Citrus Sinensis ID: 011389

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------
Protein Sequence
MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKVLYCPSW
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccEEEEccEEEEEccEEEEcccccccccEEEEEcEEEEcccccEEEEEEEEEccccccccccccccccccccEEEEcccccccccEEcccEEEEEcccccccccccccccEEEEEEEEccccEEEccccccccccccccccHHHHHHHcccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHcccccccccccccHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEccccccccccccccccccccccccccHHHHHHHEEccHHHcccccHHHHHHHHcccccccccHHHHHHHHcccccHHHHHHHHcccccccccccccccccccccccccEEEEEEEEcccEEEEccEEEEEccccccccEEEEEEEEEEcccccEEEEEEEEEcHHHHHHHcccccccccccEEEEccccccccHHHEcccEEEEEEcccEEcccccccccEEEEEEEcccccEEEEccccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHcccccccHHEcccHHHcEEEEcccc
Coil and Loop (DISEMBL)
mgnrrfaqvstsdededvpppssrtrkseeNKEQQSLRQSKRKRIklqeeedyeepeeERKASKRerrdkgkvreaekprndgvedeeeeeeeeeqpqedakpvgelvrfsgkgrgrrshyeafefdgnkyeledpvlltpedtnqkpYVAIIKEITqskdgsmmvtgqwfyrpeeadrkgggnwlsrdtRELFYSfhrdevpaesvmHKCVVHfvpihkqlpnrkqhpgfiVQKVYDTVERKLWKltdkdyednKQHEIDLLVQKTQarlgdlpdiepeetAAREQEDQLKAKRSLRkknispldvsreedsttrsdqyvkaetpgsctsnaSEYYNILSKFKALTGETHRDKWLERLLQGLQYICNsadsihadqngkggckgvdhesedksvgtengsrekgqkngksfiwpdTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLngelepskilnmspnelkvlycpsw
Flexible Loop (DISEMBL)
mgnrrfaqvstsdededvpppssrtrkseenkeqqslrqskrkriklqeeedyeepeeerkaskrerrdkgkvreaekprndgvedeeeeeeeeeqpqedakpvgelvrfsgkgrgrrshyeafefdgnkyeLEDPVLLtpedtnqkpyVAIIKEitqskdgsmmVTGQWFYRpeeadrkgggnwlsRDTRELFYSFHRDEVPAESVMHKCVVHFVPIhkqlpnrkqhpgfiVQKVYDTVERKLWKLtdkdyednkqHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLkakrslrkknispldvsreedsttrsdqyvkaetpgsctsnaSEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDhesedksvgtengsrekgqkngksfiwPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGelepskilnmspnelkvlycpsw
Low Complexity Region (SEG)
MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQeeedyeepeeerkaskrerrdkGKVREAEKPRNDGVedeeeeeeeeeqpqedAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKVLYCPSW
Disordered region (IsUnstruct)
************************************************************************************************************************YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLV*********************************************************************SEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSI*************************************SFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILN****ELKVLYC***
Disordered Region (DISOPRED)
*********************************************************************************************************************RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQK********************************************************************EYYNILSKFKALTGETHRDKWLERLLQGLQYICN********************************************IWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKVLYCPS*
Disordered Region (DISEMBL)
******************************************************************************************************PVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPE****************LRKKNIS************************SCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQN*****************************NGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKVLYCPSW
Disordered Region (DISPRO)
*******************************************R*KLQ*******************************************************************GRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPD******************RSLRKKNISPLDV*****************TPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNS****************************************KSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKVLYCPSW
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGNRRFAQVSTSDEDEDVPPPSSRTRKSExxxxxxxxxxxxxxxxxxxxxxDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELKVLYCPSW
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	487	2.2.26 [Sep-21-2011]
Q8BSQ9	1634	Protein polybromo-1 OS=Mu	yes	no	0.275	0.082	0.256	4e-08
Q86U86	1689	Protein polybromo-1 OS=Ho	no	no	0.211	0.060	0.283	4e-08
Q90941	1633	Protein polybromo-1 OS=Ga	yes	no	0.197	0.058	0.292	6e-08
Q3UHR0	2643	BAH and coiled-coil domai	no	no	0.201	0.037	0.287	0.0002
P53236	928	Chromatin structure-remod	yes	no	0.281	0.147	0.283	0.0003

>sp|Q8BSQ9|PB1_MOUSE Protein polybromo-1 OS=Mus musculus GN=Pbrm1 PE=1 SV=4

 Score = 60.1 bits (144), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 37/144 (25%), Positives = 67/144 (46%), Gaps = 10/144 (6%)

Query: 111  SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQW 170
            +G     R++ +   F  + Y + D V + P + N +P++  I+ + +   G   + G W
Sbjct: 938  TGLSGLHRTYSQDCSFKNSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCW 997

Query: 171  FYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP--NRKQH 228
            FYRP E        +L    +E+F S + ++VP   ++ KCVV FV  + +L   N +  
Sbjct: 998  FYRPNETFHLATRKFLE---KEVFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDE 1054

Query: 229  PGFIVQKVYDTVER-----KLWKL 247
              F+ +  Y    +     KLW +
Sbjct: 1055 DVFVCESRYSAKTKSFKKIKLWTM 1078

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology) (By similarity). Act as a negative regulator of cell proliferation.
Mus musculus (taxid: 10090)

>sp|Q86U86|PB1_HUMAN Protein polybromo-1 OS=Homo sapiens GN=PBRM1 PE=1 SV=1

 Score = 59.7 bits (143), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/106 (28%), Positives = 53/106 (50%), Gaps = 3/106 (2%)

Query: 111  SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQW 170
            +G     R++ +   F  + Y + D V + P + N +P++  I+ + +   G   + G W
Sbjct: 938  AGLSGLHRTYSQDCSFKNSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCW 997

Query: 171  FYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFV 216
            FYRP E        +L    +E+F S + ++VP   ++ KCVV FV
Sbjct: 998  FYRPNETFHLATRKFLE---KEVFKSDYYNKVPVSKILGKCVVMFV 1040

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Act as a negative regulator of cell proliferation.

Homo sapiens (taxid: 9606)

>sp|Q90941|PB1_CHICK Protein polybromo-1 OS=Gallus gallus GN=PBRM1 PE=1 SV=1

 Score = 59.3 bits (142), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 51/99 (51%), Gaps = 3/99 (3%)

Query: 118  RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEA 177
            R++ +   F  + Y + D V + P + N +P++  I+ + +   G   + G WFYRP E 
Sbjct: 943  RTYSQDCSFKNSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNET 1002

Query: 178  DRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFV 216
                   +L    +E+F S + ++VP   ++ KCVV FV
Sbjct: 1003 FHLATRKFLE---KEVFKSDYYNKVPVSKILGKCVVMFV 1038

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).

Gallus gallus (taxid: 9031)

>sp|Q3UHR0|BAHC1_MOUSE BAH and coiled-coil domain-containing protein 1 OS=Mus musculus GN=Bahcc1 PE=2 SV=2

 Score = 47.4 bits (111), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/101 (28%), Positives = 45/101 (44%), Gaps = 3/101 (2%)

Query: 113  KGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFY 172
            KG+ R+  Y+A         + D  +         PY+  I+ + +S   +M+V  +WFY
Sbjct: 2501 KGKARKLFYKAIVRGKETLRIGDCAVFLSAGRPNLPYIGRIESLWESWGSNMVVKVKWFY 2560

Query: 173  RPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVV 213
             PEE      G   S     L+ S H DE   +++ HKC V
Sbjct: 2561 HPEETKL---GKRQSDGKNALYQSCHEDENDVQTISHKCQV 2598

Mus musculus (taxid: 10090)

>sp|P53236|RSC1_YEAST Chromatin structure-remodeling complex subunit RSC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RSC1 PE=1 SV=1

 Score = 47.4 bits (111), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 46/162 (28%), Positives = 74/162 (45%), Gaps = 25/162 (15%)

Query: 93  EEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLL-TPEDTNQKPYVA 151
           E  +P ED  P GEL          R   +  E +  KY++ D VLL  P D N KP V 
Sbjct: 342 ELSKPDEDYLPEGEL----------RYPLDDVEINDEKYQIGDWVLLHNPNDIN-KPIVG 390

Query: 152 IIKEITQSKDGSMMVTGQWFYRPEE----ADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207
            I  +  + DG+  +   W++RPE+     DR    N + +  +      +RD  P + +
Sbjct: 391 QIFRLWSTTDGNKWLNACWYFRPEQTVHRVDRLFYKNEVMKTGQ------YRDH-PIQDI 443

Query: 208 MHKC-VVHFVPIHKQLPNRKQH-PGFIVQKVYDTVERKLWKL 247
             KC V+HF    +  P+ K + P F+ +  Y+  ++   K+
Sbjct: 444 KGKCYVIHFTRFQRGDPSTKVNGPQFVCEFRYNESDKVFNKI 485

Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is involved in meiotic sporulation through regulating IME2 expression.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	487
224058512	611	predicted protein [Populus trichocarpa]	0.965	0.769	0.706	0.0
224071890	607	predicted protein [Populus trichocarpa]	0.944	0.757	0.694	1e-180
225426420	595	PREDICTED: uncharacterized protein LOC10	0.913	0.747	0.652	1e-179
449452318	610	PREDICTED: uncharacterized protein LOC10	0.958	0.765	0.664	1e-174
297742521	1085	unnamed protein product [Vitis vinifera]	0.794	0.356	0.744	1e-173
449528690	467	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.958	1.0	0.662	1e-173
359474210	584	PREDICTED: uncharacterized protein LOC10	0.891	0.743	0.637	1e-172
356528332	605	PREDICTED: uncharacterized protein LOC10	0.936	0.753	0.669	1e-166
356528334	596	PREDICTED: uncharacterized protein LOC10	0.917	0.75	0.665	1e-162
356513389	571	PREDICTED: uncharacterized protein LOC10	0.780	0.665	0.729	1e-161

>gi|224058512|ref|XP_002299533.1| predicted protein [Populus trichocarpa] gi|222846791|gb|EEE84338.1| predicted protein [Populus trichocarpa]

 Score =  639 bits (1649), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 341/483 (70%), Positives = 388/483 (80%), Gaps = 13/483 (2%)

Query: 1   MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEER 60
           MGNRRFAQVSTSDE+++ PP   + R S        + + KRK++KLQEEE+ EE  E  
Sbjct: 1   MGNRRFAQVSTSDEEDEAPP---KARSSSTTTRPGDISERKRKKMKLQEEEEEEE--EVV 55

Query: 61  KASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSH 120
              +   R + K+RE +       E EE+ EEEEE PQEDAKPVG+  R SGKGRGRR+H
Sbjct: 56  TTRRGRGRPRKKLREEKSEDEVEEELEEDPEEEEEVPQEDAKPVGDSTRVSGKGRGRRTH 115

Query: 121 YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK 180
           Y+AFEFDGN+YELEDPVLL PED  QKPYVAIIK+I+Q+KDGSMMVTGQWFYRPEEA+RK
Sbjct: 116 YDAFEFDGNRYELEDPVLLVPEDKEQKPYVAIIKDISQTKDGSMMVTGQWFYRPEEAERK 175

Query: 181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTV 240
           GGG+W SRDTRELFYSFHRDEVPAESVMHKCVVHFVP+HKQLPNRKQ+PGFIV+KVYDTV
Sbjct: 176 GGGSWQSRDTRELFYSFHRDEVPAESVMHKCVVHFVPVHKQLPNRKQYPGFIVRKVYDTV 235

Query: 241 ERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAR---EQEDQLKAKRSL 297
           ERKLWKLTDKDYEDNKQHEIDLLVQKT +R+GDLPDIE E+  A    E ED  KAKR+L
Sbjct: 236 ERKLWKLTDKDYEDNKQHEIDLLVQKTLSRMGDLPDIEVEDAPAAAPPELEDPTKAKRTL 295

Query: 298 RKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLE 357
           R+K +SPLDV+REE++TTRSD + KAETPGSCT N SEYY IL KF ALTG+THRDKWLE
Sbjct: 296 RRKTVSPLDVTREEEATTRSDNF-KAETPGSCTGNGSEYYAILVKFDALTGDTHRDKWLE 354

Query: 358 RLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDT 417
           RLLQ +QY+C S++S   D   KGG  GVDH+ E KS G  NGS E    N KSF WP+ 
Sbjct: 355 RLLQCIQYMCISSNSTLDDDKIKGGSDGVDHKKEQKSQGAANGSEE----NSKSFPWPEA 410

Query: 418 AIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPN 477
           A+ AV+ALEKASHD LS DFQKYNQKLRQL+FNLK+ A LARRLLN ELEPSKILNMSPN
Sbjct: 411 AVPAVSALEKASHDALSSDFQKYNQKLRQLVFNLKNNAFLARRLLNRELEPSKILNMSPN 470

Query: 478 ELK 480
           ELK
Sbjct: 471 ELK 473

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224071890|ref|XP_002303589.1| predicted protein [Populus trichocarpa] gi|222841021|gb|EEE78568.1| predicted protein [Populus trichocarpa]

 Score =  638 bits (1646), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 336/484 (69%), Positives = 379/484 (78%), Gaps = 24/484 (4%)

Query: 1   MGNRRFAQVSTSDEDEDVPP--PSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEE 58
           MGNRRFAQVSTSDE+E+ PP  PS  T+    N  +    + KRK+I+LQEEE+      
Sbjct: 1   MGNRRFAQVSTSDEEEEAPPKAPSLLTKTKPVNNSEM---ERKRKKIELQEEEEV----- 52

Query: 59  ERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRR 118
              A  R R   G+ R+  +      E  EEE E EE PQEDAKP G L R SGKGRGRR
Sbjct: 53  ---AVTRRR---GRPRKKVR-----EEKSEEEVEVEEVPQEDAKPAGVLTRVSGKGRGRR 101

Query: 119 SHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEAD 178
           +H++AFEFDGN+YELEDPVLL PED  QKPYVAIIK+I+Q+K GSMMVTGQWFYRPEEA+
Sbjct: 102 THFDAFEFDGNRYELEDPVLLVPEDKEQKPYVAIIKDISQTKHGSMMVTGQWFYRPEEAE 161

Query: 179 RKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYD 238
           RKGGG+W SRDTRELFYSFH DEVPAESVMHKCVVHFVPIHKQLPNRKQ+PGFIVQKVYD
Sbjct: 162 RKGGGSWQSRDTRELFYSFHHDEVPAESVMHKCVVHFVPIHKQLPNRKQYPGFIVQKVYD 221

Query: 239 TVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEE--TAAREQEDQLKAKRS 296
           TVERKLWKLTDKDYE NKQH IDLLVQKT +R+GDLPDIE E+  TAA EQED +KAKR+
Sbjct: 222 TVERKLWKLTDKDYEYNKQHGIDLLVQKTLSRMGDLPDIEIEDAPTAAPEQEDPVKAKRT 281

Query: 297 LRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWL 356
           LR+KN+SPLDV+REE++T R D  +KAETPGSC SN SEY+ IL KF ALTG+T RDKWL
Sbjct: 282 LRRKNVSPLDVTREEEATGRPDN-LKAETPGSCPSNDSEYHAILVKFDALTGDTLRDKWL 340

Query: 357 ERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPD 416
           ERLLQ +QY+C+S +    D   KGG  G DH+ E KS G  NGS E   K GKSF W D
Sbjct: 341 ERLLQSIQYMCSSPNCTLDDGKLKGGSDGGDHKKEQKSQGAANGSEENSAKVGKSFPWLD 400

Query: 417 TAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSP 476
            A+ AV+ALEKASHD LS DFQKYNQKLRQL FNLK+ A LARRLLN ELEPSK+LNMSP
Sbjct: 401 AAVPAVSALEKASHDALSSDFQKYNQKLRQLAFNLKNNAFLARRLLNKELEPSKMLNMSP 460

Query: 477 NELK 480
           NELK
Sbjct: 461 NELK 464

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225426420|ref|XP_002270094.1| PREDICTED: uncharacterized protein LOC100251356 isoform 1 [Vitis vinifera]

 Score =  634 bits (1636), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 313/480 (65%), Positives = 371/480 (77%), Gaps = 35/480 (7%)

Query: 1   MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEER 60
           MGNRR A+++TSD++++  PPS   R      E+Q  RQ +RK+IKL             
Sbjct: 1   MGNRRIARITTSDDEDEAQPPS---RLHSPEMEKQQPRQRRRKKIKL------------- 44

Query: 61  KASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSH 120
                             P  +   ++E +  +EE PQEDAKP+G+ VR SGKGRGRRSH
Sbjct: 45  ------------------PEEEEEREKETQSGDEEAPQEDAKPIGDAVRVSGKGRGRRSH 86

Query: 121 YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK 180
           YEAFEFDGN+Y+LEDPVLL PED  QKPYVAIIK+ITQ+++GS+MVTGQWFYRPEEA++K
Sbjct: 87  YEAFEFDGNRYDLEDPVLLVPEDEKQKPYVAIIKDITQTREGSIMVTGQWFYRPEEAEKK 146

Query: 181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTV 240
           GGG+W S DTRELFYSFHRDEVPAESVMHKCVVHFVP++KQLPNRKQ PGFIVQ+VYDTV
Sbjct: 147 GGGSWKSSDTRELFYSFHRDEVPAESVMHKCVVHFVPLNKQLPNRKQFPGFIVQRVYDTV 206

Query: 241 ERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKK 300
           ERKLW+LTDKDYEDN QHE+DLLVQKT++RLG+L DIE EE  A EQEDQ K+KR+LRKK
Sbjct: 207 ERKLWRLTDKDYEDNLQHEVDLLVQKTRSRLGELFDIEIEEVVA-EQEDQTKSKRTLRKK 265

Query: 301 NISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLL 360
           N+SPLDV+R++++TTR DQ++K ETPGSCTSN SEY  IL  FKALTGETHRDKWLE+LL
Sbjct: 266 NMSPLDVTRDDEATTRFDQHLKPETPGSCTSNMSEYCTILVNFKALTGETHRDKWLEKLL 325

Query: 361 QGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIA 420
           QG+Q +C S D +H D   KGG    DH S++    T +GS  K    G+SFIWPD A+ 
Sbjct: 326 QGIQSVCCSDDDVHRDDKEKGGSGDSDHASDNNRTETAHGSDAKSLTAGRSFIWPDAAVP 385

Query: 421 AVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELK 480
           AVTALE+AS D  S DFQKYNQK+RQL+FNLK+  LLARRLLNGELEPSKILNMSPNELK
Sbjct: 386 AVTALEQASQDAFSSDFQKYNQKMRQLVFNLKNNPLLARRLLNGELEPSKILNMSPNELK 445

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452318|ref|XP_004143906.1| PREDICTED: uncharacterized protein LOC101218620 [Cucumis sativus]

 Score =  617 bits (1592), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 319/480 (66%), Positives = 392/480 (81%), Gaps = 13/480 (2%)

Query: 1   MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEER 60
           MGNRRFAQVSTSDE+++VP    ++  S++N     +R+ KRK++KLQEEE+  E +E+ 
Sbjct: 1   MGNRRFAQVSTSDEEDEVPAMKQQSSNSDDN---LPIRR-KRKKMKLQEEEEEVEGDEKH 56

Query: 61  KASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSH 120
           + S++      K  EA K      + E+E++++++Q QEDAKP+G++VR SGKGRGR++H
Sbjct: 57  RRSRKSSNKGEKKMEASK----QQQAEDEDDDDDDQSQEDAKPIGDVVRVSGKGRGRKNH 112

Query: 121 YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK 180
           Y AFE+DGN+Y+LEDPVLL PED +QKPYVAIIK+ITQ+KDG MMVTGQWFYRPEEA++K
Sbjct: 113 YNAFEYDGNRYDLEDPVLLVPEDKDQKPYVAIIKDITQNKDG-MMVTGQWFYRPEEAEKK 171

Query: 181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTV 240
           GGG+W S DTRELFYSFHRD+VPAESVMHKCVVHFVP+HKQLP RKQHPGFIV+KVYDTV
Sbjct: 172 GGGSWQSHDTRELFYSFHRDQVPAESVMHKCVVHFVPLHKQLPIRKQHPGFIVRKVYDTV 231

Query: 241 ERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKK 300
           ERKLWKLTDKDYED+KQ EID LV+KT ARLGDLPDIEPE+  A +QEDQLK KRS ++K
Sbjct: 232 ERKLWKLTDKDYEDSKQQEIDELVKKTMARLGDLPDIEPEDAPA-DQEDQLKTKRSFKRK 290

Query: 301 NISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLL 360
           NISPLDV+R+E  TTRSD   KAETPGSCT+N SEYY+IL  F+ LTGETHRD+WLE+LL
Sbjct: 291 NISPLDVTRDESETTRSDLSSKAETPGSCTTNRSEYYSILEIFEVLTGETHRDRWLEKLL 350

Query: 361 QGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIA 420
           +G+QYIC+S +  H    GK    GV+ E+++  +     + EK  K+ KSFIWPD A+ 
Sbjct: 351 EGVQYICHSPEKTHEGDIGKTAANGVNLENKNPELSI---AAEKNAKSSKSFIWPDAAVP 407

Query: 421 AVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELK 480
           A+TALEK S+D LS DFQKYNQK+RQL+FNLK+T LLA+RLLNGELEPSKILNMSPNELK
Sbjct: 408 AITALEKVSNDALSADFQKYNQKMRQLVFNLKNTRLLAQRLLNGELEPSKILNMSPNELK 467

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742521|emb|CBI34670.3| unnamed protein product [Vitis vinifera]

 Score =  615 bits (1585), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 289/388 (74%), Positives = 333/388 (85%), Gaps = 1/388 (0%)

Query: 93  EEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAI 152
           +EE PQEDAKP+G+ VR SGKGRGRRSHYEAFEFDGN+Y+LEDPVLL PED  QKPYVAI
Sbjct: 31  DEEAPQEDAKPIGDAVRVSGKGRGRRSHYEAFEFDGNRYDLEDPVLLVPEDEKQKPYVAI 90

Query: 153 IKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCV 212
           IK+ITQ+++GS+MVTGQWFYRPEEA++KGGG+W S DTRELFYSFHRDEVPAESVMHKCV
Sbjct: 91  IKDITQTREGSIMVTGQWFYRPEEAEKKGGGSWKSSDTRELFYSFHRDEVPAESVMHKCV 150

Query: 213 VHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLG 272
           VHFVP++KQLPNRKQ PGFIVQ+VYDTVERKLW+LTDKDYEDN QHE+DLLVQKT++RLG
Sbjct: 151 VHFVPLNKQLPNRKQFPGFIVQRVYDTVERKLWRLTDKDYEDNLQHEVDLLVQKTRSRLG 210

Query: 273 DLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSN 332
           +L DIE EE  A EQEDQ K+KR+LRKKN+SPLDV+R++++TTR DQ++K ETPGSCTSN
Sbjct: 211 ELFDIEIEEVVA-EQEDQTKSKRTLRKKNMSPLDVTRDDEATTRFDQHLKPETPGSCTSN 269

Query: 333 ASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESED 392
            SEY  IL  FKALTGETHRDKWLE+LLQG+Q +C S D +H D   KGG    DH S++
Sbjct: 270 MSEYCTILVNFKALTGETHRDKWLEKLLQGIQSVCCSDDDVHRDDKEKGGSGDSDHASDN 329

Query: 393 KSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
               T +GS  K    G+SFIWPD A+ AVTALE+AS D  S DFQKYNQK+RQL+FNLK
Sbjct: 330 NRTETAHGSDAKSLTAGRSFIWPDAAVPAVTALEQASQDAFSSDFQKYNQKMRQLVFNLK 389

Query: 453 STALLARRLLNGELEPSKILNMSPNELK 480
           +  LLARRLLNGELEPSKILNMSPNELK
Sbjct: 390 NNPLLARRLLNGELEPSKILNMSPNELK 417

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449528690|ref|XP_004171336.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized LOC101218620, partial [Cucumis sativus]

 Score =  613 bits (1582), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 318/480 (66%), Positives = 391/480 (81%), Gaps = 13/480 (2%)

Query: 1   MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEER 60
           MGNRRFAQVSTSDE+++VP    ++  S++N     +R+ KRK++KLQEEE+  E +E+ 
Sbjct: 1   MGNRRFAQVSTSDEEDEVPAMKQQSSNSDDN---LPIRR-KRKKMKLQEEEEEVEGDEKH 56

Query: 61  KASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSH 120
           + S++      K  EA K      + E+E++++++Q QEDAKP+G++VR SGKGRGR++H
Sbjct: 57  RRSRKSSNKGEKKMEASK----QQQAEDEDDDDDDQSQEDAKPIGDVVRVSGKGRGRKNH 112

Query: 121 YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK 180
           Y AFE+DGN+Y+LEDPVLL PED +QKPYVAIIK+ITQ+KDG MMVTGQWFYRPEEA++K
Sbjct: 113 YNAFEYDGNRYDLEDPVLLVPEDKDQKPYVAIIKDITQNKDG-MMVTGQWFYRPEEAEKK 171

Query: 181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTV 240
           GGG+W S DTRELFYSFHRD+VPAESVMHKCVVHFVP+HKQLP RKQHPGFIV+KVYDTV
Sbjct: 172 GGGSWQSHDTRELFYSFHRDQVPAESVMHKCVVHFVPLHKQLPIRKQHPGFIVRKVYDTV 231

Query: 241 ERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKK 300
           ERKLWKLTDKDYED+KQ EID LV+KT ARLGDLPDIEPE+  A +QEDQLK KRS ++ 
Sbjct: 232 ERKLWKLTDKDYEDSKQQEIDELVKKTMARLGDLPDIEPEDAPA-DQEDQLKTKRSFKRX 290

Query: 301 NISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLL 360
           NISPLDV+R+E  TTRSD   KAETPGSCT+N SEYY+IL  F+ LTGETHRD+WLE+LL
Sbjct: 291 NISPLDVTRDESETTRSDLSSKAETPGSCTTNRSEYYSILEIFEVLTGETHRDRWLEKLL 350

Query: 361 QGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIA 420
           +G+QYIC+S +  H    GK    GV+ E+++  +     + EK  K+ KSFIWPD A+ 
Sbjct: 351 EGVQYICHSPEKTHEGDIGKTAANGVNLENKNPELSI---AAEKNAKSSKSFIWPDAAVP 407

Query: 421 AVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELK 480
           A+TALEK S+D LS DFQKYNQK+RQL+FNLK+T LLA+RLLNGELEPSKILNMSPNELK
Sbjct: 408 AITALEKVSNDALSADFQKYNQKMRQLVFNLKNTRLLAQRLLNGELEPSKILNMSPNELK 467

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359474210|ref|XP_003631417.1| PREDICTED: uncharacterized protein LOC100251356 isoform 2 [Vitis vinifera]

 Score =  610 bits (1573), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 306/480 (63%), Positives = 364/480 (75%), Gaps = 46/480 (9%)

Query: 1   MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEER 60
           MGNRR A+++TSD++++  PPS   R      E+Q  RQ +RK+IKL             
Sbjct: 1   MGNRRIARITTSDDEDEAQPPS---RLHSPEMEKQQPRQRRRKKIKL------------- 44

Query: 61  KASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSH 120
                             P  +   ++E +  +EE PQEDAKP+G+ VR SGKGRGRRSH
Sbjct: 45  ------------------PEEEEEREKETQSGDEEAPQEDAKPIGDAVRVSGKGRGRRSH 86

Query: 121 YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK 180
           YEAFEFDGN+Y+LEDPVLL PED  QKPYVAIIK+ITQ+++GS+MVTGQWFYRPEEA++K
Sbjct: 87  YEAFEFDGNRYDLEDPVLLVPEDEKQKPYVAIIKDITQTREGSIMVTGQWFYRPEEAEKK 146

Query: 181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTV 240
           GGG+W S DTRELFYSFHRDEVPAESVMHKCVVHFVP++KQLPNRKQ PGFIVQ+VYDTV
Sbjct: 147 GGGSWKSSDTRELFYSFHRDEVPAESVMHKCVVHFVPLNKQLPNRKQFPGFIVQRVYDTV 206

Query: 241 ERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKK 300
           ERKLW+LTDKDYEDN QHE+DLLVQKT++RLG+L DIE EE  A EQEDQ K+KR+LRKK
Sbjct: 207 ERKLWRLTDKDYEDNLQHEVDLLVQKTRSRLGELFDIEIEEVVA-EQEDQTKSKRTLRKK 265

Query: 301 NISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLL 360
           N+SPLDV+R++++TTR DQ++K ETPGSCTSN SEY  IL  FKALTGETHRDKWLE+LL
Sbjct: 266 NMSPLDVTRDDEATTRFDQHLKPETPGSCTSNMSEYCTILVNFKALTGETHRDKWLEKLL 325

Query: 361 QGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIA 420
           QG+Q +C S D +H D   KGG    DH S++    T +GS  K           + A+ 
Sbjct: 326 QGIQSVCCSDDDVHRDDKEKGGSGDSDHASDNNRTETAHGSDAK-----------NAAVP 374

Query: 421 AVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILNMSPNELK 480
           AVTALE+AS D  S DFQKYNQK+RQL+FNLK+  LLARRLLNGELEPSKILNMSPNELK
Sbjct: 375 AVTALEQASQDAFSSDFQKYNQKMRQLVFNLKNNPLLARRLLNGELEPSKILNMSPNELK 434

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528332|ref|XP_003532758.1| PREDICTED: uncharacterized protein LOC100787670 isoform 1 [Glycine max]

 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 326/487 (66%), Positives = 382/487 (78%), Gaps = 31/487 (6%)

Query: 1   MGNRRFAQVSTS-DEDEDVPPPSSRTRKS-----EENKEQQSLRQSKRKRIKLQEEEDYE 54
           MGNRRF QV+TS DEDE  PPP    ++S     EEN+ +Q  +Q KRKR+KLQEEE+ E
Sbjct: 1   MGNRRFTQVATSEDEDEAPPPPPPPKQQSSVSAPEENRSKQ--QQRKRKRMKLQEEEEEE 58

Query: 55  EPEEERKASK-RERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGK 113
           E +EE K  K R+ +DK                EE   EEEE PQEDAKP+GE VR SGK
Sbjct: 59  EEKEEEKKKKKRKIKDK---------------QEERSNEEEEPPQEDAKPIGEPVRLSGK 103

Query: 114 GRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYR 173
           GRGR+ HYE+FE+DGN+Y LEDP+LLTPED +QKPYVAIIK+ITQS +GSMMVTGQWFYR
Sbjct: 104 GRGRKKHYESFEYDGNQYMLEDPILLTPEDKDQKPYVAIIKDITQSLNGSMMVTGQWFYR 163

Query: 174 PEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIV 233
           PEEA+RKGGG+W SRDTRELFYSFHRD+VPAESVMHKCVVHFVPIHKQLPNRKQHPGFIV
Sbjct: 164 PEEAERKGGGSWQSRDTRELFYSFHRDDVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIV 223

Query: 234 QKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKA 293
           QKVYDTVERKLWKLTDKDYEDNKQ EID LVQKT  RLG+L DIEPEE  A +QED +K 
Sbjct: 224 QKVYDTVERKLWKLTDKDYEDNKQQEIDELVQKTLKRLGELLDIEPEEPVA-DQEDLMKN 282

Query: 294 KRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRD 353
           KR LRKK+ISPLDVS+EE++T + DQ +K ETP SC +NASE+Y IL  F  LTG+THRD
Sbjct: 283 KRILRKKSISPLDVSKEEETTRKGDQPLKPETPWSCINNASEHYRILVDFNVLTGDTHRD 342

Query: 354 KWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFI 413
           K LE+LLQ ++++ NS DSI  ++ G       ++ S +KS+ + N  ++      K F+
Sbjct: 343 KCLEKLLQSVEFMFNSDDSIKREEKGNDNSDATNNGSNNKSLESVNECKD------KPFV 396

Query: 414 WPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILN 473
           WPD A+ AV ALEKASHDTLS D+QKYNQKLRQL+FNLK+ A+LARRLLNGELEPSKILN
Sbjct: 397 WPDDAVPAVVALEKASHDTLSSDYQKYNQKLRQLVFNLKNNAILARRLLNGELEPSKILN 456

Query: 474 MSPNELK 480
           M+PNELK
Sbjct: 457 MTPNELK 463

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528334|ref|XP_003532759.1| PREDICTED: uncharacterized protein LOC100787670 isoform 2 [Glycine max]

 Score =  577 bits (1486), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 324/487 (66%), Positives = 375/487 (77%), Gaps = 40/487 (8%)

Query: 1   MGNRRFAQVSTS-DEDEDVPPPSSRTRKS-----EENKEQQSLRQSKRKRIKLQEEEDYE 54
           MGNRRF QV+TS DEDE  PPP    ++S     EEN+ +Q  +Q KRKR+KLQEEE+ E
Sbjct: 1   MGNRRFTQVATSEDEDEAPPPPPPPKQQSSVSAPEENRSKQ--QQRKRKRMKLQEEEEEE 58

Query: 55  EPEEERKASK-RERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGK 113
           E +EE K  K R+ +DK                EE   EEEE PQEDAKP+GE VR SGK
Sbjct: 59  EEKEEEKKKKKRKIKDK---------------QEERSNEEEEPPQEDAKPIGEPVRLSGK 103

Query: 114 GRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYR 173
           GRGR+ HYE+FE+DGN+Y LEDP+LLTPED +QKPYVAIIK+ITQS +GSMMVTGQWFYR
Sbjct: 104 GRGRKKHYESFEYDGNQYMLEDPILLTPEDKDQKPYVAIIKDITQSLNGSMMVTGQWFYR 163

Query: 174 PEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIV 233
           PEEA+RKGGG+W SRDTRELFYSFHRD+VPAESVMHKCVVHFVPIHKQLPNRKQHPGFIV
Sbjct: 164 PEEAERKGGGSWQSRDTRELFYSFHRDDVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIV 223

Query: 234 QKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKA 293
           QKVYDTVERKLWKLTDKDYEDNKQ EID LVQKT  RLG+L DIEPEE  A +QED +K 
Sbjct: 224 QKVYDTVERKLWKLTDKDYEDNKQQEIDELVQKTLKRLGELLDIEPEEPVA-DQEDLMKN 282

Query: 294 KRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRD 353
           KR LRKK+ISPLDVS+EE++T + DQ +K ETP SC +NASE+Y IL  F  LTG+THRD
Sbjct: 283 KRILRKKSISPLDVSKEEETTRKGDQPLKPETPWSCINNASEHYRILVDFNVLTGDTHRD 342

Query: 354 KWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFI 413
           K LE+LLQ ++++ NS DSI  ++ G            D S  T NGS  K  ++   + 
Sbjct: 343 KCLEKLLQSVEFMFNSDDSIKREEKGN-----------DNSDATNNGSNNKSLESVNEY- 390

Query: 414 WPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGELEPSKILN 473
               A+ AV ALEKASHDTLS D+QKYNQKLRQL+FNLK+ A+LARRLLNGELEPSKILN
Sbjct: 391 ---DAVPAVVALEKASHDTLSSDYQKYNQKLRQLVFNLKNNAILARRLLNGELEPSKILN 447

Query: 474 MSPNELK 480
           M+PNELK
Sbjct: 448 MTPNELK 454

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513389|ref|XP_003525396.1| PREDICTED: uncharacterized protein LOC100796051 [Glycine max]

 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 280/384 (72%), Positives = 322/384 (83%), Gaps = 4/384 (1%)

Query: 97  PQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEI 156
           PQEDAKP+GE VR SGKGRGR+ HYE+FE+DGN+Y LEDP+LLTPED +QKPYVAIIK+I
Sbjct: 88  PQEDAKPIGEPVRLSGKGRGRKKHYESFEYDGNQYTLEDPILLTPEDKDQKPYVAIIKDI 147

Query: 157 TQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFV 216
           TQS +GSMMVTGQWFYRPEEA+RKGGG+W S DTRELFYSFHRD+VPAESVMHKCVVHFV
Sbjct: 148 TQSLNGSMMVTGQWFYRPEEAERKGGGSWQSCDTRELFYSFHRDDVPAESVMHKCVVHFV 207

Query: 217 PIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPD 276
           PIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQ EID LVQKT  RLG L D
Sbjct: 208 PIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQQEIDELVQKTLQRLGKLLD 267

Query: 277 IEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEY 336
           IEPEE  A +QED +K KR LRKK+ISPLDVS+EE++T + DQ +K ETP SC +NASE+
Sbjct: 268 IEPEEPVA-DQEDLMKNKRILRKKSISPLDVSKEEETTRQGDQPLKPETPWSCVNNASEH 326

Query: 337 YNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVG 396
           Y IL  F ALTG+THRDK LE+LLQ +Q++ NS DSI  ++ G       ++ S +KS+ 
Sbjct: 327 YRILVDFNALTGDTHRDKCLEKLLQSVQFMFNSDDSIKKEEKGNDNSGAANNGSNNKSLE 386

Query: 397 TENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTAL 456
           + N   E   K+ K F+WPD A+ AV ALEKASHDTLS D+QKYNQKLRQL+FNLK+ A+
Sbjct: 387 SAN---ECEDKSSKPFVWPDDAVPAVVALEKASHDTLSSDYQKYNQKLRQLVFNLKNNAI 443

Query: 457 LARRLLNGELEPSKILNMSPNELK 480
           LARRLLNGELEPS ILNM+PNELK
Sbjct: 444 LARRLLNGELEPSIILNMTPNELK 467

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	487
TAIR|locus:2123136	587	AT4G11560 [Arabidopsis thalian	0.751	0.623	0.636	8.5e-134
TAIR|locus:2040209	380	AT2G25120 [Arabidopsis thalian	0.402	0.515	0.529	9.3e-67
TAIR|locus:2097134	380	AT3G43990 [Arabidopsis thalian	0.435	0.557	0.465	5.4e-63
TAIR|locus:2121601	360	AT4G23120 [Arabidopsis thalian	0.431	0.583	0.486	2.6e-57
TAIR|locus:2097915	1613	SUO "'shuttle' in chinese" [Ar	0.297	0.089	0.369	7.9e-20
TAIR|locus:2097925	1611	AT3G48060 [Arabidopsis thalian	0.297	0.090	0.369	1.3e-19
ZFIN|ZDB-GENE-010501-3	1648	pbrm1l "polybromo 1, like" [Da	0.260	0.077	0.305	8.1e-08
TAIR|locus:2120693	234	EBS "EARLY BOLTING IN SHORT DA	0.213	0.444	0.330	1.6e-07
UNIPROTKB|E1BNH8	1664	E1BNH8 "Uncharacterized protei	0.390	0.114	0.227	3.7e-07
UNIPROTKB|E7EVG2	1461	PBRM1 "Protein polybromo-1" [H	0.390	0.130	0.227	8.7e-07

TAIR|locus:2123136 AT4G11560 [Arabidopsis thaliana (taxid:3702)]

 Score = 1241 (441.9 bits), Expect = 8.5e-134, Sum P(2) = 8.5e-134
 Identities = 242/380 (63%), Positives = 293/380 (77%)

Query:   101 AKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK 160
             A PVG+ V  +GKG+G+R+H+  F +DGN Y+LE PVLL PED +QKPYVAIIK+ITQ+K
Sbjct:   101 ACPVGDSVNVTGKGKGKRTHFNQFAYDGNTYDLEVPVLLVPEDKSQKPYVAIIKDITQTK 160

Query:   161 DGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHK 220
             DGSMM+ GQWFYRPEEA+++GGGNW S DTRELFYSFHRDEVPAESVMH+CVV+FVP HK
Sbjct:   161 DGSMMILGQWFYRPEEAEKRGGGNWQSSDTRELFYSFHRDEVPAESVMHRCVVYFVPAHK 220

Query:   221 QLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPE 280
             QLP RK +PGFIV+KVYDTVE+KLWKLTDKDYED+KQ EID+LV+KT   LGDLPD+E E
Sbjct:   221 QLPKRKNNPGFIVRKVYDTVEKKLWKLTDKDYEDSKQREIDVLVKKTMNVLGDLPDLESE 280

Query:   281 ETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNIL 340
             +    +QE+ LKAKRS RK NISP+DV REED++      +KAETPGS    +SE+Y IL
Sbjct:   281 DMLV-DQENVLKAKRSFRKVNISPVDVRREEDAS------LKAETPGSGAGISSEHYAIL 333

Query:   341 SKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENG 400
              KF +LTG+ HRDK L +LL+ +Q+IC   ++  A    K G      E ++K    ENG
Sbjct:   334 EKFDSLTGDAHRDKCLGKLLEAVQHICYIPENKQAGDEAKVGSDASHLEQDEKDTKPENG 393

Query:   401 SREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARR 460
               EK       F+WPD A+  V ALE ASH +L+ DFQKYNQK+R L+FNLK+TALLARR
Sbjct:   394 KDEK-------FLWPDAAVPQVCALENASHASLASDFQKYNQKMRTLVFNLKNTALLARR 446

Query:   461 LLNGELEPSKILNMSPNELK 480
             LLNGELEP+ ILNMSP ELK
Sbjct:   447 LLNGELEPATILNMSPTELK 466

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

TAIR|locus:2040209 AT2G25120 [Arabidopsis thaliana (taxid:3702)]

 Score = 566 (204.3 bits), Expect = 9.3e-67, Sum P(3) = 9.3e-67
 Identities = 107/202 (52%), Positives = 149/202 (73%)

Query:   101 AKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEI-TQS 159
             AKP+GE+ + +GKG+ ++SH++ F F GN+Y LED V L P+D N KPY AIIK+I   +
Sbjct:    66 AKPLGEVSKVTGKGKKKKSHFKTFTFRGNQYALEDSVQLVPDDPNSKPYCAIIKDIYIPN 125

Query:   160 KDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIH 219
             K+  + +   WFYRPE+ D+K  G W S+D+R LFYSFHRDEV AESV HKCVV+FVP +
Sbjct:   126 KEKYVKLAVHWFYRPEDVDKKHVGKWESKDSRNLFYSFHRDEVFAESVKHKCVVNFVPEN 185

Query:   220 KQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEP 279
             KQ+PNR++HP FIVQ VYD V++K+ K TDK+++ ++++EID LV KT  RLGDLPDIE 
Sbjct:   186 KQIPNRREHPCFIVQNVYDFVKKKVRKFTDKNFDVHQKNEIDRLVAKTSLRLGDLPDIEK 245

Query:   280 EETAAREQEDQLKAKRSLRKKN 301
             ++          K KR++++K+
Sbjct:   246 DQVTKTS-----KGKRTVQRKS 262

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2097134 AT3G43990 [Arabidopsis thaliana (taxid:3702)]

 Score = 509 (184.2 bits), Expect = 5.4e-63, Sum P(3) = 5.4e-63
 Identities = 102/219 (46%), Positives = 148/219 (67%)

Query:   101 AKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEI-TQS 159
             AK +G+ ++F+GKG+ ++ HYE FEF G +Y L+D VLL PED  QK Y+AIIK+I +Q 
Sbjct:    54 AKSIGKPIKFTGKGQNKKCHYETFEFHGKQYRLKDFVLLYPEDNKQKEYIAIIKDIYSQE 113

Query:   160 KDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIH 219
             KDG + +  QWFYR E+ + K  G W + + RE+F+SFH DEV AESV +KC+V+FVP  
Sbjct:   114 KDGLVKMEVQWFYRREDIEEKHFGKWKTENPREIFFSFHCDEVFAESVKYKCLVYFVPDD 173

Query:   220 KQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEP 279
             KQ+PNR  H GFIVQ VYD V +K+ K + + +E+ ++ EID+LV KT +R+G+L D+E 
Sbjct:   174 KQIPNRIHHSGFIVQMVYDNVRKKVRKFSHEGFEEEQKFEIDMLVAKTVSRIGNLVDVEK 233

Query:   280 EETAAREQEDQLKAKRSLRK-KNISPLDVSREEDSTTRS 317
              +T    +      KR +RK + +S   +S + +S   S
Sbjct:   234 VQTTTIPRR-----KRIVRKCERMSSNPISEKLESLPSS 267

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2121601 AT4G23120 [Arabidopsis thaliana (taxid:3702)]

 Score = 515 (186.3 bits), Expect = 2.6e-57, Sum P(2) = 2.6e-57
 Identities = 107/220 (48%), Positives = 150/220 (68%)

Query:   101 AKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEI-TQS 159
             A+ +G   + +GKG  ++ HY+ F+F  NKY LED VLL PED  +KPYVAIIK+I TQ 
Sbjct:    29 AQAIGLSHKCTGKGEKKKCHYKTFQFHANKYGLEDSVLLVPED-GEKPYVAIIKDIYTQR 87

Query:   160 KDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIH 219
             K+G + +  QW YRPEE ++K  GNW S+ +R+LFYSFHRDEV AESV   C+VHFV  +
Sbjct:    88 KEGHVKLEVQWLYRPEEVEKKYVGNWKSKGSRDLFYSFHRDEVFAESVKDDCIVHFVQEN 147

Query:   220 KQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEP 279
             KQ+PNR++HPGFIVQ VYD V++KL KLT   ++  ++ EID  V+KT  R+G L DI  
Sbjct:   148 KQIPNRRKHPGFIVQHVYDNVKKKLRKLTFNGFDLQQKREIDHFVEKTILRIGHLRDI-- 205

Query:   280 EETAAREQEDQL-KAKRSLRKKNI-SPLDVSREEDSTTRS 317
                  +EQ+  + ++KR++ +  I   ++ SRE ++   S
Sbjct:   206 ----VKEQKTLISRSKRTVPQSYIIKAVETSRESNNVVNS 241

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2097915 SUO "'shuttle' in chinese" [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 7.9e-20, Sum P(2) = 7.9e-20
 Identities = 55/149 (36%), Positives = 85/149 (57%)

Query:   123 AFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGG 182
             +F  DG K  + D  L  P   +  P++ II+ I   ++  + +   W YRP E  + G 
Sbjct:    43 SFSKDGRKISVGDCALFKPPQ-DCPPFIGIIRLIIAEEEDKLKLGVNWLYRPTEL-KLGK 100

Query:   183 GNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVER 242
             G  L  +  ELFYSFH D +PA S++H C V F+P   +LP+      F+ ++VYD    
Sbjct:   101 GILLEAEPNELFYSFHEDNIPAASLLHPCKVAFLPRGVELPSGIS--SFVCRRVYDVTNE 158

Query:   243 KLWKLTDKDYEDNKQHEIDLLVQKTQARL 271
             +LW LTD+DY D++Q E+D L+ KT++ +
Sbjct:   159 RLWWLTDQDYIDDRQLEVDKLLCKTRSEM 187

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0016021 "integral to membrane" evidence=IEA

GO:0000932 "cytoplasmic mRNA processing body" evidence=IDA

GO:0031053 "primary miRNA processing" evidence=IMP

GO:0035278 "negative regulation of translation involved in gene silencing by miRNA" evidence=IDA

TAIR|locus:2097925 AT3G48060 [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 1.3e-19, Sum P(2) = 1.3e-19
 Identities = 55/149 (36%), Positives = 85/149 (57%)

Query:   123 AFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGG 182
             +F  DG K  + D  L  P   +  P++ II+ I   ++  + +   W YRP E  + G 
Sbjct:    43 SFSKDGRKISVGDCALFKPPQ-DCPPFIGIIRLIIAEEEDKLKLGVNWLYRPTEL-KLGK 100

Query:   183 GNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVER 242
             G  L  +  ELFYSFH D +PA S++H C V F+P   +LP+      F+ ++VYD    
Sbjct:   101 GILLEAEPNELFYSFHEDNIPAASLLHPCKVAFLPRGVELPSGIS--SFVCRRVYDVTNE 158

Query:   243 KLWKLTDKDYEDNKQHEIDLLVQKTQARL 271
             +LW LTD+DY D++Q E+D L+ KT++ +
Sbjct:   159 RLWWLTDQDYIDDRQLEVDKLLCKTRSEM 187

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005576 "extracellular region" evidence=ISM

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0016021 "integral to membrane" evidence=IEA

ZFIN|ZDB-GENE-010501-3 pbrm1l "polybromo 1, like" [Danio rerio (taxid:7955)]

 Score = 160 (61.4 bits), Expect = 8.1e-08, P = 8.1e-08
 Identities = 41/134 (30%), Positives = 68/134 (50%)

Query:   116 GRRSHY-EAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRP 174
             G +S Y +   F+ N Y + D V + P + N +P+V  I+++ + + G   + G WFYRP
Sbjct:   926 GSQSSYSQDCSFENNTYSIGDYVYVQPAEANLQPHVVCIEKLWKDESGQQWMYGCWFYRP 985

Query:   175 EEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQL-PNR-KQHPGFI 232
             EE        +L +   E+F S + + VP   ++ KC V FV  + +L P   K    ++
Sbjct:   986 EETFHLATRKFLEK---EIFKSDYNNRVPFSKILGKCFVLFVKDYFKLQPEGFKPEDVYV 1042

Query:   233 VQKVYDTVERKLWK 246
              +  Y TV  K +K
Sbjct:  1043 CESRY-TVRTKAFK 1055

GO:0003677 "DNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

TAIR|locus:2120693 EBS "EARLY BOLTING IN SHORT DAYS" [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 1.6e-07, P = 1.6e-07
 Identities = 36/109 (33%), Positives = 55/109 (50%)

Query:   118 RSHYEAFEFDG-NKY-ELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPE 175
             R   +++   G NK     D VL+ P D  + PYVA +++I      ++ V  +W+YRPE
Sbjct:    16 RKELDSYTIKGTNKVVRAGDCVLMRPSDAGKPPYVARVEKIEADARNNVKVHCRWYYRPE 75

Query:   176 EADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN 224
             E+    GG       +ELF S H D   A ++  KC+VH    + +L N
Sbjct:    76 ESL---GGRRQFHGAKELFLSDHFDVQSAHTIEGKCIVHTFKNYTRLEN 121

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009845 "seed germination" evidence=IMP

GO:0009911 "positive regulation of flower development" evidence=IGI

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

UNIPROTKB|E1BNH8 E1BNH8 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 154 (59.3 bits), Expect = 3.7e-07, P = 3.7e-07
 Identities = 46/202 (22%), Positives = 91/202 (45%)

Query:   118 RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEA 177
             R++ +   F  + Y + D V + P + N +P++  I+ + +   G   + G WFYRP E 
Sbjct:   920 RTYSQDCSFKNSMYHVGDYVYVEPSEVNLQPHIVCIERLWEDSAGEKWLYGCWFYRPNET 979

Query:   178 DRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQL-P-NRKQHPGFIVQK 235
                    +L +   E+F S + ++VP   ++ KCVV FV  + +L P N +    F+ + 
Sbjct:   980 FHLATRKFLEK---EVFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDEDVFVCES 1036

Query:   236 VYDTVER-----KLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQ 290
              Y    +     KLW +         + ++ L V +  +   +    + E+     ++ +
Sbjct:  1037 RYSAKTKSFKKIKLWTMPVSSVRFVPR-DVPLPVVRVASVFANADKADDEKNTDNSEDSR 1095

Query:   291 LKAKRSLRK-KNISPLDVSREE 311
              +   +L K K   P+++S  E
Sbjct:  1096 TEDSCNLEKEKEDVPVEMSNGE 1117

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0007507 "heart development" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0001890 "placenta development" evidence=IEA

GO:0000776 "kinetochore" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E7EVG2 PBRM1 "Protein polybromo-1" [Homo sapiens (taxid:9606)]

 Score = 150 (57.9 bits), Expect = 8.7e-07, P = 8.7e-07
 Identities = 46/202 (22%), Positives = 91/202 (45%)

Query:   118 RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEA 177
             R++ +   F  + Y + D V + P + N +P++  I+ + +   G   + G WFYRP E 
Sbjct:   944 RTYSQDCSFKNSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNET 1003

Query:   178 DRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQL-P-NRKQHPGFIVQK 235
                    +L +   E+F S + ++VP   ++ KCVV FV  + +L P N +    F+ + 
Sbjct:  1004 FHLATRKFLEK---EVFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDEDVFVCES 1060

Query:   236 VYDTVER-----KLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQ 290
              Y    +     KLW +         + ++ L V +  +   +    + E+     ++ +
Sbjct:  1061 RYSAKTKSFKKIKLWTMPISSVRFVPR-DVPLPVVRVASVFANADKGDDEKNTDNSEDSR 1119

Query:   291 LKAKRSLRK-KNISPLDVSREE 311
              +   +L K K   P+++S  E
Sbjct:  1120 AEDNFNLEKEKEDVPVEMSNGE 1141

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	487
cd04713	146	cd04713, BAH_plant_3, BAH, or Bromo Adjacent Homol	2e-79
smart00439	121	smart00439, BAH, Bromo adjacent homology domain	1e-21
cd04370	123	cd04370, BAH, BAH, or Bromo Adjacent Homology doma	1e-19
pfam01426	120	pfam01426, BAH, BAH domain	2e-19
cd04714	121	cd04714, BAH_BAHCC1, BAH, or Bromo Adjacent Homolo	3e-15
cd04717	121	cd04717, BAH_polybromo, BAH, or Bromo Adjacent Hom	4e-09
smart00510	102	smart00510, TFS2M, Domain in the central regions o	9e-09
pfam07500	115	pfam07500, TFIIS_M, Transcription factor S-II (TFI	7e-08
cd04716	122	cd04716, BAH_plantDCM_I, BAH, or Bromo Adjacent Ho	6e-05
cd04721	130	cd04721, BAH_plant_1, BAH, or Bromo Adjacent Homol	1e-04
cd04710	135	cd04710, BAH_fungalPHD, BAH, or Bromo Adjacent Hom	3e-04
cd04712	130	cd04712, BAH_DCM_I, BAH, or Bromo Adjacent Homolog	3e-04
cd11486	635	cd11486, SLC5sbd_SGLT1, Na(+)/glucose cotransporte	4e-04
cd04715	159	cd04715, BAH_Orc1p_like, BAH, or Bromo Adjacent Ho	0.001
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.004

>gnl|CDD|240064 cd04713, BAH_plant_3, BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

 Score =  243 bits (622), Expect = 2e-79
 Identities = 94/147 (63%), Positives = 117/147 (79%), Gaps = 1/147 (0%)

Query: 111 SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQW 170
           +GKG+ ++ HY +FE DGNKY LED VLL PED +QKPY+AIIK+I + ++GS+ +  QW
Sbjct: 1   TGKGKKKKCHYTSFEKDGNKYRLEDCVLLVPED-DQKPYIAIIKDIYKQEEGSLKLEVQW 59

Query: 171 FYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPG 230
            YRPEE ++K GGNW + D RELFYSFHRDEVPAESV+H C V FVP  KQ+P RK H G
Sbjct: 60  LYRPEEIEKKKGGNWKAEDPRELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSG 119

Query: 231 FIVQKVYDTVERKLWKLTDKDYEDNKQ 257
           FIV++VYD V +KLWKLTD+DYED +Q
Sbjct: 120 FIVRRVYDNVNKKLWKLTDQDYEDERQ 146

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 146

>gnl|CDD|214664 smart00439, BAH, Bromo adjacent homology domain

 Score = 90.0 bits (224), Expect = 1e-21
 Identities = 36/124 (29%), Positives = 54/124 (43%), Gaps = 8/124 (6%)

Query: 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS--MMVTGQWFYRPEEADRKGGGNWLS 187
              + D VL+ P+D ++  Y+  I+EI ++K  S   MV  +WFYRPEE           
Sbjct: 1   TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNSESKMVRVRWFYRPEE---TVLEKAAL 57

Query: 188 RDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRK---QHPGFIVQKVYDTVERKL 244
            D  E+F S   D VP   ++ KC V +   +  L       +   F  +  YD  +   
Sbjct: 58  FDKNEVFLSDEYDTVPLSDIIGKCNVLYKSDYPGLRPEGSIGEPDVFFCESAYDPEKGSF 117

Query: 245 WKLT 248
            KL 
Sbjct: 118 KKLP 121

Length = 121

>gnl|CDD|239835 cd04370, BAH, BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif)

 Score = 84.4 bits (209), Expect = 1e-19
 Identities = 46/128 (35%), Positives = 64/128 (50%), Gaps = 12/128 (9%)

Query: 128 GNKYELEDPVLLTPEDT--NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEE--ADRKGGG 183
           G  YE+ D V + P+D+  +  PY+A I+E+ +  +GS  V  +WFYRPEE         
Sbjct: 1   GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSP-- 58

Query: 184 NWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPI---HKQLPNRKQHPGFIVQKVYDTV 240
                  RELF S H DE+P ES++ KC V FV      KQ PN+     F  +  YD  
Sbjct: 59  ---FALRRELFLSDHLDEIPVESIIGKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPT 115

Query: 241 ERKLWKLT 248
            ++   L 
Sbjct: 116 TKEFKALE 123

BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions. Length = 123

>gnl|CDD|216495 pfam01426, BAH, BAH domain

 Score = 83.5 bits (207), Expect = 2e-19
 Identities = 41/122 (33%), Positives = 57/122 (46%), Gaps = 6/122 (4%)

Query: 129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSR 188
             Y + D VL+ P+D  + PYV  I+EI + KDGS MV  +WFYRPEE      G     
Sbjct: 1   ETYSVGDFVLVEPDDAGEPPYVGRIEEIFEDKDGSKMVHVRWFYRPEET-VHRLGRA--F 57

Query: 189 DTRELFYSFHRDEVPAESVMHKCVVHFV---PIHKQLPNRKQHPGFIVQKVYDTVERKLW 245
           +  E+F S   D+VP E ++ KC V         +      +   F  + +YD       
Sbjct: 58  NKDEVFLSDECDDVPLEDIIGKCNVIIKSDPESLQPRKINGEPDVFFCELLYDPERGSFK 117

Query: 246 KL 247
           KL
Sbjct: 118 KL 119

This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction. Length = 120

>gnl|CDD|240065 cd04714, BAH_BAHCC1, BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins

 Score = 71.7 bits (176), Expect = 3e-15
 Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 3/95 (3%)

Query: 135 DPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELF 194
           D VL         PYVA I+ + +  +G+M+V  +W+YRPEE     GG   +   +ELF
Sbjct: 8   DCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETK---GGRKPNHGEKELF 64

Query: 195 YSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHP 229
            S H+DE   +++ HKC V     +++L   K+ P
Sbjct: 65  ASDHQDENSVQTIEHKCYVLTFAEYERLARVKKKP 99

BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 121

>gnl|CDD|240068 cd04717, BAH_polybromo, BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2

 Score = 54.1 bits (131), Expect = 4e-09
 Identities = 30/93 (32%), Positives = 43/93 (46%), Gaps = 11/93 (11%)

Query: 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEE----ADRKGGG 183
           G +Y + D V +   +   KP +  I+ + + +DG     G WFYRPEE      RK   
Sbjct: 1   GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYK 60

Query: 184 NWLSRDTRELFYSFHRDEVPAESVMHKCVVHFV 216
           N       E+F S   + VP E ++ KC V  V
Sbjct: 61  N-------EVFKSPLYETVPVEEIVGKCAVMDV 86

The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 121

>gnl|CDD|128786 smart00510, TFS2M, Domain in the central regions of transcription elongation factor S-II (and elsewhere)

 Score = 52.7 bits (127), Expect = 9e-09
 Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 412 FIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKS--TALLARRLLNGELEPS 469
            + P      + A   +   T     +KY  K R L FNLK      L R++LNGE+ P 
Sbjct: 25  ELDPTELAVQIEAEMFSEFGT---TDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPE 81

Query: 470 KILNMSPNEL 479
           K+  M+  EL
Sbjct: 82  KLATMTAEEL 91

Length = 102

>gnl|CDD|219433 pfam07500, TFIIS_M, Transcription factor S-II (TFIIS), central domain

 Score = 50.3 bits (121), Expect = 7e-08
 Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 424 ALEKASHDTLSLDFQKYNQKLRQLLFNLKS--TALLARRLLNGELEPSKILNMSPNELK 480
            +E+          +KY  K R L+FNLK      L R++LNGE+ P +++NMSP EL 
Sbjct: 36  EIEEELFKLYGNTGKKYKNKYRSLMFNLKDPKNPDLRRKVLNGEISPERLVNMSPEELA 94

Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity. Length = 115

>gnl|CDD|240067 cd04716, BAH_plantDCM_I, BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants

 Score = 42.4 bits (100), Expect = 6e-05
 Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 3/97 (3%)

Query: 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDT 190
           Y L D   +   +  ++P++  I E  +  DG    T QWFYR E+   +        D 
Sbjct: 4   YNLGDDAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQATNH--DK 60

Query: 191 RELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQ 227
           + +FYS  +++ P + ++ K  +  VP +     +K 
Sbjct: 61  KRVFYSEIKNDNPLDCLISKVKILQVPPNVGTKRKKP 97

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 122

>gnl|CDD|240072 cd04721, BAH_plant_1, BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 10/84 (11%)

Query: 127 DGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWL 186
           +G    + D V +  E+ ++  YVA I+++ + K GS MV  +WF+  +E      G  L
Sbjct: 4   NGVTISVHDFVYVLSEEEDR--YVAYIEDLYEDKKGSKMVKVRWFHTTDEV-----GAAL 56

Query: 187 SRDT---RELFYSFHRDEVPAESV 207
           S D+   RE+F S +   +  E +
Sbjct: 57  SPDSVNPREIFLSPNLQVISVECI 80

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 130

>gnl|CDD|240061 cd04710, BAH_fungalPHD, BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains

 Score = 40.8 bits (96), Expect = 3e-04
 Identities = 29/125 (23%), Positives = 49/125 (39%), Gaps = 18/125 (14%)

Query: 127 DGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD------------GSMMVTGQWFYRP 174
           +G   ++ D + ++ E   +  Y+  I E     +                V   W+YRP
Sbjct: 8   NGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRP 67

Query: 175 EEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKC-VVHFVPIHKQLPNRKQHPGFIV 233
            +  R+     +  D+R L+ S H D  P  SV  KC V H   I      +K+   F  
Sbjct: 68  RDISRR-----VVADSRLLYASMHSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYF 122

Query: 234 QKVYD 238
            +++D
Sbjct: 123 DQLFD 127

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 135

>gnl|CDD|240063 cd04712, BAH_DCM_I, BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1

 Score = 40.5 bits (95), Expect = 3e-04
 Identities = 25/89 (28%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 158 QSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCV-VHFV 216
           +  DGS M  G+W YR  +      GN+ +   RELF +     +  + +  +   VH V
Sbjct: 43  KGSDGSKMFHGRWLYRGCDTVL---GNYANE--RELFLTNECTCLELDLLSTEIKGVHKV 97

Query: 217 PIHKQLPNRKQHPGFIVQKVYDTVERKLW 245
                 P  K  P F V++ Y   ER  +
Sbjct: 98  DWSGT-PWGKGLPEFFVRQSYYWPERGAF 125

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 130

>gnl|CDD|212055 cd11486, SLC5sbd_SGLT1, Na(+)/glucose cotransporter SGLT1;solute binding domain

 Score = 42.6 bits (100), Expect = 4e-04
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 36  SLRQSKRKRIKLQEEEDYEEPEEERKASKRERRDKGKVREAEK-----PRNDGVEDEEEE 90
           SLR S  +RI L  ++  E+ +E    +  ER+  G  R+A        +    +  EEE
Sbjct: 536 SLRNSTEERIDLDADDWTEDEDENEMETDEERKKPGCCRKAYNWFCGFDQGKAPKLTEEE 595

Query: 91  EEEEEQPQEDA--KPV 104
           E   +    D   KP+
Sbjct: 596 EAALKMKMTDTSEKPL 611

Human SGLT1 (hSGLT1) is a high-affinity/low-capacity glucose transporter, which can also transport galactose. In the transport mechanism, two Na+ ions first bind to the extracellular side of the transporter and induce a conformational change in the glucose binding site. This results in an increased affinity for glucose. A second conformational change in the transporter follows, bringing the Na+ and glucose binding sites to the inner surface of the membrane. Glucose is then released, followed by the Na+ ions. In the process, hSGLT1 is also able to transport water and urea and may be a major pathway for transport of these across the intestinal brush-border membrane. hSGLT1 is encoded by the SLC5A1 gene and expressed mostly in the intestine, but also in the trachea, kidney, heart, brain, testis, and prostate. The WHO/UNICEF oral rehydration solution (ORS) for the treatment of secretory diarrhea contains salt and glucose. The glucose, along with sodium ions, is transported by hSGLT1 and water is either co-transported along with these or follows by osmosis. Mutations in SGLT1 are associated with intestinal glucose galactose malabsorption (GGM). Up-regulation of intestinal SGLT1 may protect against enteric infections. SGLT1 is expressed in colorectal, head and neck, and prostate tumors. Epidermal growth factor receptor (EGFR) functions in cell survival by stabilizing SGLT1, and thereby maintaining intracellular glucose levels. SGLT1 is predicted to have 14 membrane-spanning regions. This subgroup belongs to the solute carrier 5 (SLC5)transporter family. Length = 635

>gnl|CDD|240066 cd04715, BAH_Orc1p_like, BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 33/109 (30%), Positives = 49/109 (44%), Gaps = 11/109 (10%)

Query: 112 GKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEI--TQSKDGSMMVTGQ 169
           GK +  +  Y +F +DG +Y L D V +   + + +PY+  I +I  T    G   V   
Sbjct: 12  GKKKDGQF-YRSFTYDGVEYRLYDDVYV--HNGDSEPYIGKIIKIYETAIDSGKKKVKVI 68

Query: 170 WFYRPEEADRKGGGNWLSRDTRELFYSFHRDE-----VPAESVMHKCVV 213
           WF+RP E  R        R   E+F +  R E        ES++ KC V
Sbjct: 69  WFFRPSEI-RMELKGEPKRHINEVFLACGRGEGLANINLLESIIGKCNV 116

Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Length = 159

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 4/82 (4%)

Query: 24  RTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEERKASKRERRDKGKVREAEKPRNDG 83
           +TR +E+N+ +   ++  +KR   + E + E  +E   A  R R  +  V+  +K   D 
Sbjct: 334 KTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDA 393

Query: 84  VEDEEEEEEEEE----QPQEDA 101
             +E+   E EE     PQ +A
Sbjct: 394 SPNEDTPSENEESKGSPPQVEA 415

Length = 429

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

 Score = 39.7 bits (92), Expect = 0.004
 Identities = 28/158 (17%), Positives = 70/158 (44%)

Query: 4    RRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEERKAS 63
            ++  +     E E+        +  EENK + +    K +  K + EE  +  E+E+KA+
Sbjct: 1632 KKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAA 1691

Query: 64   KRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEA 123
            +  +++  + ++AE+ +    E++++ EE ++  +E+     E  + + + + +    + 
Sbjct: 1692 EALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKK 1751

Query: 124  FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD 161
             E +  K            +  +K   A+I+E    +D
Sbjct: 1752 DEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEED 1789

Length = 2084

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	487
KOG1886	464	consensus BAH domain proteins [Transcription]	100.0
cd04713	146	BAH_plant_3 BAH, or Bromo Adjacent Homology domain	100.0
cd04716	122	BAH_plantDCM_I BAH, or Bromo Adjacent Homology dom	99.94
cd04715	159	BAH_Orc1p_like BAH, or Bromo Adjacent Homology dom	99.94
cd04717	121	BAH_polybromo BAH, or Bromo Adjacent Homology doma	99.94
cd04714	121	BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain,	99.93
cd04370	123	BAH BAH, or Bromo Adjacent Homology domain (also c	99.93
smart00439	120	BAH Bromo adjacent homology domain.	99.93
cd04710	135	BAH_fungalPHD BAH, or Bromo Adjacent Homology doma	99.93
PF01426	119	BAH: BAH domain; InterPro: IPR001025 The BAH (brom	99.92
cd04721	130	BAH_plant_1 BAH, or Bromo Adjacent Homology domain	99.91
cd04709	164	BAH_MTA BAH, or Bromo Adjacent Homology domain, as	99.91
cd04708	202	BAH_plantDCM_II BAH, or Bromo Adjacent Homology do	99.89
cd04712	130	BAH_DCM_I BAH, or Bromo Adjacent Homology domain,	99.89
smart00510	102	TFS2M Domain in the central regions of transcripti	99.89
cd04760	124	BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain	99.88
PF07500	115	TFIIS_M: Transcription factor S-II (TFIIS), centra	99.85
TIGR01385	299	TFSII transcription elongation factor S-II. This m	99.85
cd04720	179	BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology do	99.82
cd04719	128	BAH_Orc1p_animal BAH, or Bromo Adjacent Homology d	99.81
cd04718	148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	99.79
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	99.76
cd04711	137	BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domai	99.75
KOG1827	629	consensus Chromatin remodeling complex RSC, subuni	99.52
KOG1634	778	consensus Predicted transcription factor DATF1, co	99.02
KOG3554	693	consensus Histone deacetylase complex, MTA1 compon	98.77
COG5076	371	Transcription factor involved in chromatin remodel	92.28

>KOG1886 consensus BAH domain proteins [Transcription]

Probab=100.00  E-value=1e-43  Score=370.95  Aligned_cols=337  Identities=40%  Similarity=0.663  Sum_probs=302.1

Q ss_pred             hhhhhccCCCCCccccccceeecCCCCCcceeeeEEEEcCeEEee-CCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceEE
Q 011389           89 EEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYEL-EDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMMV  166 (487)
Q Consensus        89 ~~~~~~~~~~~~a~~iG~pvk~~gKG~~~R~~Y~sf~~dG~~YrV-GD~VyV~~e~~~~~pyIArI~~I~e~~d-G~~~V  166 (487)
                      ...+.++++.++|.|+|...++.|+|+.+++||.+|.+.|..|.. ||+|++.+++++.+||||+|++||.+.. +.+.+
T Consensus         8 ~~~~~~~~~~~~a~~~g~a~~~qGv~~~k~~h~~t~~~~~g~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~   87 (464)
T KOG1886|consen    8 PKLKSELRPRDEASSMGDANKEQGVGGVKSLHFETFIYRGGRYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKV   87 (464)
T ss_pred             ccccccCCccchhhhhhhhhhhccccccccccccceeeccCcccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcce
Confidence            345567899999999999999999999999999999999988888 9999999999999999999999998765 68999


Q ss_pred             EEEEeecccccCCCCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCCCCCCCCceEEeeeeecCCcEEee
Q 011389          167 TGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWK  246 (487)
Q Consensus       167 rVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp~~~~~~~F~Cr~vYD~~~kkl~~  246 (487)
                      +|+|||||+|+.....+.|....++|||+|+|+|++++++|.++|.|+|++.|.+++.+..+++|+|+++||..+.++|.
T Consensus        88 ev~W~YrPee~~~~~~~~~~a~~~relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~  167 (464)
T KOG1886|consen   88 EVQWFYRPEESEGGGSGKWGAKQPRELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRK  167 (464)
T ss_pred             ecccccCCCccCCCCCCCcccCCCccccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccC
Confidence            99999999999988788888889999999999999999999999999999999999988889999999999999999999


Q ss_pred             cCCcchhcccchhhhHHHHHHhhhcCCCCCCCccccccchhhhhhhcccccccCCCCCCcccccccccCcccccccccCC
Q 011389          247 LTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETP  326 (487)
Q Consensus       247 L~dkdy~~~~q~Evd~ll~kt~~riG~l~d~~~~e~~~~~~~~~~~~k~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  326 (487)
                      +++.+|....+.++|.++.++..++|++++.....+.     ..++++++.++++++  .++|.                
T Consensus       168 ~~~~~~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~t~-----~~~~~~~~~~~s~~~--~~~r~----------------  224 (464)
T KOG1886|consen  168 LRDGDFGDGQKLEIDMLVPKTGPRRGTLPDPKKVQTL-----NAAASKRSQQKSEIS--SLSRA----------------  224 (464)
T ss_pred             ccccchhcccccCCccchhhhcccCCCCCCccccccc-----cccccceeccccccc--ccccc----------------
Confidence            9999999999999999999999999999999999833     577888999988887  22222                


Q ss_pred             CccCCCCchhHHHHhhcccccChhHHHHHHHHHHHHH-hhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccc
Q 011389          327 GSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGL-QYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKG  405 (487)
Q Consensus       327 ~~~~~~~~~~~~~l~~~~~~tgd~~RDk~le~L~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (487)
                           ..+.++.||..|..+||++.|||+++.||+++ +..|.++.....                              
T Consensus       225 -----ss~~~~~~~e~~~~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~------------------------------  269 (464)
T KOG1886|consen  225 -----SSSVDGEILESFDLLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPA------------------------------  269 (464)
T ss_pred             -----ccccccccccCCCCCCCcccccccccccchhhccccccccccCCC------------------------------
Confidence                 34467788999999999999999999999999 777766633221                              


Q ss_pred             cCCCCCCCChhHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhccCCHHHHhhhhcC-CCCccccccCChhhcCCCCC
Q 011389          406 QKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNG-ELEPSKILNMSPNELKVLYC  484 (487)
Q Consensus       406 ~~~~~~~~wp~~v~~~a~~iE~a~~~~~~~~~~~Yk~K~Rsl~fNLK~Np~Lr~rvl~G-ei~p~~l~~Mt~~Ema~~~~  484 (487)
                        .+.+-.||+.++..+.+||.+.|+.+..+..+|.++++.|+++||+-..|+.+.++| ++.|+-.+.|.+-++.++.+
T Consensus       270 --~~~~~~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k~~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~  347 (464)
T KOG1886|consen  270 --GDQGSLWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLKGQALLKPEPLNPGETKPEPKQELHPPSFPDGQS  347 (464)
T ss_pred             --cccccCCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhcchhhhccccCCCcccCchhhhhccCCCCCCCcc
Confidence              233338999999999999999999999888999999999999999999999999999 59999999999998888776


Q ss_pred             C
Q 011389          485 P  485 (487)
Q Consensus       485 ~  485 (487)
                      +
T Consensus       348 ~  348 (464)
T KOG1886|consen  348 S  348 (464)
T ss_pred             C
Confidence            4

>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

Probab=100.00  E-value=7.7e-36  Score=273.52  Aligned_cols=146  Identities=64%  Similarity=1.163  Sum_probs=134.1

Q ss_pred             cCCCCCcceeeeEEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCC
Q 011389          111 SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDT  190 (487)
Q Consensus       111 ~gKG~~~R~~Y~sf~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~  190 (487)
                      +|||.++|+||++|.++|++|+|||+|||.+++ +.+||||+|++||++.+|.++|+|+|||||+||.....+.+..+++
T Consensus         1 ~~~~~~~~~~y~s~~~dg~~y~vgD~Vlv~~~~-~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~   79 (146)
T cd04713           1 TGKGKKKKCHYTSFEKDGNKYRLEDCVLLVPED-DQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDP   79 (146)
T ss_pred             CCCCccceeeeeeEEECCEEEECCCEEEEeCCC-CCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCC
Confidence            489999999999999999999999999999876 4899999999999998899999999999999998655555555679


Q ss_pred             CeeEeeCCcccccccccceecEEEEcCccccCCCCCCCCceEEeeeeecCCcEEeecCCcchhcccc
Q 011389          191 RELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQ  257 (487)
Q Consensus       191 nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp~~~~~~~F~Cr~vYD~~~kkl~~L~dkdy~~~~q  257 (487)
                      ||||+|.|.|.+|+++|+|||+|++.+++.++|.....++|||++.||...++||+|+++||++++|
T Consensus        80 ~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~~~~~~~~~~~~~  146 (146)
T cd04713          80 RELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLWKLTDQDYEDERQ  146 (146)
T ss_pred             CeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEeeccccccccccC
Confidence            9999999999999999999999999999999887666789999999999999999999999997754

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants

Probab=99.94  E-value=6.7e-27  Score=208.91  Aligned_cols=118  Identities=22%  Similarity=0.406  Sum_probs=104.5

Q ss_pred             CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCccccccccc
Q 011389          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV  207 (487)
Q Consensus       128 G~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI  207 (487)
                      |+.|++||+|||.+++ +.++|||+|.+||++.+|..+|+|+|||||+||.....  ...++++|||+|+|+|++|++||
T Consensus         1 g~~~~lgD~V~v~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~--~~~~~~rEvFlS~~~D~~pl~~I   77 (122)
T cd04716           1 GITYNLGDDAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQ--ATNHDKKRVFYSEIKNDNPLDCL   77 (122)
T ss_pred             CcEEEcCCEEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhccccc--cccCCCceEEEecccCccchhhe
Confidence            6789999999999986 59999999999999999999999999999999986322  24579999999999999999999


Q ss_pred             ceecEEEEcCccccCC---CCCCCCceEEeeeeecCCcEEeecC
Q 011389          208 MHKCVVHFVPIHKQLP---NRKQHPGFIVQKVYDTVERKLWKLT  248 (487)
Q Consensus       208 ~GKC~V~~~~ey~~lp---~~~~~~~F~Cr~vYD~~~kkl~~L~  248 (487)
                      +|||+|++++++..++   ....+..|||++.|+..-.+|..|+
T Consensus        78 ~~Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~~~~  121 (122)
T cd04716          78 ISKVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQTLR  121 (122)
T ss_pred             eeeeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheEeCC
Confidence            9999999999998874   2334789999999999888887775

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins

Probab=99.94  E-value=2.4e-26  Score=213.78  Aligned_cols=138  Identities=25%  Similarity=0.385  Sum_probs=114.5

Q ss_pred             CccccccceeecCCCCCcceeeeEEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC--CceEEEEEEeeccccc
Q 011389          100 DAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD--GSMMVTGQWFYRPEEA  177 (487)
Q Consensus       100 ~a~~iG~pvk~~gKG~~~R~~Y~sf~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~d--G~~~VrVqWFYRPeEt  177 (487)
                      -++|.|.|.+..+     ++||.++.++|..|++||+|||.+++  .+||||+|.+||+..+  |..+++|+|||||+||
T Consensus         4 ~~~~~g~~~~~~~-----~~~Y~s~~~~g~~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~   76 (159)
T cd04715           4 WGVKRGEGGKKKD-----GQFYRSFTYDGVEYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEI   76 (159)
T ss_pred             cceecccccccCC-----ceEEEEEEECCEEEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHh
Confidence            3578888888765     67999999999999999999999854  8999999999999865  8899999999999999


Q ss_pred             CCCCCCCCCCCCCCeeEeeCCc-----ccccccccceecEEEEcCccccCCCC--C--CCCceEEeeeeecCCcEEe
Q 011389          178 DRKGGGNWLSRDTRELFYSFHR-----DEVPAESVMHKCVVHFVPIHKQLPNR--K--QHPGFIVQKVYDTVERKLW  245 (487)
Q Consensus       178 ~~~~~g~~~~~~~nELFlS~h~-----D~iplesI~GKC~V~~~~ey~~lp~~--~--~~~~F~Cr~vYD~~~kkl~  245 (487)
                      .+...+. +.+.+||||+|.|.     +++|+++|+|||.|+++++|...+..  .  ....|++.+.||...++..
T Consensus        77 ~~~~~~~-~~~~~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~~~~s~~~~~~~~~~f~~~f~~~~~~~~  152 (159)
T cd04715          77 RMELKGE-PKRHINEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRNPQPSDGIPTSADFLFPCNFDVGRCVIV  152 (159)
T ss_pred             ccccccC-cccCCCcEEEecCcCccccccCcHHHccceeEEEEehHhhhCCCCcCCccccCcceeeeEEEecCceec
Confidence            8644333 34689999999986     66899999999999999999875421  2  3456788888888776654

Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2

Probab=99.94  E-value=1.6e-26  Score=204.67  Aligned_cols=117  Identities=25%  Similarity=0.401  Sum_probs=103.1

Q ss_pred             CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCccccccccc
Q 011389          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV  207 (487)
Q Consensus       128 G~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI  207 (487)
                      |..|++||+|||.+++.+.++|||+|.+||++.+|..+|+|+|||||+||.+...+.   .++||||+|.+.+++|+++|
T Consensus         1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~---~~~~Evfls~~~d~~~~~~I   77 (121)
T cd04717           1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRK---FYKNEVFKSPLYETVPVEEI   77 (121)
T ss_pred             CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccc---cccCceEEcCccccccHHHh
Confidence            678999999999998755889999999999998899999999999999998765543   48999999999999999999


Q ss_pred             ceecEEEEcCccccCC-C-CCCCCceEEeeeeecCCcEEeec
Q 011389          208 MHKCVVHFVPIHKQLP-N-RKQHPGFIVQKVYDTVERKLWKL  247 (487)
Q Consensus       208 ~GKC~V~~~~ey~~lp-~-~~~~~~F~Cr~vYD~~~kkl~~L  247 (487)
                      +|||.|++..+|.+.. . ....+.|+|++.||...+.|..+
T Consensus        78 ~~kc~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~~  119 (121)
T cd04717          78 VGKCAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKI  119 (121)
T ss_pred             cCeeEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEecc
Confidence            9999999999998864 2 22458899999999988877654

The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins

Probab=99.93  E-value=2.1e-26  Score=204.84  Aligned_cols=112  Identities=27%  Similarity=0.439  Sum_probs=99.3

Q ss_pred             CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCccccccccc
Q 011389          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV  207 (487)
Q Consensus       128 G~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI  207 (487)
                      |.+|++||+|||.+++.+.+||||+|.+||++.+|.++|+|+|||||+||.++..   ..+++||||+|+|.|++|+++|
T Consensus         1 ~~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~---~~~~~~EvF~S~~~d~~~~~~I   77 (121)
T cd04714           1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRK---PNHGEKELFASDHQDENSVQTI   77 (121)
T ss_pred             CCEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCccc---ccCCCCceEecCCcccccHHHh
Confidence            5789999999999987568899999999999988999999999999999986433   3479999999999999999999


Q ss_pred             ceecEEEEcCccccCCC-----CCCCCceEEeeeeecCCc
Q 011389          208 MHKCVVHFVPIHKQLPN-----RKQHPGFIVQKVYDTVER  242 (487)
Q Consensus       208 ~GKC~V~~~~ey~~lp~-----~~~~~~F~Cr~vYD~~~k  242 (487)
                      +|||.|+++++|.++..     ....+.|+|+..||+...
T Consensus        78 ~gkc~V~~~~ey~~~~~~~~~~~~~~d~~~Ce~~yn~~~~  117 (121)
T cd04714          78 EHKCYVLTFAEYERLARVKKKPQDGVDFYYCAGTYNPDTG  117 (121)
T ss_pred             CcccEEEehhHheecccccCCCCcCCCEEEEeccCCCCcC
Confidence            99999999999988652     235789999999998754

BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif)

Probab=99.93  E-value=9.9e-26  Score=194.82  Aligned_cols=117  Identities=38%  Similarity=0.646  Sum_probs=103.4

Q ss_pred             CeEEeeCCeEEEcCCCC--CCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCccccccc
Q 011389          128 GNKYELEDPVLLTPEDT--NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAE  205 (487)
Q Consensus       128 G~~YrVGD~VyV~~e~~--~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iple  205 (487)
                      |.+|++||+|||.+++.  ..++|||+|.+||++.+|.++|+|+|||||+||.+...+   .+.+||||+|+++++++++
T Consensus         1 g~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~---~~~~~Elf~s~~~~~i~v~   77 (123)
T cd04370           1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSP---FALRRELFLSDHLDEIPVE   77 (123)
T ss_pred             CCEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhcccccc---ccccceeEEecCccccCHH
Confidence            67999999999999874  478999999999999999999999999999999964432   4699999999999999999


Q ss_pred             ccceecEEEEcCccccCC---CCCCCCceEEeeeeecCCcEEeec
Q 011389          206 SVMHKCVVHFVPIHKQLP---NRKQHPGFIVQKVYDTVERKLWKL  247 (487)
Q Consensus       206 sI~GKC~V~~~~ey~~lp---~~~~~~~F~Cr~vYD~~~kkl~~L  247 (487)
                      +|.|||.|++..++.+..   ....++.|||++.||..+.+|..+
T Consensus        78 ~I~gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~~  122 (123)
T cd04370          78 SIIGKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKAL  122 (123)
T ss_pred             HhccccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEeC
Confidence            999999999999988763   444678999999999988877654

BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.

>smart00439 BAH Bromo adjacent homology domain

Probab=99.93  E-value=1.1e-25  Score=195.18  Aligned_cols=116  Identities=31%  Similarity=0.464  Sum_probs=102.2

Q ss_pred             EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCc-eEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCcccccccccc
Q 011389          130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS-MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVM  208 (487)
Q Consensus       130 ~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~-~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI~  208 (487)
                      .|++||+|||.+++...++|||+|.+||++.+|. ++++|+|||||+||.+...+   ..++||||+|++++++++++|+
T Consensus         1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~---~~~~~Elf~s~~~~~i~~~~I~   77 (120)
T smart00439        1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAA---LFDKNEVFLSDEYDTVPLSDII   77 (120)
T ss_pred             CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccccccc---cCCCcceEEEccCccCChHHee
Confidence            4799999999998766899999999999998888 89999999999999875443   3589999999999999999999


Q ss_pred             eecEEEEcCccccCCCCC---CCCceEEeeeeecCCcEEeecC
Q 011389          209 HKCVVHFVPIHKQLPNRK---QHPGFIVQKVYDTVERKLWKLT  248 (487)
Q Consensus       209 GKC~V~~~~ey~~lp~~~---~~~~F~Cr~vYD~~~kkl~~L~  248 (487)
                      |||.|++.++|.+.+...   ..+.|||++.||...++|.+++
T Consensus        78 ~kc~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~~~  120 (120)
T smart00439       78 GKCNVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKKLP  120 (120)
T ss_pred             eEEEEEEcchhcccccccCCCCCCeEEEEEEEccccCcccCCC
Confidence            999999999998865322   4689999999999988887663

>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains

Probab=99.93  E-value=1.2e-25  Score=203.98  Aligned_cols=118  Identities=24%  Similarity=0.441  Sum_probs=101.6

Q ss_pred             EEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC------------CceEEEEEEeecccccCCCCCCCCCCCCCC
Q 011389          124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD------------GSMMVTGQWFYRPEEADRKGGGNWLSRDTR  191 (487)
Q Consensus       124 f~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~d------------G~~~VrVqWFYRPeEt~~~~~g~~~~~~~n  191 (487)
                      +..+|..|++||+|||.++++++|+|||+|++|+...+            +..+|+|+|||||+||....     .++++
T Consensus         5 ~~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~-----~~d~r   79 (135)
T cd04710           5 VLKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV-----VADSR   79 (135)
T ss_pred             EccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc-----cCCce
Confidence            35689999999999999998889999999999998542            34689999999999986321     46999


Q ss_pred             eeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEee
Q 011389          192 ELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWK  246 (487)
Q Consensus       192 ELFlS~h~D~iplesI~GKC~V~~~~ey~~lp-~~~~~~~F~Cr~vYD~~~kkl~~  246 (487)
                      |||+|+|.|++|+++|.|||+|++..++..+. ....+++|||.++||+.++|+++
T Consensus        80 elf~S~h~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~~~  135 (135)
T cd04710          80 LLYASMHSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRYYD  135 (135)
T ss_pred             EEEEEeeEeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhccC
Confidence            99999999999999999999999999887654 23357999999999999998863

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation

Probab=99.92  E-value=1.5e-25  Score=194.30  Aligned_cols=115  Identities=37%  Similarity=0.622  Sum_probs=100.3

Q ss_pred             eEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCc--eEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCcccccccc
Q 011389          129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS--MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAES  206 (487)
Q Consensus       129 ~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~--~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iples  206 (487)
                      ++|++||||||.+++...++|||+|.+||++.++.  ++|+|+|||||+||..   +.  ...+||||+|++++++|+++
T Consensus         1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~---~~--~~~~~Elf~s~~~~~~~~~~   75 (119)
T PF01426_consen    1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSL---GK--TFSPRELFLSDHCDDIPVES   75 (119)
T ss_dssp             EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTT---GG--HSCTTEEEEEEEEEEEEGGG
T ss_pred             CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECcccccc---cc--cCCCCEEEEECcEeEEehhh
Confidence            58999999999999878999999999999998877  9999999999999932   11  23569999999999999999


Q ss_pred             cceecEEEEcCccccCCCCC--CCCceEEeeeeecCCcEEeecC
Q 011389          207 VMHKCVVHFVPIHKQLPNRK--QHPGFIVQKVYDTVERKLWKLT  248 (487)
Q Consensus       207 I~GKC~V~~~~ey~~lp~~~--~~~~F~Cr~vYD~~~kkl~~L~  248 (487)
                      |.|||.|++..++.+.....  .++.|||++.||...++|..++
T Consensus        76 I~gkc~V~~~~~~~~~~~~~~~~~~~F~cr~~yd~~~~~f~~~~  119 (119)
T PF01426_consen   76 IRGKCNVLHLEDYEQARPYGKEEPDTFFCRYAYDPQKKRFKKLP  119 (119)
T ss_dssp             EEEEEEEEEHHHHTTGCCHCHHTTTEEEEEEEEETTTTEEEE-S
T ss_pred             EEeeeEEEECCccccccccccCCCCEEEEEEEEeCCcCEEeCCC
Confidence            99999999999988865332  6799999999999999998764

The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....

>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

Probab=99.91  E-value=8.6e-25  Score=197.21  Aligned_cols=120  Identities=22%  Similarity=0.329  Sum_probs=103.1

Q ss_pred             EEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCccccc
Q 011389          124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVP  203 (487)
Q Consensus       124 f~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~ip  203 (487)
                      |..||.+|++||||||.+++  .++|||+|.+||++.+|.++|+|+||+||+|+.+.....  .+.+||||+|++.+++|
T Consensus         1 ~~r~~~~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~--~~~~~EvFlS~~~d~i~   76 (130)
T cd04721           1 FCRNGVTISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPD--SVNPREIFLSPNLQVIS   76 (130)
T ss_pred             CccCCEEEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCC--CCCCCeEEEcCCccccc
Confidence            46799999999999999875  778999999999998999999999999999998743332  26999999999999999


Q ss_pred             ccccceecEEEEcCccccCCC----CCCCCceEEeeeeecCCcEEeec
Q 011389          204 AESVMHKCVVHFVPIHKQLPN----RKQHPGFIVQKVYDTVERKLWKL  247 (487)
Q Consensus       204 lesI~GKC~V~~~~ey~~lp~----~~~~~~F~Cr~vYD~~~kkl~~L  247 (487)
                      +++|.|||+||+..+|.++..    ......|+|++.||....+.+++
T Consensus        77 ~~~I~gk~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~~~~~fd~  124 (130)
T cd04721          77 VECIDGLATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNNKVKPFDI  124 (130)
T ss_pred             hHHeeeeeEECCHHHHhhhhccccCccccccEEEEEEecCCCCceeee
Confidence            999999999999999988642    12357999999999876655544

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins

Probab=99.91  E-value=1.7e-24  Score=202.25  Aligned_cols=117  Identities=21%  Similarity=0.326  Sum_probs=100.6

Q ss_pred             CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCC----CC---------------CCCCC
Q 011389          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKG----GG---------------NWLSR  188 (487)
Q Consensus       128 G~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~----~g---------------~~~~~  188 (487)
                      ++.|+|||||||.++. +.|++||+|++||++.+|.++|+|+|||||+||+...    .+               .....
T Consensus         1 ~~~yrvGD~Vy~~~~~-~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~   79 (164)
T cd04709           1 ANMYRVGDYVYFESSP-NNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQL   79 (164)
T ss_pred             CcEEecCCEEEEECCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhcc
Confidence            3689999999999884 7788999999999999999999999999999986411    11               11335


Q ss_pred             CCCeeEeeCCcccccccccceecEEEEcCccccCCC-CCCCCceEEeeeeecCCcEEe
Q 011389          189 DTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN-RKQHPGFIVQKVYDTVERKLW  245 (487)
Q Consensus       189 ~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp~-~~~~~~F~Cr~vYD~~~kkl~  245 (487)
                      +.+|||+|.|.+.+|+++|+|||.|++..+|..+.. ....++|||+.+||+.+++|.
T Consensus        80 ~~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~  137 (164)
T cd04709          80 RHRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLL  137 (164)
T ss_pred             CcceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeec
Confidence            899999999999999999999999999999988753 335799999999999999995

The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants

Probab=99.89  E-value=4.1e-23  Score=198.10  Aligned_cols=124  Identities=27%  Similarity=0.382  Sum_probs=104.7

Q ss_pred             EEEcCeEEeeCCeEEEcCCC-----------------CCCCCeEEEEeEEeeCCCC------ceEEEEEEeecccccCCC
Q 011389          124 FEFDGNKYELEDPVLLTPED-----------------TNQKPYVAIIKEITQSKDG------SMMVTGQWFYRPEEADRK  180 (487)
Q Consensus       124 f~~dG~~YrVGD~VyV~~e~-----------------~~~~pyIArI~~I~e~~dG------~~~VrVqWFYRPeEt~~~  180 (487)
                      |.++|++|++||+|||.|+.                 ...+++||+|.+|+..+++      ..+|+|+|||||+||.. 
T Consensus         1 f~~~Gv~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~-   79 (202)
T cd04708           1 FVYDGVTYSVGDFLYVSPDAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSP-   79 (202)
T ss_pred             CcCCCEEEecCCeEEECcccccccccccccccccccCCCCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCc-
Confidence            57899999999999999981                 1357889999999986544      68999999999999853 


Q ss_pred             CCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEeecCCc
Q 011389          181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLTDK  250 (487)
Q Consensus       181 ~~g~~~~~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp-~~~~~~~F~Cr~vYD~~~kkl~~L~dk  250 (487)
                        ....+++.+|||+|++.+++|+.+|.|||.|++..++..+. ....++.|||+..||+.++.|-+||..
T Consensus        80 --~~~y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~~lP~~  148 (202)
T cd04708          80 --EKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLKQLPPN  148 (202)
T ss_pred             --ccceecCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccCCCCch
Confidence              22345699999999999999999999999999998876543 123479999999999999999888776

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1

Probab=99.89  E-value=9.6e-23  Score=183.93  Aligned_cols=114  Identities=20%  Similarity=0.263  Sum_probs=99.0

Q ss_pred             cCeEEeeCCeEEEcCCCCC----------CCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEee
Q 011389          127 DGNKYELEDPVLLTPEDTN----------QKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYS  196 (487)
Q Consensus       127 dG~~YrVGD~VyV~~e~~~----------~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS  196 (487)
                      .|..|+|||+|+|.++++.          .++||++|..||++.+|.++|+|+|||||+||.+..     .+++||||||
T Consensus         2 ~~~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~-----~~~~~ElFLS   76 (130)
T cd04712           2 HGLTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN-----YANERELFLT   76 (130)
T ss_pred             CCCEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc-----cCCCceEEEe
Confidence            5788999999999998755          489999999999999999999999999999999643     4799999999


Q ss_pred             CCccccccc----ccceecEEEEcCccccCCCCCCCCceEEeeeeecCCcEEeecC
Q 011389          197 FHRDEVPAE----SVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLT  248 (487)
Q Consensus       197 ~h~D~iple----sI~GKC~V~~~~ey~~lp~~~~~~~F~Cr~vYD~~~kkl~~L~  248 (487)
                      +||+++++.    .|++||.|++...+...   ..+..|+|+..|++..+.|..|+
T Consensus        77 d~c~~~~~~~~~~~I~~k~~V~~~~~~~~~---~~~~~F~r~syy~~e~~~F~~l~  129 (130)
T cd04712          77 NECTCLELDLLSTEIKGVHKVDWSGTPWGK---GLPEFFVRQSYYWPERGAFTSLK  129 (130)
T ss_pred             ccccccccccccceeEEEEEEEEecCcCCc---CCCCEEEEEEEECccCCceEcCC
Confidence            999999999    99999999998766531   24566777777787999998875

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere)

Probab=99.89  E-value=3.2e-23  Score=179.96  Aligned_cols=92  Identities=32%  Similarity=0.448  Sum_probs=81.4

Q ss_pred             hhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHHHHHH
Q 011389          349 ETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKA  428 (487)
Q Consensus       349 d~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~iE~a  428 (487)
                      |.+||+|+++||++|+..+..+...                                          ..+..+|.+||.+
T Consensus         1 d~~R~~~~~~L~~al~~~~~~~~~~------------------------------------------~~~~~lA~~IE~~   38 (102)
T smart00510        1 DKVRDKCQEMLYKALQKISDPEEIE------------------------------------------LDPTELAVQIEAE   38 (102)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCCccc------------------------------------------ccHHHHHHHHHHH
Confidence            5799999999999999887655110                                          1344789999999


Q ss_pred             HHHhcCCChHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCC
Q 011389          429 SHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVL  482 (487)
Q Consensus       429 ~~~~~~~~~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~  482 (487)
                      +|..++...++|++|+|||+||||  +||+||++||+|+|+|++||+||++|||+.
T Consensus        39 lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~vl~G~i~p~~lv~Ms~~ElAs~   94 (102)
T smart00510       39 MFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPEKLATMTAEELASA   94 (102)
T ss_pred             HHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCH
Confidence            999998878899999999999999  899999999999999999999999999974

>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins

Probab=99.88  E-value=8e-23  Score=182.95  Aligned_cols=112  Identities=22%  Similarity=0.327  Sum_probs=96.4

Q ss_pred             CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCccccccccc
Q 011389          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV  207 (487)
Q Consensus       128 G~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI  207 (487)
                      |..|.+||+|+|.+++++.++|||+|..||++.+|.+||+|+|||||+||.++..     ++++|||||++|+++++.+|
T Consensus         1 g~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~~-----~~~kEvFlsd~c~d~~l~~I   75 (124)
T cd04760           1 GEELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGET-----SDPLELFLVDECEDMALSSI   75 (124)
T ss_pred             CCEEecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCccccccc-----CCCcEEEeecccCCcchHHh
Confidence            5789999999999988789999999999999999999999999999999996442     69999999999999999999


Q ss_pred             ceecEEEEcCcc--------ccCCC---CCCCCceEEeeeeecCCcEE
Q 011389          208 MHKCVVHFVPIH--------KQLPN---RKQHPGFIVQKVYDTVERKL  244 (487)
Q Consensus       208 ~GKC~V~~~~ey--------~~lp~---~~~~~~F~Cr~vYD~~~kkl  244 (487)
                      .+||+|+..++-        ...+.   .....+|||++.||+...+|
T Consensus        76 ~~Kv~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf  123 (124)
T cd04760          76 HGKVNVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARF  123 (124)
T ss_pred             eeeeEEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhcc
Confidence            999999998765        22221   12357899999999866554

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites

Probab=99.85  E-value=1.3e-21  Score=172.17  Aligned_cols=99  Identities=35%  Similarity=0.506  Sum_probs=87.8

Q ss_pred             cChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHHHH
Q 011389          347 TGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALE  426 (487)
Q Consensus       347 tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~iE  426 (487)
                      |++++|++|+++|+++|....... .   .                                      +..+..+|.+||
T Consensus         1 ~~~~~R~k~~~~L~~~l~~~~~~~-~---~--------------------------------------~~~~~~lA~~IE   38 (115)
T PF07500_consen    1 TNDKVRDKARKLLYKALQKRSDEQ-D---D--------------------------------------PEDAKELAKEIE   38 (115)
T ss_dssp             -TCHHHHHHHHHHHHHHHHCCCCC-C---C--------------------------------------TCCHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHhcCccc-c---c--------------------------------------hhHHHHHHHHHH
Confidence            789999999999999998875442 1   0                                      457889999999


Q ss_pred             HHHHHhcCCChHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCCCCCCC
Q 011389          427 KASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVLYCPSW  487 (487)
Q Consensus       427 ~a~~~~~~~~~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~~~~~~  487 (487)
                      .++|..|+.+..+|++|+|||+||||  +||.||.+|++|+|+|.+||+||++|||+.-...|
T Consensus        39 ~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~~~il~g~i~p~~lv~ms~~Elas~e~k~~  101 (115)
T PF07500_consen   39 EALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLRRRILSGEISPEELVTMSPEELASEELKEE  101 (115)
T ss_dssp             HHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHHHHHHHSSSTTCHHHHCTTTTTTTSCCCCC
T ss_pred             HHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHHHHHHcCCCCHHHHhcCCHHHhCCHHHHHH
Confidence            99999997778899999999999999  89999999999999999999999999999876643

TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.

>TIGR01385 TFSII transcription elongation factor S-II

Probab=99.85  E-value=1.9e-21  Score=197.12  Aligned_cols=95  Identities=23%  Similarity=0.332  Sum_probs=83.7

Q ss_pred             ccChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHHH
Q 011389          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTAL  425 (487)
Q Consensus       346 ~tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~i  425 (487)
                      +|||++||+|+++||+||+..++.+...                                          .++..+|.+|
T Consensus       133 ~t~d~~Rdk~r~~L~~aL~~~~~~~~~~------------------------------------------~~~~~lA~~i  170 (299)
T TIGR01385       133 VTNDKVRDKCRELLYDALAKDSDHPPQS------------------------------------------IDPEAKAIQI  170 (299)
T ss_pred             cCCcHHHHHHHHHHHHHHhhcCCCCccc------------------------------------------cCHHHHHHHH
Confidence            6999999999999999999876543110                                          0233689999


Q ss_pred             HHHHHHhcCCChHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCC
Q 011389          426 EKASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVL  482 (487)
Q Consensus       426 E~a~~~~~~~~~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~  482 (487)
                      |.+||..++.++.+|++|||||+||||  +||+||++||+|+|+|++||+||++|||+.
T Consensus       171 E~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~  229 (299)
T TIGR01385       171 EELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASA  229 (299)
T ss_pred             HHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCH
Confidence            999999999888899999999999998  799999999999999999999999999974

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p

Probab=99.82  E-value=5.8e-20  Score=174.04  Aligned_cols=119  Identities=17%  Similarity=0.235  Sum_probs=98.8

Q ss_pred             cCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceEEEEEEeecccccCCCCC-CCCC-----CCCCCeeEeeCCc
Q 011389          127 DGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMMVTGQWFYRPEEADRKGG-GNWL-----SRDTRELFYSFHR  199 (487)
Q Consensus       127 dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~d-G~~~VrVqWFYRPeEt~~~~~-g~~~-----~~~~nELFlS~h~  199 (487)
                      +|.+|++||+|+|.++. ..++|||+|.+|+.+.. +.+.+.|+|||||.|+..... +.+.     ...+||||+|.|.
T Consensus        49 d~~~~~vGD~Vlik~~~-~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~  127 (179)
T cd04720          49 DGLELSVGDTILVKDDV-ANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAEL  127 (179)
T ss_pred             CCeEEeCCCEEEEeCCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEeccc
Confidence            89999999999999986 48999999999998765 568999999999999964221 1110     2348999999999


Q ss_pred             ccccccccceecEEEEcCccccCCC--CCCCCceEEeeeeecCCcEEee
Q 011389          200 DEVPAESVMHKCVVHFVPIHKQLPN--RKQHPGFIVQKVYDTVERKLWK  246 (487)
Q Consensus       200 D~iplesI~GKC~V~~~~ey~~lp~--~~~~~~F~Cr~vYD~~~kkl~~  246 (487)
                      +.+++.+|+|||+||+..+|.++..  .....+||||++||+....|..
T Consensus       128 d~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~  176 (179)
T cd04720         128 SEIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVW  176 (179)
T ss_pred             ceEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEcc
Confidence            9999999999999999999987642  2346899999999998886644

The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p

Probab=99.81  E-value=7.3e-20  Score=164.94  Aligned_cols=113  Identities=27%  Similarity=0.406  Sum_probs=93.7

Q ss_pred             eEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCC---ceEEEEEEeecccccCCCC---CCCCCCCCCCeeEeeCCc---
Q 011389          129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDG---SMMVTGQWFYRPEEADRKG---GGNWLSRDTRELFYSFHR---  199 (487)
Q Consensus       129 ~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG---~~~VrVqWFYRPeEt~~~~---~g~~~~~~~nELFlS~h~---  199 (487)
                      .+|+|||||+|.+++. .++|||+|++|+++.+|   ...++|||||||+|+++..   .|+  ..+++|||+++|.   
T Consensus         2 ~~i~vGd~VlI~~~d~-~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~--~~~~~EvF~~~~~~~~   78 (128)
T cd04719           2 LTIEVGDFVLIEGEDA-DGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGR--EPHSQEVFFYSRSSCD   78 (128)
T ss_pred             eEEecCCEEEEECCCC-CCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccC--CCCCcEEEEecCcccc
Confidence            4799999999999874 88999999999998765   5699999999999997422   222  2489999999987   


Q ss_pred             ccccccccceecEEEEcCccccCCC--CCCCCceEEeeeeecCCcEE
Q 011389          200 DEVPAESVMHKCVVHFVPIHKQLPN--RKQHPGFIVQKVYDTVERKL  244 (487)
Q Consensus       200 D~iplesI~GKC~V~~~~ey~~lp~--~~~~~~F~Cr~vYD~~~kkl  244 (487)
                      +++++++|.|+|.|+...+|.+++.  ......||+++.+|.+..+.
T Consensus        79 ~~i~~etI~gkc~V~~~~~y~~l~~~~~~~~~~~F~r~~~~~k~~~~  125 (128)
T cd04719          79 NDIDAETIIGKVRVEPVEPKTDLPETKKKTGGPLFVKRYWDTKTFRS  125 (128)
T ss_pred             CcEeHHHcccEEEEEEcCCccchhhhccccCceEEEEEEeccccccc
Confidence            4899999999999999999999883  23456788889988766543

Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

Probab=99.79  E-value=1.9e-20  Score=171.74  Aligned_cols=98  Identities=18%  Similarity=0.340  Sum_probs=86.7

Q ss_pred             CCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCCC
Q 011389          145 NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN  224 (487)
Q Consensus       145 ~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp~  224 (487)
                      ...+|||+|.+||++. |..+|+|+|||||+||.++..   ..++.+|||+|+|.|++++++|+|||.||++.+|.++..
T Consensus        50 ~~~~~vArIekiW~~~-G~~~~~grWy~rPEET~~gr~---~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~  125 (148)
T cd04718          50 SGDLWLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQ---PHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASN  125 (148)
T ss_pred             cCchHHHHHHHHHhcc-CceEEEEEEEeCchhccCccc---cccccceeeeccccccccHHHHhcccEEcCHHHcccccC
Confidence            3678999999999986 999999999999999997443   456999999999999999999999999999999988653


Q ss_pred             CCCCCceEEeeeeecCCcEEeec
Q 011389          225 RKQHPGFIVQKVYDTVERKLWKL  247 (487)
Q Consensus       225 ~~~~~~F~Cr~vYD~~~kkl~~L  247 (487)
                      . ..++|+|+..||...+.|..+
T Consensus       126 ~-g~Dvy~Ce~~Yd~~~~~Fkr~  147 (148)
T cd04718         126 D-GDDVFLCEYEYDVHWQSFKRL  147 (148)
T ss_pred             C-CCceEEEEEEEhhhcCceeec
Confidence            3 568999999999999888654

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]

Probab=99.76  E-value=1.1e-18  Score=175.65  Aligned_cols=96  Identities=26%  Similarity=0.365  Sum_probs=83.2

Q ss_pred             cccChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHH
Q 011389          345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA  424 (487)
Q Consensus       345 ~~tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~  424 (487)
                      .+++|+.|++|+++||.||....... .                          .               ...+..+|.+
T Consensus       129 ~~~~d~~r~k~~e~l~~al~~~~~~~-~--------------------------~---------------~~~~~~~a~~  166 (296)
T KOG1105|consen  129 PITNDPVRDKCRELLYAALTTEDDSR-V--------------------------T---------------GADPLELAVQ  166 (296)
T ss_pred             CCCCchHHHHHHHHHHHHhccccccc-c--------------------------c---------------CCCHHHHHHH
Confidence            46899999999999999998322111 0                          0               2356799999


Q ss_pred             HHHHHHHhcCCChHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCC
Q 011389          425 LEKASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVL  482 (487)
Q Consensus       425 iE~a~~~~~~~~~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~  482 (487)
                      ||.+||..++.+..+|+++|||++||||  |||+||++||.|+|+|++|++||++|||+-
T Consensus       167 iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~  226 (296)
T KOG1105|consen  167 IEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASE  226 (296)
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccH
Confidence            9999999999999999999999999996  799999999999999999999999999973

>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins

Probab=99.75  E-value=1.6e-18  Score=156.81  Aligned_cols=114  Identities=18%  Similarity=0.216  Sum_probs=88.1

Q ss_pred             CCeEEEcCCCCCCCCeEEEEeEEeeCCCC-------ceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCcccccccc
Q 011389          134 EDPVLLTPEDTNQKPYVAIIKEITQSKDG-------SMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAES  206 (487)
Q Consensus       134 GD~VyV~~e~~~~~pyIArI~~I~e~~dG-------~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iples  206 (487)
                      +|+|-=.+-+.+.|++||||++|...+++       .++|+|+|||||+||..+... ..+.+.||||+|+|.+++|+.+
T Consensus        13 ~~~~~~~~~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~-ayhsDirevy~Sd~~~~~~~~~   91 (137)
T cd04711          13 SDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKA-TYHADINMLYWSDEEATVDFSA   91 (137)
T ss_pred             ccccccccCCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEeccccccccccc-ccccceeeEEeecceeecChhh
Confidence            34444445556789999999999875432       578999999999999853221 1356789999999999999999


Q ss_pred             cceecEEEEcCcccc-CC--CCCCCCceEEeeeeecCCcEEeecC
Q 011389          207 VMHKCVVHFVPIHKQ-LP--NRKQHPGFIVQKVYDTVERKLWKLT  248 (487)
Q Consensus       207 I~GKC~V~~~~ey~~-lp--~~~~~~~F~Cr~vYD~~~kkl~~L~  248 (487)
                      |.|||.|++..+... +.  ....++.|||+.+||..++.|.++|
T Consensus        92 I~GKC~V~~~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~d~p  136 (137)
T cd04711          92 VQGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFEDPP  136 (137)
T ss_pred             ccceEEEEeccccchhHHHHhcCCCcceEEhhhhccccCcccCCC
Confidence            999999997654432 21  2346899999999999999887654

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]

Probab=99.52  E-value=1.2e-14  Score=158.28  Aligned_cols=118  Identities=27%  Similarity=0.401  Sum_probs=107.6

Q ss_pred             EEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCccccc
Q 011389          124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVP  203 (487)
Q Consensus       124 f~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~ip  203 (487)
                      +.++|..|.+||+||+.+..++.++.|++|..+|+..+|..++.+||||||++|.|..++.|   ..+|||.+..+.+++
T Consensus       184 ~~i~~~~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F---~k~Evfkt~~~~~~~  260 (629)
T KOG1827|consen  184 VEIDGTKYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKF---YKQEVFKTSLYRDDL  260 (629)
T ss_pred             ccccCcccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccccch---hcccceecccccccH
Confidence            78899999999999999988779999999999999999999999999999999999998888   999999999999999


Q ss_pred             ccccceecEEEEcCccccCC--CCCCCCceEEeeeeecCCcEE
Q 011389          204 AESVMHKCVVHFVPIHKQLP--NRKQHPGFIVQKVYDTVERKL  244 (487)
Q Consensus       204 lesI~GKC~V~~~~ey~~lp--~~~~~~~F~Cr~vYD~~~kkl  244 (487)
                      ++-|+|+|.|+++..|....  .....+.|+|++.|+...+.|
T Consensus       261 ~q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K~f  303 (629)
T KOG1827|consen  261 VQRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLKKF  303 (629)
T ss_pred             HHHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchhhh
Confidence            99999999999999997753  334578999999998765443

>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]

Probab=99.02  E-value=7.8e-11  Score=130.80  Aligned_cols=77  Identities=31%  Similarity=0.480  Sum_probs=69.3

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHhcC-CChHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCCCC
Q 011389          408 NGKSFIWPDTAIAAVTALEKASHDTLS-LDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVLYC  484 (487)
Q Consensus       408 ~~~~~~wp~~v~~~a~~iE~a~~~~~~-~~~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~~~  484 (487)
                      +.+.+.||..++.   .||..+|..|+ +-+.+|++|+|||+||||  +||.||.+|+.|+|+|++|++|+++|||..-.
T Consensus       262 g~k~~~d~~ll~~---~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL  338 (778)
T KOG1634|consen  262 GEKQLQDPNLLLE---KIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPEL  338 (778)
T ss_pred             ccccccchhhHhh---hhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchH
Confidence            4667888986544   99999999999 556799999999999996  69999999999999999999999999999988


Q ss_pred             CCC
Q 011389          485 PSW  487 (487)
Q Consensus       485 ~~~  487 (487)
                      |.|
T Consensus       339 ~~~  341 (778)
T KOG1634|consen  339 AEW  341 (778)
T ss_pred             HHH
Confidence            877

>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]

Probab=98.77  E-value=6.5e-10  Score=116.93  Aligned_cols=136  Identities=21%  Similarity=0.325  Sum_probs=106.6

Q ss_pred             eEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCC-------CCC-----------------C
Q 011389          129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK-------GGG-----------------N  184 (487)
Q Consensus       129 ~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~-------~~g-----------------~  184 (487)
                      ..|+|||+|||.... ..|+.|-+|+++.++.+|.+..+|..|||..||...       ..+                 .
T Consensus         4 n~y~vgd~vYf~~ss-s~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e   82 (693)
T KOG3554|consen    4 NMYRVGDYVYFENSS-SNPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAE   82 (693)
T ss_pred             ccceecceEEEecCC-CChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhh
Confidence            379999999999887 556679999999999999999999999999998630       001                 0


Q ss_pred             C-----------------CCCCCCeeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEee
Q 011389          185 W-----------------LSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWK  246 (487)
Q Consensus       185 ~-----------------~~~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp-~~~~~~~F~Cr~vYD~~~kkl~~  246 (487)
                      +                 +..-.+|||+|-+....|+..|.|||.|....+...+- .....++||+..|||+..++|. 
T Consensus        83 ~EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLL-  161 (693)
T KOG3554|consen   83 IEEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLL-  161 (693)
T ss_pred             hhhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhh-
Confidence            0                 11246899999999999999999999999987655432 2335689999999999998884 


Q ss_pred             cCCcchh---cccchhhhHHHHHH
Q 011389          247 LTDKDYE---DNKQHEIDLLVQKT  267 (487)
Q Consensus       247 L~dkdy~---~~~q~Evd~ll~kt  267 (487)
                       .|+..+   +..|.+|+..|...
T Consensus       162 -ADkGeIRVG~kYQA~i~e~l~Eg  184 (693)
T KOG3554|consen  162 -ADKGEIRVGEKYQADIPEWLEEG  184 (693)
T ss_pred             -ccCcceeecccccccchHHHHhc
Confidence             566543   55677788887644

>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

Probab=92.28  E-value=0.019  Score=60.42  Aligned_cols=96  Identities=11%  Similarity=-0.004  Sum_probs=81.5

Q ss_pred             eEEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCccc
Q 011389          122 EAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDE  201 (487)
Q Consensus       122 ~sf~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~  201 (487)
                      ....+.+....+|+++++.+......|.++.+..+|.+.++..+.-++|||||.++.+.....   ...+++.+....+.
T Consensus       268 ~~~~i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~  344 (371)
T COG5076         268 ESVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKL---FFDNCVMYNGEVTD  344 (371)
T ss_pred             hhhcccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccch---hhhcccccchhhhh
Confidence            344566779999999999998888999999999999988888888999999999777654433   48899999999999


Q ss_pred             ccccccceecEEEEcCccc
Q 011389          202 VPAESVMHKCVVHFVPIHK  220 (487)
Q Consensus       202 iplesI~GKC~V~~~~ey~  220 (487)
                      +......+.|.|.....+.
T Consensus       345 ~~~~~~~~~~~~~~~~~~~  363 (371)
T COG5076         345 YYKNANVLEDFVIKKTRLI  363 (371)
T ss_pred             hhhhccchhhhHhhhhhhh
Confidence            9999999999998876554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	487
1w4s_A	174	Crystal Structure Of The Proximal Bah Domain Of Pol		3e-08

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	487
1w4s_A	174	Polybromo, polybromo 1 protein; BAH, bromo-associa	4e-39
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	7e-19
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	2e-06
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	2e-18
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	5e-08
4dov_A	163	ORC1, origin recognition complex subunit 1; DNA re	1e-11
3ndq_A	108	Transcription elongation factor A protein 1; helix	4e-08
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	3e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
3po3_S	178	Transcription elongation factor S-II; RNA polymera	5e-04

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A* Length = 1330

 Score = 89.2 bits (220), Expect = 7e-19
 Identities = 43/276 (15%), Positives = 88/276 (31%), Gaps = 37/276 (13%)

Query: 6   FAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEERKASKR 65
           F++     + ED      R R       QQ              +    +   +   + R
Sbjct: 345 FSEQIEKYDKEDKENAMKRRRCGVCEVCQQPE----------CGKCKACKDMVKFGGTGR 394

Query: 66  ERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSG----------KGR 115
            ++   K R       +  +DEE +++  E P       G+  + +           K  
Sbjct: 395 SKQACLKRRCPNLAVKEADDDEEADDDVSEMPSPKKLHQGKKKKQNKDRISWLGQPMKIE 454

Query: 116 GRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPE 175
             R++Y+    D    E+ D V + P+D+++  Y+A +  + + K+G MM    WF    
Sbjct: 455 ENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGT 514

Query: 176 EADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQL------------P 223
           +            D  ELF     + +    +  K  V +    +              P
Sbjct: 515 DTVLGATS-----DPLELFLVGECENMQLSYIHSKVKVIYKAPSENWAMEGGTDPETTLP 569

Query: 224 NRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHE 259
             +    +  Q  Y+    +          ++ +H+
Sbjct: 570 GAEDGKTYFFQLWYNQEYARFESPPKTQPTEDNKHK 605

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A* Length = 1330

 Score = 49.2 bits (116), Expect = 2e-06
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 10/142 (7%)

Query: 115 RGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK------DGSMMVTG 168
           R ++       +  +  +  D +  +  D  +   +  IKEI   K      +  + +  
Sbjct: 672 RPKKDPVNETLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIHCGKKKGKVNEADIKLRL 731

Query: 169 QWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP---NR 225
             FYRPE   R   G++ + D   L++S     V    V  +C V +     +     ++
Sbjct: 732 YKFYRPENTHRSYNGSYHT-DINMLYWSDEEAVVNFSDVQGRCTVEYGEDLLESIQDYSQ 790

Query: 226 KQHPGFIVQKVYDTVERKLWKL 247
                F   + Y++  +     
Sbjct: 791 GGPDRFYFLEAYNSKTKNFEDP 812

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A* Length = 1002

 Score = 87.6 bits (216), Expect = 2e-18
 Identities = 37/208 (17%), Positives = 75/208 (36%), Gaps = 23/208 (11%)

Query: 28  SEENKEQQSLRQSKRKRIKLQEEEDYEEPEEER--------KASKRERRDKGKVREAEKP 79
            E++  +      KR+R  + E     E  + +          S R ++   + R     
Sbjct: 38  IEKDDREDKENAFKRRRCGVCEVCQQPECGKCKACKDMVKFGGSGRSKQACQERRCPNMA 97

Query: 80  RNDGVEDEEEEEEEEEQPQEDAKPVGELVRF----------SGKGRGRRSHYEAFEFDGN 129
             +  +DEE ++   E P       G+  +           + K  G++S+Y+    D  
Sbjct: 98  MKEADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAE 157

Query: 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRD 189
             E+ D V + P+D+++  Y+A +  + +      M    WF    +      G   + D
Sbjct: 158 TLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVL---GA--TSD 212

Query: 190 TRELFYSFHRDEVPAESVMHKCVVHFVP 217
             ELF     +++    +  K  V +  
Sbjct: 213 PLELFLVDECEDMQLSYIHSKVKVIYKA 240

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A* Length = 1002

 Score = 54.9 bits (131), Expect = 5e-08
 Identities = 33/218 (15%), Positives = 67/218 (30%), Gaps = 23/218 (10%)

Query: 40  SKRKRIKLQEEEDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQE 99
           S  +  +++++E     E+      R                DGV    E      +   
Sbjct: 297 SCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSS 356

Query: 100 DAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQS 159
             K            R R+   +   +  +  +  D +  +  D  +   +  IKEI   
Sbjct: 357 PVK------------RPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCP 404

Query: 160 K-------DGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCV 212
           K       +  + +    FYRPE   +    ++ + D   L++S     V  ++V  +C 
Sbjct: 405 KKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHA-DINLLYWSDEEAVVDFKAVQGRCT 463

Query: 213 VHFVPIHKQLPNRKQHPG---FIVQKVYDTVERKLWKL 247
           V +     +        G   F   + Y+   +     
Sbjct: 464 VEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDP 501

>4dov_A ORC1, origin recognition complex subunit 1; DNA replication, replication; 1.70A {Mus musculus} PDB: 4dow_A* Length = 163

 Score = 61.6 bits (149), Expect = 1e-11
 Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 18/140 (12%)

Query: 115 RGRRSHYEAFEFDGNK-----YELEDPVLLTPEDTNQKPYVAIIK---EITQSKDGSMMV 166
           +  +  Y       N       ++   VL+  ED N+KPYVA +    +           
Sbjct: 18  KQFQQMYREICMKINDGSEIHIKVGQFVLIQGED-NKKPYVAKLIELFQNGAEVPPKKCA 76

Query: 167 TGQWFYRPEE---ADRKGGGNWLSRDTRELFYSFHRD---EVPAESVMHKCVVHFVPIHK 220
             QWF R  E   + R   G       +E+F+    D   ++  E+++    V  +   +
Sbjct: 77  RVQWFVRFLEIPVSKRHLLGRSP--PAQEIFWYDCSDWDNKINVETIIGPVQVVALAPEE 134

Query: 221 QLP-NRKQHPGFIVQKVYDT 239
            +P ++K      V+  ++ 
Sbjct: 135 VIPVDQKSEETLFVKLSWNK 154

>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens} Length = 108

 Score = 50.4 bits (120), Expect = 4e-08
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 415 PDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKST--ALLARRLLNGELEPSKIL 472
                   + +E+A +  +     KY  ++R  + NLK      L + +L G + P    
Sbjct: 38  GADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFA 97

Query: 473 NMSPNELK 480
            M+  E+ 
Sbjct: 98  RMTAEEMA 105

>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 120

 Score = 48.4 bits (115), Expect = 3e-07
 Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 404 KGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRL 461
           K   +    +  + A    T +EK           KY  K R L+FNLK     +L +++
Sbjct: 26  KRLTDSNLKVPEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKV 85

Query: 462 LNGELEPSKILNMSPNELK 480
           L GE+ P  ++ MSP EL 
Sbjct: 86  LKGEVTPDHLIRMSPEELA 104

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 47.1 bits (111), Expect = 3e-06
 Identities = 13/80 (16%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 22  SSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEERKASKRERRDKGKVREAEKPRN 81
           +   R ++E +  +  R+ +RKR++  +       +E R+ +K++  +  + +  +  +N
Sbjct: 75  AQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKN 134

Query: 82  DGVEDEEEEEEEEEQPQEDA 101
             + +   ++   +QP  D 
Sbjct: 135 K-INNRIADKAFYQQPDADI 153

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 3e-05
 Identities = 50/321 (15%), Positives = 86/321 (26%), Gaps = 119/321 (37%)

Query: 250 KDYEDN-----KQHEIDLLVQKTQA-----RLGDLPDIEPEETAAREQEDQLKA-----K 294
           KD +D       + EID ++    A     RL      + EE   +  E+ L+       
Sbjct: 36  KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM 95

Query: 295 RSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNI--LSKFKALTGETHR 352
             ++ +   P         +  +  Y++        +     YN+  L  +  L      
Sbjct: 96  SPIKTEQRQP---------SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR----- 141

Query: 353 DKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSF 412
            + L  L +  + +      I     G  G  G       K+    +       +    F
Sbjct: 142 -QALLEL-RPAKNVL-----ID----GVLGS-G-------KTWVALDVCLSYKVQCKMDF 182

Query: 413 --IW--------PDTAIAAVTAL---------EKASH-DTLSLDFQKYNQKLRQLL---- 448
              W        P+T +  +  L          ++ H   + L       +LR+LL    
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242

Query: 449 -------------------FNLKSTALLARR------LLNGE-------------LEP-- 468
                              FNL    LL  R       L+               L P  
Sbjct: 243 YENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE 302

Query: 469 -----SKILNMSPNELKVLYC 484
                 K L+  P +L     
Sbjct: 303 VKSLLLKYLDCRPQDLPREVL 323

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Length = 178

 Score = 40.2 bits (93), Expect = 5e-04
 Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 415 PDTAIAAVTALEKASHDTLSLD--FQKYNQKLRQLLFNLKST--ALLARRLLNGELEPSK 470
           P + +    A+E   +   + D     Y  + R +  N+ S     L  ++ NG++ P  
Sbjct: 37  PQSILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEF 96

Query: 471 ILNMSPNEL 479
           +      +L
Sbjct: 97  LATCDAKDL 105

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	487
1w4s_A	174	Polybromo, polybromo 1 protein; BAH, bromo-associa	99.96
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	99.93
2lw4_A	113	Transcription elongation factor A protein 2; struc	99.92
3ndq_A	108	Transcription elongation factor A protein 1; helix	99.92
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	99.91
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	99.9
3po3_S	178	Transcription elongation factor S-II; RNA polymera	99.88
4dov_A	163	ORC1, origin recognition complex subunit 1; DNA re	99.83
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	99.79
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.79
4ft4_B	784	DNA (cytosine-5)-methyltransferase 1; chromodomain	99.79
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	99.76
2fl7_A	232	Regulatory protein SIR3; ORC, silencing, chromatin	99.28
1m4z_A	238	Origin recognition complex subunit 1; DNA replicat	99.28

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A*

Probab=99.93  E-value=5.7e-26  Score=258.54  Aligned_cols=141  Identities=20%  Similarity=0.286  Sum_probs=122.3

Q ss_pred             CccccccceeecCCCCCcceeeeEEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCC
Q 011389          100 DAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADR  179 (487)
Q Consensus       100 ~a~~iG~pvk~~gKG~~~R~~Y~sf~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~  179 (487)
                      ...|+|.|+    ++..++.+|+++.++|.+|+|||||||.++++..+||||+|++||++.+|.+||+|+|||||+||.+
T Consensus       132 ~~~W~G~p~----k~~~~~~~Y~s~~v~g~~i~VGD~V~v~~~d~~~ppyIarIe~m~ed~~g~k~~~v~Wf~rp~ET~l  207 (1002)
T 3swr_A          132 RISWVGEAV----KTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVL  207 (1002)
T ss_dssp             CEEEESCCC----CCBTTEEECSEEEETTEEEETTCEEEECBSSTTSCCEEEEEEEEEEETTTEEEEEEEEEEEGGGSTT
T ss_pred             cccccCccc----ccccCceeeeEEEECCEEEecCCEEEEecCCCCCCceEEEEEEEeecCCCCeEEEEEEEecchhccc
Confidence            446999999    4555799999999999999999999999988778889999999999988999999999999999987


Q ss_pred             CCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccc----------cCC-CCCCCCceEEeeeeecCCcEEeecC
Q 011389          180 KGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHK----------QLP-NRKQHPGFIVQKVYDTVERKLWKLT  248 (487)
Q Consensus       180 ~~~g~~~~~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~----------~lp-~~~~~~~F~Cr~vYD~~~kkl~~L~  248 (487)
                      +..     ++++|||+|+||+++++++|+|||+|++...+.          ..+ ....+++|||+..||..+++|.+|+
T Consensus       208 g~~-----~~~~ElFlsd~cd~~~l~~I~gkc~V~~~~~~~~w~~~~~~~~~~~~~~~~~~~ffc~~~Y~~~~~~F~~lp  282 (1002)
T 3swr_A          208 GAT-----SDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPP  282 (1002)
T ss_dssp             GGG-----SCTTEEEEEEEEEEEEGGGEEEEECEEECCCCTTGGGCTTCCCCCSCCCCCCTSEEEEEEEETTTTEEECCC
T ss_pred             ccC-----CCCCceEeeccccCCcHHHhceeeEEEEccCCcchhhhcccccccccccCCCCeEEEEEEECCCCCcccCCC
Confidence            432     589999999999999999999999999975511          111 1123689999999999999999997


Q ss_pred             C
Q 011389          249 D  249 (487)
Q Consensus       249 d  249 (487)
                      .
T Consensus       283 ~  283 (1002)
T 3swr_A          283 K  283 (1002)
T ss_dssp             C
T ss_pred             h
Confidence            6

>2lw4_A Transcription elongation factor A protein 2; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.92  E-value=2.9e-26  Score=201.06  Aligned_cols=101  Identities=22%  Similarity=0.231  Sum_probs=87.6

Q ss_pred             cccChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHH
Q 011389          345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA  424 (487)
Q Consensus       345 ~~tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~  424 (487)
                      .+|||++||+|+++||+||+...+....                                          ..++..+|.+
T Consensus         6 p~t~D~vRdk~~e~L~~aL~~~~~~~~~------------------------------------------~~~~~~~A~~   43 (113)
T 2lw4_A            6 PVTCDAVRNKCREMLTAALQTDHDHVAI------------------------------------------GADCERLSAQ   43 (113)
T ss_dssp             CCCCSTTHHHHHHHHHHHHHSSTHHHHH------------------------------------------TCCHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHHHcCCCcccc------------------------------------------cchHHHHHHH
Confidence            4699999999999999999764332200                                          1145588999


Q ss_pred             HHHHHHHhcCCChHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCCCCCCC
Q 011389          425 LEKASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVLYCPSW  487 (487)
Q Consensus       425 iE~a~~~~~~~~~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~~~~~~  487 (487)
                      ||.++|..|++++.+|++|+|||+||||  +||+||++||+|+|+|++||+||++|||+--...|
T Consensus        44 IE~~~f~~~~~~~~~Yk~k~Rsl~~NLkd~~Np~Lr~~vl~G~i~p~~l~~Ms~eEmAs~elk~~  108 (113)
T 2lw4_A           44 IEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELKEI  108 (113)
T ss_dssp             HHHHHHHHHTCTTTHHHHHHHHHHHHHHCSSSSHHHHHHHTTSSCHHHHHHSCHHHHHCTTTTTC
T ss_pred             HHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHH
Confidence            9999999998888899999999999997  69999999999999999999999999999877766

>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens}

Probab=99.92  E-value=5.5e-26  Score=197.84  Aligned_cols=95  Identities=21%  Similarity=0.205  Sum_probs=81.9

Q ss_pred             ccChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHHH
Q 011389          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTAL  425 (487)
Q Consensus       346 ~tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~i  425 (487)
                      +|||++||||+++||+||+..++.+..                                          ..++..+|.+|
T Consensus        11 ~t~d~vR~k~~~lL~~aL~~~~d~~~~------------------------------------------~~~~~~lA~~I   48 (108)
T 3ndq_A           11 STSDSVRLKCREMLAAALRTGDDYIAI------------------------------------------GADEEELGSQI   48 (108)
T ss_dssp             CCCCHHHHHHHHHHHHHTTGGGHHHHH------------------------------------------TCCHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHcCCCCCcc------------------------------------------cccHHHHHHHH
Confidence            599999999999999999886533210                                          01566899999


Q ss_pred             HHHHHHhcCCChHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCC
Q 011389          426 EKASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVL  482 (487)
Q Consensus       426 E~a~~~~~~~~~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~  482 (487)
                      |.++|..|+.++.+||+|+|||+||||  +||+||++||+|+|+|++||+||++|||+-
T Consensus        49 E~~if~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmAS~  107 (108)
T 3ndq_A           49 EEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD  107 (108)
T ss_dssp             HHHHHHHHCSSSHHHHHHHHHHHHHHTCTTCHHHHHHHHHTSSCHHHHHHCCTTTC---
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHHHHHHHHcCCcCHHHHhCCCHHHccCC
Confidence            999999998877899999999999998  799999999999999999999999999973

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A*

Probab=99.91  E-value=9e-25  Score=254.05  Aligned_cols=141  Identities=18%  Similarity=0.309  Sum_probs=118.6

Q ss_pred             CccccccceeecCCCCCcceeeeEEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCC
Q 011389          100 DAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADR  179 (487)
Q Consensus       100 ~a~~iG~pvk~~gKG~~~R~~Y~sf~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~  179 (487)
                      +-+|+|.|++..    .+++||+++.++|.+|+|||||||.+++++.++|||+|++||++.+|..||+|+|||||+||.+
T Consensus       443 ~i~W~G~p~k~~----~~~~~Y~~~~v~g~~~~vGD~V~v~~~d~~~p~yiarIe~iwe~~dg~~~~~~~WfyRp~ETvl  518 (1330)
T 3av4_A          443 RISWLGQPMKIE----ENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVL  518 (1330)
T ss_dssp             CEEEESSCSCCC------CEEECSEEEESSEEETTCEEEECBCCSSCCCEEEEEEEEEEETTCCEEEEEEEEEEGGGSTT
T ss_pred             CceEccCceecc----CCceeeeEEEECCEEEecCCEEEEeCCCCCCCCEEEEEeeeeecCCCCEEEEEEEEEchHHccc
Confidence            455999988444    3699999999999999999999999887667899999999999999999999999999999986


Q ss_pred             CCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCc---cccC----CCC-----CCCCceEEeeeeecCCcEEeec
Q 011389          180 KGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPI---HKQL----PNR-----KQHPGFIVQKVYDTVERKLWKL  247 (487)
Q Consensus       180 ~~~g~~~~~~~nELFlS~h~D~iplesI~GKC~V~~~~e---y~~l----p~~-----~~~~~F~Cr~vYD~~~kkl~~L  247 (487)
                      +.     .++++|||+|+|+|++++++|+|||.|+++..   |...    +..     .....|||+..||...++|+++
T Consensus       519 g~-----~~~~rElFlS~~~d~~~l~~I~gKC~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~F~C~~~Yd~~~~~F~~l  593 (1330)
T 3av4_A          519 GA-----TSDPLELFLVGECENMQLSYIHSKVKVIYKAPSENWAMEGGTDPETTLPGAEDGKTYFFQLWYNQEYARFESP  593 (1330)
T ss_dssp             GG-----GSCTTEEEEEEEEEEEEGGGEEEEECEEECCCCTTSTTCCC-------------CCEEEEEEEETTTTEEECC
T ss_pred             cc-----ccCCCeEEEecccccCcHHHhcceeEEEEeccchhhhhhcccCccccccccccCCceEEEeEECCccCccCCc
Confidence            33     26999999999999999999999999999766   3221    111     2356899999999999999999


Q ss_pred             CC
Q 011389          248 TD  249 (487)
Q Consensus       248 ~d  249 (487)
                      +.
T Consensus       594 p~  595 (1330)
T 3av4_A          594 PK  595 (1330)
T ss_dssp             CC
T ss_pred             Cc
Confidence            77

>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.90  E-value=4.4e-24  Score=189.01  Aligned_cols=103  Identities=26%  Similarity=0.370  Sum_probs=90.0

Q ss_pred             ccChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHHH
Q 011389          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTAL  425 (487)
Q Consensus       346 ~tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~i  425 (487)
                      .++|.+||+|+++|+++|.....+.+..                        .              . ..++..+|.+|
T Consensus         7 ~~~d~~Rd~~r~~L~eaL~~~~~~~~~~------------------------~--------------~-~~~~~~lA~~I   47 (120)
T 2dme_A            7 GSADQIRQSVRHSLKDILMKRLTDSNLK------------------------V--------------P-EEKAAKVATKI   47 (120)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHTTTTCC------------------------C--------------C-HHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHHHHhccccccc------------------------c--------------c-hhHHHHHHHHH
Confidence            3679999999999999998876543110                        0              0 34788999999


Q ss_pred             HHHHHHhcCCChHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCCCCCCC
Q 011389          426 EKASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVLYCPSW  487 (487)
Q Consensus       426 E~a~~~~~~~~~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~~~~~~  487 (487)
                      |.+||..|+.++.+|++|+|||+||||  +||+||++||+|+|+|++||+||++|||+.-...|
T Consensus        48 E~~lf~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmAS~elk~~  111 (120)
T 2dme_A           48 EKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAW  111 (120)
T ss_dssp             HHHHHHHHCSCSHHHHHHHHHHTHHHHSSSCCSHHHHHHHTSSCTTHHHHSCTTTTTTCCSTTT
T ss_pred             HHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHH
Confidence            999999998888899999999999998  79999999999999999999999999999887776

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A

Probab=99.88  E-value=4.2e-23  Score=193.95  Aligned_cols=93  Identities=17%  Similarity=0.283  Sum_probs=82.7

Q ss_pred             ccChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHHH
Q 011389          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTAL  425 (487)
Q Consensus       346 ~tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~i  425 (487)
                      +|||++||+|+++||+||+..++++                                            |..++.+|.+|
T Consensus        12 ~~~d~vRdk~~~lL~~aL~~~~~~~--------------------------------------------~~~~~~~A~~I   47 (178)
T 3po3_S           12 IYHHKLRDQVLKALYDVLAKESEHP--------------------------------------------PQSILHTAKAI   47 (178)
T ss_dssp             ---CHHHHHHHHHHHHHTTSSSSCS--------------------------------------------TTHHHHHHHHH
T ss_pred             cCCChHHHHHHHHHHHHHhcCCCCc--------------------------------------------hhhHHHHHHHH
Confidence            6999999999999999999876544                                            55889999999


Q ss_pred             HHHHHHhcCC-ChH-HHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCC
Q 011389          426 EKASHDTLSL-DFQ-KYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVL  482 (487)
Q Consensus       426 E~a~~~~~~~-~~~-~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~  482 (487)
                      |.+||..+++ ++. +|++|+|||+||||  +||+||++||+|+|+|.+||+||++|||+.
T Consensus        48 E~~if~~~~~~~~~k~Yk~k~Rsl~~NLKd~~N~~Lr~~vl~g~isp~~lv~Ms~eElas~  108 (178)
T 3po3_S           48 ESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPA  108 (178)
T ss_dssp             HHHHHHHTSCSSSSTHHHHHHHHHHHHHHSSSCSHHHHHHHHCCCTTHHHHCCTTTTSSCS
T ss_pred             HHHHHHHhcCCCchhhhhhhhhHHHHHcCCCCCHHHHHHHhcCCCCHHHHHhcCchhhCCH
Confidence            9999999986 344 89999999999998  799999999999999999999999999985

>4dov_A ORC1, origin recognition complex subunit 1; DNA replication, replication; 1.70A {Mus musculus} PDB: 4dow_A*

Probab=99.83  E-value=9.9e-20  Score=168.02  Aligned_cols=140  Identities=22%  Similarity=0.279  Sum_probs=110.5

Q ss_pred             cccccceeecCCCCCcceeeeEEEE--cC---eEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCC---CCceEEEEEEeec
Q 011389          102 KPVGELVRFSGKGRGRRSHYEAFEF--DG---NKYELEDPVLLTPEDTNQKPYVAIIKEITQSK---DGSMMVTGQWFYR  173 (487)
Q Consensus       102 ~~iG~pvk~~gKG~~~R~~Y~sf~~--dG---~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~---dG~~~VrVqWFYR  173 (487)
                      .|+|.|+ ...|  ..-.+|+++.+  +|   .++++||||+|.+++ ...||||+|+.|+++.   ...+.++||||||
T Consensus         8 sW~g~~l-~drk--l~~~~Y~~~~v~~~~~~~~~i~vGd~VLI~~~D-~~~PyVAki~~lye~~~e~~~~k~A~VQWy~R   83 (163)
T 4dov_A            8 SWVGRPL-PNRK--QFQQMYREICMKINDGSEIHIKVGQFVLIQGED-NKKPYVAKLIELFQNGAEVPPKKCARVQWFVR   83 (163)
T ss_dssp             EEESCCC-CCCC--TTEEEESEEEEECTTSCEEEEETTCEEEECCSS-SSCCEEEEEEEEEEETTSSSCEEEEEEEEEEE
T ss_pred             EEeccCc-CCCc--ccceeeeEEEEecCCCCCeEEeeCCEEEEeCCc-ccCChhHHHHHHHhccccCCCceEEEEEeeec
Confidence            5899998 3221  23568999988  56   899999999999887 4778999999999852   3468899999999


Q ss_pred             ccccCCCCCCCC--CCCCCCeeEeeCCcc---cccccccceecEEEEcCccccCCCC-CCCCceEEeeeeecCCcEEeec
Q 011389          174 PEEADRKGGGNW--LSRDTRELFYSFHRD---EVPAESVMHKCVVHFVPIHKQLPNR-KQHPGFIVQKVYDTVERKLWKL  247 (487)
Q Consensus       174 PeEt~~~~~g~~--~~~~~nELFlS~h~D---~iplesI~GKC~V~~~~ey~~lp~~-~~~~~F~Cr~vYD~~~kkl~~L  247 (487)
                      |+|++... .++  ...+.+|||+++|.+   .+++++|+|+|.|+....+..+|.. ....+||.+..+|..  +|.-|
T Consensus        84 ~~EiP~~k-~~l~g~~~~~qEIF~~d~~~~d~~I~aeTIi~~c~V~~~~~~e~~p~~~~~e~t~FvklsWd~k--~f~pl  160 (163)
T 4dov_A           84 FLEIPVSK-RHLLGRSPPAQEIFWYDCSDWDNKINVETIIGPVQVVALAPEEVIPVDQKSEETLFVKLSWNKK--DFAPL  160 (163)
T ss_dssp             GGGSCTTT-GGGGCSCCCTTEEEEECCSCSCCEEEGGGEEEEEEEEECCTTCCCCSSCCCCSEEEEEEEECSS--CEEEC
T ss_pred             hhhccccc-hhhccCCCCCCeEEEecCCCCcccccHHHeeeceEEEEcCCccccCCCcccceEEEEEEEecCC--cceeC
Confidence            99998522 111  114689999999874   7899999999999999999999844 557899999999964  34444


Q ss_pred             C
Q 011389          248 T  248 (487)
Q Consensus       248 ~  248 (487)
                      +
T Consensus       161 ~  161 (163)
T 4dov_A          161 P  161 (163)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A*

Probab=99.79  E-value=2.6e-19  Score=204.12  Aligned_cols=133  Identities=21%  Similarity=0.284  Sum_probs=110.3

Q ss_pred             cceeeeEEEEcCeEEeeCCeEEEcCCC-----------------------------------------CCCCCeEEEEeE
Q 011389          117 RRSHYEAFEFDGNKYELEDPVLLTPED-----------------------------------------TNQKPYVAIIKE  155 (487)
Q Consensus       117 ~R~~Y~sf~~dG~~YrVGD~VyV~~e~-----------------------------------------~~~~pyIArI~~  155 (487)
                      ++.+|.+|.++|.+|++||||||.|+.                                         ...|++||+|++
T Consensus       321 ~~~~~~~~~~~g~~y~vgD~Vyl~p~~~~f~~~~~~~~~~~~~~~vd~~~ype~yrk~~~~~kg~n~~~~~P~~IgrI~~  400 (1002)
T 3swr_A          321 SRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKE  400 (1002)
T ss_dssp             SCEEESEEEETTEEEETTCEEEECTTSCCCSSCCCCCCCCSCSCCCCTTTCTTSGGGHHHHHTCCCCCCCCCCEEEEEEE
T ss_pred             CcEEEEEEEECCEEEecCCEEEECCcccccccccccccccccccccccccchhhhhccchhccccccCCCCCceeeEEeE
Confidence            478999999999999999999999832                                         134778999999


Q ss_pred             EeeCCCCc-------eEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCC---CC
Q 011389          156 ITQSKDGS-------MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP---NR  225 (487)
Q Consensus       156 I~e~~dG~-------~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp---~~  225 (487)
                      ||....+.       ++|+|+|||||+||++... ...+++.||||+|+|.+++|+.+|+|||.|++..++....   ..
T Consensus       401 i~~~~~~~~~~~~~~~~v~v~~fyRPed~~~~~~-~~~~~D~~elf~S~~~~~~~~~~i~GkC~V~~~~d~~~~~~~~~~  479 (1002)
T 3swr_A          401 IFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTP-ASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSM  479 (1002)
T ss_dssp             EEECCCSSSSCCSSCCEEEEEECBCGGGSTTCGG-GGSSSCTTEEEECCCEEEEEGGGCCEEEEEEEGGGCSSCHHHHHH
T ss_pred             EEecCCccccCCCccEEEEEEEEECccccccccc-ccccCCcceEEEecceeccCHHHcceEEEEEEeccccccchhhcc
Confidence            99766544       9999999999999985432 2345689999999999999999999999999998876432   11


Q ss_pred             CCCCceEEeeeeecCCcEEeecCCc
Q 011389          226 KQHPGFIVQKVYDTVERKLWKLTDK  250 (487)
Q Consensus       226 ~~~~~F~Cr~vYD~~~kkl~~L~dk  250 (487)
                      ..++.|||..+||..++.|..++..
T Consensus       480 ~~p~~fyf~~~Yd~~~~~f~~~p~~  504 (1002)
T 3swr_A          480 GGPNRFYFLEAYNAKSKSFEDPPNH  504 (1002)
T ss_dssp             TSSSEEEEEEEEETTTTEEECCCST
T ss_pred             CCCCeEEEEEEEeCCCCeeecCccc
Confidence            2458899999999999999887643

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A

Probab=99.79  E-value=9.8e-20  Score=184.00  Aligned_cols=95  Identities=19%  Similarity=0.296  Sum_probs=84.7

Q ss_pred             cccChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHH
Q 011389          345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA  424 (487)
Q Consensus       345 ~~tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~  424 (487)
                      ..|||.+||+|+++|+++|+...++.                                            |.++..+|.+
T Consensus       142 ~~~~d~~R~k~r~~L~~aL~~~~~~~--------------------------------------------~~~~~~~A~~  177 (309)
T 1pqv_S          142 AIYHHKLRDQVLKALYDVLAKESEHP--------------------------------------------PQSILHTAKA  177 (309)
T ss_pred             CcCChHHHHHHHHHHHHHHhcCCCcc--------------------------------------------chhHHHHHHH
Confidence            35899999999999999998653322                                            3477899999


Q ss_pred             HHHHHHHhcCCChHH--HHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCCC
Q 011389          425 LEKASHDTLSLDFQK--YNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVLY  483 (487)
Q Consensus       425 iE~a~~~~~~~~~~~--Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~~  483 (487)
                      ||.+||..|++++.+  |++|||||+||||  +||.||++||+|+|+|++||+||++|||+..
T Consensus       178 IE~al~~~~~~~~~~~~Yk~k~Rsl~~NLKd~~N~~Lr~~vl~g~i~p~~lv~Ms~eElasde  240 (309)
T 1pqv_S          178 IESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAP  240 (309)
T ss_pred             HHHHHHHHhCCCchhHHHHHHHHHHHHHcCcCCChHHHHHHHcCCCCHHHHhcCCHHHhCCHH
Confidence            999999999877666  9999999999998  7999999999999999999999999999863

>4ft4_B DNA (cytosine-5)-methyltransferase 1; chromodomain, BAH domain, DNA methyltransferase domain, H3K9 binding, methylation, transferase; HET: DNA MLY SAH; 2.70A {Zea mays} PDB: 4ft2_A* 4fsx_A*

Probab=99.79  E-value=1.2e-19  Score=201.43  Aligned_cols=132  Identities=19%  Similarity=0.316  Sum_probs=107.8

Q ss_pred             cceeeeEEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccCCCC----CCCCCCCCCCe
Q 011389          117 RRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKG----GGNWLSRDTRE  192 (487)
Q Consensus       117 ~R~~Y~sf~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~----~g~~~~~~~nE  192 (487)
                      .|+||.++.++|+.|+|||||||+.+. +.++|||+|.+||++.+|..+|+|+|||||+||+...    ...-..++.||
T Consensus        44 ~~~~~~~~~~~~~~~~~~d~~~v~~~~-~~~~~i~~i~~~~~~~~~~~~~~~~~~~r~~d~~~~~~~~~~~~~~~~d~~~  122 (784)
T 4ft4_B           44 ARCHYRSAKVDNVVYCLGDDVYVKAGE-NEADYIGRITEFFEGTDQCHYFTCRWFFRAEDTVINSLVSISVDGHKHDPRR  122 (784)
T ss_dssp             EEEECSEEEETTEEEETTCEEEECCST-TSCCEEEEEEEEEEETTSCEEEEEEEEEEGGGSTTGGGGGCCBTTBCCCTTB
T ss_pred             cceeeeeeeECCEEEeCCCeEEEeCCC-CCCCEEEEEEEEEEcCCCCEEEEEEEeeChhhhcccccccccccccccccce
Confidence            489999999999999999999999865 6789999999999999999999999999999997522    11123468999


Q ss_pred             eEeeCCcccccccccceecEEEEcCccccCCC---CCCCCceEEeeeeecCCcEEeecCC
Q 011389          193 LFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN---RKQHPGFIVQKVYDTVERKLWKLTD  249 (487)
Q Consensus       193 LFlS~h~D~iplesI~GKC~V~~~~ey~~lp~---~~~~~~F~Cr~vYD~~~kkl~~L~d  249 (487)
                      ||+|++++++++++|+|||+|+++....+++.   ......|||.+.|.....++-.++.
T Consensus       123 ~~~s~~~~~~~~~~i~~k~~v~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~  182 (784)
T 4ft4_B          123 VFLSEEKNDNVLDCIISKVKIVHVDPNMDPKAKAQLIESCDLYYDMSYSVAYSTFANISS  182 (784)
T ss_dssp             EEEEEEEEEEEGGGEEEECCEEECCTTSCHHHHHHHHHHCSEEESEEEETGGGEEEEC--
T ss_pred             EEEeCcEEEechHHeeeeEEEEeeCccccchhhhhccCCcceEeccccCccccCccCCCc
Confidence            99999999999999999999999876555431   1113469999999877776666543

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A*

Probab=99.76  E-value=1e-18  Score=203.59  Aligned_cols=133  Identities=23%  Similarity=0.309  Sum_probs=109.8

Q ss_pred             cceeeeEEEEcCeEEeeCCeEEEcCCC-----------------------------------------CCCCCeEEEEeE
Q 011389          117 RRSHYEAFEFDGNKYELEDPVLLTPED-----------------------------------------TNQKPYVAIIKE  155 (487)
Q Consensus       117 ~R~~Y~sf~~dG~~YrVGD~VyV~~e~-----------------------------------------~~~~pyIArI~~  155 (487)
                      ++.+|.+|.++|.+|++||||||.|+.                                         ...|++||+|.+
T Consensus       633 ~~~~Y~~~~~~g~~Y~vgD~Vyl~p~~f~~~~~~~~~~~~~~~~~~~~~~ype~yrk~~~~~kg~~~~~~~Py~IgqI~e  712 (1330)
T 3av4_A          633 GRVYCSSITKNGVVYRLGDSVYLPPEAFTFNIKVASPVKRPKKDPVNETLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKE  712 (1330)
T ss_dssp             SSEEEEEEEETTEEEETTCEEEECTTSCCCCCCC-------CCCCCCTTTCSSGGGGGC-------CCCCCCCEEEEEEE
T ss_pred             CceeeeEEEECCEEEecCCEEEECcccccccccccccccccccccccccccchhhhcccccccccccCCCCCceEEEEEE
Confidence            478999999999999999999998761                                         135568999999


Q ss_pred             EeeCCC------CceEEEEEEeecccccCCCCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccC--C-CCC
Q 011389          156 ITQSKD------GSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQL--P-NRK  226 (487)
Q Consensus       156 I~e~~d------G~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~l--p-~~~  226 (487)
                      ||.+.+      +..+|+|+|||||+||.+...+ ....+.||||+|++.+++|+++|.|||.|++..++...  + ...
T Consensus       713 I~~~~~s~~~~~~~~~vrV~wFyRPedt~~~~~~-~~~~D~nELf~S~~~~~vp~~~I~GKC~V~~~~d~~~~i~~y~~~  791 (1330)
T 3av4_A          713 IHCGKKKGKVNEADIKLRLYKFYRPENTHRSYNG-SYHTDINMLYWSDEEAVVNFSDVQGRCTVEYGEDLLESIQDYSQG  791 (1330)
T ss_dssp             CCCCEETTEECSSCCEEEEEEEECTTTSTTGGGT-TTTSCTTBCEEEEEEEEEEGGGCCEEEEEEESTTCSSCHHHHHHT
T ss_pred             EEecCCccccCCCceEEEEEEeeChhhccccccc-ccccCcceEEeeccceecCHHHcCceEEEEecccccccccccccC
Confidence            997654      5799999999999999864322 23469999999999999999999999999999887663  1 122


Q ss_pred             CCCceEEeeeeecCCcEEeecCCc
Q 011389          227 QHPGFIVQKVYDTVERKLWKLTDK  250 (487)
Q Consensus       227 ~~~~F~Cr~vYD~~~kkl~~L~dk  250 (487)
                      .++.|||+..||..++.|-.+|..
T Consensus       792 g~d~Fy~~~~Yd~~~k~~~~~P~~  815 (1330)
T 3av4_A          792 GPDRFYFLEAYNSKTKNFEDPPNH  815 (1330)
T ss_dssp             STTEEEESCEEETTTTEEECCCGG
T ss_pred             CCCeEEEEEEecccCCeeccCchH
Confidence            468999999999999988765443

>2fl7_A Regulatory protein SIR3; ORC, silencing, chromatin, transcription; 1.85A {Saccharomyces cerevisiae} PDB: 2fvu_A 3tu4_K*

Probab=99.28  E-value=2.8e-12  Score=124.55  Aligned_cols=125  Identities=12%  Similarity=0.106  Sum_probs=93.5

Q ss_pred             cCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCC-CCceEEEEEEeecccccCC-------CCC-----CCCCC------
Q 011389          127 DGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK-DGSMMVTGQWFYRPEEADR-------KGG-----GNWLS------  187 (487)
Q Consensus       127 dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~-dG~~~VrVqWFYRPeEt~~-------~~~-----g~~~~------  187 (487)
                      ||+.|++||+|.|..+. .+.+.|+.|..|.-+. +..+.+.|.||+|..|+..       .+.     +...+      
T Consensus        49 Dg~~~~~GDsVlv~~~~-~~sysv~LI~eIrl~t~~n~vei~v~wylR~~Ei~~~~~~~~~~P~~~~~~~~~~~~~~~~~  127 (232)
T 2fl7_A           49 DGLSFGKGESVIFNDNV-TETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFF  127 (232)
T ss_dssp             TCCEECTTCEEEEEETT-TTEEEEEEEEEEEC-----CCEEEEEEEECGGGSCHHHHHHHHCHHHHHTTCCHHHHHHHHH
T ss_pred             CCcEEeCCCEEEEecCC-CCceEEEEEEEEEecCCCceEEEEEEEeecHHHcCchhhhhhcCchhcccccchhhhhhhhh
Confidence            89999999999998754 4566788888887665 5678999999999999964       111     00112      


Q ss_pred             --CCCCeeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEeecCCcch
Q 011389          188 --RDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLTDKDY  252 (487)
Q Consensus       188 --~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp-~~~~~~~F~Cr~vYD~~~kkl~~L~dkdy  252 (487)
                        ...||||+|.+.+.|-+.+|+++|+|+...+|.++. +.....+||||++||+....|..+.-.++
T Consensus       128 ~~~~~nELflTa~l~eI~l~diI~~anVls~~Ef~~l~~d~~~~~tFf~R~~cd~~~~~f~~iD~~~~  195 (232)
T 2fl7_A          128 NEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQI  195 (232)
T ss_dssp             HHSCTTEEEEEEEEEEECGGGEEEECEEECTTTC-------CTTTEEEEEEECCTTSCSCEECCHHHH
T ss_pred             cccccceEEEeccHHHHHHHhhhhheEeccHHHHHHhcccccCCceEEEEEEEcCCcCccccccHHHH
Confidence              589999999999999999999999999999999763 23346899999999997776765543444

>1m4z_A Origin recognition complex subunit 1; DNA replication, transcriptional silencing, chromatin, BAH D gene regulation; 2.20A {Saccharomyces cerevisiae} SCOP: b.34.12.1 PDB: 1zhi_A 1zbx_A

Probab=99.28  E-value=1.5e-12  Score=126.76  Aligned_cols=126  Identities=17%  Similarity=0.151  Sum_probs=99.7

Q ss_pred             cCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCC-CCceEEEEEEeecccccCC-------CCC-----CCCCC------
Q 011389          127 DGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK-DGSMMVTGQWFYRPEEADR-------KGG-----GNWLS------  187 (487)
Q Consensus       127 dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~-dG~~~VrVqWFYRPeEt~~-------~~~-----g~~~~------  187 (487)
                      ||+.|++||+|.|..+. .+.+.|+.|..|.-+. +..+.+.|.||+|..|+..       .+.     +...+      
T Consensus        49 Dg~~~~~GDsVlv~~~~-~~sysv~LI~eIrl~t~~n~vei~v~wylR~~Ei~~~~~~~~~~P~~~~~~~~~~~~~~~~~  127 (238)
T 1m4z_A           49 DGIKLGRGDSVVMHNEA-AGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFS  127 (238)
T ss_dssp             TCCEECTTCEEEEEETT-TTEEEEEEEEEEEEETTTTEEEEEEEEEECGGGSCHHHHHHHHCHHHHHSCCCHHHHHHHHH
T ss_pred             CCcEEeCCCEEEEecCC-CCceEEEEEEEEEecCCCceEEEEEEEeecHHHcCchhhhhhcCchhcccccchhhhhhhhh
Confidence            89999999999998754 4566788888887665 5678999999999999964       111     00112      


Q ss_pred             --CCCCeeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEeecCCcchh
Q 011389          188 --RDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLTDKDYE  253 (487)
Q Consensus       188 --~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp-~~~~~~~F~Cr~vYD~~~kkl~~L~dkdy~  253 (487)
                        ...||||+|.+.+.|-+.+|+++|+|+...+|.++. +.....+||||++||+....|..+.-.++.
T Consensus       128 ~~~~~nELflTa~l~eI~l~diI~~anVls~~Ef~~i~~d~~~~~tFf~R~~cd~~~~~f~~iD~~~~~  196 (238)
T 1m4z_A          128 ETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVK  196 (238)
T ss_dssp             HHSCTTEEEEEEEEEEECGGGEEEEEEEECHHHHHHHGGGCCTTTEEEEEEECCTTSCCCEECCHHHHH
T ss_pred             cccccceEEEeccHHHHhHHhhhhheEeccHHHHhhhccccccCceEEEEEEEcCCcCccccccHHHHH
Confidence              589999999999999999999999999999998763 224468999999999987777665444443

---

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	487
d1m4za_	217	b.34.12.1 (A:) Origin-recognition complex protein	2e-17
d1enwa_	114	a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak	7e-07

>d1m4za_ b.34.12.1 (A:) Origin-recognition complex protein 120kDa subunit, Orc1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 217

class: All beta proteins
fold: SH3-like barrel
superfamily: BAH domain
family: BAH domain
domain: Origin-recognition complex protein 120kDa subunit, Orc1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 78.8 bits (194), Expect = 2e-17
 Identities = 24/198 (12%), Positives = 49/198 (24%), Gaps = 32/198 (16%)

Query: 99  EDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQ 158
           E    +    +   +   +  HY     DG K    D V++  E       V +I+E+  
Sbjct: 21  EQGNIIDGGQKRLRRRGAKTEHYLKRSSDGIKLGRGDSVVMHNEAAG-TYSVYMIQELRL 79

Query: 159 S-----------------------KDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFY 195
           +                                    RP            + +  EL+ 
Sbjct: 80  NTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLN--YYNKLFSETANKNELYL 137

Query: 196 SFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPG-FIVQKVYDTVERKL-----WKLTD 249
           +    E+   + +    V      + L         F V+ + +    K        +  
Sbjct: 138 TAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKA 197

Query: 250 KDYEDNKQHEIDLLVQKT 267
              +   +   + L   T
Sbjct: 198 YIKKVEPREAQEYLKDLT 215

>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 114

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: Elongation factor TFIIS domain 2
family: Elongation factor TFIIS domain 2
domain: Elongation factor TFIIS domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.6 bits (108), Expect = 7e-07
 Identities = 11/69 (15%), Positives = 26/69 (37%), Gaps = 4/69 (5%)

Query: 415 PDTAIAAVTALEKASHDTL--SLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSK 470
           P + +    A+E   +       +   Y  + R +  N+   +   L  ++ NG++ P  
Sbjct: 42  PQSILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEF 101

Query: 471 ILNMSPNEL 479
           +      +L
Sbjct: 102 LATCDAKDL 110

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	487
d1enwa_	114	Elongation factor TFIIS domain 2 {Baker's yeast (S	99.86
d1m4za_	217	Origin-recognition complex protein 120kDa subunit,	99.68

>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: Elongation factor TFIIS domain 2
family: Elongation factor TFIIS domain 2
domain: Elongation factor TFIIS domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=3.8e-23  Score=179.43  Aligned_cols=94  Identities=19%  Similarity=0.295  Sum_probs=84.8

Q ss_pred             cccChhHHHHHHHHHHHHHhhhhcCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCChhHHHHHHHH
Q 011389          345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA  424 (487)
Q Consensus       345 ~~tgd~~RDk~le~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~v~~~a~~  424 (487)
                      .+|+|.+||+|+++|+++|+....++                                            ++.++.+|.+
T Consensus        16 ~~~~d~~R~~~~~~L~~aL~~~~~~~--------------------------------------------~~~~~~la~~   51 (114)
T d1enwa_          16 AIYHHKLRDQVLKALYDVLAKESEHP--------------------------------------------PQSILHTAKA   51 (114)
T ss_dssp             CSSTTTTHHHHHHHHHHHHHHHCSSS--------------------------------------------CSCHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhCcCccc--------------------------------------------hhHHHHHHHH
Confidence            57999999999999999998765444                                            5578899999


Q ss_pred             HHHHHHHhcCCC--hHHHHHHHHHHHHhcc--CCHHHHhhhhcCCCCccccccCChhhcCCC
Q 011389          425 LEKASHDTLSLD--FQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKVL  482 (487)
Q Consensus       425 iE~a~~~~~~~~--~~~Yk~K~Rsl~fNLK--~Np~Lr~rvl~Gei~p~~l~~Mt~~Ema~~  482 (487)
                      ||.++|..|+..  ..+|++|+|||+||||  +||+||++|++|+|+|++|+.||++|||+.
T Consensus        52 IE~~lf~~~~~~~~~~~Y~~k~rsi~~NLkd~~N~~L~~~v~~g~i~p~~l~~M~~~ElaP~  113 (114)
T d1enwa_          52 IESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPA  113 (114)
T ss_dssp             HTTTTTSSCTTTTTHHHHHHHHHHHHHHHTTSCCCCTTTHHHHCSSCCSSHHHHTTTTTCSC
T ss_pred             HHHHHHHHhcccCCcHHHHHHHHHHHHHcCccchHHHHHHHHcCCCCHHHHhCCCHHHcCCC
Confidence            999999998753  4589999999999998  799999999999999999999999999985

>d1m4za_ b.34.12.1 (A:) Origin-recognition complex protein 120kDa subunit, Orc1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: SH3-like barrel
superfamily: BAH domain
family: BAH domain
domain: Origin-recognition complex protein 120kDa subunit, Orc1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.68  E-value=1.3e-18  Score=165.77  Aligned_cols=135  Identities=16%  Similarity=0.126  Sum_probs=101.2

Q ss_pred             CCCCcceeeeEEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCC-ceEEEEEEeecccccCCCC----------
Q 011389          113 KGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDG-SMMVTGQWFYRPEEADRKG----------  181 (487)
Q Consensus       113 KG~~~R~~Y~sf~~dG~~YrVGD~VyV~~e~~~~~pyIArI~~I~e~~dG-~~~VrVqWFYRPeEt~~~~----------  181 (487)
                      ++++...+|-....||.+|++||+|||.++. +.++|||+|.+|..+..+ ...+-+.||+|..|..-..          
T Consensus        35 r~~~~~~~~~~r~~D~~e~~~GD~Vlvk~~~-~~~~~v~iI~ei~~~~~~~~~e~~~~~~lr~~e~~~~~~~~~~~~~~~  113 (217)
T d1m4za_          35 RRGAKTEHYLKRSSDGIKLGRGDSVVMHNEA-AGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDAN  113 (217)
T ss_dssp             -----CEEEEEETTTCCEECTTCEEEEEETT-TTEEEEEEEEEEEEETTTTEEEEEEEEEECGGGSCHHHHHHHHCHHHH
T ss_pred             cCCCCCcEEEEEecCCeEEecCCEEEEeCCC-CCCceEEEEeeeccCcccchheeeeecccchhhhccchhhhhccccee
Confidence            3444455666666799999999999999775 578899999999877654 4566666676666643100          


Q ss_pred             ----------CCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEeecC
Q 011389          182 ----------GGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLT  248 (487)
Q Consensus       182 ----------~g~~~~~~~nELFlS~h~D~iplesI~GKC~V~~~~ey~~lp-~~~~~~~F~Cr~vYD~~~kkl~~L~  248 (487)
                                .+......+||||+|++++++++++|+|||+|++..+|..+. .....++|||+++||+..++|..+.
T Consensus       114 w~~~p~e~~~~k~r~~~~~~ElflT~~~d~i~~~~I~~k~~V~s~~ef~~~~~~~~~~~~F~cr~~~D~~~~~f~~id  191 (217)
T d1m4za_         114 ILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDIN  191 (217)
T ss_dssp             HSCCCHHHHHHHHHHHSCTTEEEEEEEEEEECGGGEEEEEEEECHHHHHHHGGGCCTTTEEEEEEECCTTSCCCEECC
T ss_pred             eecCchhhhhhccccccCcceeEecCccceeehhheeeeEEEecHHHhcchhhccCCCCeEEEEEEEcCCCCceeecc
Confidence                      111123578999999999999999999999999999986543 2345789999999999999998764