cr~~~~~~~~~   66 (72)
T 2djb_A           13 TPYILCSICKGYLIDA-TTITECLHTFCKSCIVRHFYY-----------SNRCPKCNIVVHQTQPL   66 (72)
T ss_dssp             CGGGSCTTTSSCCSSC-EECSSSCCEECHHHHHHHHHH-----------CSSCTTTCCCCCSSCSC
T ss_pred             CCCCCCCCCChHHHCc-CEECCCCCHHHHHHHHHHHHc-----------CCcCCCcCcccCccccc
Confidence            3457899999999875 55 599999999999999743           35899999998877654

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.23  E-value=6.8e-12  Score=83.29  Aligned_cols=54  Identities=13%  Similarity=0.243  Sum_probs=44.4

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .+...|+||.+.+.+ ++.++|||.||..|+..|+.          .+...||.||.++...++.
T Consensus         6 ~~~~~C~IC~~~~~~-Pv~~~CgH~fc~~Ci~~~~~----------~~~~~CP~C~~~~~~~~l~   59 (78)
T 1t1h_A            6 PEYFRCPISLELMKD-PVIVSTGQTYERSSIQKWLD----------AGHKTCPKSQETLLHAGLT   59 (78)
T ss_dssp             SSSSSCTTTSCCCSS-EEEETTTEEEEHHHHHHHHT----------TTCCBCTTTCCBCSSCCCE
T ss_pred             cccCCCCCccccccC-CEEcCCCCeecHHHHHHHHH----------HCcCCCCCCcCCCChhhCc
Confidence            356789999999987 48899999999999999973          2356899999988766543

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.23  E-value=7.1e-12  Score=80.33  Aligned_cols=55  Identities=31%  Similarity=0.609  Sum_probs=43.9

Q ss_pred             Cccccccccc-cccCCC---eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEE
Q 028376           23 DEETCPICQE-KLGNQK---MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAY   87 (210)
Q Consensus        23 ~~~~C~iC~~-~~~~~~---~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~   87 (210)
                      +...|+||.+ .+.++.   ++++|||.||..|+.+|+.+          ....||.||.++...++..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~----------~~~~CP~Cr~~~~~~~~~~   60 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----------GAGNCPECGTPLRKSNFRV   60 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHT----------TSSSCTTTCCCCSSCCCEE
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHc----------CCCcCCCCCCcccccccee
Confidence            4578999999 666542   46899999999999999642          3468999999998887653

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.23  E-value=9e-12  Score=82.01  Aligned_cols=52  Identities=29%  Similarity=0.632  Sum_probs=42.1

Q ss_pred             CCccccccccccccCCCeecC-CCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           22 ADEETCPICQEKLGNQKMVFQ-CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~-CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .+...|+||++.+.+ ++.++ |||.||..|+..|+..         .....||+||.++...
T Consensus        13 ~~~~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~---------~~~~~CP~Cr~~~~~~   65 (74)
T 2yur_A           13 PDELLCLICKDIMTD-AVVIPCCGNSYCDECIRTALLE---------SDEHTCPTCHQNDVSP   65 (74)
T ss_dssp             CGGGSCSSSCCCCTT-CEECSSSCCEECTTHHHHHHHH---------SSSSCCSSSCCSSCCT
T ss_pred             CCCCCCcCCChHHhC-CeEcCCCCCHHHHHHHHHHHHh---------cCCCcCCCCCCcCCCc
Confidence            345789999999987 48888 9999999999999864         2346899999975443

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=1e-11  Score=84.19  Aligned_cols=56  Identities=29%  Similarity=0.690  Sum_probs=45.0

Q ss_pred             CCccccccccccccC---CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           22 ADEETCPICQEKLGN---QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .+...|+||++.+..   .+++++|||.||..|+..|+..        ......||.||.++...++
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~--------~~~~~~CP~Cr~~~~~~~i   71 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLAS--------SINGVRCPFCSKITRITSL   71 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHH--------CSSCBCCTTTCCCBCCSST
T ss_pred             cCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHc--------CCCCcCCCCCCCcccchhH
Confidence            355789999998875   1478899999999999999865        2345789999999877654

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.21  E-value=4.3e-12  Score=82.60  Aligned_cols=57  Identities=26%  Similarity=0.664  Sum_probs=45.4

Q ss_pred             cCCCCccccccccccccCC------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           19 LSKADEETCPICQEKLGNQ------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        19 l~~~~~~~C~iC~~~~~~~------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +...+...|+||++.+.++      .+.++|||.||..|+.+|+..           ...||.||.++...++.
T Consensus         5 ~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-----------~~~CP~Cr~~~~~~~~~   67 (71)
T 3ng2_A            5 LRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-----------ANTCPTCRKKINHKRYH   67 (71)
T ss_dssp             -CCTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHH-----------CSBCTTTCCBCCCCSCC
T ss_pred             CCCCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHc-----------CCCCCCCCCccChhhee
Confidence            3456778999999987652      178999999999999999754           24899999998877653

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=99.21  E-value=7.6e-12  Score=79.64  Aligned_cols=54  Identities=26%  Similarity=0.641  Sum_probs=44.3

Q ss_pred             CccccccccccccCC------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEE
Q 028376           23 DEETCPICQEKLGNQ------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAY   87 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~   87 (210)
                      +...|+||++.+.++      .+.++|||.||..|+.+|++.           ...||.||.++...++..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-----------~~~CP~Cr~~~~~~~~~~   61 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-----------ANTCPTCRKKINHKRYHP   61 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHH-----------CSBCTTTCCBCTTTCEEE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHc-----------CCCCCCCCccCCccceee
Confidence            567899999987652      278899999999999999754           348999999998887653

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=2e-11  Score=81.98  Aligned_cols=58  Identities=34%  Similarity=0.725  Sum_probs=46.4

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .+...|+||.+.+.+ ++.++|||.||..|+..|+.....     ......||.||..+...++
T Consensus        17 ~~~~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~~~~~-----~~~~~~CP~Cr~~~~~~~~   74 (85)
T 2ecv_A           17 KEEVTCPICLELLTQ-PLSLDCGHSFCQACLTANHKKSML-----DKGESSCPVCRISYQPENI   74 (85)
T ss_dssp             CCCCCCTTTCSCCSS-CBCCSSSCCBCTTHHHHHHHHHHH-----TTSCCCCTTTCCSSCSSSC
T ss_pred             cCCCCCCCCCcccCC-ceeCCCCCHHHHHHHHHHHHHhhc-----CCCCCcCCCCCCccCHHhc
Confidence            356789999999887 478899999999999999866332     1346789999999887654

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.18  E-value=4.1e-11  Score=80.44  Aligned_cols=59  Identities=32%  Similarity=0.599  Sum_probs=47.1

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .+...|+||.+.+.+ +++++|||.||..|+..|+.....     ......||.||..+...++.
T Consensus        17 ~~~~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~~~~~-----~~~~~~CP~Cr~~~~~~~~~   75 (85)
T 2ecw_A           17 KEEVTCPICLELLKE-PVSADCNHSFCRACITLNYESNRN-----TDGKGNCPVCRVPYPFGNLK   75 (85)
T ss_dssp             CTTTSCTTTCSCCSS-CEECTTSCCBCHHHHHHHHHHSBC-----TTSCBCCTTTCCCCCTTCCE
T ss_pred             ccCCCCcCCChhhCc-ceeCCCCCHHHHHHHHHHHHhccC-----CCCCCCCCCCCCcCCHHhCC
Confidence            346789999999887 488999999999999999865220     13467899999998877654

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.18  E-value=2.4e-11  Score=83.21  Aligned_cols=49  Identities=31%  Similarity=0.714  Sum_probs=41.0

Q ss_pred             CCccccccccccccCCCeecC-CCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           22 ADEETCPICQEKLGNQKMVFQ-CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~-CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      .+...|+||.+.+.+ ++.++ |||.||..|+..|+..         .....||.||.++
T Consensus        11 ~~~~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~---------~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           11 PDELLCLICKDIMTD-AVVIPCCGNSYCDECIRTALLE---------SDEHTCPTCHQND   60 (92)
T ss_dssp             CTTTEETTTTEECSS-CEECTTTCCEECHHHHHHHHHH---------CTTCCCTTTCCSS
T ss_pred             CcCCCCCCCChhhcC-ceECCCCCCHHHHHHHHHHHHh---------cCCCcCcCCCCcC
Confidence            345789999999987 48888 9999999999999754         2346899999986

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.18  E-value=5.3e-12  Score=82.38  Aligned_cols=52  Identities=21%  Similarity=0.411  Sum_probs=42.8

Q ss_pred             CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      ..+...|+||++.+.+ ++.++|||.||..|+..|+           .....||+||..+...+
T Consensus        12 ~~~~~~C~IC~~~~~~-~~~~~CgH~fC~~Ci~~~~-----------~~~~~CP~Cr~~~~~~~   63 (71)
T 2d8t_A           12 SLTVPECAICLQTCVH-PVSLPCKHVFCYLCVKGAS-----------WLGKRCALCRQEIPEDF   63 (71)
T ss_dssp             SSSCCBCSSSSSBCSS-EEEETTTEEEEHHHHHHCT-----------TCSSBCSSSCCBCCHHH
T ss_pred             CCCCCCCccCCcccCC-CEEccCCCHHHHHHHHHHH-----------HCCCcCcCcCchhCHhh
Confidence            3456789999999887 4888999999999999995           23468999999887654

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=99.16  E-value=1.3e-11  Score=85.98  Aligned_cols=53  Identities=25%  Similarity=0.624  Sum_probs=43.8

Q ss_pred             CccccccccccccCCCee-cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMV-FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~-~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +...|+||++.+.++ +. ++|||.||..|+..|+...          ...||.||.++...++.
T Consensus        21 ~~~~C~IC~~~~~~p-~~~~~CgH~FC~~Ci~~~~~~~----------~~~CP~Cr~~~~~~~l~   74 (100)
T 3lrq_A           21 EVFRCFICMEKLRDA-RLCPHCSKLCCFSCIRRWLTEQ----------RAQCPHCRAPLQLRELV   74 (100)
T ss_dssp             HHTBCTTTCSBCSSE-EECTTTCCEEEHHHHHHHHHHT----------CSBCTTTCCBCCGGGCE
T ss_pred             CCCCCccCCccccCc-cccCCCCChhhHHHHHHHHHHC----------cCCCCCCCCcCCHHHhH
Confidence            456899999999875 66 9999999999999997541          25899999998766554

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.16  E-value=1.3e-11  Score=91.06  Aligned_cols=47  Identities=28%  Similarity=0.655  Sum_probs=39.9

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ...|+||.+.+.+ +++++|||.||..|+..|+           .....||.||.++..
T Consensus        53 ~~~C~iC~~~~~~-~~~~~CgH~fc~~Ci~~~~-----------~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYFIE-AVTLNCAHSFCSYCINEWM-----------KRKIECPICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBCSS-EEEETTSCEEEHHHHHHHT-----------TTCSBCTTTCCBCCC
T ss_pred             cCCCcccCcccCC-ceECCCCCCccHHHHHHHH-----------HcCCcCCCCCCcCCC
Confidence            4579999999987 5889999999999999995           345689999998754

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=99.15  E-value=3.1e-11  Score=74.50  Aligned_cols=50  Identities=28%  Similarity=0.693  Sum_probs=40.6

Q ss_pred             CCCccccccccccccC---CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           21 KADEETCPICQEKLGN---QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ..+...|+||++.+.+   ..++++|||.||..|+.+|+..           ...||+||.++.
T Consensus         2 ~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-----------~~~CP~Cr~~~~   54 (55)
T 2ecm_A            2 SSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKE-----------GYRCPLCSGPSS   54 (55)
T ss_dssp             CSCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHH-----------TCCCTTSCCSSC
T ss_pred             CCCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHc-----------CCcCCCCCCcCC
Confidence            3466899999998754   2577899999999999999754           258999998764

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.15  E-value=3.5e-11  Score=76.51  Aligned_cols=46  Identities=35%  Similarity=0.870  Sum_probs=38.3

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      .+...|+||++.+.+ +++++|||.||..|+..|++.        ......||+|
T Consensus        18 ~~~~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~~--------~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQK-PVTIDCGHNFCLKCITQIGET--------SCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSS-CEECTTSSEECHHHHHHHHHH--------CSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCC-eEEeCCCCcchHHHHHHHHHc--------CCCCCcCcCC
Confidence            356789999999987 488899999999999999864        2345689998

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=99.15  E-value=2.7e-11  Score=86.20  Aligned_cols=68  Identities=29%  Similarity=0.491  Sum_probs=47.5

Q ss_pred             CchHHHHHh----cCCCCccccccccccccCCC-----------------eecCCCCcchHhhHHHHHHHhhhccccCCC
Q 028376           10 NSTKHRIES----LSKADEETCPICQEKLGNQK-----------------MVFQCGHFTCCKCFFAMTEQRLIHDNKVKN   68 (210)
Q Consensus        10 ~~~~~~~~~----l~~~~~~~C~iC~~~~~~~~-----------------~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~   68 (210)
                      ...++++..    +....+..|+||++.+..+.                 .+++|||.||..|+..|+....      ..
T Consensus         7 ~~p~~~i~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~------~~   80 (114)
T 1v87_A            7 GEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN------KD   80 (114)
T ss_dssp             CCHHHHHHHHEEECSSCCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTC------CS
T ss_pred             CChHHHHHHHHHhccCCCCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHccc------CC
Confidence            344455544    34455679999999885421                 2789999999999999985411      13


Q ss_pred             ccccccCCcccccCC
Q 028376           69 EWVMCPTCRQRTDIG   83 (210)
Q Consensus        69 ~~~~CP~Cr~~~~~~   83 (210)
                      ....||+||..+...
T Consensus        81 ~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           81 GSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCCBCTTTCCBSSSC
T ss_pred             CCCcCCCCCCccCCC
Confidence            456899999987543

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=99.14  E-value=1.8e-11  Score=79.07  Aligned_cols=49  Identities=33%  Similarity=0.681  Sum_probs=41.2

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      .+...|+||++.+.++.+.++|||.||..|+..|++.           ...||.||.++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~-----------~~~CP~Cr~~~~   51 (68)
T 1chc_A            3 TVAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQ-----------NPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHH-----------SCSTTTTCCCCC
T ss_pred             CCCCCCeeCCccccCCcEecCCCCeeHHHHHHHHHhC-----------cCcCcCCChhhH
Confidence            3567899999998875588999999999999999743           258999999875

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.14  E-value=3.4e-11  Score=79.89  Aligned_cols=54  Identities=26%  Similarity=0.553  Sum_probs=42.8

Q ss_pred             CCccccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           22 ADEETCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .+...|+||++.+..+  ...++|||.||..|+.+|++           ....||+||..+...++.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~-----------~~~~CP~Cr~~~~~~~~~   68 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLE-----------QHDSCPVCRKSLTGQNTA   68 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHT-----------TTCSCTTTCCCCCCSCSC
T ss_pred             CCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHH-----------cCCcCcCcCCccCCcccC
Confidence            3567899999987643  25579999999999999963           235899999998877654

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=99.13  E-value=3.9e-11  Score=79.75  Aligned_cols=57  Identities=30%  Similarity=0.677  Sum_probs=43.0

Q ss_pred             CCccccccccccccC-CCeecC--CCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376           22 ADEETCPICQEKLGN-QKMVFQ--CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA   88 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~-~~~~~~--CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~   88 (210)
                      .+...|+||++++.. +..+++  |||.||..|+..+.          ......||.||.++....+.+.
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~----------~~~~~~CP~CR~~~~~~~~~~~   68 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIR----------TDENGLCPACRKPYPEDPAVYK   68 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHT----------TSSCSBCTTTCCBCSSCSSCCC
T ss_pred             ccCCcCCccCccCccccccccccCCCCCcCHHHHHHHH----------hcCCCCCCCCCCccCCCchhhc
Confidence            456789999998853 234444  99999999999873          1345689999999988766443

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=2.6e-11  Score=81.09  Aligned_cols=48  Identities=27%  Similarity=0.545  Sum_probs=40.7

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      .+...|+||++.+.+ +++++|||.||..|+..|++.           ...||+||.++.
T Consensus        13 ~~~~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~~-----------~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN-PVVTKCRHYFCESCALEHFRA-----------TPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS-EEECTTSCEEEHHHHHHHHHH-----------CSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC-eeEccCCCHhHHHHHHHHHHC-----------CCcCCCcCcccc
Confidence            345689999999987 488999999999999999743           348999999875

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.13  E-value=2e-11  Score=86.51  Aligned_cols=53  Identities=26%  Similarity=0.638  Sum_probs=43.2

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ...|+||.+.+.++ +.++|||.||..|+..|+..        ......||.||.++...++
T Consensus        21 ~~~C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~~--------~~~~~~CP~Cr~~~~~~~~   73 (112)
T 1jm7_A           21 ILECPICLELIKEP-VSTKCDHIFCKFCMLKLLNQ--------KKGPSQCPLCKNDITKRSL   73 (112)
T ss_dssp             HTSCSSSCCCCSSC-CBCTTSCCCCSHHHHHHHHS--------SSSSCCCTTTSCCCCTTTC
T ss_pred             CCCCcccChhhcCe-EECCCCCHHHHHHHHHHHHh--------CCCCCCCcCCCCcCCHhhc
Confidence            46899999998874 77999999999999999754        2334689999998876543

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.13  E-value=1.4e-11  Score=81.77  Aligned_cols=59  Identities=27%  Similarity=0.641  Sum_probs=44.5

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      .+...|+||.+.+.+ ++.++|||.||..|+..|+......    ......||.||.++...++
T Consensus        10 ~~~~~C~IC~~~~~~-p~~l~CgH~fC~~Ci~~~~~~~~~~----~~~~~~CP~Cr~~~~~~~l   68 (79)
T 2egp_A           10 QEEVTCPICLELLTE-PLSLDCGHSLCRACITVSNKEAVTS----MGGKSSCPVCGISYSFEHL   68 (79)
T ss_dssp             CCCCEETTTTEECSS-CCCCSSSCCCCHHHHSCCCCCCSSS----CCCCCCCSSSCCCCCSSGG
T ss_pred             ccCCCCcCCCcccCC-eeECCCCCHHHHHHHHHHHHhcccC----CCCCCcCCCCCCcCCHhhC
Confidence            356789999999887 4778999999999999985321100    1336789999999876543

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=1.4e-11  Score=80.08  Aligned_cols=53  Identities=30%  Similarity=0.669  Sum_probs=43.7

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEE
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAY   87 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~   87 (210)
                      .+...|+||++.+.+  ++++|||.||..|+..|+           .....||.||.++...+..+
T Consensus        13 ~~~~~C~IC~~~~~~--~~~~CgH~fc~~Ci~~~~-----------~~~~~CP~Cr~~~~~~~~~~   65 (70)
T 2ecn_A           13 TDEEECCICMDGRAD--LILPCAHSFCQKCIDKWS-----------DRHRNCPICRLQMTGANESS   65 (70)
T ss_dssp             CCCCCCSSSCCSCCS--EEETTTEEECHHHHHHSS-----------CCCSSCHHHHHCTTCCCCCC
T ss_pred             CCCCCCeeCCcCccC--cccCCCCcccHHHHHHHH-----------HCcCcCCCcCCcccCCCccc
Confidence            456789999998876  889999999999999994           45678999999987665433

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=2.3e-11  Score=78.59  Aligned_cols=50  Identities=28%  Similarity=0.751  Sum_probs=40.5

Q ss_pred             CCccccccccccccCC------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           22 ADEETCPICQEKLGNQ------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      .+...|+||++.+.++      .++++|||.||..|+..|+..           ...||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-----------~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-----------ANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHH-----------CSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHc-----------CCCCCCCCCccCc
Confidence            4567899999987652      178999999999999999754           3489999998753

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}

Probab=99.10  E-value=5.7e-11  Score=76.88  Aligned_cols=51  Identities=25%  Similarity=0.451  Sum_probs=40.3

Q ss_pred             CCccccccccccccC--CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           22 ADEETCPICQEKLGN--QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~--~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .+...|+||++.+..  ..+.++|||.||..|+..|+..           ...||+||..+...
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~-----------~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLIT-----------NKKCPICRVDIEAQ   64 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHH-----------CSBCTTTCSBSCSC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHc-----------CCCCcCcCccccCc
Confidence            455789999988753  3467899999999999999754           23699999987653

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=99.09  E-value=2.9e-11  Score=83.97  Aligned_cols=48  Identities=29%  Similarity=0.546  Sum_probs=39.8

Q ss_pred             ccccccccccccCCCeec-CCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           24 EETCPICQEKLGNQKMVF-QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~-~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ...|+||.+.+.++ +.+ +|||.||..|+..|+.           ....||.||..+...
T Consensus        22 ~~~C~IC~~~~~~p-~~~~~CgH~fC~~Ci~~~~~-----------~~~~CP~Cr~~~~~~   70 (99)
T 2y43_A           22 LLRCGICFEYFNIA-MIIPQCSHNYCSLCIRKFLS-----------YKTQCPTCCVTVTEP   70 (99)
T ss_dssp             HTBCTTTCSBCSSE-EECTTTCCEEEHHHHHHHHT-----------TCCBCTTTCCBCCGG
T ss_pred             CCCcccCChhhCCc-CEECCCCCHhhHHHHHHHHH-----------CCCCCCCCCCcCChh
Confidence            46899999999875 555 9999999999999963           346899999987654

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}

Probab=99.09  E-value=3.6e-11  Score=86.97  Aligned_cols=48  Identities=25%  Similarity=0.488  Sum_probs=40.7

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ...|+||.+.+.+ ++.++|||.||..|+..|+.          .....||.||.++..
T Consensus        52 ~~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~----------~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFR-PITTVCQHNVCKDCLDRSFR----------AQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSS-EEECTTSCEEEHHHHHHHHH----------TTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcC-cEEeeCCCcccHHHHHHHHh----------HCcCCCCCCCccCCC
Confidence            4679999999987 48899999999999999974          234589999998865

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=99.08  E-value=7.7e-11  Score=72.75  Aligned_cols=49  Identities=24%  Similarity=0.548  Sum_probs=38.5

Q ss_pred             CCccccccccccccCC--CeecC-CCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           22 ADEETCPICQEKLGNQ--KMVFQ-CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~--~~~~~-CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      .+...|+||++.+...  ...++ |||.||..|+.+|+           .....||+||.++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~-----------~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWL-----------GSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTT-----------TTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHH-----------HcCCcCcCCCCEeE
Confidence            4567899999988652  35565 99999999999995           33568999998764

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.06  E-value=6.1e-11  Score=78.07  Aligned_cols=51  Identities=22%  Similarity=0.503  Sum_probs=40.7

Q ss_pred             CCccccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           22 ADEETCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .+...|+||++.+..+  ...++|||.||..|+..|+..           ...||+||..+...
T Consensus        21 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~-----------~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A           21 SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA-----------NRTCPICRADSGPS   73 (75)
T ss_dssp             SSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHH-----------CSSCTTTCCCCCCC
T ss_pred             CCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHc-----------CCcCcCcCCcCCCC
Confidence            4567899999987653  266899999999999999754           24899999987653

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.05  E-value=1.3e-10  Score=80.93  Aligned_cols=52  Identities=13%  Similarity=0.075  Sum_probs=43.7

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +...||||.+.+.+| ++++|||.||..|+..|+           .....||.|+.++...+++
T Consensus        28 ~~~~CpI~~~~m~dP-V~~~cGhtf~r~~I~~~l-----------~~~~~cP~~~~~l~~~~L~   79 (100)
T 2kre_A           28 DEFRDPLMDTLMTDP-VRLPSGTIMDRSIILRHL-----------LNSPTDPFNRQTLTESMLE   79 (100)
T ss_dssp             TTTBCTTTCSBCSSE-EEETTTEEEEHHHHHHHT-----------TSCSBCSSSCCBCCTTSSE
T ss_pred             HhhCCcCccCcccCC-eECCCCCEEchHHHHHHH-----------HcCCCCCCCCCCCChhhce
Confidence            457899999999984 889999999999999995           2346899999998776543

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A

Probab=99.05  E-value=1.1e-10  Score=82.33  Aligned_cols=49  Identities=20%  Similarity=0.481  Sum_probs=40.5

Q ss_pred             CccccccccccccCCCeec-CCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGNQKMVF-QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~-~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      +...|+||.+.+.++ +.+ +|||.||..|+..|+.           ....||.||..+...
T Consensus        14 ~~~~C~IC~~~~~~p-~~~~~CgH~fC~~Ci~~~~~-----------~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDA-TTIIECLHSFCKTCIVRYLE-----------TSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSSE-EEETTTCCEEEHHHHHHHHT-----------SCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhCc-CEeCCCCChhhHHHHHHHHH-----------hCCcCcCCCcccccc
Confidence            457899999999875 665 9999999999999963           236899999987654

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.04  E-value=1.1e-10  Score=78.10  Aligned_cols=52  Identities=21%  Similarity=0.429  Sum_probs=39.5

Q ss_pred             CCccccccccccccCC-------------C-eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           22 ADEETCPICQEKLGNQ-------------K-MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~-------------~-~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      .++..|+||++.+...             . ++.+|||.||..|+.+|+           .....||+||.++...+
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl-----------~~~~~CP~CR~~~~~~~   78 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWV-----------KQNNRCPLCQQDWVVQR   78 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHT-----------TTCCBCTTTCCBCCEEE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHH-----------HhCCCCCCcCCCcchhh
Confidence            4567899999888542             2 344699999999999996           33458999999876543

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=99.04  E-value=1.3e-10  Score=79.42  Aligned_cols=49  Identities=24%  Similarity=0.493  Sum_probs=38.8

Q ss_pred             CccccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           23 DEETCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      +...|+||++.+...  ...++|||.||..|+..|+.           ....||+||..+..
T Consensus        39 ~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~-----------~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           39 QEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQ-----------KSGTCPVCRCMFPP   89 (91)
T ss_dssp             SCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHT-----------TTCBCTTTCCBSSC
T ss_pred             CCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHH-----------cCCcCcCcCccCCC
Confidence            456799999887642  35689999999999999963           33589999998754

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.03  E-value=9.5e-11  Score=73.04  Aligned_cols=46  Identities=30%  Similarity=0.714  Sum_probs=37.3

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      .+...|+||++.+.++ ++++|||.||..|+..|+..        ......||+|
T Consensus        13 ~~~~~C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~~--------~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP-VIIECGHNFCKACITRWWED--------LERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC-CCCSSCCCCCHHHHHHHTTS--------SCCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc-EeCCCCCccCHHHHHHHHHh--------cCCCCCCCCC
Confidence            3567899999999874 78999999999999999532        1356789988

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=99.03  E-value=1e-10  Score=79.03  Aligned_cols=52  Identities=13%  Similarity=0.057  Sum_probs=43.6

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +...|+||.+.+.+ +++++|||.||..|+..|+..           ...||.|+.++...+++
T Consensus        13 ~~~~CpI~~~~m~d-PV~~~cGhtf~r~~I~~~l~~-----------~~~cP~~~~~l~~~~l~   64 (85)
T 2kr4_A           13 DEFRDPLMDTLMTD-PVRLPSGTVMDRSIILRHLLN-----------SPTDPFNRQMLTESMLE   64 (85)
T ss_dssp             TTTBCTTTCSBCSS-EEECTTSCEEEHHHHHHHHHH-----------CSBCTTTCCBCCGGGCE
T ss_pred             hheECcccCchhcC-CeECCCCCEECHHHHHHHHhc-----------CCCCCCCcCCCChHhcc
Confidence            46789999999998 489999999999999999753           35899999988765543

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B

Probab=99.03  E-value=9.7e-11  Score=88.79  Aligned_cols=47  Identities=34%  Similarity=0.725  Sum_probs=39.1

Q ss_pred             cccccccccccCCCeec-CCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           25 ETCPICQEKLGNQKMVF-QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~-~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ..|+||.+.+.++ +.+ +|||.||..|+..|+..          ....||.||.++..
T Consensus        55 ~~C~IC~~~~~~p-~~~~~CgH~fC~~Ci~~~~~~----------~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           55 LMCPICLDMLKNT-MTTKECLHRFCADCIITALRS----------GNKECPTCRKKLVS  102 (165)
T ss_dssp             HBCTTTSSBCSSE-EEETTTCCEEEHHHHHHHHHT----------TCCBCTTTCCBCCS
T ss_pred             CCCcccChHhhCc-CEeCCCCChhHHHHHHHHHHh----------CcCCCCCCCCcCCC
Confidence            4899999999885 555 99999999999999742          34689999998754

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A

Probab=99.02  E-value=1.5e-10  Score=82.93  Aligned_cols=54  Identities=22%  Similarity=0.442  Sum_probs=44.5

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .+...|+||.+.+.++ +.++|||.||..|+..|+...          ...||.||.++...++.
T Consensus        16 ~~~~~C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~~~----------~~~CP~Cr~~~~~~~~~   69 (118)
T 3hct_A           16 ESKYECPICLMALREA-VQTPCGHRFCKACIIKSIRDA----------GHKCPVDNEILLENQLF   69 (118)
T ss_dssp             CGGGBCTTTCSBCSSE-EECTTSCEEEHHHHHHHHHHH----------CSBCTTTCCBCCGGGCE
T ss_pred             CCCCCCCcCChhhcCe-EECCcCChhhHHHHHHHHhhC----------CCCCCCCCCCcCHHhcc
Confidence            3457899999999874 889999999999999997542          23899999998876654

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens}

Probab=99.01  E-value=1.1e-10  Score=87.27  Aligned_cols=50  Identities=24%  Similarity=0.520  Sum_probs=41.8

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      +...|+||.+.+.+ ++.++|||.||..|+..|+..          ....||+||.++...
T Consensus        77 ~~~~C~IC~~~~~~-pv~~~CgH~fC~~Ci~~~~~~----------~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ-PVTTECFHNVCKDCLQRSFKA----------QVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSS-EEECTTSCEEEHHHHHHHHHT----------TCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcC-CEEcCCCCchhHHHHHHHHHh----------CCCcCCCCCccCCCC
Confidence            34689999999987 488999999999999999742          345899999988765

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.01  E-value=8.5e-10  Score=90.10  Aligned_cols=69  Identities=14%  Similarity=0.165  Sum_probs=63.2

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC-CceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN-NITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~-gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      ..+.|+.+|.+.|..+..  ++.|+||||||+.++++|+..|... |+++.+++|+|+      ..+|.++++.|+++
T Consensus        93 ~~s~K~~~L~~ll~~~~~--~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~------~~~R~~~i~~F~~~  162 (271)
T 1z5z_A           93 RRSGKMIRTMEIIEEALD--EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELS------KKERDDIISKFQNN  162 (271)
T ss_dssp             TTCHHHHHHHHHHHHHHH--TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSC------HHHHHHHHHHHHHC
T ss_pred             ccCHHHHHHHHHHHHHHh--CCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCC------HHHHHHHHHHhcCC
Confidence            458999999999998864  4789999999999999999999985 999999999987      99999999999983

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.00  E-value=3e-10  Score=78.74  Aligned_cols=53  Identities=15%  Similarity=0.029  Sum_probs=44.4

Q ss_pred             CCccccccccccccCCCeecCCC-CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           22 ADEETCPICQEKLGNQKMVFQCG-HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~Cg-H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .+.+.||||.+.+.+ +++++|| |.||..||..|+.           ....||.||.++...+++
T Consensus        20 p~~~~CpI~~~~m~d-PV~~~cG~htf~r~cI~~~l~-----------~~~~cP~~~~~l~~~~L~   73 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD-PVVLPSSRVTVDRSTIARHLL-----------SDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             CTTTBCTTTCSBCSS-EEECTTTCCEEEHHHHHHHTT-----------TSCBCTTTCSBCCTTTSE
T ss_pred             cHhcCCcCccccccC-CeECCCCCeEECHHHHHHHHH-----------hCCCCCCCCCCCChhhce
Confidence            356789999999998 4999999 9999999999952           245899999998776654

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1

Probab=98.98  E-value=1.8e-10  Score=82.19  Aligned_cols=51  Identities=24%  Similarity=0.574  Sum_probs=42.5

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ...|+||.+.+.+ ++.++|||.||..|+..|+..          ....||.||.++...++
T Consensus        23 ~~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~~----------~~~~CP~Cr~~~~~~~~   73 (116)
T 1rmd_A           23 SISCQICEHILAD-PVETSCKHLFCRICILRCLKV----------MGSYCPSCRYPCFPTDL   73 (116)
T ss_dssp             HTBCTTTCSBCSS-EEECTTSCEEEHHHHHHHHHH----------TCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCcHhcC-cEEcCCCCcccHHHHHHHHhH----------CcCcCCCCCCCCCHhhc
Confidence            4689999999987 488999999999999999754          13579999998876654

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}

Probab=98.98  E-value=7e-11  Score=84.25  Aligned_cols=49  Identities=35%  Similarity=0.750  Sum_probs=40.6

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      +...|+||.+.+.+ ++.++|||.||..|+..|+.          .....||.||..+..
T Consensus        14 ~~~~C~iC~~~~~~-p~~~~CgH~fC~~Ci~~~~~----------~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVE-PVTLPCNHTLCKPCFQSTVE----------KASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSS-CEECTTSCEECHHHHCCCCC----------TTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCc-eeEcCCCCHHhHHHHHHHHh----------HCcCCCCCCCcccCc
Confidence            45789999999987 58889999999999999852          335789999998754

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.96  E-value=4.8e-10  Score=73.45  Aligned_cols=50  Identities=24%  Similarity=0.474  Sum_probs=39.4

Q ss_pred             CCccccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           22 ADEETCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      .+...|+||++.+..+  ..+++|||.||..|+.+|+..           ...||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-----------~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEV-----------RKVCPLCNMPVLQ   64 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHH-----------CSBCTTTCCBCSS
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHc-----------CCcCCCcCccccc
Confidence            4467899999988653  244599999999999999754           2389999998754

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.96  E-value=4.8e-10  Score=81.38  Aligned_cols=56  Identities=25%  Similarity=0.635  Sum_probs=45.5

Q ss_pred             CCccccccccccccCC------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376           22 ADEETCPICQEKLGNQ------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA   88 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~   88 (210)
                      .+...|+||++.+.++      .+.++|||.||..|+.+|++           ....||.||..+...++...
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~-----------~~~~CP~Cr~~~~~~~l~~l   66 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----------NANTCPTCRKKINHKRYHPI   66 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHT-----------TCSBCTTTCCBCTTTCEEEC
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHH-----------hCCCCCCCCCcCcccccccc
Confidence            4567999999988653      27899999999999999963           33589999999988877543

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.96  E-value=1.5e-10  Score=71.98  Aligned_cols=47  Identities=26%  Similarity=0.549  Sum_probs=38.6

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .+...|+||.+.+.++ ++++|||.||..|+..+              ...||.||..+...
T Consensus         4 ~~~~~C~IC~~~~~~p-~~l~CgH~fC~~Ci~~~--------------~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP-KLLPCLHTLCSGCLEAS--------------GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCCSSCSSSCSSCBCC-SCSTTSCCSBTTTCSSS--------------SSSCSSCCSSSSCC
T ss_pred             ccCCCceEeCCccCCe-EEcCCCCcccHHHHccC--------------CCCCCcCCcEeecC
Confidence            4567899999999874 88999999999998652              35899999987653

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.93  E-value=2.6e-10  Score=81.57  Aligned_cols=47  Identities=23%  Similarity=0.560  Sum_probs=39.2

Q ss_pred             CccccccccccccCCCeec-CCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGNQKMVF-QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~-~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      +...|+||.+.+.++ +.+ +|||.||..|+..|+           .  ..||.||.++...
T Consensus        21 ~~~~C~IC~~~~~~p-v~~~~CgH~fC~~Ci~~~~-----------~--~~CP~Cr~~~~~~   68 (117)
T 1jm7_B           21 KLLRCSRCTNILREP-VCLGGCEHIFCSNCVSDCI-----------G--TGCPVCYTPAWIQ   68 (117)
T ss_dssp             HTTSCSSSCSCCSSC-BCCCSSSCCBCTTTGGGGT-----------T--TBCSSSCCBCSCS
T ss_pred             hCCCCCCCChHhhCc-cEeCCCCCHHHHHHHHHHh-----------c--CCCcCCCCcCccc
Confidence            457899999999875 666 999999999999984           2  5899999987543

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=1.2e-09  Score=75.04  Aligned_cols=59  Identities=24%  Similarity=0.492  Sum_probs=45.4

Q ss_pred             CCccccccccccccCCCeecC-CCCcchHhhHHHHHHHhhhccccCCCccccccC--Cccc-ccCCCeE
Q 028376           22 ADEETCPICQEKLGNQKMVFQ-CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPT--CRQR-TDIGNIA   86 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~-CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~--Cr~~-~~~~~l~   86 (210)
                      .+...||||++.+.++ ++++ |||.||..||..|+.....     ......||+  |+.. +...+++
T Consensus         5 ~~~~~CPI~~~~~~dP-V~~~~cGh~f~r~cI~~~l~~~~~-----~~~~~~CP~tgc~~~~l~~~~L~   67 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKP-VKNKVCGHTYEEDAIVRMIESRQK-----RKKKAYCPQIGCSHTDIRKSDLI   67 (94)
T ss_dssp             SSCCBCTTTCSBCSSE-EEESSSCCEEEHHHHHHHHHHHHT-----TTCCBCCCSTTCCCCCBCGGGEE
T ss_pred             CcEeECcCcCchhcCC-EEcCCCCCeecHHHHHHHHHHccC-----cCCCCCCCcCcCcccccCHhhCc
Confidence            3567899999999985 8885 9999999999999865310     124568999  8876 7666654

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=98.90  E-value=3e-10  Score=72.58  Aligned_cols=51  Identities=31%  Similarity=0.667  Sum_probs=39.7

Q ss_pred             cCCCCccccccccccccCCCeec--CCCCc-chHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           19 LSKADEETCPICQEKLGNQKMVF--QCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        19 l~~~~~~~C~iC~~~~~~~~~~~--~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      +.+.+...|+||++...+. +++  +|||. ||.+|+..|...           ...||+||.++.
T Consensus         3 l~~~~~~~C~IC~~~~~~~-~~~~~pCgH~~~C~~C~~~~~~~-----------~~~CPiCR~~i~   56 (64)
T 2vje_A            3 LPLNAIEPCVICQGRPKNG-CIVHGKTGHLMACFTCAKKLKKR-----------NKPCPVCRQPIQ   56 (64)
T ss_dssp             --CGGGSCCTTTSSSCSCE-EEEETTEEEEEECHHHHHHHHHT-----------TCCCTTTCCCCC
T ss_pred             CCCCCcCCCCcCCCCCCCE-EEECCCCCChhhHHHHHHHHHHc-----------CCcCCCcCcchh
Confidence            3455678999999988774 655  99999 899999998532           347999999874

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=98.89  E-value=8e-10  Score=77.63  Aligned_cols=49  Identities=16%  Similarity=0.344  Sum_probs=39.4

Q ss_pred             CCccccccccccccCC-----------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           22 ADEETCPICQEKLGNQ-----------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~-----------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      .++..|+||++.+...                 .++++|||.||..|+..|+.           ....||+||..+.
T Consensus        35 ~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~-----------~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           35 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK-----------TRQVCPLDNREWE  100 (106)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHT-----------TCSBCSSSCSBCC
T ss_pred             CCCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHH-----------cCCcCcCCCCcce
Confidence            4567899999887643                 25589999999999999963           3568999999864

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*

Probab=98.89  E-value=8.8e-10  Score=93.58  Aligned_cols=52  Identities=29%  Similarity=0.574  Sum_probs=43.2

Q ss_pred             ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      ...|+||++.+.+ ++.++|||.||..|+..|+..          ....||.||.++....++
T Consensus       332 ~~~C~ICle~~~~-pv~lpCGH~FC~~Ci~~wl~~----------~~~~CP~CR~~i~~~~~i  383 (389)
T 2y1n_A          332 FQLCKICAENDKD-VKIEPCGHLMCTSCLTSWQES----------EGQGCPFCRCEIKGTEPI  383 (389)
T ss_dssp             SSBCTTTSSSBCC-EEEETTCCEECHHHHHHHHHH----------TCSBCTTTCCBCCEEEEC
T ss_pred             CCCCCccCcCCCC-eEEeCCCChhhHHHHHHHHhc----------CCCCCCCCCCccCCceeE
Confidence            4789999999877 588999999999999999742          345899999998776544

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.88  E-value=6.2e-10  Score=73.28  Aligned_cols=53  Identities=28%  Similarity=0.679  Sum_probs=40.9

Q ss_pred             HHHHHhcCCCCccccccccccccCCCeecCCCCc-chHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           13 KHRIESLSKADEETCPICQEKLGNQKMVFQCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        13 ~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ++.++.+  .+...|+||++.+.+ +++++|||. ||..|+...               ..||.||.++...
T Consensus        16 ~~~~~~~--~~~~~C~IC~~~~~~-~~~~pCgH~~~C~~C~~~~---------------~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           16 EEQLRRL--QEEKLCKICMDRNIA-IVFVPCGHLVTCKQCAEAV---------------DKCPMCYTVITFK   69 (75)
T ss_dssp             HHHHHHH--HHHHSCSSSCSSCCC-BCCSSSCCCCBCHHHHHHC---------------SBCTTTCCBCCCC
T ss_pred             HHHHHcC--CCCCCCCcCCCCCCC-EEEecCCCHHHHHHHhhCC---------------CCCccCCceecCc
Confidence            4444444  245689999999887 488999999 999999643               4899999988653

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.88  E-value=1e-09  Score=89.42  Aligned_cols=53  Identities=13%  Similarity=-0.028  Sum_probs=43.2

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +...|+||.+.+.+ |++++|||.||..|+..|+..         + ...||.||.++...+++
T Consensus       207 ~~~~c~i~~~~~~d-Pv~~~~gh~f~~~~i~~~~~~---------~-~~~cP~~~~~~~~~~l~  259 (281)
T 2c2l_A          207 DYLCGKISFELMRE-PCITPSGITYDRKDIEEHLQR---------V-GHFNPVTRSPLTQEQLI  259 (281)
T ss_dssp             STTBCTTTCSBCSS-EEECSSCCEEETTHHHHHHHH---------T-CSSCTTTCCCCCGGGCE
T ss_pred             cccCCcCcCCHhcC-CeECCCCCEECHHHHHHHHHH---------C-CCCCcCCCCCCchhcCc
Confidence            45789999999998 499999999999999999854         1 12499999988765543

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}

Probab=98.87  E-value=3.5e-10  Score=83.60  Aligned_cols=51  Identities=22%  Similarity=0.480  Sum_probs=41.6

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .+...|+||.+.+.++ +.++|||.||..|+..|+.          .....||.||.++...
T Consensus        29 ~~~~~C~IC~~~~~~p-v~~~CgH~FC~~Ci~~~~~----------~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           29 EAKYLCSACRNVLRRP-FQAQCGHRYCSFCLASILS----------SGPQNCAACVHEGIYE   79 (141)
T ss_dssp             CGGGBCTTTCSBCSSE-EECTTSCEEEHHHHHHHGG----------GSCEECHHHHHTTCCC
T ss_pred             CcCcCCCCCChhhcCc-EECCCCCccCHHHHHHHHh----------cCCCCCCCCCCccccc
Confidence            4567899999999875 8899999999999999963          2335899999976443

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.84  E-value=1.8e-09  Score=82.58  Aligned_cols=53  Identities=13%  Similarity=-0.011  Sum_probs=43.5

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +...||||.+.+.+ |++++|||.||..|+..|+..         .+ ..||.|+.++...++.
T Consensus       105 ~~f~CPI~~elm~D-PV~~~~Ghtfer~~I~~~l~~---------~~-~tcP~t~~~l~~~~L~  157 (179)
T 2f42_A          105 DYLCGKISFELMRE-PCITPSGITYDRKDIEEHLQR---------VG-HFDPVTRSPLTQDQLI  157 (179)
T ss_dssp             GGGBCTTTCSBCSS-EEECTTSCEEEHHHHHHHHHH---------TC-SBCTTTCCBCCGGGCE
T ss_pred             HhhcccCccccCCC-CeECCCCCEECHHHHHHHHHh---------CC-CCCCCCcCCCChhhCc
Confidence            45789999999998 589999999999999999854         11 2699999988766543

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.84  E-value=4.1e-09  Score=97.98  Aligned_cols=71  Identities=15%  Similarity=0.233  Sum_probs=64.6

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      .|.|+..|.+.|..+..  .+.|+||||||+.++++|+..|...||+|.+++|+|+      ..+|.++|++|+.++..
T Consensus       554 ~s~K~~~L~~lL~~~~~--~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~------~~eR~~~i~~F~~~~~~  624 (800)
T 3mwy_W          554 SSGKMVLLDQLLTRLKK--DGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVP------SAQRRISIDHFNSPDSN  624 (800)
T ss_dssp             TCHHHHHHHHHHHHHTT--TTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSC------HHHHHHHHHTTSSTTCS
T ss_pred             cChHHHHHHHHHHHHhh--CCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCC------HHHHHHHHHHhhCCCCC
Confidence            58899999999998864  4789999999999999999999999999999999987      99999999999985443

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=98.82  E-value=8.3e-10  Score=72.50  Aligned_cols=44  Identities=32%  Similarity=0.751  Sum_probs=37.3

Q ss_pred             CccccccccccccCCCeecCCCCc-chHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      +...|+||++.+.+ ++.++|||. ||..|+..|               ..||.||.++..
T Consensus        23 ~~~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~---------------~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIA-IVFVPCGHLVTCKQCAEAV---------------DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCC-EEEETTCCBCCCHHHHTTC---------------SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCC-EEEcCCCChhHHHHhhhcC---------------ccCCCcCcCccC
Confidence            34689999999887 488899999 999998765               489999998754

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=98.82  E-value=2.2e-09  Score=81.60  Aligned_cols=54  Identities=22%  Similarity=0.442  Sum_probs=44.7

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .+...|+||.+.+.++ +.++|||.||..|+..|+...          ...||.||.++...++.
T Consensus        16 ~~~~~C~IC~~~~~~p-v~~~CgH~fC~~Ci~~~~~~~----------~~~CP~Cr~~~~~~~~~   69 (170)
T 3hcs_A           16 ESKYECPICLMALREA-VQTPCGHRFCKACIIKSIRDA----------GHKCPVDNEILLENQLF   69 (170)
T ss_dssp             CGGGBCTTTCSBCSSE-EECTTSCEEEHHHHHHHHHHH----------CSBCTTTCCBCCGGGCE
T ss_pred             CCCCCCCCCChhhcCc-EECCCCCHHHHHHHHHHHHhC----------CCCCCCCccCcchhhhh
Confidence            4567999999999874 889999999999999997541          23899999998876654

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.80  E-value=3.4e-09  Score=68.39  Aligned_cols=46  Identities=28%  Similarity=0.655  Sum_probs=38.5

Q ss_pred             CCCccccccccccccCCCeecCCCCc-chHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           21 KADEETCPICQEKLGNQKMVFQCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~~~~~~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      +.+...|.||++...+ .++++|||. ||..|+...               ..||+||.++..
T Consensus        12 ~~~~~~C~IC~~~~~~-~v~~pCgH~~~C~~C~~~~---------------~~CP~CR~~i~~   58 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVN-WVLLPCRHTCLCDGCVKYF---------------QQCPMCRQFVQE   58 (68)
T ss_dssp             CCCSSCCSSSSSSCCC-CEETTTTBCCSCTTHHHHC---------------SSCTTTCCCCCC
T ss_pred             CCCCCCCCCcCcCCCC-EEEECCCChhhhHHHHhcC---------------CCCCCCCcchhc
Confidence            3456789999998876 589999999 999999843               389999998755

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=98.79  E-value=1e-09  Score=69.86  Aligned_cols=47  Identities=21%  Similarity=0.670  Sum_probs=37.6

Q ss_pred             CccccccccccccCCCeec--CCCCc-chHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           23 DEETCPICQEKLGNQKMVF--QCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~--~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ....|+||++...+. +++  +|||. ||..|...+.+.           ...||+||.++.
T Consensus         6 ~~~~C~IC~~~~~~~-~~~~~pCgH~~~C~~C~~~~~~~-----------~~~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRDG-NIIHGRTGHLVTCFHCARRLKKA-----------GASCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSCE-EEEETTEEEEEECHHHHHHHHHT-----------TCBCTTTCCBCC
T ss_pred             cCCCCcccCCcCCCe-EEEecCCCCHhHHHHHHHHHHHh-----------CCcCCCcCchhh
Confidence            456899999987763 555  99998 999999988532           258999999874

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.79  E-value=1.9e-09  Score=74.06  Aligned_cols=55  Identities=20%  Similarity=0.521  Sum_probs=41.1

Q ss_pred             CCccccccccccccCCCee--cCCCCcchHhhHHHHHHHhhhccccCCCccccccC--Cccc
Q 028376           22 ADEETCPICQEKLGNQKMV--FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPT--CRQR   79 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~--~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~--Cr~~   79 (210)
                      .+...|+||++.+..+..+  .+|||.||.+|+..+++......   ......||.  |+..
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g---~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEG---LETAISCPDAACPKQ   61 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHC---SCCCEECSCTTCSSC
T ss_pred             CCCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcC---CcccccCccccCCCC
Confidence            4567899999987654333  37999999999999987654321   124578999  9987

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=98.77  E-value=3e-09  Score=77.15  Aligned_cols=56  Identities=25%  Similarity=0.640  Sum_probs=45.4

Q ss_pred             CCCCccccccccccccCC------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           20 SKADEETCPICQEKLGNQ------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        20 ~~~~~~~C~iC~~~~~~~------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      ...+...|+||++.+..+      .+.++|||.||..|+.+|++.           ...||+||..+..+++.
T Consensus        68 i~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-----------~~~CP~Cr~~~~~~~~~  129 (133)
T 4ap4_A           68 IGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-----------ANTCPTCRKKINHKRYH  129 (133)
T ss_dssp             CSSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHH-----------CSBCTTTCCBCCGGGEE
T ss_pred             cCCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHc-----------CCCCCCCCCcCChhcce
Confidence            346678899999887642      277899999999999999754           34899999999888765

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=98.74  E-value=1.8e-09  Score=71.82  Aligned_cols=53  Identities=28%  Similarity=0.671  Sum_probs=41.0

Q ss_pred             HHHHHhcCCCCccccccccccccCCCeecCCCCc-chHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           13 KHRIESLSKADEETCPICQEKLGNQKMVFQCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        13 ~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ++.++.+.  +...|+||++.+.+ +++++|||. ||..|+..+               ..||.||.++...
T Consensus         9 ~~~~~~l~--~~~~C~IC~~~~~~-~v~~pCgH~~~C~~C~~~~---------------~~CP~Cr~~i~~~   62 (79)
T 2yho_A            9 QEKLRKLK--EAMLCMVCCEEEIN-STFCPCGHTVCCESCAAQL---------------QSCPVCRSRVEHV   62 (79)
T ss_dssp             HHHHHHHH--HHTBCTTTSSSBCC-EEEETTCBCCBCHHHHTTC---------------SBCTTTCCBCCEE
T ss_pred             HHHHHcCC--CCCEeEEeCcccCc-EEEECCCCHHHHHHHHHhc---------------CcCCCCCchhhCe
Confidence            34444443  34689999998887 588999999 999998765               2899999987664

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=98.73  E-value=2.5e-08  Score=90.62  Aligned_cols=70  Identities=11%  Similarity=0.285  Sum_probs=61.5

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      ..|.|+..|...+..+.. .++.|+||||||+.++++|+..|...|+.|.+++|+|+      ..+|.+++++|+++
T Consensus       396 ~~s~K~~~l~~ll~~~~~-~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~------~~~R~~~i~~F~~~  465 (644)
T 1z3i_X          396 QLSGKMLVLDYILAMTRT-TTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMS------IKKRAKIVERFNNP  465 (644)
T ss_dssp             GGSHHHHHHHHHHHHHHH-HCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCC------HHHHHHHHHHHHST
T ss_pred             ccChHHHHHHHHHHHHhh-cCCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCC------HHHHHHHHHHhcCC
Confidence            347898877777666653 46889999999999999999999999999999999987      99999999999983

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=98.72  E-value=3.2e-09  Score=85.24  Aligned_cols=55  Identities=20%  Similarity=0.300  Sum_probs=43.4

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccC--CcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPT--CRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~--Cr~~~~~~~l~   86 (210)
                      ....||||++.+.+|...+.|||.||..|+..|++.         .+...||+  |+..+...++.
T Consensus       180 ~el~CPIcl~~f~DPVts~~CGHsFcR~cI~~~~~~---------~~~~~CPvtGCr~~l~~~dL~  236 (267)
T 3htk_C          180 IELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQG---------YTTRDCPQAACSQVVSMRDFV  236 (267)
T ss_dssp             CCSBCTTTSSBCSSEEEESSSCCEEEHHHHHHHSTT---------CSCEECSGGGCSCEECGGGEE
T ss_pred             eeeECcCccCcccCCeeeCCCCCcccHHHHHHHHHh---------CCCCCCCcccccCcCchhhCC
Confidence            456799999999986334699999999999999532         24468999  99988777654

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=98.72  E-value=1.8e-09  Score=77.05  Aligned_cols=52  Identities=15%  Similarity=0.328  Sum_probs=1.9

Q ss_pred             CCCccccccccccccCC-----------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           21 KADEETCPICQEKLGNQ-----------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~-----------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      +.+...|+||++.+..+                 .+.++|+|.||..|+.+|+..           ...||+||.++...
T Consensus        45 d~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~-----------~~~CP~Cr~~~~~~  113 (117)
T 4a0k_B           45 DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-----------RQVCPLDNREWEFQ  113 (117)
T ss_dssp             CCCC----------------------------------------------------------------------------
T ss_pred             cCCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHc-----------CCcCCCCCCeeeee
Confidence            34567899999887642                 233699999999999999643           45899999986543

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.65  E-value=3e-08  Score=65.99  Aligned_cols=53  Identities=17%  Similarity=0.476  Sum_probs=41.5

Q ss_pred             CCcccccccccccc-CCCeecCCC-----CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           22 ADEETCPICQEKLG-NQKMVFQCG-----HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        22 ~~~~~C~iC~~~~~-~~~~~~~Cg-----H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .+...|.||++.+. ...++++|.     |.|+..|+.+|+..         .....||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~---------~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKS---------SDTRCCELCKYEFIME   71 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHH---------HCCSBCSSSCCBCCCC
T ss_pred             CCCCCCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhh---------CCCCCCCCCCCeeecC
Confidence            45678999998764 234778996     99999999999865         2345899999988655

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.50  E-value=9.3e-08  Score=60.20  Aligned_cols=54  Identities=9%  Similarity=0.004  Sum_probs=44.9

Q ss_pred             ccccccccccccCCCeec-CCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEcc
Q 028376           24 EETCPICQEKLGNQKMVF-QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYAD   89 (210)
Q Consensus        24 ~~~C~iC~~~~~~~~~~~-~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~   89 (210)
                      ...|+||.+.+.++ +++ +|||+|+..|+.+|+...           ..||+.+.++...+++...
T Consensus         3 ~~~CpIs~~~m~dP-V~~~~sG~~yer~~I~~~l~~~-----------~~cP~t~~~L~~~~Lip~~   57 (61)
T 2bay_A            3 HMLCAISGKVPRRP-VLSPKSRTIFEKSLLEQYVKDT-----------GNDPITNEPLSIEEIVEIV   57 (61)
T ss_dssp             -CCCTTTCSCCSSE-EEETTTTEEEEHHHHHHHHHHH-----------SBCTTTCCBCCGGGCEECC
T ss_pred             eEEecCCCCCCCCC-EEeCCCCcEEcHHHHHHHHHhC-----------CCCcCCcCCCChhhcEECc
Confidence            36799999999985 787 999999999999998641           2599999999988876543

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=98.48  E-value=3.8e-07  Score=79.87  Aligned_cols=69  Identities=14%  Similarity=0.165  Sum_probs=62.8

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC-CceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN-NITCIKMKGENHKLPSANLQHRNALQKELTRH  195 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~-gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~  195 (210)
                      ..+.|+.++++.|.++..  ++.|+|||++|..+++.+...|... |+.+..++|+|+      ..+|.+++++|+++
T Consensus       322 ~~s~K~~~l~~~l~~~~~--~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~------~~~R~~~~~~F~~~  391 (500)
T 1z63_A          322 RRSGKMIRTMEIIEEALD--EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELS------KKERDDIISKFQNN  391 (500)
T ss_dssp             TTCHHHHHHHHHHHHHHT--TTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSC------HHHHHHHHHHHHHC
T ss_pred             hcchhHHHHHHHHHHHHc--cCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCC------HHHHHHHHHHhcCC
Confidence            457999999999988763  5889999999999999999999986 999999999987      99999999999984

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=98.42  E-value=7e-07  Score=76.56  Aligned_cols=73  Identities=14%  Similarity=0.225  Sum_probs=64.3

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeC--------CCCCCcchhhHhhhHHHH
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG--------ENHKLPSANLQHRNALQK  190 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G--------~m~~~~~~~~~~R~~~l~  190 (210)
                      ..+.|+.+|++.|..+....++.|+|||+++..+++.+...|...|+.+..++|        +|+      ..+|.++++
T Consensus       340 ~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~------~~~r~~~~~  413 (494)
T 1wp9_A          340 LDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLS------QREQKLILD  413 (494)
T ss_dssp             CSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------------CCHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCC------HHHHHHHHH
Confidence            567899999999998876677899999999999999999999999999999999        755      999999999


Q ss_pred             HHhhcCC
Q 028376          191 ELTRHMP  197 (210)
Q Consensus       191 ~F~~~~p  197 (210)
                      .|+++..
T Consensus       414 ~F~~~~~  420 (494)
T 1wp9_A          414 EFARGEF  420 (494)
T ss_dssp             HHHHTSC
T ss_pred             HHhcCCc
Confidence            9998543

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.42  E-value=7.8e-08  Score=80.88  Aligned_cols=54  Identities=30%  Similarity=0.712  Sum_probs=42.0

Q ss_pred             chHHHHHhcCCCCccccccccccccCCCeecCCCCc-chHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           11 STKHRIESLSKADEETCPICQEKLGNQKMVFQCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        11 ~~~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ..++.++.+.  +...|+||++.+.+ ++.++|||. ||..|+..+               ..||.||.++..
T Consensus       284 ~~~~~~~~l~--~~~~C~IC~~~~~~-~v~lpCgH~~fC~~C~~~~---------------~~CP~CR~~i~~  338 (345)
T 3t6p_A          284 SLEEQLRRLQ--EERTCKVCMDKEVS-VVFIPCGHLVVCQECAPSL---------------RKCPICRGIIKG  338 (345)
T ss_dssp             CHHHHHHHHH--TTCBCTTTSSSBCC-EEEETTCCEEECTTTGGGC---------------SBCTTTCCBCCE
T ss_pred             cHHHHHHhCc--CCCCCCccCCcCCc-eEEcCCCChhHhHHHHhcC---------------CcCCCCCCCccC
Confidence            3444555443  34789999999887 488899999 999998865               489999998753

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=98.38  E-value=2.7e-07  Score=76.76  Aligned_cols=55  Identities=13%  Similarity=0.221  Sum_probs=49.6

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH  175 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~  175 (210)
                      ..|.|+.-|-+.|..+++  .+.|++||||++.+||++|..|...|+.|.|+||+..
T Consensus       106 ~~SGKf~~L~~LL~~l~~--~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~  160 (328)
T 3hgt_A          106 ENSGKFSVLRDLINLVQE--YETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSI  160 (328)
T ss_dssp             HTCHHHHHHHHHHHHHTT--SCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC
T ss_pred             HcCccHHHHHHHHHHHHh--CCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCch
Confidence            369999988888888875  4789999999999999999999999999999999954

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.33  E-value=3.6e-07  Score=59.65  Aligned_cols=51  Identities=22%  Similarity=0.365  Sum_probs=39.6

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ....|.||.+.+.....-..|+|.|+..|+.+|++.         .....||.||.....
T Consensus        14 ~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~---------~~~~~CP~Cr~~w~~   64 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQS---------NAEPRCPHCNDYWPH   64 (74)
T ss_dssp             SSCBCSSSCCBCSSSEECSSSCCEECHHHHHHHSTT---------CSSCCCTTTCSCCCS
T ss_pred             CCCcCcchhhHcccCCccCCCCchhhHHHHHHHHHh---------cCCCCCCCCcCcCCC
Confidence            447899999988754344599999999999999732         233789999987653

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.25  E-value=3.8e-07  Score=62.20  Aligned_cols=47  Identities=21%  Similarity=0.503  Sum_probs=38.7

Q ss_pred             ccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      -|++|.-++..-+.+.||.|+||.+|...|..          .....||.|+.++..
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~----------~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEK----------KGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHH----------TTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHh----------ccCCCCcCcCCeeee
Confidence            58999988877678899999999999998842          345689999998754

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=98.21  E-value=7.6e-06  Score=61.80  Aligned_cols=68  Identities=9%  Similarity=0.065  Sum_probs=60.2

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      .+.|+++|.+.|...    +..|+|||+.+....+.+...|...|++...++|.|+      ..+|..+++.|+++..
T Consensus        15 ~~~K~~~L~~ll~~~----~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~------~~~r~~~~~~f~~g~~   82 (172)
T 1t5i_A           15 DNEKNRKLFDLLDVL----EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMP------QEERLSRYQQFKDFQR   82 (172)
T ss_dssp             GGGHHHHHHHHHHHS----CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTSC
T ss_pred             hHHHHHHHHHHHHhC----CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCC------HHHHHHHHHHHHCCCC
Confidence            467999988877643    5679999999999999999999999999999999977      9999999999997443

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=98.18  E-value=4.9e-06  Score=63.70  Aligned_cols=68  Identities=15%  Similarity=0.169  Sum_probs=53.3

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      .+.|+++|++.|...   .++.|+|||+++....+.+...|...|++...+.|+|+      ..+|..+++.|+.+.
T Consensus        29 ~~~K~~~L~~ll~~~---~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~------~~~r~~~~~~f~~g~   96 (185)
T 2jgn_A           29 ESDKRSFLLDLLNAT---GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRS------QRDREEALHQFRSGK   96 (185)
T ss_dssp             GGGHHHHHHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------------CHHHHHHHHTS
T ss_pred             cHHHHHHHHHHHHhc---CCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCC------HHHHHHHHHHHHcCC
Confidence            468999999888753   36789999999999999999999999999999999977      999999999999744

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=98.17  E-value=9.9e-06  Score=60.50  Aligned_cols=68  Identities=13%  Similarity=0.170  Sum_probs=60.3

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..+.|++.|.+.|...    ++.|+|||.++....+.+...|...|++...++|+|+      ..+|..+++.|+.+.
T Consensus        18 ~~~~K~~~L~~ll~~~----~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~------~~~r~~~~~~f~~g~   85 (163)
T 2hjv_A           18 REENKFSLLKDVLMTE----NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMI------QEDRFDVMNEFKRGE   85 (163)
T ss_dssp             CGGGHHHHHHHHHHHH----CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTS
T ss_pred             ChHHHHHHHHHHHHhc----CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCC------HHHHHHHHHHHHcCC
Confidence            3468999998887653    4679999999999999999999999999999999977      999999999999743

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.16  E-value=1.9e-06  Score=53.89  Aligned_cols=53  Identities=25%  Similarity=0.458  Sum_probs=40.5

Q ss_pred             CCCCccccccccccccCCCeecCCC--C---cchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           20 SKADEETCPICQEKLGNQKMVFQCG--H---FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        20 ~~~~~~~C~iC~~~~~~~~~~~~Cg--H---~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      -+++...|.||++.... ..++||.  |   .|+..|+.+|+..         .+...||+|+.++..
T Consensus         2 e~~~~~~CrIC~~~~~~-~l~~PC~C~gs~~~~H~~Cl~~W~~~---------~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            2 EDEDVPVCWICNEELGN-ERFRACGCTGELENVHRSCLSTWLTI---------SRNTACQICGVVYNT   59 (60)
T ss_dssp             TTCSCCEETTTTEECSC-CCCCSCCCSSGGGSCCHHHHHHHHHH---------HTCSBCTTTCCBCCC
T ss_pred             CCCCCCEeEEeecCCCC-ceecCcCCCCchhhhHHHHHHHHHHh---------CCCCccCCCCCeeec
Confidence            35667899999887655 4678865  4   8999999999864         234689999998753

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=98.08  E-value=2e-05  Score=58.84  Aligned_cols=65  Identities=17%  Similarity=0.183  Sum_probs=58.3

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      .|+++|.+.+...    +..|+|||..+....+.+...|...|+....++|.|+      ..+|..+++.|+.+.
T Consensus        16 ~K~~~l~~ll~~~----~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~------~~~r~~~~~~f~~g~   80 (165)
T 1fuk_A           16 YKYECLTDLYDSI----SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLP------QQERDTIMKEFRSGS   80 (165)
T ss_dssp             GHHHHHHHHHHHT----TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTS
T ss_pred             hHHHHHHHHHHhC----CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCC------HHHHHHHHHHHHcCC
Confidence            4999888877753    5689999999999999999999999999999999977      999999999999743

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=98.06  E-value=1.3e-05  Score=61.66  Aligned_cols=66  Identities=9%  Similarity=0.198  Sum_probs=58.2

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ...|+..|++.|..     .+.|+|||+++....+.+...|...|++...++|.|+      ..+|.++++.|+++.
T Consensus        39 ~~~K~~~L~~~l~~-----~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~------~~~R~~~l~~F~~g~  104 (191)
T 2p6n_A           39 EEAKMVYLLECLQK-----TPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKD------QEERTKAIEAFREGK  104 (191)
T ss_dssp             GGGHHHHHHHHHTT-----SCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSC------HHHHHHHHHHHHHTS
T ss_pred             hHHHHHHHHHHHHh-----CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCC------HHHHHHHHHHHhcCC
Confidence            46899988877753     2459999999999999999999999999999999977      999999999999743

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=97.99  E-value=2.9e-05  Score=58.55  Aligned_cols=65  Identities=12%  Similarity=0.116  Sum_probs=57.5

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      .|+++|.+.+..    .+..|+|||.++....+.+...|...|+....++|.|+      ..+|..+++.|+++.
T Consensus        20 ~K~~~L~~ll~~----~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~------~~~R~~~~~~f~~g~   84 (175)
T 2rb4_A           20 DKYQALCNIYGS----ITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELT------VEQRASIIQRFRDGK   84 (175)
T ss_dssp             HHHHHHHHHHTT----SCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCC------HHHHHHHHHHHHTTS
T ss_pred             hHHHHHHHHHHh----CCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCC------HHHHHHHHHHHHcCC
Confidence            488888776653    35679999999999999999999999999999999977      999999999999743

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}

Probab=97.94  E-value=5.5e-06  Score=68.86  Aligned_cols=60  Identities=15%  Similarity=0.254  Sum_probs=39.7

Q ss_pred             CccccccccccccCCC-------eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           23 DEETCPICQEKLGNQK-------MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~-------~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      ...+|+||...+.+..       ...+|||.|+..|+.+|++.....-..-..-...||.||.++..
T Consensus       307 ~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             SCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             CCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            4568999987765411       13589999999999999976321100001223579999998754

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=97.93  E-value=9.5e-06  Score=71.36  Aligned_cols=69  Identities=12%  Similarity=0.135  Sum_probs=40.2

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC------------CceEEEeeCCCCCCcchhhHhhhH
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN------------NITCIKMKGENHKLPSANLQHRNA  187 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~------------gi~~~~~~G~m~~~~~~~~~~R~~  187 (210)
                      .+.|+.+|++.|.+.....++.|+|||+++..+++.+...|...            |..+..++|+|+      ..+|.+
T Consensus       370 ~~~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~------~~~R~~  443 (556)
T 4a2p_A          370 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMT------LPSQKG  443 (556)
T ss_dssp             CCHHHHHHHHHHHHHHHHCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC--------------------------
T ss_pred             CChHHHHHHHHHHHHhcCCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccC------HHHHHH
Confidence            58899999999988776677899999999999999999999887            566666677766      999999


Q ss_pred             HHHHHhh
Q 028376          188 LQKELTR  194 (210)
Q Consensus       188 ~l~~F~~  194 (210)
                      +++.|++
T Consensus       444 ~~~~F~~  450 (556)
T 4a2p_A          444 VLDAFKT  450 (556)
T ss_dssp             -------
T ss_pred             HHHHhcc
Confidence            9999998

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=97.92  E-value=1.3e-05  Score=70.35  Aligned_cols=69  Identities=12%  Similarity=0.090  Sum_probs=41.3

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCC------------ceEEEeeCCCCCCcchhhHhhhH
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN------------ITCIKMKGENHKLPSANLQHRNA  187 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~g------------i~~~~~~G~m~~~~~~~~~~R~~  187 (210)
                      .+.|+++|++.|.++....++.|+|||+++..+++.+...|...|            ..+..++|+|+      ..+|.+
T Consensus       369 ~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~------~~~R~~  442 (555)
T 3tbk_A          369 ENPKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMT------LPAQKC  442 (555)
T ss_dssp             CCHHHHHHHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-----------------------
T ss_pred             CCHHHHHHHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccC------HHHHHH
Confidence            478999999999988877788999999999999999999999875            35555566866      999999


Q ss_pred             HHHHHhh
Q 028376          188 LQKELTR  194 (210)
Q Consensus       188 ~l~~F~~  194 (210)
                      +++.|++
T Consensus       443 ~~~~F~~  449 (555)
T 3tbk_A          443 VLEAFRA  449 (555)
T ss_dssp             -------
T ss_pred             HHHHHhc
Confidence            9999997

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=97.78  E-value=2.2e-05  Score=74.13  Aligned_cols=69  Identities=12%  Similarity=0.135  Sum_probs=40.2

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC------------CceEEEeeCCCCCCcchhhHhhhH
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN------------NITCIKMKGENHKLPSANLQHRNA  187 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~------------gi~~~~~~G~m~~~~~~~~~~R~~  187 (210)
                      .+.|+..|++.|.......++.|+|||+++..+++.|...|..+            |..+..++|+|+      ..+|.+
T Consensus       611 ~~~K~~~L~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~------~~eR~~  684 (936)
T 4a2w_A          611 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMT------LPSQKG  684 (936)
T ss_dssp             CCHHHHHHHHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC-------------------------
T ss_pred             CCHHHHHHHHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCC------HHHHHH
Confidence            47899999999998776677899999999999999999999987            666666677766      999999


Q ss_pred             HHHHHhh
Q 028376          188 LQKELTR  194 (210)
Q Consensus       188 ~l~~F~~  194 (210)
                      +++.|+.
T Consensus       685 il~~Fr~  691 (936)
T 4a2w_A          685 VLDAFKT  691 (936)
T ss_dssp             -------
T ss_pred             HHHHhhc
Confidence            9999997

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=97.77  E-value=2.5e-05  Score=72.45  Aligned_cols=69  Identities=12%  Similarity=0.135  Sum_probs=39.7

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC------------CceEEEeeCCCCCCcchhhHhhhH
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN------------NITCIKMKGENHKLPSANLQHRNA  187 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~------------gi~~~~~~G~m~~~~~~~~~~R~~  187 (210)
                      .+.|+..|++.|.......++.|+|||+++..+++.|...|..+            |..+..++|+|+      ..+|..
T Consensus       611 ~~~K~~~L~~lL~~~~~~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~------~~eR~~  684 (797)
T 4a2q_A          611 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMT------LPSQKG  684 (797)
T ss_dssp             CCHHHHHHHHHHHHHHHHCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC-------------------------
T ss_pred             CChHHHHHHHHHHHHhccCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCC------HHHHHH
Confidence            48899999999988766677899999999999999999999884            666677788866      999999


Q ss_pred             HHHHHhh
Q 028376          188 LQKELTR  194 (210)
Q Consensus       188 ~l~~F~~  194 (210)
                      +++.|++
T Consensus       685 ~l~~F~~  691 (797)
T 4a2q_A          685 VLDAFKT  691 (797)
T ss_dssp             -------
T ss_pred             HHHHhhc
Confidence            9999998

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=97.76  E-value=0.00011  Score=57.24  Aligned_cols=68  Identities=7%  Similarity=0.155  Sum_probs=60.3

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ....|+++|.+.+..    .++.++|||.......+.+...|...|+....++|+|+      ..+|.++++.|+++.
T Consensus        14 ~~~~k~~~l~~ll~~----~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~------~~~r~~~~~~f~~g~   81 (212)
T 3eaq_A           14 PVRGRLEVLSDLLYV----ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLS------QGERERVLGAFRQGE   81 (212)
T ss_dssp             CTTSHHHHHHHHHHH----HCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSC------HHHHHHHHHHHHSSS
T ss_pred             CHHHHHHHHHHHHHh----CCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCC------HHHHHHHHHHHHCCC
Confidence            447899999988764    24679999999999999999999999999999999977      999999999999754

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=97.71  E-value=5.8e-05  Score=71.53  Aligned_cols=68  Identities=12%  Similarity=0.121  Sum_probs=61.4

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHH-hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFI-ANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~-~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..+.|+.+|.+.|..    .++.|+|||+++...++.+...|. ..|+++..++|+|+      ..+|.++++.|++++
T Consensus       486 ~~~~K~~~L~~ll~~----~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~------~~~R~~~l~~F~~g~  554 (968)
T 3dmq_A          486 NFDPRVEWLMGYLTS----HRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMS------IIERDRAAAWFAEED  554 (968)
T ss_dssp             TTSHHHHHHHHHHHH----TSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSC------TTHHHHHHHHHHSTT
T ss_pred             CccHHHHHHHHHHHh----CCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCC------HHHHHHHHHHHhCCC
Confidence            457899999988875    568999999999999999999999 47999999999977      999999999999854

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=97.58  E-value=5.2e-05  Score=68.90  Aligned_cols=73  Identities=10%  Similarity=0.119  Sum_probs=58.3

Q ss_pred             CCchHHHHHHHHHHHHhcCC-CCcEEEEcchHHHHHHHHHHHHhC------CceEEEeeCC--------CCCCcchhhHh
Q 028376          120 YGTKIEAVTRRILWIKSTDP-KAKILVFSSWNDVLDVLEHAFIAN------NITCIKMKGE--------NHKLPSANLQH  184 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~-~~K~iVFSQf~~~L~li~~~L~~~------gi~~~~~~G~--------m~~~~~~~~~~  184 (210)
                      .+.|++.|++.|.......+ +.|+|||+++..+.+.|...|..+      |++...|+|+        |+      ..+
T Consensus       379 ~~~k~~~L~~~L~~~~~~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~------~~e  452 (699)
T 4gl2_A          379 ENEKLTKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMT------QNE  452 (699)
T ss_dssp             ---CSSCSHHHHHHHHHHSSSCCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCC------HHH
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCC------HHH
Confidence            46788888888887666666 899999999999999999999998      9999999999        77      999


Q ss_pred             hhHHHHHHhhcCCC
Q 028376          185 RNALQKELTRHMPS  198 (210)
Q Consensus       185 R~~~l~~F~~~~p~  198 (210)
                      |.++++.|+++..+
T Consensus       453 R~~~~~~F~~g~~~  466 (699)
T 4gl2_A          453 QKEVISKFRTGKIN  466 (699)
T ss_dssp             HHHHHHHHCC---C
T ss_pred             HHHHHHHHhcCCCc
Confidence            99999999985544

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=96.70  E-value=1.1e-05  Score=60.62  Aligned_cols=67  Identities=18%  Similarity=0.141  Sum_probs=58.1

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|++.|.+.+..    .++.|+|||.++....+.+...|...|+....++|.|+      ..+|..+++.|+++..
T Consensus        15 ~~k~~~l~~ll~~----~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~------~~~r~~~~~~f~~g~~   81 (170)
T 2yjt_D           15 EHKTALLVHLLKQ----PEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMV------QGKRNEAIKRLTEGRV   81 (170)
Confidence            5688877776654    34679999999999999999999999999999999977      9999999999997543

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=97.44  E-value=0.00023  Score=64.60  Aligned_cols=73  Identities=12%  Similarity=0.122  Sum_probs=46.4

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCC----ceEEEeeC--------CCCCCcchhhHhhhH
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN----ITCIKMKG--------ENHKLPSANLQHRNA  187 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~g----i~~~~~~G--------~m~~~~~~~~~~R~~  187 (210)
                      .+.|+..|.+.|.......++.++|||+++....+.+...|...|    ++...+.|        +|+      ..+|.+
T Consensus       378 ~~~k~~~L~~ll~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~------~~eR~~  451 (696)
T 2ykg_A          378 ENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMT------LPAQKC  451 (696)
T ss_dssp             CCHHHHHHHHHHHHHHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC--------------------------
T ss_pred             CCHHHHHHHHHHHHHhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCC------HHHHHH
Confidence            568999999999887666678899999999999999999999999    99999966        655      999999


Q ss_pred             HHHHHhh-cCCC
Q 028376          188 LQKELTR-HMPS  198 (210)
Q Consensus       188 ~l~~F~~-~~p~  198 (210)
                      +++.|+. +...
T Consensus       452 v~~~F~~~g~~~  463 (696)
T 2ykg_A          452 ILDAFKASGDHN  463 (696)
T ss_dssp             ---------CCS
T ss_pred             HHHHHHhcCCcc
Confidence            9999997 4443

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=97.40  E-value=0.00074  Score=55.55  Aligned_cols=68  Identities=7%  Similarity=0.159  Sum_probs=60.3

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..+.|+++|.+.+...    ++.++|||.......+.+...|...|+....++|.|+      ..+|.++++.|.++.
T Consensus        11 ~~~~K~~~L~~ll~~~----~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~------~~~r~~~~~~f~~g~   78 (300)
T 3i32_A           11 PVRGRLEVLSDLLYVA----SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMS------QGERERVMGAFRQGE   78 (300)
T ss_dssp             CSSSHHHHHHHHHHHH----CCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCC------THHHHHHHHHHHHTS
T ss_pred             CHHHHHHHHHHHHHhc----CCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCC------HHHHHHHHHHhhcCC
Confidence            4468999998877643    3789999999999999999999999999999999977      999999999999854

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=97.23  E-value=0.0014  Score=54.76  Aligned_cols=68  Identities=9%  Similarity=0.032  Sum_probs=58.8

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ...|...|.+.+..    .+..|+|||.......+.+...|...|+....++|+|+      ..+|..+++.|+++..
T Consensus       234 ~~~~~~~l~~~l~~----~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~------~~~r~~~~~~f~~~~~  301 (391)
T 1xti_A          234 DNEKNRKLFDLLDV----LEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMP------QEERLSRYQQFKDFQR  301 (391)
T ss_dssp             GGGHHHHHHHHHHH----SCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTCC
T ss_pred             chhHHHHHHHHHHh----cCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCC------HHHHHHHHHHHhcCCC
Confidence            45677777776664    35789999999999999999999999999999999977      9999999999997543

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=97.08  E-value=0.0019  Score=53.17  Aligned_cols=68  Identities=13%  Similarity=0.117  Sum_probs=58.9

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ....|+++|.+.+.     .++.|+|||.......+.+...|...|+....++|+|+      ..+|..+++.|+++..
T Consensus       222 ~~~~~~~~l~~~l~-----~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~------~~~r~~~~~~f~~~~~  289 (367)
T 1hv8_A          222 NENERFEALCRLLK-----NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLS------QSQREKVIRLFKQKKI  289 (367)
T ss_dssp             CGGGHHHHHHHHHC-----STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSC------HHHHHHHHHHHHTTSS
T ss_pred             ChHHHHHHHHHHHh-----cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCC------HHHHHHHHHHHHcCCC
Confidence            34578887776664     46789999999999999999999999999999999977      9999999999997543

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=97.04  E-value=0.0022  Score=54.09  Aligned_cols=67  Identities=16%  Similarity=0.215  Sum_probs=57.9

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|++.|.+.+...    ...|+|||.......+.+...|...|+....++|.|+      ..+|..+++.|+++..
T Consensus       261 ~~k~~~l~~~~~~~----~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~------~~~r~~~~~~f~~g~~  327 (410)
T 2j0s_A          261 EWKFDTLCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMP------QKERESIMKEFRSGAS  327 (410)
T ss_dssp             THHHHHHHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSC------HHHHHHHHHHHHHTSS
T ss_pred             HhHHHHHHHHHHhc----CCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCC------HHHHHHHHHHHHCCCC
Confidence            34888877776654    3569999999999999999999999999999999977      9999999999998543

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=96.97  E-value=0.0037  Score=52.70  Aligned_cols=69  Identities=14%  Similarity=0.169  Sum_probs=59.3

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ...|...|.+.+...   .++.|+|||.......+.+...|...|+....++|.|+      ..+|..+++.|+++..
T Consensus       259 ~~~~~~~l~~~l~~~---~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~------~~~r~~~~~~f~~g~~  327 (417)
T 2i4i_A          259 ESDKRSFLLDLLNAT---GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRS------QRDREEALHQFRSGKS  327 (417)
T ss_dssp             GGGHHHHHHHHHHTC---CTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHHTSS
T ss_pred             cHhHHHHHHHHHHhc---CCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCC------HHHHHHHHHHHHcCCC
Confidence            456777777766542   35789999999999999999999999999999999977      9999999999997544

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=96.90  E-value=0.0042  Score=51.67  Aligned_cols=60  Identities=12%  Similarity=0.128  Sum_probs=52.2

Q ss_pred             HHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          132 LWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       132 ~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..+....+..|+|||.......+.+...|...|+....++|.|+      ..+|..+++.|+.+..
T Consensus       235 ~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~------~~~r~~~~~~f~~g~~  294 (395)
T 3pey_A          235 TELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQ------TQERDRLIDDFREGRS  294 (395)
T ss_dssp             HHHHTTTTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSC------HHHHHHHHHHHHTTSC
T ss_pred             HHHHHhccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCC------HHHHHHHHHHHHCCCC
Confidence            33334456789999999999999999999999999999999977      9999999999998543

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=96.89  E-value=0.0034  Score=53.85  Aligned_cols=66  Identities=11%  Similarity=0.092  Sum_probs=57.6

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ...|...|++.|...     ..++|||.......+.+...|...|++...++|.|+      ..+|.++++.|+++.
T Consensus       285 ~~~k~~~l~~~l~~~-----~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~------~~~R~~~l~~F~~g~  350 (434)
T 2db3_A          285 KYAKRSKLIEILSEQ-----ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRL------QSQREQALRDFKNGS  350 (434)
T ss_dssp             GGGHHHHHHHHHHHC-----CTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSC------HHHHHHHHHHHHTSS
T ss_pred             cHHHHHHHHHHHHhC-----CCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCC------HHHHHHHHHHHHcCC
Confidence            457888888777642     345999999999999999999999999999999977      999999999999754

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=96.82  E-value=0.0011  Score=52.68  Aligned_cols=53  Identities=21%  Similarity=0.344  Sum_probs=40.0

Q ss_pred             CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      .....|.+|.+.+.....-..|+|.|+..|+..|++.         .....||.|+......
T Consensus       178 ~~i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~---------~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          178 DAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQS---------NAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TTCCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTT---------CSSCBCTTTCCBCCSC
T ss_pred             CCCCcCcchhhHHhCCcccCccChHHHHHHHHHHHHh---------CCCCCCCCCCCCCCCC
Confidence            3567899999988764333469999999999999632         3456899999875443

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=96.77  E-value=0.004  Score=52.20  Aligned_cols=68  Identities=12%  Similarity=0.157  Sum_probs=57.7

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ...|+..+...+..    .+..|+|||.......+.+...|...|+....++|+|+      ..+|..+++.|+++..
T Consensus       242 ~~~k~~~l~~~~~~----~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~------~~~r~~~~~~f~~g~~  309 (400)
T 1s2m_A          242 ERQKLHCLNTLFSK----LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMK------QQERNKVFHEFRQGKV  309 (400)
T ss_dssp             GGGHHHHHHHHHHH----SCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSC------HHHHHHHHHHHHTTSS
T ss_pred             hhhHHHHHHHHHhh----cCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCC------HHHHHHHHHHHhcCCC
Confidence            35677776665553    35679999999999999999999999999999999977      9999999999997543

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=96.68  E-value=0.008  Score=53.03  Aligned_cols=67  Identities=7%  Similarity=0.072  Sum_probs=58.5

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|++.|++.|..    .++.++|||.......+.+...|...|+....|+|+|+      ..+|..+++.|.++..
T Consensus       221 ~~~~~~l~~~l~~----~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~------~~~R~~~~~~f~~g~~  287 (523)
T 1oyw_A          221 FKPLDQLMRYVQE----QRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLE------NNVRADVQEKFQRDDL  287 (523)
T ss_dssp             SSHHHHHHHHHHH----TTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTSC
T ss_pred             CCHHHHHHHHHHh----cCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCC------HHHHHHHHHHHHcCCC
Confidence            4677777777764    36789999999999999999999999999999999977      9999999999998543

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=96.64  E-value=0.0058  Score=51.23  Aligned_cols=67  Identities=13%  Similarity=0.121  Sum_probs=56.7

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+..|.+.+..    .+..|+|||.......+.+...|...|+....++|.|+      ..+|..+++.|+.+..
T Consensus       251 ~~~~~~l~~~~~~----~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~------~~~r~~~~~~f~~g~~  317 (412)
T 3fht_A          251 DEKFQALCNLYGA----ITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMM------VEQRAAVIERFREGKE  317 (412)
T ss_dssp             HHHHHHHHHHHHH----HSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSC------HHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHHHHhh----cCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCC------HHHHHHHHHHHHCCCC
Confidence            3566666665554    34679999999999999999999999999999999977      9999999999997543

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=96.59  E-value=0.0036  Score=52.64  Aligned_cols=67  Identities=16%  Similarity=0.222  Sum_probs=53.2

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+..+.+.+.    ..+..|+|||.......+.+...|...|+....++|+|+      ..+|..+++.|+++..
T Consensus       265 ~~~~~~l~~~~~----~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~------~~~r~~~~~~f~~g~~  331 (414)
T 3eiq_A          265 EWKLDTLCDLYE----TLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMD------QKERDVIMREFRSGSS  331 (414)
T ss_dssp             TTHHHHHHHHHH----SSCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CH------HHHHHHHHHHHSCC--
T ss_pred             HhHHHHHHHHHH----hCCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCC------HHHHHHHHHHHHcCCC
Confidence            347777666555    345679999999999999999999999999999999966      9999999999987443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=96.36  E-value=0.014  Score=50.75  Aligned_cols=69  Identities=7%  Similarity=0.046  Sum_probs=56.1

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      .|.+.+.+.+.+... ....++|||.. +...+.+...|...|.+...++|.|+      ..+|.++++.|+++..+
T Consensus       331 ~~~~~l~~~l~~~~~-~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~------~~~r~~i~~~f~~g~~~  399 (510)
T 2oca_A          331 KRNKWIAKLAIKLAQ-KDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVD------TETRNIMKTLAENGKGI  399 (510)
T ss_dssp             HHHHHHHHHHHHHHT-TTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTT------HHHHHHHHHHHHHCCSC
T ss_pred             HHHHHHHHHHHHHHh-cCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCC------HHHHHHHHHHHhCCCCC
Confidence            455666666666553 45678899999 88888899999999999999999977      99999999999985544

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=96.35  E-value=0.018  Score=51.61  Aligned_cols=55  Identities=2%  Similarity=-0.016  Sum_probs=50.1

Q ss_pred             cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          137 TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..++.++|||.......+.+...|...|+....|+|+|+      ..+|.++++.|..+..
T Consensus       264 ~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~------~~~R~~~~~~F~~g~~  318 (591)
T 2v1x_A          264 RYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLE------PEDKTTVHRKWSANEI  318 (591)
T ss_dssp             TTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTSS
T ss_pred             hccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCC------HHHHHHHHHHHHcCCC
Confidence            346789999999999999999999999999999999977      9999999999997543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=96.26  E-value=0.013  Score=52.05  Aligned_cols=70  Identities=16%  Similarity=0.214  Sum_probs=56.7

Q ss_pred             CchHHHHHHHHHHHH-hcCCCCcEEEEcchHHHHHHHHHHHHhC---CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          121 GTKIEAVTRRILWIK-STDPKAKILVFSSWNDVLDVLEHAFIAN---NITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       121 SsKi~al~~~L~~~~-~~~~~~K~iVFSQf~~~L~li~~~L~~~---gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..++..+++.|.... ...++.|+|||.......+.+...|...   |+....++|.|+      ..+|..+++.|..+.
T Consensus       268 ~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~------~~~R~~~~~~F~~g~  341 (579)
T 3sqw_A          268 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKIT------QNKRTSLVKRFKKDE  341 (579)
T ss_dssp             THHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSC------HHHHHHHHHHHHHCS
T ss_pred             hhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCC------HHHHHHHHHHhhcCC
Confidence            344545555554433 3367889999999999999999999987   999999999977      999999999999844

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=96.20  E-value=0.015  Score=51.25  Aligned_cols=70  Identities=17%  Similarity=0.239  Sum_probs=57.3

Q ss_pred             CchHHHHHHHHHHH-HhcCCCCcEEEEcchHHHHHHHHHHHHhC---CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          121 GTKIEAVTRRILWI-KSTDPKAKILVFSSWNDVLDVLEHAFIAN---NITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       121 SsKi~al~~~L~~~-~~~~~~~K~iVFSQf~~~L~li~~~L~~~---gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..++..+++.+... ....++.++|||..-....+.+...|...   |++...++|.|+      ..+|..+++.|.++.
T Consensus       319 ~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~------~~~R~~~~~~f~~g~  392 (563)
T 3i5x_A          319 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKIT------QNKRTSLVKRFKKDE  392 (563)
T ss_dssp             THHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSC------HHHHHHHHHHHHHCS
T ss_pred             HhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCC------HHHHHHHHHHHhcCC
Confidence            44555555555443 33467889999999999999999999986   999999999977      999999999999854

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=96.09  E-value=0.03  Score=50.82  Aligned_cols=69  Identities=16%  Similarity=0.082  Sum_probs=60.1

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ...++..|++.|..+...  +.++|||+.-....+.+...|...|++...++|.|+      ..+|..+++.|..+.
T Consensus       421 ~~~~~~~Ll~~l~~~~~~--~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~------~~~R~~~~~~f~~g~  489 (664)
T 1c4o_A          421 TENQILDLMEGIRERAAR--GERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELD------AFKRQALIRDLRLGH  489 (664)
T ss_dssp             STTHHHHHHHHHHHHHHT--TCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCC------HHHHHHHHHHHHTTS
T ss_pred             ccchHHHHHHHHHHHHhc--CCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCC------HHHHHHHHHHhhcCC
Confidence            346788888888876643  679999999999999999999999999999999977      999999999998744

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=96.06  E-value=0.0049  Score=53.16  Aligned_cols=66  Identities=15%  Similarity=0.259  Sum_probs=53.7

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      ..+.|+..|.+.|..    .++.|+|||+++...++.+...|.   +  ..++|.|+      ..+|.++++.|+++..+
T Consensus       332 ~~~~k~~~l~~~l~~----~~~~k~lvF~~~~~~~~~l~~~l~---~--~~~~g~~~------~~~R~~~~~~F~~g~~~  396 (472)
T 2fwr_A          332 NSKNKIRKLREILER----HRKDKIIIFTRHNELVYRISKVFL---I--PAITHRTS------REEREEILEGFRTGRFR  396 (472)
T ss_dssp             SCSHHHHHHHHHHHH----TSSSCBCCBCSCHHHHHHHHHHTT---C--CBCCSSSC------SHHHHTHHHHHHHSSCS
T ss_pred             cChHHHHHHHHHHHh----CCCCcEEEEECCHHHHHHHHHHhC---c--ceeeCCCC------HHHHHHHHHHHhCCCCC
Confidence            356788888877765    468899999999999999998884   3  35789977      99999999999986554


Q ss_pred             C
Q 028376          199 S  199 (210)
Q Consensus       199 ~  199 (210)
                      +
T Consensus       397 v  397 (472)
T 2fwr_A          397 A  397 (472)
T ss_dssp             B
T ss_pred             E
Confidence            4

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=96.02  E-value=0.034  Score=50.47  Aligned_cols=69  Identities=13%  Similarity=0.069  Sum_probs=60.0

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..++..|++.|..+..  .+.++|||+.-....+.+...|..+|++...++|.|+      ..+|..+++.|..+..
T Consensus       428 ~~~~~~Ll~~l~~~~~--~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~------~~~R~~~l~~f~~g~~  496 (661)
T 2d7d_A          428 EGQIDDLIGEIQARIE--RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIK------TLERIEIIRDLRLGKY  496 (661)
T ss_dssp             TTHHHHHHHHHHHHHT--TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCC------HHHHHHHHHHHHHTSC
T ss_pred             cchHHHHHHHHHHHHh--cCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCC------HHHHHHHHHHHhcCCe
Confidence            4678888888887663  3679999999999999999999999999999999977      9999999999997443

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=95.77  E-value=0.0045  Score=42.19  Aligned_cols=33  Identities=18%  Similarity=0.531  Sum_probs=25.2

Q ss_pred             CccccccccccccCCCee--cCCCCcchHhhHHHH
Q 028376           23 DEETCPICQEKLGNQKMV--FQCGHFTCCKCFFAM   55 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~--~~CgH~fC~~C~~~~   55 (210)
                      +...|++|.+.+..+++.  +.|+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            457899999753223455  899999999999973

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=95.28  E-value=0.033  Score=49.52  Aligned_cols=67  Identities=16%  Similarity=0.158  Sum_probs=50.6

Q ss_pred             hHHHHHHHHHHHH-hcCCCCcEEEEcchHHHHHHHHHHHHhCCce--------EEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376          123 KIEAVTRRILWIK-STDPKAKILVFSSWNDVLDVLEHAFIANNIT--------CIKMKGENHKLPSANLQHRNALQKELT  193 (210)
Q Consensus       123 Ki~al~~~L~~~~-~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~--------~~~~~G~m~~~~~~~~~~R~~~l~~F~  193 (210)
                      +...+.+.|..+. ..++..|+|||++.....+.+...|...+..        ...++|.|+       .+|.+++++|+
T Consensus       421 r~~~i~~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~-------~~r~~~l~~F~  493 (590)
T 3h1t_A          421 RTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG-------KIGKGHLSRFQ  493 (590)
T ss_dssp             THHHHHHHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH-------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh-------HHHHHHHHHHh
Confidence            4455555554432 2366789999999999999999999887654        567899853       36999999999


Q ss_pred             hcC
Q 028376          194 RHM  196 (210)
Q Consensus       194 ~~~  196 (210)
                      +++
T Consensus       494 ~~~  496 (590)
T 3h1t_A          494 ELE  496 (590)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            844

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=95.09  E-value=0.0037  Score=52.09  Aligned_cols=65  Identities=15%  Similarity=0.155  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      |...+.+.+..    .+..|+|||.......+.+...|...|+....++|+|+      ..+|..+++.|+++..
T Consensus       246 ~~~~l~~~~~~----~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~------~~~r~~~~~~f~~~~~  310 (394)
T 1fuu_A          246 KYECLTDLYDS----ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLP------QQERDTIMKEFRSGSS  310 (394)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             HHHHHHHHHhc----CCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCC------HHHHHHHHHHHHCCCC
Confidence            55555544433    34679999999999999999999999999999999977      9999999999987443

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=93.00  E-value=0.15  Score=33.63  Aligned_cols=55  Identities=25%  Similarity=0.584  Sum_probs=39.8

Q ss_pred             cCCCCccccccccccccCC----C--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           19 LSKADEETCPICQEKLGNQ----K--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        19 l~~~~~~~C~iC~~~~~~~----~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ++......|.||.+.+...    +  ..-.|+-..|+.|++--.          ..+...||.|..++...
T Consensus        11 ~~~~~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYEr----------keG~q~CpqCktrYkr~   71 (93)
T 1weo_A           11 LKNLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYER----------REGTQNCPQCKTRYKRL   71 (93)
T ss_dssp             CSCCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHH----------HTSCSSCTTTCCCCCCC
T ss_pred             ccccCCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHH----------hccCccccccCCccccc
Confidence            4556678999998875421    1  224788899999998542          36778999999988643

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=92.98  E-value=0.34  Score=44.62  Aligned_cols=64  Identities=13%  Similarity=0.068  Sum_probs=52.7

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..|..+|++.|......  +.++|||+......+.|...|...||++..+.|+        ..+|.+.+-.|..
T Consensus       457 ~eK~~al~~~I~~~~~~--gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgk--------q~~rE~~ii~~ag  520 (822)
T 3jux_A          457 KEKYEKIVEEIEKRYKK--GQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAK--------YHEKEAEIVAKAG  520 (822)
T ss_dssp             HHHHHHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSC--------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhC--CCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCC--------chHHHHHHHHhCC
Confidence            46889999999876433  5689999999999999999999999999999998        5566666655543

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=92.82  E-value=0.11  Score=33.60  Aligned_cols=48  Identities=27%  Similarity=0.575  Sum_probs=36.5

Q ss_pred             CCCccccccccccccCCCeecCC----CCcchHhhHHHHHHHhhhccccCCCccccccC
Q 028376           21 KADEETCPICQEKLGNQKMVFQC----GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPT   75 (210)
Q Consensus        21 ~~~~~~C~iC~~~~~~~~~~~~C----gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~   75 (210)
                      ......|.+|.+.+++. ...+|    +|.||..|-...++++.      .....-||.
T Consensus        12 ~~a~l~CtlC~erLEdt-HFVQCPsv~~HkFCFpCsr~sIk~q~------~~~EvyCPS   63 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDT-HFVQCPSVPSHKFCFPCSRESIKAQG------ATGEVYCPS   63 (93)
T ss_dssp             SCCSCCCSSSCSCCSST-TSEECSSCSSCEECHHHHHHHHHHHH------SSSCCCCTT
T ss_pred             CCCeeEeecchhhhccC-ceeeCCCccCCeeeccccHHHHHhcC------CCCcEECCC
Confidence            34557899999999874 45556    79999999999988754      355667775

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=92.65  E-value=0.2  Score=40.35  Aligned_cols=50  Identities=16%  Similarity=0.221  Sum_probs=43.2

Q ss_pred             cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          137 TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ...+.|+|||.......+.+...|.    ....++|.|+      ..+|.++++.|+++.
T Consensus       217 ~~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~------~~~r~~~~~~f~~~~  266 (337)
T 2z0m_A          217 ENKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLP------QSVRNRNIDAFREGE  266 (337)
T ss_dssp             TCCCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSC------HHHHHHHHHHHHTTS
T ss_pred             hCCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCC------HHHHHHHHHHHHcCC
Confidence            3567899999999999999888887    4678999977      999999999999744

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=92.08  E-value=0.027  Score=48.56  Aligned_cols=68  Identities=13%  Similarity=0.119  Sum_probs=0.0

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      ..|...|.+.+..    .+..++|||.......+.+...|...|+....++|.|+      ..+|..+++.|.++...
T Consensus       318 ~~~~~~l~~~~~~----~~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~------~~~R~~~~~~f~~g~~~  385 (479)
T 3fmp_B          318 DEKFQALCNLYGA----ITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMM------VEQRAAVIERFREGKEK  385 (479)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHhh----ccCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCC------HHHHHHHHHHHHcCCCc
Confidence            3455555554443    34579999999999999999999999999999999976      99999999999985443

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=92.04  E-value=0.28  Score=45.59  Aligned_cols=66  Identities=12%  Similarity=0.073  Sum_probs=52.5

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR  194 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~  194 (210)
                      ..|..+|++.|....  ..+..+|||+.-....+.|...|...||++..+.|.+.      ..+|.-+.+.|+.
T Consensus       424 ~~K~~al~~~i~~~~--~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~------~rEa~iia~agr~  489 (853)
T 2fsf_A          424 AEKIQAIIEDIKERT--AKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFH------ANEAAIVAQAGYP  489 (853)
T ss_dssp             HHHHHHHHHHHHHHH--TTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCH------HHHHHHHHTTTST
T ss_pred             HHHHHHHHHHHHHHh--cCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChh------HHHHHHHHhcCCC
Confidence            568999999887654  33668999999999999999999999999999999943      4444444455554

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=91.95  E-value=0.21  Score=46.43  Aligned_cols=54  Identities=17%  Similarity=0.164  Sum_probs=46.3

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH  175 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~  175 (210)
                      ...|..+|++.|......  +..+|||+.-....+.|...|...||++..+.|.+.
T Consensus       414 ~~~K~~al~~~i~~~~~~--~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~  467 (844)
T 1tf5_A          414 MEGKFKAVAEDVAQRYMT--GQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNH  467 (844)
T ss_dssp             HHHHHHHHHHHHHHHHHH--TCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCH
T ss_pred             HHHHHHHHHHHHHHHHhc--CCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCcc
Confidence            357899999988865432  567999999999999999999999999999999944

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=91.43  E-value=0.36  Score=45.18  Aligned_cols=53  Identities=15%  Similarity=0.119  Sum_probs=45.9

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH  175 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~  175 (210)
                      ..|..+|++.|.....  .+..+|||+.-....+.|...|...||++..+.|.+.
T Consensus       443 ~~K~~al~~~i~~~~~--~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~  495 (922)
T 1nkt_A          443 EAKYIAVVDDVAERYA--KGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYH  495 (922)
T ss_dssp             HHHHHHHHHHHHHHHH--TTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCH
T ss_pred             HHHHHHHHHHHHHHHh--cCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChh
Confidence            4689999999976543  3567999999999999999999999999999999943

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=89.53  E-value=0.53  Score=45.46  Aligned_cols=54  Identities=2%  Similarity=-0.028  Sum_probs=48.0

Q ss_pred             CCCcEEEEcchHHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          139 PKAKILVFSSWNDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       139 ~~~K~iVFSQf~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      .+.+++||......++.+...|...  |++...++|.|+      ..+|.++++.|.++..+
T Consensus       811 ~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~------~~eR~~il~~F~~g~~~  866 (1151)
T 2eyq_A          811 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMR------ERELERVMNDFHHQRFN  866 (1151)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCC------HHHHHHHHHHHHTTSCC
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCC------HHHHHHHHHHHHcCCCc
Confidence            4789999999999999999999987  899999999987      99999999999975443

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=88.94  E-value=0.57  Score=43.24  Aligned_cols=67  Identities=13%  Similarity=0.220  Sum_probs=56.8

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh-----------CCceEEEeeCCCCCCcchhhHhhhHHH
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA-----------NNITCIKMKGENHKLPSANLQHRNALQ  189 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~-----------~gi~~~~~~G~m~~~~~~~~~~R~~~l  189 (210)
                      ..+++++++.+..+....+..++|||..-....+.+...|..           .|+....+.|+|+      ..+|.+++
T Consensus       284 ~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~------~~eR~~v~  357 (773)
T 2xau_A          284 RDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLP------PHQQQRIF  357 (773)
T ss_dssp             SCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCC------HHHHGGGG
T ss_pred             hhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCC------HHHHHHHH
Confidence            456777777877776666788999999999888888888875           7899999999977      99999999


Q ss_pred             HHHh
Q 028376          190 KELT  193 (210)
Q Consensus       190 ~~F~  193 (210)
                      +.|.
T Consensus       358 ~~f~  361 (773)
T 2xau_A          358 EPAP  361 (773)
T ss_dssp             SCCC
T ss_pred             hhcc
Confidence            9997

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=88.85  E-value=1.8  Score=29.80  Aligned_cols=50  Identities=14%  Similarity=0.241  Sum_probs=44.0

Q ss_pred             EEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          143 ILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       143 ~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      .+|||+-+..|.-|-...+..|++.+.+.....      .+.|..-|++|.+..-+
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqd------ekrrrerleefekqgvd   54 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQD------EKRRRERLEEFEKQGVD   54 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSC------HHHHHHHHHHHHTTTCE
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCch------HHHHHHHHHHHHHcCCc
Confidence            489999999999999999999999998888755      89999999999975444

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=87.59  E-value=0.91  Score=37.99  Aligned_cols=60  Identities=10%  Similarity=0.028  Sum_probs=48.7

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEE-EeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCI-KMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~-~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|.+.|.+.|...     +.++|||.......+.+...|...|+... .++|.          +|.  ++.|+++..
T Consensus       238 ~~~~~~l~~~l~~~-----~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----------~r~--~~~f~~g~~  298 (414)
T 3oiy_A          238 SRSKEKLVELLEIF-----RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----------EKN--FEDFKVGKI  298 (414)
T ss_dssp             SCCHHHHHHHHHHH-----CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----------HHH--HHHHHTTSC
T ss_pred             cCHHHHHHHHHHHc-----CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----------chH--HHHHhCCCC
Confidence            36788887777651     47999999999999999999999999987 77773          444  999998543

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=82.71  E-value=2.9  Score=39.70  Aligned_cols=66  Identities=6%  Similarity=-0.039  Sum_probs=52.5

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCc------------------------------------
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNI------------------------------------  165 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi------------------------------------  165 (210)
                      .++.+|++.|..    .+..++|||..-....+.+...|...|+                                    
T Consensus       322 ~~~~~li~~l~~----~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~  397 (997)
T 4a4z_A          322 KTWPEIVNYLRK----RELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSL  397 (997)
T ss_dssp             THHHHHHHHHHH----TTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHh----CCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHH
Confidence            456677766653    4568999999999999988888877666                                    


Q ss_pred             ---eEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          166 ---TCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       166 ---~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                         +...++|+|+      ...|..+++.|..+.-
T Consensus       398 l~~gi~~~H~gl~------~~~R~~v~~~F~~G~~  426 (997)
T 4a4z_A          398 LERGIAVHHGGLL------PIVKELIEILFSKGFI  426 (997)
T ss_dssp             HTTTEEEECTTSC------HHHHHHHHHHHHTTCC
T ss_pred             hhcCeeeecCCCC------HHHHHHHHHHHHCCCC
Confidence               3577899977      9999999999998543

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=82.48  E-value=0.088  Score=35.37  Aligned_cols=40  Identities=33%  Similarity=0.699  Sum_probs=28.5

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ..||.|..++...     =++.+|..|-..+            .....||.|..++.
T Consensus        33 ~~CP~Cq~eL~~~-----g~~~hC~~C~~~f------------~~~a~CPdC~q~Le   72 (101)
T 2jne_A           33 LHCPQCQHVLDQD-----NGHARCRSCGEFI------------EMKALCPDCHQPLQ   72 (101)
T ss_dssp             CBCSSSCSBEEEE-----TTEEEETTTCCEE------------EEEEECTTTCSBCE
T ss_pred             ccCccCCCcceec-----CCEEECccccchh------------hccccCcchhhHHH
Confidence            7899999877532     1455688886654            45568999988764

>3ipz_A Monothiol glutaredoxin-S14, chloroplastic; electron transport, PL redox-active center, transit peptide, transport, oxidoreduc; 2.40A {Arabidopsis thaliana} PDB: 2lku_A

Probab=82.19  E-value=3.2  Score=27.98  Aligned_cols=34  Identities=9%  Similarity=0.092  Sum_probs=30.1

Q ss_pred             CCcEEEEcc------hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376          140 KAKILVFSS------WNDVLDVLEHAFIANNITCIKMKGE  173 (210)
Q Consensus       140 ~~K~iVFSQ------f~~~L~li~~~L~~~gi~~~~~~G~  173 (210)
                      ..+++||+.      |-.+-..+...|...||.|..++=.
T Consensus        17 ~~~Vvvy~k~t~~~p~Cp~C~~ak~~L~~~gi~~~~~dI~   56 (109)
T 3ipz_A           17 SEKVVLFMKGTRDFPMCGFSNTVVQILKNLNVPFEDVNIL   56 (109)
T ss_dssp             SSSEEEEESBCSSSBSSHHHHHHHHHHHHTTCCCEEEEGG
T ss_pred             cCCEEEEEecCCCCCCChhHHHHHHHHHHcCCCcEEEECC
Confidence            569999998      8899999999999999999888654

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}

Probab=81.73  E-value=1.4  Score=30.60  Aligned_cols=47  Identities=21%  Similarity=0.411  Sum_probs=35.7

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      +.|..|..++........=|..||..|..+.             ..+.|..|+.++...+
T Consensus        31 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~-------------~~~~C~~C~~~I~~~~   77 (126)
T 2xqn_T           31 FCCFDCDSILAGEIYVMVNDKPVCKPCYVKN-------------HAVVCQGCHNAIDPEV   77 (126)
T ss_dssp             SBCTTTCCBCTTSEEEEETTEEEEHHHHHHH-------------SCCBCTTTCSBCCTTS
T ss_pred             CCcCCCCCCCCcCEEEeECCEEechHHhCcC-------------cCccCcccCCcCCcCc
Confidence            5677788877654456677899999999875             2358999999998643

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=80.78  E-value=1.5  Score=36.78  Aligned_cols=54  Identities=22%  Similarity=0.554  Sum_probs=38.5

Q ss_pred             ccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      .||+=...+..+..-..|.|+-|.+-. .+++...      ....-.||+|.+.+...+|.
T Consensus       251 ~CPlS~~ri~~PvRg~~C~HlQCFDl~-sfL~~~~------~~~~W~CPIC~k~~~~~dL~  304 (371)
T 3i2d_A          251 QCPISYTRMKYPSKSINCKHLQCFDAL-WFLHSQL------QIPTWQCPVCQIDIALENLA  304 (371)
T ss_dssp             BCTTTSSBCSSEEEETTCCSSCCEEHH-HHHHHHH------HSCCCBCTTTCCBCCGGGEE
T ss_pred             cCCCccccccccCcCCcCCCcceECHH-HHHHHhh------cCCceeCCCCCcccCHHHee
Confidence            488888778776666899999775542 3333222      24567899999999888876

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=80.39  E-value=1.2  Score=27.11  Aligned_cols=41  Identities=27%  Similarity=0.645  Sum_probs=30.1

Q ss_pred             cccccccccccCCC--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           25 ETCPICQEKLGNQK--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        25 ~~C~iC~~~~~~~~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      ..|..|...+.+..  .-..|++.||.+|=.=+           ...-..||.|
T Consensus        16 ~~C~~C~~~~~~~~~y~C~~C~~~FC~dCD~fi-----------He~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFV-----------HDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTSEEECCTTTTCCBCHHHHHTT-----------TTTSCSSSTT
T ss_pred             CcccccCcccCCCccEECCccCcCcccchhHHH-----------HhhccCCcCC
Confidence            46999998885432  23689999999996533           3556689988

>2lqo_A Putative glutaredoxin RV3198.1/MT3292; TRX fold, oxidoreductase; NMR {Mycobacterium tuberculosis}

Probab=80.18  E-value=2.5  Score=27.91  Aligned_cols=46  Identities=17%  Similarity=0.239  Sum_probs=34.6

Q ss_pred             CCcEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHH
Q 028376          140 KAKILVFSS-WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKE  191 (210)
Q Consensus       140 ~~K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~  191 (210)
                      +.+++|||. |-.+-..+...|+++||+|..++=...      ...|+..++.
T Consensus         3 ta~I~vYs~~~Cp~C~~aK~~L~~~gi~y~~idi~~d------~~~~~~~~~~   49 (92)
T 2lqo_A            3 TAALTIYTTSWCGYCLRLKTALTANRIAYDEVDIEHN------RAAAEFVGSV   49 (92)
T ss_dssp             SSCEEEEECTTCSSHHHHHHHHHHTTCCCEEEETTTC------HHHHHHHHHH
T ss_pred             CCcEEEEcCCCCHhHHHHHHHHHhcCCceEEEEcCCC------HHHHHHHHHH
Confidence            468899986 667777788999999999998887644      5556554443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	210
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.001
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	0.003

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 36.5 bits (84), Expect = 2e-04
 Identities = 16/54 (29%), Positives = 17/54 (31%), Gaps = 11/54 (20%)

Query: 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78
          E CPIC E   N  M   C H  C  C      Q              CP C+ 
Sbjct: 6  ERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQN-----------PTCPLCKV 48

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.0 bits (77), Expect = 0.001
 Identities = 5/60 (8%), Positives = 10/60 (16%), Gaps = 11/60 (18%)

Query: 26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85
           C I  +      +  +                          +    P   +   I  I
Sbjct: 2  LCAISGKVPRRPVLSPKSRTIFEKSLLEQY-----------VKDTGNDPITNEPLSIEEI 50

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.6 bits (76), Expect = 0.003
 Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 2/42 (4%)

Query: 10 NSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKC 51
            ++  ++ L       C  C   L     +  C H  C  C
Sbjct: 10 AHSRAALDRLE--KLLRCSRCTNILREPVCLGGCEHIFCSNC 49

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	210
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.36
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.32
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.29
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.29
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.26
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.26
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.25
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.22
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.2
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.2
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.16
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.16
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.15
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.12
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.07
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.93
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.92
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.77
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.57
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.38
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.25
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.18
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	98.12
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	98.08
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	98.0
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	97.97
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	97.95
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.93
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	97.86
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	97.8
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	95.53
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	94.47
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	92.55
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	92.07
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	91.37
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	90.01
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	89.09
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	88.35
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	87.73
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	87.17
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	86.26
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	80.26

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=2.3e-13  Score=89.24  Aligned_cols=51  Identities=29%  Similarity=0.607  Sum_probs=42.3

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      +...|+||++.+.+ +++++|||.||.+|+..|+..          +...||+||..+...+
T Consensus        22 ~~~~C~IC~~~~~~-~~~~~CgH~fC~~Ci~~wl~~----------~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          22 TFQLCKICAENDKD-VKIEPCGHLMCTSCLTSWQES----------EGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             CTTBCTTTSSSBCC-EECSSSCCEECHHHHHHHHHT----------TCCSCTTTCCCCCCCC
T ss_pred             CCCCCccCCCcCCC-eEEeCCCCeeeHHHHHHHHHH----------CcCcCCCCCcCccCCc
Confidence            34579999999887 589999999999999999742          3457999999987654

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.32  E-value=2.8e-13  Score=90.01  Aligned_cols=50  Identities=24%  Similarity=0.584  Sum_probs=42.1

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      ..|+||.+.+.+ +++++|||.||..|+.+|++.          ....||.||.++...++
T Consensus        24 l~C~IC~~~~~~-pv~~~CgH~FC~~Ci~~~~~~----------~~~~CP~Cr~p~~~~~l   73 (86)
T d1rmda2          24 ISCQICEHILAD-PVETSCKHLFCRICILRCLKV----------MGSYCPSCRYPCFPTDL   73 (86)
T ss_dssp             TBCTTTCSBCSS-EEECTTSCEEEHHHHHHHHHH----------TCSBCTTTCCBCCGGGC
T ss_pred             cCCccCCcchhc-ceecCCCChhhHHHHHHHHhh----------CCCcCcccCCCCChhhc
Confidence            479999999987 589999999999999999753          23479999998876654

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=6.3e-13  Score=83.87  Aligned_cols=54  Identities=28%  Similarity=0.552  Sum_probs=41.7

Q ss_pred             CccccccccccccC----CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGN----QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~----~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      ++..|+||++.+..    ..++++|||.||.+|+..|+..          ....||.||.++...++.
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~----------~~~~CP~CR~~i~~~~~~   59 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----------GAGNCPECGTPLRKSNFR   59 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHT----------TSSSCTTTCCCCSSCCCE
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCc----------CcCCCCCCCcCccccccc
Confidence            56899999876422    1356799999999999999743          234799999999877653

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.29  E-value=6.9e-13  Score=84.46  Aligned_cols=48  Identities=33%  Similarity=0.691  Sum_probs=40.2

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ...+|+||++.+.++.++++|||.||..|+.+|++.           ...||+||.++.
T Consensus         4 ~~d~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~-----------~~~CP~CR~~i~   51 (68)
T d1chca_           4 VAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQ-----------NPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHH-----------SCSTTTTCCCCC
T ss_pred             CCCCCccCCcCccCCcEEeCCCCcCcHHHHHHHHHh-----------CCcCCCCCcchH
Confidence            346799999998776677999999999999999854           347999999763

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=1.2e-12  Score=90.08  Aligned_cols=61  Identities=25%  Similarity=0.595  Sum_probs=46.1

Q ss_pred             HHHHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376           13 KHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN   84 (210)
Q Consensus        13 ~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   84 (210)
                      +.+++.+.  +...|+||.+.+.++ +.++|||.||..|+..|+..        ......||.||.++...+
T Consensus        12 ~~~~~~l~--~~l~CpIC~~~~~~p-v~~~CgH~fC~~Ci~~~~~~--------~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          12 QNVINAMQ--KILECPICLELIKEP-VSTKCDHIFCKFCMLKLLNQ--------KKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             HHHHHHHH--HHTSCSSSCCCCSSC-CBCTTSCCCCSHHHHHHHHS--------SSSSCCCTTTSCCCCTTT
T ss_pred             HHHHHhcc--cCcCCCccCchhCCe-EEcCCCCchhhHHHHHHHHH--------CCCCCcCcCCCCcCChhh
Confidence            33444443  346899999999874 78999999999999999754        234568999999876554

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=4.1e-13  Score=91.58  Aligned_cols=69  Identities=19%  Similarity=0.378  Sum_probs=50.2

Q ss_pred             CchhhhhccCchHHHHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376            1 MTEEVVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      |.++....-....+.++.+.  +...|+||.+.+.++..+++|||.||..|+.+|+.             ..||.||.++
T Consensus         1 ~~p~~~~~~~~~~~~l~~l~--~~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~-------------~~CP~Cr~~~   65 (97)
T d1jm7b_           1 MEPDGRGAWAHSRAALDRLE--KLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG-------------TGCPVCYTPA   65 (97)
T ss_dssp             CCSSTTCCCHHHHHHHHHHH--HTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT-------------TBCSSSCCBC
T ss_pred             CCCCcccccHhHHHHHHhhh--hcCCCccCCchhhcCceeCCCCCchhHHHHHHHHh-------------ccccccCCcC
Confidence            34444555555666666664  34689999999988644579999999999999841             2599999887


Q ss_pred             cCCC
Q 028376           81 DIGN   84 (210)
Q Consensus        81 ~~~~   84 (210)
                      ...+
T Consensus        66 ~~~~   69 (97)
T d1jm7b_          66 WIQD   69 (97)
T ss_dssp             SCSS
T ss_pred             chhh
Confidence            6554

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.25  E-value=1.8e-12  Score=79.29  Aligned_cols=51  Identities=10%  Similarity=0.012  Sum_probs=43.4

Q ss_pred             ccccccccccCCCeec-CCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376           26 TCPICQEKLGNQKMVF-QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA   88 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~-~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~   88 (210)
                      .|+||.+.+.++ +++ .|||+||.+|+.+|+++           ...||.||.++..++++.+
T Consensus         2 ~C~Ic~~~~~~P-v~~~~cGh~fc~~cI~~~l~~-----------~~~CP~c~~~l~~~dLipi   53 (56)
T d2baya1           2 LCAISGKVPRRP-VLSPKSRTIFEKSLLEQYVKD-----------TGNDPITNEPLSIEEIVEI   53 (56)
T ss_dssp             CCTTTCSCCSSE-EEETTTTEEEEHHHHHHHHHH-----------HSBCTTTCCBCCGGGCEEC
T ss_pred             CCccCCchHHhc-CccCCCCCcccHHHHHHHHhh-----------ccCCCccCCcCCHHhceeC
Confidence            699999999885 655 79999999999999865           2379999999999988654

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=2.2e-12  Score=77.61  Aligned_cols=48  Identities=29%  Similarity=0.685  Sum_probs=37.2

Q ss_pred             cccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           25 ETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        25 ~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      .+|+||++.+...   ..+++|||.||..|+.+|++          .....||+||.++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~----------~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRT----------DENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTT----------TSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHh----------hcCCCCCccCCcCCC
Confidence            3799999887532   24568999999999999952          334579999998764

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.20  E-value=6e-12  Score=88.11  Aligned_cols=69  Identities=30%  Similarity=0.489  Sum_probs=48.6

Q ss_pred             cCchHHHHHh----cCCCCccccccccccccCC-----------------CeecCCCCcchHhhHHHHHHHhhhccccCC
Q 028376            9 SNSTKHRIES----LSKADEETCPICQEKLGNQ-----------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVK   67 (210)
Q Consensus         9 ~~~~~~~~~~----l~~~~~~~C~iC~~~~~~~-----------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~   67 (210)
                      +...++++++    ++...+..|+||++.+...                 ..+++|||.||..||..|++...      .
T Consensus         6 s~~pe~v~~~~~e~~~~~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~------~   79 (114)
T d1v87a_           6 SGEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN------K   79 (114)
T ss_dssp             SCCHHHHHHHHEEECSSCCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTC------C
T ss_pred             CCCCHHHHHHHHHHhcccccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcC------c
Confidence            3444555544    4455677899999876431                 25689999999999999986532      2


Q ss_pred             CccccccCCcccccCC
Q 028376           68 NEWVMCPTCRQRTDIG   83 (210)
Q Consensus        68 ~~~~~CP~Cr~~~~~~   83 (210)
                      .....||+||..+...
T Consensus        80 ~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          80 DGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SSCCBCTTTCCBSSSC
T ss_pred             CCCCccccccchhccC
Confidence            3456899999876443

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.20  E-value=1.6e-11  Score=101.62  Aligned_cols=71  Identities=11%  Similarity=0.275  Sum_probs=63.7

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..|.|+..|.+.|..+.. .+++|+||||||+.+|++|+..|...||.|.+++|+++      ..+|.+++++|+++.
T Consensus        98 ~~S~Kl~~L~~ll~~~~~-~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~------~~~R~~~i~~F~~~~  168 (346)
T d1z3ix1          98 QLSGKMLVLDYILAMTRT-TTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMS------IKKRAKIVERFNNPS  168 (346)
T ss_dssp             GGSHHHHHHHHHHHHHHH-HCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCC------HHHHHHHHHHHHSTT
T ss_pred             ccCHHHHHHHHHHHHHHH-hcCCceeEEeehhhhhHHHHHHHhhhhccccccccchh------HHHHHHHHHhhhccc
Confidence            458999988888877654 46899999999999999999999999999999999988      999999999999744

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.16  E-value=9.5e-12  Score=75.59  Aligned_cols=48  Identities=25%  Similarity=0.563  Sum_probs=37.4

Q ss_pred             CCccccccccccccCC--Ce-ecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376           22 ADEETCPICQEKLGNQ--KM-VFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT   80 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~--~~-~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~   80 (210)
                      ++..+|+||++.+...  .. ++.|||.||..|+.+|+           .....||+||.++
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl-----------~~~~~CP~CR~~i   53 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWL-----------GSHSTCPLCRLTV   53 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTT-----------TTCCSCSSSCCCS
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHH-----------HhCCcCCCCCCEe
Confidence            3556899999988642  23 34799999999999996           3345899999875

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.16  E-value=9.6e-12  Score=81.56  Aligned_cols=52  Identities=13%  Similarity=-0.019  Sum_probs=43.5

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI   85 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   85 (210)
                      +...|+||.+.+.++ ++++|||.||..|+..|+..          ....||.||.++...++
T Consensus         6 ~~l~CpIc~~l~~dP-v~~~cGhtfc~~ci~~~l~~----------~~~~cP~c~~~l~~~~l   57 (80)
T d2c2la2           6 DYLCGKISFELMREP-CITPSGITYDRKDIEEHLQR----------VGHFNPVTRSPLTQEQL   57 (80)
T ss_dssp             STTBCTTTCSBCSSE-EECSSCCEEETTHHHHHHHH----------TCSSCTTTCCCCCGGGC
T ss_pred             ccccCcCcCchhhhh-cccCCcCeecHHHHHHHHhc----------CCccCCCcccccccccc
Confidence            567899999999985 89999999999999999754          23479999998766554

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.15  E-value=1.3e-11  Score=80.59  Aligned_cols=53  Identities=13%  Similarity=0.248  Sum_probs=44.5

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +...|+||.+.+.++ ++++|||.||..|+..|++          .....||.|+.++...++.
T Consensus         7 ~~l~CpIc~~~m~dP-V~~~cgh~fc~~ci~~~~~----------~~~~~cP~~~~~l~~~~l~   59 (78)
T d1t1ha_           7 EYFRCPISLELMKDP-VIVSTGQTYERSSIQKWLD----------AGHKTCPKSQETLLHAGLT   59 (78)
T ss_dssp             SSSSCTTTSCCCSSE-EEETTTEEEEHHHHHHHHT----------TTCCBCTTTCCBCSSCCCE
T ss_pred             ccCCCcCcCchhhCc-eEccCCCcchHHHHHHHHH----------HCCCCCCcccccCCccccc
Confidence            568899999999985 8899999999999999973          2345799999988777654

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=5.8e-12  Score=76.79  Aligned_cols=46  Identities=26%  Similarity=0.574  Sum_probs=38.0

Q ss_pred             CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      +...|+||++.+.+ +++++|||.||..|+.++              ...||.||.++...
T Consensus         5 ~~l~C~IC~~~~~~-p~~lpCgH~fC~~Ci~~~--------------~~~CP~Cr~~~~~~   50 (56)
T d1bora_           5 QFLRCQQCQAEAKC-PKLLPCLHTLCSGCLEAS--------------GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSCBC-CSCSTTSCCSBTTTCSSS--------------SSSCSSCCSSSSCC
T ss_pred             CCCCCcccCcccCC-CEEecCCCHHhHHHHHcC--------------CCcCcCCCCcccCC
Confidence            34689999999987 588999999999998543              35799999988765

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.07  E-value=1.6e-10  Score=90.97  Aligned_cols=71  Identities=17%  Similarity=0.191  Sum_probs=63.0

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC-CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN-NITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~-gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+|+.+|++.|..+..  ++.|+||||+|...+++|+..|... |+.+.+++|+++      ..+|.+++++|++ +|
T Consensus        66 ~~S~K~~~l~~~l~~~~~--~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~------~~~R~~~i~~F~~-~~  136 (244)
T d1z5za1          66 RRSGKMIRTMEIIEEALD--EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELS------KKERDDIISKFQN-NP  136 (244)
T ss_dssp             TTCHHHHHHHHHHHHHHH--TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSC------HHHHHHHHHHHHH-CT
T ss_pred             hhhhHHHHHHHHHHhhcc--cccceEEEeeceehHHHHHHHHHhhccceEEEEecccc------hhccchhhhhhhc-cc
Confidence            347999999999988764  4889999999999999999999865 999999999977      9999999999998 44


Q ss_pred             C
Q 028376          198 S  198 (210)
Q Consensus       198 ~  198 (210)
                      +
T Consensus       137 ~  137 (244)
T d1z5za1         137 S  137 (244)
T ss_dssp             T
T ss_pred             c
Confidence            3

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=98.93  E-value=3.5e-10  Score=69.78  Aligned_cols=54  Identities=22%  Similarity=0.414  Sum_probs=41.9

Q ss_pred             cCCCCccccccccccccCCCeecCC-----CCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           19 LSKADEETCPICQEKLGNQKMVFQC-----GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        19 l~~~~~~~C~iC~~~~~~~~~~~~C-----gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      |.+++...|+||++....+ .+.+|     +|.||..|+..|+..         .+...||+||+++..
T Consensus         1 ~eded~~~C~IC~~~~~~~-~~~~c~c~~c~h~~H~~Cl~~W~~~---------~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           1 MEDEDVPVCWICNEELGNE-RFRACGCTGELENVHRSCLSTWLTI---------SRNTACQICGVVYNT   59 (60)
T ss_dssp             CTTCSCCEETTTTEECSCC-CCCSCCCSSGGGSCCHHHHHHHHHH---------HTCSBCTTTCCBCCC
T ss_pred             CCCCCCCCCccCCccCCCc-eeEecccCCCCCEEcHHHHHHHHhh---------CCCCCCcccCCeeec
Confidence            4567888999999887653 44544     599999999999865         234589999998764

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.92  E-value=3.9e-10  Score=75.00  Aligned_cols=50  Identities=16%  Similarity=0.344  Sum_probs=38.3

Q ss_pred             CCccccccccccccCC-----------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376           22 ADEETCPICQEKLGNQ-----------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI   82 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~-----------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~   82 (210)
                      .....|+||.+.+...                 .++++|||.||..||.+|++           ....||+||+.+..
T Consensus        19 ~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~-----------~~~~CP~CR~~~~~   85 (88)
T d3dplr1          19 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK-----------TRQVCPLDNREWEF   85 (88)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHT-----------TCSBCSSSCSBCCE
T ss_pred             CCCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHH-----------HCCcCCCCCCcccc
Confidence            4556799998766432                 25679999999999999973           34579999998754

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=3.1e-09  Score=71.92  Aligned_cols=52  Identities=15%  Similarity=0.027  Sum_probs=42.9

Q ss_pred             CccccccccccccCCCeecCCC-CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376           23 DEETCPICQEKLGNQKMVFQCG-HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA   86 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~~~~Cg-H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   86 (210)
                      +.+.||||.+.+.++ ++++|| |.||..||.+|+           .....||.|+.++...++.
T Consensus        21 ~~f~CPI~~~lm~dP-V~~~~~~~ty~r~~I~~~l-----------~~~~~~P~~~~~l~~~~L~   73 (98)
T d1wgma_          21 DEFLDPIMSTLMCDP-VVLPSSRVTVDRSTIARHL-----------LSDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             TTTBCTTTCSBCSSE-EECTTTCCEEEHHHHHHHT-----------TTSCBCTTTCSBCCTTTSE
T ss_pred             HHhCCcCchhHHHHH-HhcccccchhhHHHHHHHH-----------HhcCCcccccccccchhhc
Confidence            468999999999985 888776 489999999996           2345799999999887764

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.57  E-value=1.6e-08  Score=67.67  Aligned_cols=54  Identities=17%  Similarity=0.412  Sum_probs=39.6

Q ss_pred             CCccccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376           22 ADEETCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ   78 (210)
Q Consensus        22 ~~~~~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~   78 (210)
                      .....|+||.+.+...  ..+++|||.||.+|+..|++......   ......||.|+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~---~~~~i~CP~~~C   58 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEG---LETAISCPDAAC   58 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHC---SCCCEECSCTTC
T ss_pred             CCCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcC---CccccCCcCCCC
Confidence            4567999999876432  24568999999999999998765432   234568998654

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.38  E-value=6.5e-07  Score=65.93  Aligned_cols=70  Identities=9%  Similarity=0.054  Sum_probs=62.3

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS  199 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~  199 (210)
                      .+.|+++|.+.|..+    ...|+|||+.+....+.+...|...|+....+.|+|+      ..+|..+++.|++++..+
T Consensus        11 ~~~K~~~L~~ll~~~----~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~------~~~r~~~l~~F~~g~~~i   80 (168)
T d1t5ia_          11 DNEKNRKLFDLLDVL----EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMP------QEERLSRYQQFKDFQRRI   80 (168)
T ss_dssp             GGGHHHHHHHHHHHS----CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTSCSE
T ss_pred             hHHHHHHHHHHHHhC----CCCeEEEEEeeeecchhhhhhhccccccccccccccc------hhhhhhhhhhhcccccee
Confidence            468999999988754    3679999999999999999999999999999999977      999999999999866543

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=98.25  E-value=1.7e-06  Score=68.64  Aligned_cols=78  Identities=14%  Similarity=0.247  Sum_probs=64.4

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCC--cchhhHhhhHHHHHHhhcC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKL--PSANLQHRNALQKELTRHM  196 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~--~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..+.|++.|.+.|.++....++.|+|||+++...++.+...|...|+++..+.|.....  ..|+..+|..+++.|+++.
T Consensus       140 ~~~pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~  219 (286)
T d1wp9a2         140 LDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE  219 (286)
T ss_dssp             CSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTS
T ss_pred             CCCcHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCC
Confidence            34689999999998887778899999999999999999999999999999998865422  2355778999999999843

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.18  E-value=3.3e-06  Score=62.11  Aligned_cols=67  Identities=12%  Similarity=0.173  Sum_probs=60.4

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+.+|.+.|..    .+..|+|||..+..+.+.+...|...|+....+.|.|+      ..+|.++++.|.++..
T Consensus        17 ~~K~~~L~~ll~~----~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~------~~~r~~~~~~f~~~~~   83 (171)
T d1s2ma2          17 RQKLHCLNTLFSK----LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMK------QQERNKVFHEFRQGKV   83 (171)
T ss_dssp             GGHHHHHHHHHHH----SCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSC------HHHHHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHh----CCCCceEEEEeeeehhhHhHHhhhcccccccccccccc------hhhhhhhhhhcccCcc
Confidence            4799999988864    46789999999999999999999999999999999977      9999999999998543

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.12  E-value=5e-06  Score=60.06  Aligned_cols=66  Identities=14%  Similarity=0.130  Sum_probs=59.0

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      ..|+++|++.|.     .++.|+|||+......+.+...|...|+....++|.|+      ..+|..+++.|..+..
T Consensus        14 ~~K~~~L~~ll~-----~~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~------~~~r~~~~~~f~~~~~   79 (155)
T d1hv8a2          14 NERFEALCRLLK-----NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLS------QSQREKVIRLFKQKKI   79 (155)
T ss_dssp             GGHHHHHHHHHC-----STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSC------HHHHHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHc-----cCCCCEEEEECchHHHHHHHhhhcccccccccccccch------hhhhhhhhhhhhcccc
Confidence            479999988764     34679999999999999999999999999999999987      9999999999998543

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.08  E-value=8.4e-06  Score=59.38  Aligned_cols=68  Identities=15%  Similarity=0.134  Sum_probs=60.4

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      ..|++.|.+.+..    .+..|+|||..+....+.+...|...|+....+.|.|+      ..+|.++++.|+.++..
T Consensus        12 e~K~~~L~~ll~~----~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~------~~~r~~~l~~f~~~~~~   79 (162)
T d1fuka_          12 EYKYECLTDLYDS----ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLP------QQERDTIMKEFRSGSSR   79 (162)
T ss_dssp             GGHHHHHHHHHHH----TTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTSCS
T ss_pred             HHHHHHHHHHHHh----CCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCc------hhhHHHHHHHHhhcccc
Confidence            4789988887764    45789999999999999999999999999999999977      99999999999985543

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=1.8e-05  Score=57.97  Aligned_cols=68  Identities=16%  Similarity=0.211  Sum_probs=60.1

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      ..|+++|.+.|...    +..|+|||.......+.+...|...|+....+.|.|+      ..+|..+++.|+++...
T Consensus        19 ~~K~~~L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~------~~~r~~~~~~fk~g~~~   86 (168)
T d2j0sa2          19 EWKFDTLCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMP------QKERESIMKEFRSGASR   86 (168)
T ss_dssp             THHHHHHHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSC------HHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhh------HHHHHHHHHHHhcCCcc
Confidence            46999999887653    4679999999999999999999999999999999977      99999999999985433

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=97.95  E-value=2.8e-05  Score=57.25  Aligned_cols=68  Identities=16%  Similarity=0.078  Sum_probs=59.2

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      +.++.|++.+.+...  .+.++|||..-..+-+.+...|..+||+...|+|.|+      ..+|.++++.|.++.-
T Consensus        15 ~qv~dll~~i~~~~~--~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~------~~eR~~~l~~F~~G~~   82 (174)
T d1c4oa2          15 NQILDLMEGIRERAA--RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELD------AFKRQALIRDLRLGHY   82 (174)
T ss_dssp             THHHHHHHHHHHHHH--TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCC------HHHHHHHHHHHHTTSC
T ss_pred             CCHHHHHHHHHHHHh--cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccc------hHHHHHHHHHHHCCCe
Confidence            456777777766543  4889999999999999999999999999999999987      9999999999998543

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.93  E-value=4.5e-06  Score=62.71  Aligned_cols=66  Identities=14%  Similarity=0.244  Sum_probs=53.9

Q ss_pred             CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376          119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS  198 (210)
Q Consensus       119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~  198 (210)
                      ..++|+++|.+.|..    .++.|+|||++|..+++.|...|...     .++|.++      ..+|.++++.|++++..
T Consensus        76 ~~~~K~~~l~~ll~~----~~~~k~lvf~~~~~~~~~l~~~l~~~-----~i~g~~~------~~~R~~~l~~F~~~~~~  140 (200)
T d2fwra1          76 NSKNKIRKLREILER----HRKDKIIIFTRHNELVYRISKVFLIP-----AITHRTS------REEREEILEGFRTGRFR  140 (200)
T ss_dssp             SCSHHHHHHHHHHHH----TSSSCBCCBCSCHHHHHHHHHHTTCC-----BCCSSSC------SHHHHTHHHHHHHSSCS
T ss_pred             CcHHHHHHHHHHHHh----CCCCcEEEEeCcHHHHHHHHhhcCcc-----eeeCCCC------HHHHHHHHHHhhcCCee
Confidence            457899998877764    46789999999999999998877433     3689977      99999999999986655


Q ss_pred             C
Q 028376          199 S  199 (210)
Q Consensus       199 ~  199 (210)
                      +
T Consensus       141 v  141 (200)
T d2fwra1         141 A  141 (200)
T ss_dssp             B
T ss_pred             e
Confidence            4

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=97.86  E-value=4.2e-05  Score=56.63  Aligned_cols=69  Identities=13%  Similarity=0.072  Sum_probs=60.5

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP  197 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p  197 (210)
                      .++++.|+..+.+...  .+.++|||..-....+.+...|+.+|++...+.|.|+      ..+|.++++.|+++.-
T Consensus        14 ~~qvd~ll~~i~~~~~--~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~------~~eR~~~l~~Fr~g~~   82 (181)
T d1t5la2          14 KGQIDDLIGEIRERVE--RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIK------TLERIEIIRDLRLGKY   82 (181)
T ss_dssp             TTHHHHHHHHHHHHHH--TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCC------HHHHHHHHHHHHHTSC
T ss_pred             CCcHHHHHHHHHHHHh--cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCcc------HHHHHHHHHHHHCCCC
Confidence            4678888888876543  3679999999999999999999999999999999977      9999999999998543

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=97.80  E-value=4.9e-05  Score=57.16  Aligned_cols=66  Identities=8%  Similarity=0.085  Sum_probs=58.6

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM  196 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~  196 (210)
                      ..|++.|++.|..    .++.|+|||.......+.+...|...|+....|+|+|+      ..+|.++++.|..+.
T Consensus        15 ~~k~~~L~~~l~~----~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~------~~~r~~~~~~f~~g~   80 (200)
T d1oywa3          15 FKPLDQLMRYVQE----QRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLE------NNVRADVQEKFQRDD   80 (200)
T ss_dssp             SSHHHHHHHHHHH----TTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC------HHHHHHHHHHHHTTS
T ss_pred             CcHHHHHHHHHHh----cCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCc------HHHHHHHHHHHhccc
Confidence            3588888887764    34679999999999999999999999999999999977      999999999999844

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.53  E-value=0.0014  Score=50.13  Aligned_cols=61  Identities=2%  Similarity=0.001  Sum_probs=48.8

Q ss_pred             chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376          122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS  199 (210)
Q Consensus       122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~  199 (210)
                      .|+++|.+.|..+     +.++|||++.....+.|...|...      |.|++.      ..+|..+++.|.++..++
T Consensus        12 ~~~~~l~~~l~~~-----~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~------~~~R~~~~~~f~~g~~~v   72 (248)
T d1gkub2          12 ESISTLSSILEKL-----GTGGIIYARTGEEAEEIYESLKNK------FRIGIV------TATKKGDYEKFVEGEIDH   72 (248)
T ss_dssp             CCTTTTHHHHTTS-----CSCEEEEESSHHHHHHHHHTTTTS------SCEEEC------TTSSSHHHHHHHHTSCSE
T ss_pred             hHHHHHHHHHHHh-----CCCEEEEECCHHHHHHHHHHHHHh------ccCCCC------HHHHHHHHHHHHhCCCeE
Confidence            4666677666532     468999999999999999999864      688865      999999999999865543

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.47  E-value=0.019  Score=34.67  Aligned_cols=50  Identities=26%  Similarity=0.546  Sum_probs=37.3

Q ss_pred             CCCCccccccccccccCCCeecCC----CCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           20 SKADEETCPICQEKLGNQKMVFQC----GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        20 ~~~~~~~C~iC~~~~~~~~~~~~C----gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      .......|.+|.+.+++. ...+|    +|.||..|-...++.+.      .+...-||.-
T Consensus         4 ~~~~~l~CtlC~erLEdt-HFVQCPsv~~HkFCFpCsr~sik~q~------~~~evyCPSG   57 (80)
T d2cs3a1           4 ANSGPLCCTICHERLEDT-HFVQCPSVPSHKFCFPCSRESIKAQG------ATGEVYCPSG   57 (80)
T ss_dssp             CSCCSCCCSSSCSCCSST-TSEECSSCSSCEECHHHHHHHHHHHH------SSSCCCCTTS
T ss_pred             CCCCceeeeeehhhhcCC-ceEeCCCCcCCceeccccHHHHHhcC------CCCcEECCCC
Confidence            344557899999999874 45556    79999999999988755      3556677753

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=92.55  E-value=0.093  Score=32.75  Aligned_cols=55  Identities=27%  Similarity=0.628  Sum_probs=39.6

Q ss_pred             cCCCCccccccccccccCC----Cee--cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376           19 LSKADEETCPICQEKLGNQ----KMV--FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG   83 (210)
Q Consensus        19 l~~~~~~~C~iC~~~~~~~----~~~--~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~   83 (210)
                      ++......|.||.+.+...    +++  --|+--.|+.|++--  +        ..+...||.|..++...
T Consensus        11 ~~~~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYE--r--------keG~q~CpqCkt~Ykr~   71 (93)
T d1weoa_          11 LKNLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYE--R--------REGTQNCPQCKTRYKRL   71 (93)
T ss_dssp             CSCCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHH--H--------HTSCSSCTTTCCCCCCC
T ss_pred             hhhcccchhhhcccccccCCCCCEEEEecccCCccchHHHHHH--H--------hccCccCcccCChhhhh
Confidence            4566778999998876421    122  478889999999843  2        35678999999987654

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=92.07  E-value=0.056  Score=42.18  Aligned_cols=51  Identities=12%  Similarity=0.019  Sum_probs=41.4

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhh----------hHHHHHHhhcC
Q 028376          140 KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHR----------NALQKELTRHM  196 (210)
Q Consensus       140 ~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R----------~~~l~~F~~~~  196 (210)
                      +.|+|||.......+.+...|.+.|+....|.|+|.      ...|          ..+|+.|.+++
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hggls------q~~R~~~gd~~i~~~~aLe~f~~G~   96 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLD------VSVIPTSGDVVVVATDALMTGFTGD   96 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC------GGGSCSSSSEEEEECTTC---CCCC
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCch------HHHHHhccchHHHHHHHHHHHhcCC
Confidence            679999999999999999999999999999999976      6555          45778887644

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=91.37  E-value=0.35  Score=34.50  Aligned_cols=51  Identities=14%  Similarity=0.111  Sum_probs=46.2

Q ss_pred             CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376          121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE  173 (210)
Q Consensus       121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~  173 (210)
                      ..|.+|+++.+.+....  +--+|||+....--+.+...|.++||++..+..+
T Consensus        17 ~eK~~AIi~eV~~~~~~--grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk   67 (175)
T d1tf5a4          17 EGKFKAVAEDVAQRYMT--GQPVLVGTVAVETSELISKLLKNKGIPHQVLNAK   67 (175)
T ss_dssp             HHHHHHHHHHHHHHHHH--TCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSS
T ss_pred             HHHHHHHHHHHHHHHhc--CCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhh
Confidence            47899999999887755  6789999999999999999999999999988877

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.01  E-value=0.13  Score=29.88  Aligned_cols=43  Identities=28%  Similarity=0.644  Sum_probs=31.4

Q ss_pred             CccccccccccccCCCe--ecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376           23 DEETCPICQEKLGNQKM--VFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC   76 (210)
Q Consensus        23 ~~~~C~iC~~~~~~~~~--~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C   76 (210)
                      ....|..|...+.+...  -..|++.||.+|=.=+           ...-..||.|
T Consensus        14 ~~~~C~gC~~~l~~~~~y~C~~C~~~FC~dCD~fi-----------He~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFV-----------HDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTSEEECCTTTTCCBCHHHHHTT-----------TTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCCceEECcCCCCccccccchhh-----------hhhhcCCCCC
Confidence            45689999988776422  2588999999996533           3556689988

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=89.09  E-value=0.17  Score=34.63  Aligned_cols=36  Identities=17%  Similarity=0.189  Sum_probs=34.2

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376          140 KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH  175 (210)
Q Consensus       140 ~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~  175 (210)
                      +.|+|||..-....+.+...|...|+....|.|.|.
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~   70 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLD   70 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCC
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhccccchhhhhccch
Confidence            569999999999999999999999999999999976

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.35  E-value=0.13  Score=25.71  Aligned_cols=29  Identities=21%  Similarity=0.608  Sum_probs=25.8

Q ss_pred             ccccccccccCCCeecCCCCcchHhhHHH
Q 028376           26 TCPICQEKLGNQKMVFQCGHFTCCKCFFA   54 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~   54 (210)
                      .|..|..++.....+..=.+.||..|.+.
T Consensus         1 ~C~~C~qPIGtksfipk~~~~yCvpCyE~   29 (32)
T d1x4ka1           1 ICHRCQQPIGTKSFIPKDNQNFCVPCYEK   29 (32)
T ss_dssp             CCSSSCCCCCSSSEEEETTEEEEHHHHHH
T ss_pred             CcccccCcccccccccCCCCceEeecchh
Confidence            38899999998889999999999999885

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.73  E-value=1.1  Score=32.83  Aligned_cols=61  Identities=13%  Similarity=0.074  Sum_probs=52.2

Q ss_pred             CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHH
Q 028376          120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQK  190 (210)
Q Consensus       120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~  190 (210)
                      ...|.+|+++.+.++...  +-=+||.+.....-+.++..|.++||+|..+..+        ..+|++.|=
T Consensus        16 ~~~K~~Avv~ei~~~h~~--GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK--------~herEAeII   76 (219)
T d1nkta4          16 EEAKYIAVVDDVAERYAK--GQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAK--------YHEQEATII   76 (219)
T ss_dssp             HHHHHHHHHHHHHHHHHT--TCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSS--------CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhc--CCCEEEeeCcHHHHHHHHHHHHHhccchhccchh--------hHHHHHHHH
Confidence            358999999999998865  6779999999999999999999999999999887        446666553

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=87.17  E-value=0.018  Score=34.85  Aligned_cols=40  Identities=33%  Similarity=0.699  Sum_probs=29.2

Q ss_pred             cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376           25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD   81 (210)
Q Consensus        25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~   81 (210)
                      ..||.|..++...     =||..|..|-..+            .....||.|+.++.
T Consensus         3 ~~CP~C~~eL~~~-----~~~~~C~~C~~~~------------~~~a~CPdC~~~Le   42 (71)
T d2jnea1           3 LHCPQCQHVLDQD-----NGHARCRSCGEFI------------EMKALCPDCHQPLQ   42 (71)
T ss_dssp             CBCSSSCSBEEEE-----TTEEEETTTCCEE------------EEEEECTTTCSBCE
T ss_pred             CcCCCccCccccc-----CCCEehhhhhhhh------------eeEEeCCccccHHH
Confidence            5799998877542     1688888886655            44568999988764

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.26  E-value=0.21  Score=24.86  Aligned_cols=29  Identities=28%  Similarity=0.689  Sum_probs=25.4

Q ss_pred             ccccccccccCCCeecCCCCcchHhhHHH
Q 028376           26 TCPICQEKLGNQKMVFQCGHFTCCKCFFA   54 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~   54 (210)
                      .|..|..++.....+..=.+.||..|.+.
T Consensus         1 ~C~~C~qPIGtkSFip~~~~~yCvpCYE~   29 (32)
T d1wyha1           1 LCSGCEQPLGSRSFVPDKGAHYCVPCYEN   29 (32)
T ss_dssp             BCTTTCCBTTTSCEEEETTEEEEHHHHHH
T ss_pred             CcccccCcccccccccCCCcEEEEecccc
Confidence            48889999988778888899999999875

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.26  E-value=0.71  Score=22.88  Aligned_cols=31  Identities=19%  Similarity=0.506  Sum_probs=25.9

Q ss_pred             ccccccccccCCCeecCCCCcchHhhHHHHH
Q 028376           26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMT   56 (210)
Q Consensus        26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~   56 (210)
                      .|.-|...+.+...+--=|-++|..|.++++
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHT
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhc
Confidence            4888988888767888889999999998873