Citrus Sinensis ID: 011020

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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-------490-----
Protein Sequence
MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLLSLPTCQPFLSGRLQG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccEEEEccEEEEEccEEEEcccccccccEEEEEEEEEEcccccEEEEEEEEEccccccccccccccccccccEEEcccccccccccccccEEEEEcccccccccccccccEEEEEEEEccccEEEEccccccccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEccccccccccccEEEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEccccccccccccccccccccccccccHHHHHHHEEccHHHcccccHHHHHHHHcccccccccHHHHHHHHcccccHHHHHHHHcccccccccccccccccccccccccEEEEEEEEcccEEEEccEEEEEccccccccEEEEEEEEEEcccccEEEEEEEEEcHHHHHHHcccccccccccEEEEccccccccHHHEcccEEEEEEcccEEcccccccccEEEEEEEcccccEEEEccccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEcccccccccccccHEEHHccccccccccccccc
Coil and Loop (DISEMBL)
mgnrrfaqvstsdededvpppssrtrkseeNKEQQSLRQSKRKRIklqeeedyeepeeERKASKRerrdkgkvreaekprndgvedeeeeeeeeeqpqedakpvgelvrfsgkgrgrrshyeafefdgnkyeledpvlltpedtnqkpYVAIIKEITqskdgsmmvtgqwfyrpeeadrkgggnwlsrdtRELFYSfhrdevpaesvmHKCVVHfvpihkqlpnrkqhpgfiVQKVYDTVERKLWKltdkdyednKQHEIDLLVQKTQarlgdlpdiepeetAAREQEDQLKAKRSLRkknispldvsreedsttrsdqyvkaetpgsctsnaSEYYNILSKFKALTGETHRDKWLERLLQGLQYICNsadsihadqngkggckgvdhesedksvgtengsrekgqkngksfiwpdTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLkrawvgpglfclsscpgphvrsptrafllslptcqpflsgrlqg
Flexible Loop (DISEMBL)
mgnrrfaqvstsdededvpppssrtrkseenkeqqslrqskrkriklqeeedyeepeeerkaskrerrdkgkvreaekprndgvedeeeeeeeeeqpqedakpvgelvrfsgkgrgrrshyeafefdgnkyeLEDPVLLtpedtnqkpyVAIIKEitqskdgsmmVTGQWFYRpeeadrkgggnwlsRDTRELFYSFHRDEVPAESVMHKCVVHFVPIhkqlpnrkqhpgfiVQKVYDTVERKLWKLtdkdyednkqHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLkakrslrkknispldvsreedsttrsdqyvkaetpgsctsnaSEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDhesedksvgtengsrekgqkngksfiwPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLlslptcqpflsgrlqg
Low Complexity Region (SEG)
MGNRRFAQVSTSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQeeedyeepeeerkaskrerrdkGKVREAEKPRNDGVedeeeeeeeeeqpqedAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLLSLPTCQPFLSGRLQG
Disordered region (IsUnstruct)
************************************************************************************************************************YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLV*********************************************************************SEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSI*************************************SFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLLSLPTCQPF*******
Disordered Region (DISOPRED)
*********************************************************************************************************************RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQ******************************************************************NASEYYNILSKFKALTGETHRDKWLERLLQGLQYI***********************************************WPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLLSLPTCQPFLSGRL**
Disordered Region (DISEMBL)
******************************************************************************************************PVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPE****************LRKKNIS************************SCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQN*****************************NGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLLSLPTCQPFLSGRLQG
Disordered Region (DISPRO)
*******************************************R*KLQ*******************************************************************GRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPD***************K**RSLRKKNISPLDV*****************TPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNS****************************************KSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLLSLPTCQPFLS*****
Transmembrane Helix (TMHMM)
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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)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGNRRFAQVSTSDEDEDVPPPSSRTRKSExxxxxxxxxxxxxxxxxxxxxxDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLLSLPTCQPFLSGRLQG
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	495	2.2.26 [Sep-21-2011]
Q8BSQ9	1634	Protein polybromo-1 OS=Mu	yes	no	0.270	0.082	0.256	5e-08
Q86U86	1689	Protein polybromo-1 OS=Ho	no	no	0.208	0.060	0.283	6e-08
Q90941	1633	Protein polybromo-1 OS=Ga	yes	no	0.193	0.058	0.292	7e-08
Q3UHR0	2643	BAH and coiled-coil domai	no	no	0.197	0.037	0.287	0.0001
P53236	928	Chromatin structure-remod	yes	no	0.276	0.147	0.283	0.0003
Q9P281	2608	BAH and coiled-coil domai	no	no	0.197	0.037	0.277	0.0008

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

 Score = 59.7 bits (143), Expect = 5e-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  FYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQL--PNRKQH 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 = 59.3 bits (142), Expect = 6e-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 = 7e-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 = 48.5 bits (114), Expect = 1e-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)

>sp|Q9P281|BAHC1_HUMAN BAH and coiled-coil domain-containing protein 1 OS=Homo sapiens GN=BAHCC1 PE=1 SV=3

 Score = 45.8 bits (107), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 113  KGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFY 172
            KG+ R+  Y+A         + D  +         PY+  I+ + +S   +M+V  +WFY
Sbjct: 2466 KGKARKLFYKAIVRGEETLRVGDCAVFLSAGRPNLPYIGRIESMWESWGSNMVVKVKWFY 2525

Query: 173  RPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVV 213
             PEE      G         L+ S H DE   +++ HKC V
Sbjct: 2526 HPEETKL---GKRQCDGKNALYQSCHEDENDVQTISHKCQV 2563

Homo sapiens (taxid: 9606)

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	495
224058512	611	predicted protein [Populus trichocarpa]	0.892	0.723	0.696	1e-166
224071890	607	predicted protein [Populus trichocarpa]	0.872	0.711	0.686	1e-166
225426420	595	PREDICTED: uncharacterized protein LOC10	0.842	0.700	0.637	1e-163
449452318	610	PREDICTED: uncharacterized protein LOC10	0.886	0.719	0.650	1e-159
297742521	1085	unnamed protein product [Vitis vinifera]	0.725	0.330	0.733	1e-158
449528690	467	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.886	0.940	0.648	1e-158
359474210	584	PREDICTED: uncharacterized protein LOC10	0.820	0.695	0.621	1e-156
356528332	605	PREDICTED: uncharacterized protein LOC10	0.864	0.707	0.657	1e-151
356513389	571	PREDICTED: uncharacterized protein LOC10	0.711	0.616	0.721	1e-147
356528334	596	PREDICTED: uncharacterized protein LOC10	0.846	0.703	0.653	1e-146

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

 Score =  590 bits (1521), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 317/455 (69%), Positives = 363/455 (79%), Gaps = 13/455 (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 AIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
           A+ AV+ALEKASHD LS DFQKYNQKLRQL+FNLK
Sbjct: 411 AVPAVSALEKASHDALSSDFQKYNQKLRQLVFNLK 445

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 =  590 bits (1520), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 313/456 (68%), Positives = 354/456 (77%), Gaps = 24/456 (5%)

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 TAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
            A+ AV+ALEKASHD LS DFQKYNQKLRQL FNLK
Sbjct: 401 AAVPAVSALEKASHDALSSDFQKYNQKLRQLAFNLK 436

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 =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 288/452 (63%), Positives = 345/452 (76%), Gaps = 35/452 (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 AVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
           AVTALE+AS D  S DFQKYNQK+RQL+FNLK
Sbjct: 386 AVTALEQASQDAFSSDFQKYNQKMRQLVFNLK 417

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 =  566 bits (1460), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 294/452 (65%), Positives = 365/452 (80%), Gaps = 13/452 (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 AVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
           A+TALEK S+D LS DFQKYNQK+RQL+FNLK
Sbjct: 408 AITALEKVSNDALSADFQKYNQKMRQLVFNLK 439

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 =  563 bits (1451), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 264/360 (73%), Positives = 307/360 (85%), Gaps = 1/360 (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

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 =  563 bits (1451), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 293/452 (64%), Positives = 364/452 (80%), Gaps = 13/452 (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 AVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
           A+TALEK S+D LS DFQKYNQK+RQL+FNLK
Sbjct: 408 AITALEKVSNDALSADFQKYNQKMRQLVFNLK 439

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 =  558 bits (1437), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 281/452 (62%), Positives = 338/452 (74%), Gaps = 46/452 (10%)

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 AVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
           AVTALE+AS D  S DFQKYNQK+RQL+FNLK
Sbjct: 375 AVTALEQASQDAFSSDFQKYNQKMRQLVFNLK 406

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 =  541 bits (1394), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 302/459 (65%), Positives = 355/459 (77%), Gaps = 31/459 (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 WPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
           WPD A+ AV ALEKASHDTLS D+QKYNQKLRQL+FNLK
Sbjct: 397 WPDDAVPAVVALEKASHDTLSSDYQKYNQKLRQLVFNLK 435

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 =  526 bits (1356), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 257/356 (72%), Positives = 296/356 (83%), Gaps = 4/356 (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 TENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
           + N   E   K+ K F+WPD A+ AV ALEKASHDTLS D+QKYNQKLRQL+FNLK
Sbjct: 387 SAN---ECEDKSSKPFVWPDDAVPAVVALEKASHDTLSSDYQKYNQKLRQLVFNLK 439

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 =  525 bits (1353), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 300/459 (65%), Positives = 348/459 (75%), Gaps = 40/459 (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 WPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
               A+ AV ALEKASHDTLS D+QKYNQKLRQL+FNLK
Sbjct: 391 ---DAVPAVVALEKASHDTLSSDYQKYNQKLRQLVFNLK 426

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	495
TAIR|locus:2123136	587	AT4G11560 [Arabidopsis thalian	0.682	0.575	0.619	1.9e-121
TAIR|locus:2040209	380	AT2G25120 [Arabidopsis thalian	0.395	0.515	0.529	9.3e-67
TAIR|locus:2121601	360	AT4G23120 [Arabidopsis thalian	0.424	0.583	0.486	6.1e-58
TAIR|locus:2097134	380	AT3G43990 [Arabidopsis thalian	0.428	0.557	0.465	6.4e-57
TAIR|locus:2097915	1613	SUO "'shuttle' in chinese" [Ar	0.292	0.089	0.369	9.4e-20
TAIR|locus:2097925	1611	AT3G48060 [Arabidopsis thalian	0.292	0.090	0.369	1.5e-19
ZFIN|ZDB-GENE-010501-3	1648	pbrm1l "polybromo 1, like" [Da	0.256	0.077	0.305	8.4e-08
TAIR|locus:2120693	234	EBS "EARLY BOLTING IN SHORT DA	0.210	0.444	0.330	1.6e-07
UNIPROTKB|E1BNH8	1664	E1BNH8 "Uncharacterized protei	0.383	0.114	0.227	3.8e-07
UNIPROTKB|E7EVG2	1461	PBRM1 "Protein polybromo-1" [H	0.383	0.130	0.227	9e-07

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

 Score = 1124 (400.7 bits), Expect = 1.9e-121, Sum P(2) = 1.9e-121
 Identities = 218/352 (61%), Positives = 267/352 (75%)

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 SREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK 452
               EK       F+WPD A+  V ALE ASH +L+ DFQKYNQK+R L+FNLK
Sbjct:   394 KDEK-------FLWPDAAVPQVCALENASHASLASDFQKYNQKMRTLVFNLK 438

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:2121601 AT4G23120 [Arabidopsis thaliana (taxid:3702)]

 Score = 515 (186.3 bits), Expect = 6.1e-58, Sum P(2) = 6.1e-58
 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:2097134 AT3G43990 [Arabidopsis thaliana (taxid:3702)]

 Score = 509 (184.2 bits), Expect = 6.4e-57, Sum P(3) = 6.4e-57
 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:2097915 SUO "'shuttle' in chinese" [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 9.4e-20, Sum P(2) = 9.4e-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 = 1.5e-19, Sum P(2) = 1.5e-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 = 8.4e-08, P = 8.4e-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 = 3.8e-07, P = 3.8e-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 = 9.0e-07, P = 9.0e-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

Your Input: gw1.I.8957.1 hypothetical protein (586 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	495
cd04713	146	cd04713, BAH_plant_3, BAH, or Bromo Adjacent Homol	1e-79
smart00439	121	smart00439, BAH, Bromo adjacent homology domain	8e-22
cd04370	123	cd04370, BAH, BAH, or Bromo Adjacent Homology doma	4e-20
pfam01426	120	pfam01426, BAH, BAH domain	1e-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
cd04716	122	cd04716, BAH_plantDCM_I, BAH, or Bromo Adjacent Ho	4e-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	5e-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	0.002
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.004

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

 Score =  244 bits (625), Expect = 1e-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 = 90.4 bits (225), Expect = 8e-22
 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 = 85.5 bits (212), Expect = 4e-20
 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 = 84.3 bits (209), Expect = 1e-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|240067 cd04716, BAH_plantDCM_I, BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants

 Score = 42.8 bits (101), Expect = 4e-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 = 40.4 bits (95), 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 = 40.1 bits (94), 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 = 42.2 bits (99), Expect = 5e-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 = 40.6 bits (95), 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 = 40.9 bits (95), Expect = 0.002
 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

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 22/63 (34%), Positives = 37/63 (58%)

Query: 41  KRKRIKLQEEEDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQED 100
           K K+I  + E+  EE ++E+K      + K +  E EK + +  ++EEEEE EEE+ +E+
Sbjct: 411 KIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEE 470

Query: 101 AKP 103
            K 
Sbjct: 471 EKK 473

Length = 482

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	495
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
cd04717	121	BAH_polybromo BAH, or Bromo Adjacent Homology doma	99.94
cd04714	121	BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain,	99.94
cd04715	159	BAH_Orc1p_like BAH, or Bromo Adjacent Homology dom	99.94
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	99.93
cd04709	164	BAH_MTA BAH, or Bromo Adjacent Homology domain, as	99.92
cd04721	130	BAH_plant_1 BAH, or Bromo Adjacent Homology domain	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,	99.88
cd04760	124	BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain	99.88
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
cd04711	137	BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domai	99.74
KOG1827	629	consensus Chromatin remodeling complex RSC, subuni	99.54
KOG3554	693	consensus Histone deacetylase complex, MTA1 compon	99.07
PF07500	115	TFIIS_M: Transcription factor S-II (TFIIS), centra	98.26
smart00510	102	TFS2M Domain in the central regions of transcripti	98.08
TIGR01385	299	TFSII transcription elongation factor S-II. This m	97.43
COG5076	371	Transcription factor involved in chromatin remodel	94.21
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	80.65

>KOG1886 consensus BAH domain proteins [Transcription]

Probab=100.00  E-value=1.4e-48  Score=407.74  Aligned_cols=311  Identities=41%  Similarity=0.687  Sum_probs=283.5

Q ss_pred             hhhhhhccCCCCCccccccceeecCCCCCcceeeeEEEEcCEEEee-CCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceE
Q 011020           88 EEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYEL-EDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMM  165 (495)
Q Consensus        88 ~~~~~~~~~~~~~a~pIG~pVK~~GKGkk~R~~Y~Sf~~dG~~YkV-GD~VyV~~ed~~e~PyIArI~eIwedkd-G~~~  165 (495)
                      +...+.++++.++|.|+|...+..|+|..+++||.+|.+.|..|.. ||.|++.+++++.+||||+|..||.... +.+.
T Consensus         7 ~~~~~~~~~~~~~a~~~g~a~~~qGv~~~k~~h~~t~~~~~g~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k   86 (464)
T KOG1886|consen    7 EPKLKSELRPRDEASSMGDANKEQGVGGVKSLHFETFIYRGGRYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVK   86 (464)
T ss_pred             cccccccCCccchhhhhhhhhhhccccccccccccceeeccCcccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcc
Confidence            3455678899999999999999999999999999999999988888 9999999999999999999999998765 5899


Q ss_pred             EEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccCCCCCCCCceEEEeeeecCCcEEe
Q 011020          166 VTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLW  245 (495)
Q Consensus       166 VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp~~~~pd~FfCr~vYD~~~kKL~  245 (495)
                      ++|+|||||+|+.....+.|....++|||+|+|+|.+++++|.++|.|++++.|.+++.+..+++|+|+.+||..+.++|
T Consensus        87 ~ev~W~YrPee~~~~~~~~~~a~~~relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~  166 (464)
T KOG1886|consen   87 VEVQWFYRPEESEGGGSGKWGAKQPRELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLR  166 (464)
T ss_pred             eecccccCCCccCCCCCCCcccCCCccccccccccchhhhhhcccceeeeccccccccccCCCCCccccccccccccccc
Confidence            99999999999998888888888999999999999999999999999999999999998888999999999999999999


Q ss_pred             ecCCchhhccccchhhHHHHHhhhhcCCCCCCCccccccchhhhhhhcccccccCCCCCccccccccccCcccccccccC
Q 011020          246 KLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAET  325 (495)
Q Consensus       246 ~L~dkDye~~~q~Evd~Ll~Kt~~rlG~L~Di~~~e~~~~~~~d~~~~k~~~r~~~~~~~~~~~~~~~~~~~~~~~k~~t  325 (495)
                      .+.+.+|....+.++|.++.++..++++++++.... +    +..++++|+.++++++  .++|.               
T Consensus       167 ~~~~~~~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~-t----~~~~~~~~~~~~s~~~--~~~r~---------------  224 (464)
T KOG1886|consen  167 KLRDGDFGDGQKLEIDMLVPKTGPRRGTLPDPKKVQ-T----LNAAASKRSQQKSEIS--SLSRA---------------  224 (464)
T ss_pred             CccccchhcccccCCccchhhhcccCCCCCCccccc-c----ccccccceeccccccc--ccccc---------------
Confidence            999999999999999999999999999999999988 3    3578889999998887  22222               


Q ss_pred             CCccCCCCchhHHHHhhhccccCCchhhhHHHHHHHHh-hhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCcccc
Q 011020          326 PGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGL-QYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREK  404 (495)
Q Consensus       326 p~~~~~~~~~~~~~l~~~~~~tg~~~rd~~l~~l~~~i-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  404 (495)
                            ..+.++.||+.|..+||+++|||.|++|++.+ +++|.++..+.+.                            
T Consensus       225 ------ss~~~~~~~e~~~~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~~----------------------------  270 (464)
T KOG1886|consen  225 ------SSSVDGEILESFDLLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPAG----------------------------  270 (464)
T ss_pred             ------ccccccccccCCCCCCCcccccccccccchhhccccccccccCCCc----------------------------
Confidence                  34467889999999999999999999999999 9999999877753                            


Q ss_pred             ccCCCCCCCCchhHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhccccccc
Q 011020          405 GQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGP  458 (495)
Q Consensus       405 ~~~~~~~~~wp~~~v~~v~ale~~~~~~~~~d~~kyn~k~~~l~~n~k~~~~~~  458 (495)
                         ...+ .|||.+|+.|.|||+++|++|+.|+.|||+|++.|++++|+..+|+
T Consensus       271 ---~~~~-~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k~~~~l~  320 (464)
T KOG1886|consen  271 ---DQGS-LWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLKGQALLK  320 (464)
T ss_pred             ---cccc-CCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhcchhhhc
Confidence               2223 8999999999999999999999999999999999999999988876

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

Probab=100.00  E-value=1.4e-35  Score=271.34  Aligned_cols=146  Identities=64%  Similarity=1.163  Sum_probs=135.1

Q ss_pred             cCCCCCcceeeeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCC
Q 011020          111 SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDT  190 (495)
Q Consensus       111 ~GKGkk~R~~Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~  190 (495)
                      +|||+++++||++|.++|++|+|||+|||.+++ +.+||||+|++||++.+|.++|+|+|||||+||.....+.+..+++
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            489999999999999999999999999999887 4899999999999998899999999999999999766666656689


Q ss_pred             CeeEeeCCcccccccceeeecEEEecCccccCCCCCCCCceEEEeeeecCCcEEeecCCchhhcccc
Q 011020          191 RELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQ  257 (495)
Q Consensus       191 nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp~~~~pd~FfCr~vYD~~~kKL~~L~dkDye~~~q  257 (495)
                      ||||+|.|.|.+|+++|+|||.|++.+++.++|.....++|||++.||..+++||+|+++||+++.|
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            9999999999999999999999999999998886666899999999999999999999999998754

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=1e-26  Score=207.93  Aligned_cols=118  Identities=22%  Similarity=0.417  Sum_probs=104.2

Q ss_pred             CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccce
Q 011020          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV  207 (495)
Q Consensus       128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI  207 (495)
                      |+.|++||+|||.+++ +.++|||+|++||++.+|..+|+|+|||||+||.....+  ..++++|||+|+|+|++|+++|
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-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQA--TNHDKKRVFYSEIKNDNPLDCL   77 (122)
T ss_pred             CcEEEcCCEEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhcccccc--ccCCCceEEEecccCccchhhe
Confidence            6789999999999987 599999999999999999999999999999999974322  4578999999999999999999


Q ss_pred             eeecEEEecCccccCC---CCCCCCceEEEeeeecCCcEEeecC
Q 011020          208 MHKCVVHFVPIHKQLP---NRKQHPGFIVQKVYDTVERKLWKLT  248 (495)
Q Consensus       208 ~GKC~V~~v~ey~qlp---~~~~pd~FfCr~vYD~~~kKL~~L~  248 (495)
                      +|||+|++++++..++   ....+++|||++.|+..-.+|..|+
T Consensus        78 ~~Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~~~~  121 (122)
T cd04716          78 ISKVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQTLR  121 (122)
T ss_pred             eeeeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheEeCC
Confidence            9999999999988873   3345799999999999877777664

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.

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

Probab=99.94  E-value=6.9e-27  Score=206.18  Aligned_cols=117  Identities=25%  Similarity=0.420  Sum_probs=103.7

Q ss_pred             CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccce
Q 011020          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV  207 (495)
Q Consensus       128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI  207 (495)
                      |..|++||+|||.+++.+.++|||+|.+||++.+|..+|+|+|||||+||.+...+.+   ++||||+|.+.+++|+++|
T Consensus         1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~---~~~Evfls~~~d~~~~~~I   77 (121)
T cd04717           1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKF---YKNEVFKSPLYETVPVEEI   77 (121)
T ss_pred             CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCcccc---ccCceEEcCccccccHHHh
Confidence            6789999999999987668899999999999988999999999999999988666544   8999999999999999999


Q ss_pred             eeecEEEecCccccCC-C-CCCCCceEEEeeeecCCcEEeec
Q 011020          208 MHKCVVHFVPIHKQLP-N-RKQHPGFIVQKVYDTVERKLWKL  247 (495)
Q Consensus       208 ~GKC~V~~v~ey~qlp-~-~~~pd~FfCr~vYD~~~kKL~~L  247 (495)
                      +|||.||++.+|.+.. . ....+.|+|+..||...+.|..+
T Consensus        78 ~~kc~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~~  119 (121)
T cd04717          78 VGKCAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKI  119 (121)
T ss_pred             cCeeEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEecc
Confidence            9999999999998874 2 22458899999999988777654

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=99.94  E-value=1e-26  Score=206.40  Aligned_cols=112  Identities=27%  Similarity=0.439  Sum_probs=99.5

Q ss_pred             CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccce
Q 011020          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV  207 (495)
Q Consensus       128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI  207 (495)
                      |.+|++||+|||.+++.+.+||||+|.+||++.+|.++|+|+|||||+||.+...   ..+++||||+|+|.|++|+++|
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            5789999999999987568899999999999988999999999999999987443   3469999999999999999999


Q ss_pred             eeecEEEecCccccCCC-----CCCCCceEEEeeeecCCc
Q 011020          208 MHKCVVHFVPIHKQLPN-----RKQHPGFIVQKVYDTVER  242 (495)
Q Consensus       208 ~GKC~V~~v~ey~qlp~-----~~~pd~FfCr~vYD~~~k  242 (495)
                      +|||.|+++++|.++..     ....+.|+|+..||+...
T Consensus        78 ~gkc~V~~~~ey~~~~~~~~~~~~~~d~~~Ce~~yn~~~~  117 (121)
T cd04714          78 EHKCYVLTFAEYERLARVKKKPQDGVDFYYCAGTYNPDTG  117 (121)
T ss_pred             CcccEEEehhHheecccccCCCCcCCCEEEEeccCCCCcC
Confidence            99999999999988652     246799999999998753

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.

>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=3.6e-26  Score=212.62  Aligned_cols=138  Identities=25%  Similarity=0.388  Sum_probs=114.3

Q ss_pred             CccccccceeecCCCCCcceeeeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC--CceEEEEEEeeccccc
Q 011020          100 DAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD--GSMMVTGQWFYRPEEA  177 (495)
Q Consensus       100 ~a~pIG~pVK~~GKGkk~R~~Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkd--G~~~VrVqWFYRPEET  177 (495)
                      -++|.|.+.+..+     ++||+++.++|..|++||+|||.+++  .+||||+|.+||+..+  |.++++|+|||||+||
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            3567777777654     56999999999999999999999865  8999999999999865  8899999999999999


Q ss_pred             ccCCCCCCcCCCCCeeEeeCCc-----ccccccceeeecEEEecCccccCC--CC--CCCCceEEEeeeecCCcEEe
Q 011020          178 DRKGGGNWLSRDTRELFYSFHR-----DEVPAESVMHKCVVHFVPIHKQLP--NR--KQHPGFIVQKVYDTVERKLW  245 (495)
Q Consensus       178 ~~~~~g~f~~~~~nELFlSdh~-----D~~PlesI~GKC~V~~v~ey~qlp--~~--~~pd~FfCr~vYD~~~kKL~  245 (495)
                      .+...+. +.+.+||||+|.|.     +++|+++|+|||.|+++++|...+  +.  .....|++.+.||+..++..
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     668999999999999999998754  11  23477888889998876653

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.

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

Probab=99.93  E-value=6e-26  Score=194.34  Aligned_cols=117  Identities=38%  Similarity=0.646  Sum_probs=103.7

Q ss_pred             CEEEeeCCeEEEcCCCC--CCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCccccccc
Q 011020          128 GNKYELEDPVLLTPEDT--NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAE  205 (495)
Q Consensus       128 G~~YkVGD~VyV~~ed~--~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~Ple  205 (495)
                      |.+|++||+|||.+++.  ..++|||+|.+||++.+|.++++|+|||||+||.+...+   .+.+||||+|++++++|++
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            67899999999999874  478999999999999899999999999999999975443   4599999999999999999


Q ss_pred             ceeeecEEEecCccccCC---CCCCCCceEEEeeeecCCcEEeec
Q 011020          206 SVMHKCVVHFVPIHKQLP---NRKQHPGFIVQKVYDTVERKLWKL  247 (495)
Q Consensus       206 sI~GKC~V~~v~ey~qlp---~~~~pd~FfCr~vYD~~~kKL~~L  247 (495)
                      +|+|||.|++..++.+..   ....++.|||++.||..+.++..+
T Consensus        78 ~I~gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~~  122 (123)
T cd04370          78 SIIGKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKAL  122 (123)
T ss_pred             HhccccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEeC
Confidence            999999999999988763   445679999999999988777654

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=6.2e-26  Score=195.05  Aligned_cols=116  Identities=31%  Similarity=0.462  Sum_probs=102.4

Q ss_pred             EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCc-eEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCccccccccee
Q 011020          130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS-MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVM  208 (495)
Q Consensus       130 ~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~-~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~  208 (495)
                      .|++||+|||.+++...++|||+|.+||++.+|. ++++|+|||||+||.+...+.   .++||||+|++++++|+++|+
T Consensus         1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~---~~~~Elf~s~~~~~i~~~~I~   77 (120)
T smart00439        1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAAL---FDKNEVFLSDEYDTVPLSDII   77 (120)
T ss_pred             CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhcccccccc---CCCcceEEEccCccCChHHee
Confidence            4899999999998866889999999999998888 899999999999999755443   489999999999999999999


Q ss_pred             eecEEEecCccccCCCCC---CCCceEEEeeeecCCcEEeecC
Q 011020          209 HKCVVHFVPIHKQLPNRK---QHPGFIVQKVYDTVERKLWKLT  248 (495)
Q Consensus       209 GKC~V~~v~ey~qlp~~~---~pd~FfCr~vYD~~~kKL~~L~  248 (495)
                      |||.|++.+++...+...   .++.|||++.||...++|+.++
T Consensus        78 ~kc~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~~~  120 (120)
T smart00439       78 GKCNVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKKLP  120 (120)
T ss_pred             eEEEEEEcchhcccccccCCCCCCeEEEEEEEccccCcccCCC
Confidence            999999999998765322   4799999999999988887653

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

Probab=99.93  E-value=5.6e-26  Score=206.21  Aligned_cols=116  Identities=24%  Similarity=0.447  Sum_probs=101.8

Q ss_pred             EEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC------------CceEEEEEEeecccccccCCCCCCcCCCCCe
Q 011020          125 EFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD------------GSMMVTGQWFYRPEEADRKGGGNWLSRDTRE  192 (495)
Q Consensus       125 ~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkd------------G~~~VrVqWFYRPEET~~~~~g~f~~~~~nE  192 (495)
                      ..+|+.|++||+|||.++++++|+|||+|++|+..++            +..+|+|+|||||+||....     .++++|
T Consensus         6 ~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~-----~~d~re   80 (135)
T cd04710           6 LKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV-----VADSRL   80 (135)
T ss_pred             ccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc-----cCCceE
Confidence            4689999999999999998889999999999998543            23689999999999986422     469999


Q ss_pred             eEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEe
Q 011020          193 LFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLW  245 (495)
Q Consensus       193 LFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~  245 (495)
                      ||+|+|.|++|+++|+|||+|++..++..+. ....+++|||.++||++++|++
T Consensus        81 lf~S~h~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~~  134 (135)
T cd04710          81 LYASMHSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRYY  134 (135)
T ss_pred             EEEEeeEeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhcc
Confidence            9999999999999999999999999887765 3445899999999999999886

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=99.93  E-value=7.2e-26  Score=194.75  Aligned_cols=115  Identities=37%  Similarity=0.622  Sum_probs=100.5

Q ss_pred             EEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCc--eEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccc
Q 011020          129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS--MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAES  206 (495)
Q Consensus       129 ~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~--~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~Ples  206 (495)
                      ++|++||+|||.+++...++|||+|.+||++.++.  ++++|+|||||+||..   +.  ...+||||+|++++++|+++
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            57999999999999878999999999999998877  9999999999999932   21  23569999999999999999


Q ss_pred             eeeecEEEecCccccCCCCC--CCCceEEEeeeecCCcEEeecC
Q 011020          207 VMHKCVVHFVPIHKQLPNRK--QHPGFIVQKVYDTVERKLWKLT  248 (495)
Q Consensus       207 I~GKC~V~~v~ey~qlp~~~--~pd~FfCr~vYD~~~kKL~~L~  248 (495)
                      |+|||.|++..++.+.....  .++.|||++.||+..++|..++
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            99999999999998765332  6899999999999999998764

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 ....

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

Probab=99.92  E-value=2.6e-25  Score=207.84  Aligned_cols=117  Identities=21%  Similarity=0.333  Sum_probs=101.3

Q ss_pred             CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccC----CCC---------------CCcCC
Q 011020          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK----GGG---------------NWLSR  188 (495)
Q Consensus       128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~----~~g---------------~f~~~  188 (495)
                      ++.|++||+|||.++. +.++|||+|++||++.+|.++|+|+|||||+||+..    ..+               ..+..
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 678889999999999999999999999999998642    111               11345


Q ss_pred             CCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEe
Q 011020          189 DTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLW  245 (495)
Q Consensus       189 ~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~  245 (495)
                      +.+|||+|.|.+++|+++|+|||.|+++.+|..+. ....+++|||+.+||+.+++|.
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            89999999999999999999999999999998876 3346899999999999999994

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.

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

Probab=99.91  E-value=2.3e-24  Score=194.39  Aligned_cols=120  Identities=22%  Similarity=0.329  Sum_probs=102.8

Q ss_pred             EEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCccccc
Q 011020          124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVP  203 (495)
Q Consensus       124 f~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~P  203 (495)
                      |..+|.++++||+|||.+++  .++|||+|.+||++.+|.++|+|+||+||+||.+.....  .+.+||||+|++.+++|
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            34689999999999999876  778999999999998999999999999999999754433  25999999999999999


Q ss_pred             ccceeeecEEEecCccccCCC----CCCCCceEEEeeeecCCcEEeec
Q 011020          204 AESVMHKCVVHFVPIHKQLPN----RKQHPGFIVQKVYDTVERKLWKL  247 (495)
Q Consensus       204 lesI~GKC~V~~v~ey~qlp~----~~~pd~FfCr~vYD~~~kKL~~L  247 (495)
                      +++|+|||+||+..+|.++..    ....+.|+|++.||....+-+++
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            999999999999999988641    12367999999999986644443

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=6.6e-23  Score=197.04  Aligned_cols=124  Identities=27%  Similarity=0.382  Sum_probs=104.7

Q ss_pred             EEEcCEEEeeCCeEEEcCCC-----------------CCCCCeEEEEeEEeeCCCC------ceEEEEEEeecccccccC
Q 011020          124 FEFDGNKYELEDPVLLTPED-----------------TNQKPYVAIIKEITQSKDG------SMMVTGQWFYRPEEADRK  180 (495)
Q Consensus       124 f~~dG~~YkVGD~VyV~~ed-----------------~~e~PyIArI~eIwedkdG------~~~VrVqWFYRPEET~~~  180 (495)
                      |+++|++|++||+|||.++.                 ...+++||+|.+|+..+++      ..+|+|+|||||+||.. 
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            56899999999999999981                 1357889999999986554      68999999999999853 


Q ss_pred             CCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEeecCCc
Q 011020          181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLTDK  250 (495)
Q Consensus       181 ~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~~L~dk  250 (495)
                        +...+++.+|||+|++.+++|+++|.|||.|++..++..+. ....++.|||+..||+.++.|.+||..
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              22235699999999999999999999999999999886653 233489999999999999999888774

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=99.88  E-value=2e-22  Score=181.81  Aligned_cols=114  Identities=20%  Similarity=0.277  Sum_probs=98.6

Q ss_pred             cCEEEeeCCeEEEcCCCCC----------CCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEee
Q 011020          127 DGNKYELEDPVLLTPEDTN----------QKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYS  196 (495)
Q Consensus       127 dG~~YkVGD~VyV~~ed~~----------e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlS  196 (495)
                      .|..|++||+|+|.++++.          .++||++|..||++.+|.+||+|+|||||+||.+..     .+++||||||
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            5778999999999998855          489999999999999999999999999999999854     4699999999


Q ss_pred             CCccccccc----ceeeecEEEecCccccCCCCCCCCceEEEeeeecCCcEEeecC
Q 011020          197 FHRDEVPAE----SVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLT  248 (495)
Q Consensus       197 dh~D~~Ple----sI~GKC~V~~v~ey~qlp~~~~pd~FfCr~vYD~~~kKL~~L~  248 (495)
                      +||++++++    .|++||.|++...+..   ...++.|+|+..|++.++.|..|+
T Consensus        77 d~c~~~~~~~~~~~I~~k~~V~~~~~~~~---~~~~~~F~r~syy~~e~~~F~~l~  129 (130)
T cd04712          77 NECTCLELDLLSTEIKGVHKVDWSGTPWG---KGLPEFFVRQSYYWPERGAFTSLK  129 (130)
T ss_pred             ccccccccccccceeEEEEEEEEecCcCC---cCCCCEEEEEEEECccCCceEcCC
Confidence            999999999    9999999998876653   124566777777787888888775

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.

>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=1.5e-22  Score=181.65  Aligned_cols=112  Identities=22%  Similarity=0.319  Sum_probs=96.2

Q ss_pred             CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccce
Q 011020          128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV  207 (495)
Q Consensus       128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI  207 (495)
                      |.+|.+||+|+|.++++..+||||+|..||++.+|.+|++|+|||||+||.+...     ++++|||+|++|+.+++.+|
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            5689999999999988789999999999999999999999999999999997543     69999999999999999999


Q ss_pred             eeecEEEecCccc--------cCC---CCCCCCceEEEeeeecCCcEE
Q 011020          208 MHKCVVHFVPIHK--------QLP---NRKQHPGFIVQKVYDTVERKL  244 (495)
Q Consensus       208 ~GKC~V~~v~ey~--------qlp---~~~~pd~FfCr~vYD~~~kKL  244 (495)
                      .+||+|+..+.-.        ..+   ....-.+|||++.||+...++
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            9999999987651        111   112348899999999966554

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.

>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=7.8e-20  Score=172.94  Aligned_cols=122  Identities=16%  Similarity=0.222  Sum_probs=100.4

Q ss_pred             EEEE-cCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceEEEEEEeecccccccCCC-CCCc-----CCCCCeeE
Q 011020          123 AFEF-DGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMMVTGQWFYRPEEADRKGG-GNWL-----SRDTRELF  194 (495)
Q Consensus       123 Sf~~-dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkd-G~~~VrVqWFYRPEET~~~~~-g~f~-----~~~~nELF  194 (495)
                      .... +|.+|++||+|+|.+++ ..++|||+|.+|+.+.. +.+.+.|+|||||.|+..... +.+.     ...+||||
T Consensus        44 l~R~~d~~~~~vGD~Vlik~~~-~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElf  122 (179)
T cd04720          44 LARDSDGLELSVGDTILVKDDV-ANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELY  122 (179)
T ss_pred             EEEccCCeEEeCCCEEEEeCCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEE
Confidence            3344 89999999999999987 48999999999998765 567999999999999964221 1111     23489999


Q ss_pred             eeCCcccccccceeeecEEEecCccccCC-C-CCCCCceEEEeeeecCCcEEe
Q 011020          195 YSFHRDEVPAESVMHKCVVHFVPIHKQLP-N-RKQHPGFIVQKVYDTVERKLW  245 (495)
Q Consensus       195 lSdh~D~~PlesI~GKC~V~~v~ey~qlp-~-~~~pd~FfCr~vYD~~~kKL~  245 (495)
                      +|.|.+.+++.+|+|||+||...+|.++. . .....+||||++||+.+..|.
T Consensus       123 lT~~~d~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~  175 (179)
T cd04720         123 LTAELSEIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFV  175 (179)
T ss_pred             EecccceEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEc
Confidence            99999999999999999999999998764 2 234689999999999887664

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=6.8e-20  Score=165.40  Aligned_cols=113  Identities=27%  Similarity=0.406  Sum_probs=94.1

Q ss_pred             EEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCC---ceEEEEEEeecccccccCC---CCCCcCCCCCeeEeeCCc---
Q 011020          129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDG---SMMVTGQWFYRPEEADRKG---GGNWLSRDTRELFYSFHR---  199 (495)
Q Consensus       129 ~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG---~~~VrVqWFYRPEET~~~~---~g~f~~~~~nELFlSdh~---  199 (495)
                      .+|+|||||+|.+++. .++|||+|++||++.++   ...++|||||||+|+++..   .+.  ..+++|||+|+|.   
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            4799999999999884 88999999999998765   5699999999999997532   222  3489999999987   


Q ss_pred             ccccccceeeecEEEecCccccCCC--CCCCCceEEEeeeecCCcEE
Q 011020          200 DEVPAESVMHKCVVHFVPIHKQLPN--RKQHPGFIVQKVYDTVERKL  244 (495)
Q Consensus       200 D~~PlesI~GKC~V~~v~ey~qlp~--~~~pd~FfCr~vYD~~~kKL  244 (495)
                      +.+++++|.|+|.|+...+|..++.  ......||+++.|+....+.
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            4899999999999999999999873  23457899999998765543

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=1.3e-20  Score=173.44  Aligned_cols=98  Identities=18%  Similarity=0.342  Sum_probs=86.8

Q ss_pred             CCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccCCC
Q 011020          145 NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN  224 (495)
Q Consensus       145 ~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp~  224 (495)
                      ...+|||+|++||++. |..+|+|+|||||+||.++...   .++.+|||+|+|.|++++++|+|||.||++.+|.++..
T Consensus        50 ~~~~~vArIekiW~~~-G~~~~~grWy~rPEET~~gr~~---~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~  125 (148)
T cd04718          50 SGDLWLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQP---HNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASN  125 (148)
T ss_pred             cCchHHHHHHHHHhcc-CceEEEEEEEeCchhccCcccc---ccccceeeeccccccccHHHHhcccEEcCHHHcccccC
Confidence            3578999999999986 9999999999999999985544   45999999999999999999999999999999988753


Q ss_pred             CCCCCceEEEeeeecCCcEEeec
Q 011020          225 RKQHPGFIVQKVYDTVERKLWKL  247 (495)
Q Consensus       225 ~~~pd~FfCr~vYD~~~kKL~~L  247 (495)
                      . ..++|||+..||...+.|..+
T Consensus       126 ~-g~Dvy~Ce~~Yd~~~~~Fkr~  147 (148)
T cd04718         126 D-GDDVFLCEYEYDVHWQSFKRL  147 (148)
T ss_pred             C-CCceEEEEEEEhhhcCceeec
Confidence            3 478999999999998887654

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.

>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=99.74  E-value=3.5e-18  Score=155.37  Aligned_cols=114  Identities=18%  Similarity=0.228  Sum_probs=88.5

Q ss_pred             CCeEEEcCCCCCCCCeEEEEeEEeeCCCC-------ceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccc
Q 011020          134 EDPVLLTPEDTNQKPYVAIIKEITQSKDG-------SMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAES  206 (495)
Q Consensus       134 GD~VyV~~ed~~e~PyIArI~eIwedkdG-------~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~Ples  206 (495)
                      +|+|-=.+-+.+.+++||||++|...+++       .++|+|+|||||+||..+.... .+.+.||||+|+|.+++|+++
T Consensus        13 ~~~~~~~~~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~a-yhsDirevy~Sd~~~~~~~~~   91 (137)
T cd04711          13 SDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKAT-YHADINMLYWSDEEATVDFSA   91 (137)
T ss_pred             ccccccccCCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccc-cccceeeEEeecceeecChhh
Confidence            34444445556789999999999876442       4689999999999999632221 245789999999999999999


Q ss_pred             eeeecEEEecCcccc-CC--CCCCCCceEEEeeeecCCcEEeecC
Q 011020          207 VMHKCVVHFVPIHKQ-LP--NRKQHPGFIVQKVYDTVERKLWKLT  248 (495)
Q Consensus       207 I~GKC~V~~v~ey~q-lp--~~~~pd~FfCr~vYD~~~kKL~~L~  248 (495)
                      |.|||.|++..+... +.  ....++.|||+.+||..++.|.++|
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            999999997766542 32  2246899999999999999886654

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=99.54  E-value=5.4e-15  Score=161.09  Aligned_cols=116  Identities=27%  Similarity=0.393  Sum_probs=107.2

Q ss_pred             EEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCccccc
Q 011020          124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVP  203 (495)
Q Consensus       124 f~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~P  203 (495)
                      +.++|..|.+||+||+.+..++..+.|++|.++|+..+|..|+.++|||||++|.|..++.|   ..+|+|.|..+.+++
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            78999999999999999988779999999999999999999999999999999999999988   999999999999999


Q ss_pred             ccceeeecEEEecCccccCC--CCCCCCceEEEeeeecCCc
Q 011020          204 AESVMHKCVVHFVPIHKQLP--NRKQHPGFIVQKVYDTVER  242 (495)
Q Consensus       204 lesI~GKC~V~~v~ey~qlp--~~~~pd~FfCr~vYD~~~k  242 (495)
                      +..|+|+|.|+++.+|....  ....-+.|.|+..|+...+
T Consensus       261 ~q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K  301 (629)
T KOG1827|consen  261 VQRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLK  301 (629)
T ss_pred             HHHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchh
Confidence            99999999999999997753  3345699999999988653

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

Probab=99.07  E-value=1.2e-11  Score=130.43  Aligned_cols=137  Identities=21%  Similarity=0.338  Sum_probs=108.8

Q ss_pred             EEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccC-------CCC-----------------C
Q 011020          129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK-------GGG-----------------N  184 (495)
Q Consensus       129 ~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~-------~~g-----------------~  184 (495)
                      ..|+|||+||+..+. .+++.|-+|+++.++.+|++..+|..|||..||...       ..+                 .
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            379999999999987 556779999999999999999999999999998741       011                 1


Q ss_pred             C-----------------cCCCCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEee
Q 011020          185 W-----------------LSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWK  246 (495)
Q Consensus       185 f-----------------~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~~  246 (495)
                      +                 +....+|||+|.+....|+..|+|||.|....+...+. +....++||+..+||+..++|  
T Consensus        83 ~EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTL--  160 (693)
T KOG3554|consen   83 IEEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTL--  160 (693)
T ss_pred             hhhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhh--
Confidence            1                 11357899999999999999999999999887766543 445679999999999998887  


Q ss_pred             cCCchhh---ccccchhhHHHHHhh
Q 011020          247 LTDKDYE---DNKQHEIDLLVQKTQ  268 (495)
Q Consensus       247 L~dkDye---~~~q~Evd~Ll~Kt~  268 (495)
                      |.|+..+   +..|.+|+..+..+.
T Consensus       161 LADkGeIRVG~kYQA~i~e~l~EgE  185 (693)
T KOG3554|consen  161 LADKGEIRVGEKYQADIPEWLEEGE  185 (693)
T ss_pred             hccCcceeecccccccchHHHHhcc
Confidence            4565543   456677877776543

>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=98.26  E-value=1.9e-06  Score=75.98  Aligned_cols=70  Identities=33%  Similarity=0.406  Sum_probs=57.3

Q ss_pred             cCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHHHH
Q 011020          347 TGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALE  426 (495)
Q Consensus       347 tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~ale  426 (495)
                      |++..||+|.+-|..++....... .   .                                      +..+..++..+|
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            789999999988888887653221 1   1                                      568899999999


Q ss_pred             HHhhhhhhhhHHHHHHHHHHHHHhhc--cccccc
Q 011020          427 KASHDTLSLDFQKYNQKLRQLLFNLK--RAWVGP  458 (495)
Q Consensus       427 ~~~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~  458 (495)
                      .|+|+.++++-.+|++|+|+|.||||  +|+-|.
T Consensus        39 ~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~   72 (115)
T PF07500_consen   39 EALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLR   72 (115)
T ss_dssp             HHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHH
T ss_pred             HHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHH
Confidence            99999998899999999999999999  665554

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.

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

Probab=98.08  E-value=6.4e-06  Score=72.14  Aligned_cols=68  Identities=26%  Similarity=0.296  Sum_probs=53.9

Q ss_pred             CchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHHHHHH
Q 011020          349 ETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKA  428 (495)
Q Consensus       349 ~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~ale~~  428 (495)
                      |..||++.+.|..+++..+.....  .                                        ..+..+..++|.+
T Consensus         1 d~~R~~~~~~L~~al~~~~~~~~~--~----------------------------------------~~~~~lA~~IE~~   38 (102)
T smart00510        1 DKVRDKCQEMLYKALQKISDPEEI--E----------------------------------------LDPTELAVQIEAE   38 (102)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCCcc--c----------------------------------------ccHHHHHHHHHHH
Confidence            467999999999998766543310  0                                        1355678899999


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhc--cccccc
Q 011020          429 SHDTLSLDFQKYNQKLRQLLFNLK--RAWVGP  458 (495)
Q Consensus       429 ~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~  458 (495)
                      +|+.++.+..+|++|+|+|.||||  +|+-|.
T Consensus        39 lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr   70 (102)
T smart00510       39 MFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLR   70 (102)
T ss_pred             HHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHH
Confidence            999999999999999999999999  776444

>TIGR01385 TFSII transcription elongation factor S-II

Probab=97.43  E-value=0.00022  Score=73.23  Aligned_cols=70  Identities=21%  Similarity=0.235  Sum_probs=55.0

Q ss_pred             ccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCch--hHHHHHH
Q 011020          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPD--TAIAAVT  423 (495)
Q Consensus       346 ~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~--~~v~~v~  423 (495)
                      +|||..||++.+-|.+++...+...                                            |+  +...+..
T Consensus       133 ~t~d~~Rdk~r~~L~~aL~~~~~~~--------------------------------------------~~~~~~~~lA~  168 (299)
T TIGR01385       133 VTNDKVRDKCRELLYDALAKDSDHP--------------------------------------------PQSIDPEAKAI  168 (299)
T ss_pred             cCCcHHHHHHHHHHHHHHhhcCCCC--------------------------------------------ccccCHHHHHH
Confidence            6999999999999999987532110                                            11  2234578


Q ss_pred             HHHHHhhhhhhhhHHHHHHHHHHHHHhhc--ccccccc
Q 011020          424 ALEKASHDTLSLDFQKYNQKLRQLLFNLK--RAWVGPG  459 (495)
Q Consensus       424 ale~~~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~~  459 (495)
                      ++|.++|+.++.+-.+|+.|+|+|.||||  +|+-|..
T Consensus       169 ~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~  206 (299)
T TIGR01385       169 QIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRH  206 (299)
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHH
Confidence            89999999999999999999999999998  6665543

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.

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

Probab=94.21  E-value=0.0058  Score=63.97  Aligned_cols=95  Identities=11%  Similarity=0.007  Sum_probs=82.9

Q ss_pred             EEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccc
Q 011020          123 AFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEV  202 (495)
Q Consensus       123 Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~  202 (495)
                      +..+.+....+|+++.+.+......|.++.+..+|.+.++..+.-++|||||.++.+.....+   ..+++.+....+.+
T Consensus       269 ~~~i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~  345 (371)
T COG5076         269 SVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLF---FDNCVMYNGEVTDY  345 (371)
T ss_pred             hhcccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchh---hhcccccchhhhhh
Confidence            345667799999999999988889999999999999988888889999999998887665544   89999999999999


Q ss_pred             cccceeeecEEEecCccc
Q 011020          203 PAESVMHKCVVHFVPIHK  220 (495)
Q Consensus       203 PlesI~GKC~V~~v~ey~  220 (495)
                      .+....+.|.|....++.
T Consensus       346 ~~~~~~~~~~~~~~~~~~  363 (371)
T COG5076         346 YKNANVLEDFVIKKTRLI  363 (371)
T ss_pred             hhhccchhhhHhhhhhhh
Confidence            999999999998776654

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

Probab=80.65  E-value=4  Score=42.56  Aligned_cols=68  Identities=26%  Similarity=0.324  Sum_probs=51.7

Q ss_pred             cccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHH
Q 011020          345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA  424 (495)
Q Consensus       345 ~~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~a  424 (495)
                      .+|.+.-|+++++.|..++.   .+.+.                                      .-.|+ ..-.+.+.
T Consensus       129 ~~~~d~~r~k~~e~l~~al~---~~~~~--------------------------------------~~~~~-~~~~~a~~  166 (296)
T KOG1105|consen  129 PITNDPVRDKCRELLYAALT---TEDDS--------------------------------------RVTGA-DPLELAVQ  166 (296)
T ss_pred             CCCCchHHHHHHHHHHHHhc---ccccc--------------------------------------cccCC-CHHHHHHH
Confidence            56799999999999999987   11111                                      11122 22334567


Q ss_pred             HHHHhhhhhhhhHHHHHHHHHHHHHhhccc
Q 011020          425 LEKASHDTLSLDFQKYNQKLRQLLFNLKRA  454 (495)
Q Consensus       425 le~~~~~~~~~d~~kyn~k~~~l~~n~k~~  454 (495)
                      +|.+.|..++.-..||-.++|..+||||..
T Consensus       167 iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~  196 (296)
T KOG1105|consen  167 IEEAIFEKLGNTDSKYKNRYRSRVSNLKDK  196 (296)
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHhhccCCC
Confidence            899999999999999999999999999854

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	495
1w4s_A	174	Crystal Structure Of The Proximal Bah Domain Of Pol		2e-08

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	495
1w4s_A	174	Polybromo, polybromo 1 protein; BAH, bromo-associa	4e-39
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	4e-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,	4e-08
4dov_A	163	ORC1, origin recognition complex subunit 1; DNA re	9e-12
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	1e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	9e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
3gdb_A	937	Endo-D, putative uncharacterized protein SPR0440;	8e-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 = 90.0 bits (222), Expect = 4e-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 = 49.6 bits (117), 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 = 4e-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 = 62.4 bits (151), Expect = 9e-12
 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

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

 Score = 48.2 bits (114), Expect = 1e-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

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

 Score = 39.4 bits (91), Expect = 9e-04
 Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 12/55 (21%)

Query: 48  QEEEDYEEPEEERKASKRERRDKGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAK 102
           Q +   +EPE  RK   RE + K   R  E        D   +  E+E  ++  K
Sbjct: 76  QADRLTQEPESIRKW--REEQRK---RLQEL-------DAASKVMEQEWREKAKK 118

>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 = 43.7 bits (102), Expect = 1e-04
 Identities = 47/333 (14%), Positives = 96/333 (28%), Gaps = 118/333 (35%)

Query: 188 RDTRELFY-SFHRD----EVP--AESVMHKCVV-HFVPIHKQLPNRKQHPGFIVQKVYDT 239
           +D   +F  +F  +    +V    +S++ K  + H +       +          +++ T
Sbjct: 19  KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHII----MSKDAVSG----TLRLFWT 70

Query: 240 VERKLWKLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAR--EQEDQLKAKRSL 297
           +  K  ++  K  E+  +     L+   +         +P        EQ D+L     +
Sbjct: 71  LLSKQEEMVQKFVEEVLRINYKFLMSPIKTE-----QRQPSMMTRMYIEQRDRLYNDNQV 125

Query: 298 RKKNISPLDVSREEDSTTRSDQYVKAETPGSCTSNASEYYNILSKFKALTGETHRDKWLE 357
                +  +VSR +                               +  L       + L 
Sbjct: 126 ----FAKYNVSRLQ------------------------------PYLKLR------QALL 145

Query: 358 RLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSF--IW- 414
             L+  + +      I     G  G  G       K+    +       +    F   W 
Sbjct: 146 E-LRPAKNVL-----ID----GVLGS-G-------KTWVALDVCLSYKVQCKMDFKIFWL 187

Query: 415 -------PDTAIAAVTAL---------EKASH-DTLSLDFQKYNQKLRQLLFN--LKRAW 455
                  P+T +  +  L          ++ H   + L       +LR+LL +   +   
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC- 246

Query: 456 VGPGLFCLSSCPGPHVRSPT--RAFLLSLPTCQ 486
               L  L      +V++     AF LS   C+
Sbjct: 247 ----LLVLL-----NVQNAKAWNAFNLS---CK 267

>3gdb_A Endo-D, putative uncharacterized protein SPR0440; alpha-beta-barrels, cell WALL, peptidoglycan-anchor, secreted, hydrolase; HET: PGE; 1.87A {Streptococcus pneumoniae} PDB: 2xqx_A Length = 937

 Score = 41.1 bits (95), Expect = 8e-04
 Identities = 19/189 (10%), Positives = 45/189 (23%)

Query: 10  STSDEDEDVPPPSSRTRKSEENKEQQSLRQSKRKRIKLQEEEDYEEPEEERKASKRERRD 69
              +E E          +      + +   S         E       EE+ +       
Sbjct: 49  DKQNEGEHARENKLEKAEGVATASETASPASNEAATTETAEAASAAKPEEKASEVVAETP 108

Query: 70  KGKVREAEKPRNDGVEDEEEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGN 129
             + +       +   +   + +E +   E  K   E+     K   +    +  +F+  
Sbjct: 109 SAEAKPKSDKETEAKPEATNQGDESKPAAEANKTEKEVQPDVPKNTEKTLKPKEIKFNSW 168

Query: 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRD 189
           +  L+       +D   +  V +    T                    + K   +     
Sbjct: 169 EELLKWEPGAREDDAINRGSVVLASRRTGHLVNEKASKEAKVQALSNTNSKAKDHASVGG 228

Query: 190 TRELFYSFH 198
                Y+F 
Sbjct: 229 EEFKAYAFD 237

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	495
1w4s_A	174	Polybromo, polybromo 1 protein; BAH, bromo-associa	99.96
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	99.94
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	99.91
4dov_A	163	ORC1, origin recognition complex subunit 1; DNA re	99.85
4ft4_B	784	DNA (cytosine-5)-methyltransferase 1; chromodomain	99.79
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	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	99.27
2dme_A	120	PHD finger protein 3; PHF3, TFS2M, glioblastoma mu	98.35
2lw4_A	113	Transcription elongation factor A protein 2; struc	98.3
3po3_S	178	Transcription elongation factor S-II; RNA polymera	98.24
3ndq_A	108	Transcription elongation factor A protein 1; helix	98.19
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	98.03

>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=99.94  E-value=3.9e-26  Score=258.86  Aligned_cols=141  Identities=20%  Similarity=0.284  Sum_probs=122.4

Q ss_pred             CccccccceeecCCCCCcceeeeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeeccccccc
Q 011020          100 DAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADR  179 (495)
Q Consensus       100 ~a~pIG~pVK~~GKGkk~R~~Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~  179 (495)
                      ...|+|.|+    |++.++.+|+++.++|.+|+|||||||.++++..+||||+|++||++.+|.+||+|+|||||+||.+
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    5556789999999999999999999999988778889999999999988999999999999999997


Q ss_pred             CCCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccc--------c--CC-CCCCCCceEEEeeeecCCcEEeecC
Q 011020          180 KGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHK--------Q--LP-NRKQHPGFIVQKVYDTVERKLWKLT  248 (495)
Q Consensus       180 ~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~--------q--lp-~~~~pd~FfCr~vYD~~~kKL~~L~  248 (495)
                      +..     ++++|||+|++|+++++++|+|||+|++...+.        .  .+ ....+++|||+..||+.+++|..|+
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     589999999999999999999999999875511        1  11 1123689999999999999999997


Q ss_pred             C
Q 011020          249 D  249 (495)
Q Consensus       249 d  249 (495)
                      .
T Consensus       283 ~  283 (1002)
T 3swr_A          283 K  283 (1002)
T ss_dssp             C
T ss_pred             h
Confidence            6

>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=1.3e-24  Score=251.73  Aligned_cols=141  Identities=18%  Similarity=0.318  Sum_probs=118.0

Q ss_pred             CccccccceeecCCCCCcceeeeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeeccccccc
Q 011020          100 DAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADR  179 (495)
Q Consensus       100 ~a~pIG~pVK~~GKGkk~R~~Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~  179 (495)
                      +-.|+|.|++..    .+++||+++.++|.+|++||||||.+++++.++|||+|++||++.+|.+||+|+|||||+||.+
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            345889888443    4689999999999999999999999887667899999999999999999999999999999986


Q ss_pred             CCCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCcccc---C----CCC-----CCCCceEEEeeeecCCcEEeec
Q 011020          180 KGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQ---L----PNR-----KQHPGFIVQKVYDTVERKLWKL  247 (495)
Q Consensus       180 ~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~q---l----p~~-----~~pd~FfCr~vYD~~~kKL~~L  247 (495)
                      ..     .++++|||+|+|+|++|+++|+|||+|++...+..   .    +..     .....|||++.||+..++|++|
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            32     25999999999999999999999999999866322   1    111     2357899999999999999999


Q ss_pred             CC
Q 011020          248 TD  249 (495)
Q Consensus       248 ~d  249 (495)
                      +.
T Consensus       594 p~  595 (1330)
T 3av4_A          594 PK  595 (1330)
T ss_dssp             CC
T ss_pred             Cc
Confidence            77

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

Probab=99.85  E-value=2.7e-20  Score=172.31  Aligned_cols=141  Identities=22%  Similarity=0.288  Sum_probs=111.1

Q ss_pred             cccccceeecCCCCCcceeeeEEEE--cC---EEEeeCCeEEEcCCCCCCCCeEEEEeEEeeC---CCCceEEEEEEeec
Q 011020          102 KPVGELVRFSGKGRGRRSHYEAFEF--DG---NKYELEDPVLLTPEDTNQKPYVAIIKEITQS---KDGSMMVTGQWFYR  173 (495)
Q Consensus       102 ~pIG~pVK~~GKGkk~R~~Y~Sf~~--dG---~~YkVGD~VyV~~ed~~e~PyIArI~eIwed---kdG~~~VrVqWFYR  173 (495)
                      .|+|.|+ ...  +....+|++|.+  .|   .++++||||+|.+++ ...||||+|++|+++   ....+.++||||||
T Consensus         8 sW~g~~l-~dr--kl~~~~Y~~~~v~~~~~~~~~i~vGd~VLI~~~D-~~~PyVAki~~lye~~~e~~~~k~A~VQWy~R   83 (163)
T 4dov_A            8 SWVGRPL-PNR--KQFQQMYREICMKINDGSEIHIKVGQFVLIQGED-NKKPYVAKLIELFQNGAEVPPKKCARVQWFVR   83 (163)
T ss_dssp             EEESCCC-CCC--CTTEEEESEEEEECTTSCEEEEETTCEEEECCSS-SSCCEEEEEEEEEEETTSSSCEEEEEEEEEEE
T ss_pred             EEeccCc-CCC--cccceeeeEEEEecCCCCCeEEeeCCEEEEeCCc-ccCChhHHHHHHHhccccCCCceEEEEEeeec
Confidence            5889988 322  233568999988  56   899999999999988 578899999999985   23468999999999


Q ss_pred             ccccccCCCCCCc--CCCCCeeEeeCCcc---cccccceeeecEEEecCccccCCCC-CCCCceEEEeeeecCCcEEeec
Q 011020          174 PEEADRKGGGNWL--SRDTRELFYSFHRD---EVPAESVMHKCVVHFVPIHKQLPNR-KQHPGFIVQKVYDTVERKLWKL  247 (495)
Q Consensus       174 PEET~~~~~g~f~--~~~~nELFlSdh~D---~~PlesI~GKC~V~~v~ey~qlp~~-~~pd~FfCr~vYD~~~kKL~~L  247 (495)
                      |+|++... ..+.  ..+.+|||+++|.+   .+.+++|+|+|.|++...+..+|.. ....+||.+..+|..  +|.-|
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            99998532 1111  14689999999984   7899999999999999999888743 567899999999954  45555


Q ss_pred             CC
Q 011020          248 TD  249 (495)
Q Consensus       248 ~d  249 (495)
                      ++
T Consensus       161 ~~  162 (163)
T 4dov_A          161 PP  162 (163)
T ss_dssp             C-
T ss_pred             CC
Confidence            43

>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=9.3e-20  Score=200.34  Aligned_cols=132  Identities=19%  Similarity=0.316  Sum_probs=108.6

Q ss_pred             cceeeeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCC----CCCCcCCCCCe
Q 011020          117 RRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKG----GGNWLSRDTRE  192 (495)
Q Consensus       117 ~R~~Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~----~g~f~~~~~nE  192 (495)
                      .++||.++.++|+.|++||+|||+++. +.++|||+|.+||++.+|..+|+|+|||||+||....    ...-..++.||
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            478999999999999999999999865 6789999999999999999999999999999998532    11123468999


Q ss_pred             eEeeCCcccccccceeeecEEEecCccccCCC---CCCCCceEEEeeeecCCcEEeecCC
Q 011020          193 LFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN---RKQHPGFIVQKVYDTVERKLWKLTD  249 (495)
Q Consensus       193 LFlSdh~D~~PlesI~GKC~V~~v~ey~qlp~---~~~pd~FfCr~vYD~~~kKL~~L~d  249 (495)
                      ||+|++++++|+++|.|||+|+++....+.+.   ......|||.+.|.....++..++.
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            99999999999999999999999877655431   1123569999999887777766643

>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=3e-19  Score=202.77  Aligned_cols=133  Identities=21%  Similarity=0.286  Sum_probs=110.3

Q ss_pred             cceeeeEEEEcCEEEeeCCeEEEcCCC-----------------------------------------CCCCCeEEEEeE
Q 011020          117 RRSHYEAFEFDGNKYELEDPVLLTPED-----------------------------------------TNQKPYVAIIKE  155 (495)
Q Consensus       117 ~R~~Y~Sf~~dG~~YkVGD~VyV~~ed-----------------------------------------~~e~PyIArI~e  155 (495)
                      ++.+|.+|.++|.+|++||+|||.++.                                         ...+++||+|.+
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            467999999999999999999999832                                         134778999999


Q ss_pred             EeeCCCCc-------eEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccCC---CC
Q 011020          156 ITQSKDGS-------MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP---NR  225 (495)
Q Consensus       156 IwedkdG~-------~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp---~~  225 (495)
                      ||....+.       ++|+|+|||||+||.+.... ...++.||||+|+|.+++|+++|+|||.|++..++....   ..
T Consensus       401 i~~~~~~~~~~~~~~~~v~v~~fyRPed~~~~~~~-~~~~D~~elf~S~~~~~~~~~~i~GkC~V~~~~d~~~~~~~~~~  479 (1002)
T 3swr_A          401 IFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPA-SYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSM  479 (1002)
T ss_dssp             EEECCCSSSSCCSSCCEEEEEECBCGGGSTTCGGG-GSSSCTTEEEECCCEEEEEGGGCCEEEEEEEGGGCSSCHHHHHH
T ss_pred             EEecCCccccCCCccEEEEEEEEECcccccccccc-cccCCcceEEEecceeccCHHHcceEEEEEEeccccccchhhcc
Confidence            99776544       89999999999999864322 335689999999999999999999999999998886542   11


Q ss_pred             CCCCceEEEeeeecCCcEEeecCCc
Q 011020          226 KQHPGFIVQKVYDTVERKLWKLTDK  250 (495)
Q Consensus       226 ~~pd~FfCr~vYD~~~kKL~~L~dk  250 (495)
                      ..++.|||..+||+.++.|..++..
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            3468899999999999999887643

>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=1.1e-18  Score=202.54  Aligned_cols=133  Identities=23%  Similarity=0.319  Sum_probs=109.7

Q ss_pred             cceeeeEEEEcCEEEeeCCeEEEcCCC-----------------------------------------CCCCCeEEEEeE
Q 011020          117 RRSHYEAFEFDGNKYELEDPVLLTPED-----------------------------------------TNQKPYVAIIKE  155 (495)
Q Consensus       117 ~R~~Y~Sf~~dG~~YkVGD~VyV~~ed-----------------------------------------~~e~PyIArI~e  155 (495)
                      ++.+|.+|.++|.+|++||||||.++.                                         ...+++||+|.+
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------CceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccC--C-CCC
Q 011020          156 ITQSKD------GSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQL--P-NRK  226 (495)
Q Consensus       156 Iwedkd------G~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~ql--p-~~~  226 (495)
                      ||.+.+      +..+|+|+|||||+||.+...+. ...+.||||+|++.+++|+++|.|||.|+++.++...  + ...
T Consensus       713 I~~~~~s~~~~~~~~~vrV~wFyRPedt~~~~~~~-~~~D~nELf~S~~~~~vp~~~I~GKC~V~~~~d~~~~i~~y~~~  791 (1330)
T 3av4_A          713 IHCGKKKGKVNEADIKLRLYKFYRPENTHRSYNGS-YHTDINMLYWSDEEAVVNFSDVQGRCTVEYGEDLLESIQDYSQG  791 (1330)
T ss_dssp             CCCCEETTEECSSCCEEEEEEEECTTTSTTGGGTT-TTSCTTBCEEEEEEEEEEGGGCCEEEEEEESTTCSSCHHHHHHT
T ss_pred             EEecCCccccCCCceEEEEEEeeChhhcccccccc-cccCcceEEeeccceecCHHHcCceEEEEecccccccccccccC
Confidence            998754      57899999999999998743222 2458999999999999999999999999999887663  2 222


Q ss_pred             CCCceEEEeeeecCCcEEeecCCc
Q 011020          227 QHPGFIVQKVYDTVERKLWKLTDK  250 (495)
Q Consensus       227 ~pd~FfCr~vYD~~~kKL~~L~dk  250 (495)
                      .++.|||+..||..++.|..++..
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            378999999999999988755443

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

Probab=99.28  E-value=3.3e-12  Score=124.28  Aligned_cols=126  Identities=12%  Similarity=0.097  Sum_probs=93.9

Q ss_pred             EcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCC-CCceEEEEEEeeccccccc-------CCC-----CCCcC-----
Q 011020          126 FDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK-DGSMMVTGQWFYRPEEADR-------KGG-----GNWLS-----  187 (495)
Q Consensus       126 ~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedk-dG~~~VrVqWFYRPEET~~-------~~~-----g~f~~-----  187 (495)
                      .+|..|++||+|.|..+. .+.+.|+.|..|.-.. +.-+.+.|+||+|..|+..       .+.     +...+     
T Consensus        48 ~Dg~~~~~GDsVlv~~~~-~~sysv~LI~eIrl~t~~n~vei~v~wylR~~Ei~~~~~~~~~~P~~~~~~~~~~~~~~~~  126 (232)
T 2fl7_A           48 SDGLSFGKGESVIFNDNV-TETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKF  126 (232)
T ss_dssp             TTCCEECTTCEEEEEETT-TTEEEEEEEEEEEC-----CCEEEEEEEECGGGSCHHHHHHHHCHHHHHTTCCHHHHHHHH
T ss_pred             cCCcEEeCCCEEEEecCC-CCceEEEEEEEEEecCCCceEEEEEEEeecHHHcCchhhhhhcCchhcccccchhhhhhhh
Confidence            389999999999998765 4566688888886554 5578999999999999975       211     11122     


Q ss_pred             ---CCCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEeecCCchh
Q 011020          188 ---RDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLTDKDY  252 (495)
Q Consensus       188 ---~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~~L~dkDy  252 (495)
                         ...||||+|.+.+.+-+.+|+++|+|+...+|..+. ......+||||.+||+...+|..+.-.++
T Consensus       127 ~~~~~~nELflTa~l~eI~l~diI~~anVls~~Ef~~l~~d~~~~~tFf~R~~cd~~~~~f~~iD~~~~  195 (232)
T 2fl7_A          127 FNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQI  195 (232)
T ss_dssp             HHHSCTTEEEEEEEEEEECGGGEEEECEEECTTTC-------CTTTEEEEEEECCTTSCSCEECCHHHH
T ss_pred             hcccccceEEEeccHHHHHHHhhhhheEeccHHHHHHhcccccCCceEEEEEEEcCCcCccccccHHHH
Confidence               589999999999999999999999999999998773 23346999999999998776766544444

>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=99.27  E-value=2.4e-12  Score=125.67  Aligned_cols=127  Identities=17%  Similarity=0.143  Sum_probs=100.1

Q ss_pred             EcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCC-CCceEEEEEEeeccccccc-------CCC-----CCCcC-----
Q 011020          126 FDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK-DGSMMVTGQWFYRPEEADR-------KGG-----GNWLS-----  187 (495)
Q Consensus       126 ~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedk-dG~~~VrVqWFYRPEET~~-------~~~-----g~f~~-----  187 (495)
                      .||..|++||+|.|..+. .+.+.|+.|..|.-+. ++-+.+.|.||+|..|+..       .+.     +...+     
T Consensus        48 ~Dg~~~~~GDsVlv~~~~-~~sysv~LI~eIrl~t~~n~vei~v~wylR~~Ei~~~~~~~~~~P~~~~~~~~~~~~~~~~  126 (238)
T 1m4z_A           48 SDGIKLGRGDSVVMHNEA-AGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLF  126 (238)
T ss_dssp             TTCCEECTTCEEEEEETT-TTEEEEEEEEEEEEETTTTEEEEEEEEEECGGGSCHHHHHHHHCHHHHHSCCCHHHHHHHH
T ss_pred             cCCcEEeCCCEEEEecCC-CCceEEEEEEEEEecCCCceEEEEEEEeecHHHcCchhhhhhcCchhcccccchhhhhhhh
Confidence            389999999999998765 4566788888886554 5578999999999999975       211     11122     


Q ss_pred             ---CCCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEeecCCchhh
Q 011020          188 ---RDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLTDKDYE  253 (495)
Q Consensus       188 ---~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~~L~dkDye  253 (495)
                         ...||||+|.+.+.+-+.+|+++|+|+...+|..+. ......+||||++||+...+|..+.-.++.
T Consensus       127 ~~~~~~nELflTa~l~eI~l~diI~~anVls~~Ef~~i~~d~~~~~tFf~R~~cd~~~~~f~~iD~~~~~  196 (238)
T 1m4z_A          127 SETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVK  196 (238)
T ss_dssp             HHHSCTTEEEEEEEEEEECGGGEEEEEEEECHHHHHHHGGGCCTTTEEEEEEECCTTSCCCEECCHHHHH
T ss_pred             hcccccceEEEeccHHHHhHHhhhhheEeccHHHHhhhccccccCceEEEEEEEcCCcCccccccHHHHH
Confidence               589999999999999999999999999999998763 224569999999999987777766444443

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

Probab=98.35  E-value=3.1e-07  Score=81.26  Aligned_cols=74  Identities=22%  Similarity=0.158  Sum_probs=59.4

Q ss_pred             ccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCC-chhHHHHHHH
Q 011020          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIW-PDTAIAAVTA  424 (495)
Q Consensus       346 ~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w-p~~~v~~v~a  424 (495)
                      .++|..||++.+.|.+.+.........                                        .. ..+++.++.+
T Consensus         7 ~~~d~~Rd~~r~~L~eaL~~~~~~~~~----------------------------------------~~~~~~~~~lA~~   46 (120)
T 2dme_A            7 GSADQIRQSVRHSLKDILMKRLTDSNL----------------------------------------KVPEEKAAKVATK   46 (120)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHTTTTC----------------------------------------CCCHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHHHHhcccccc----------------------------------------ccchhHHHHHHHH
Confidence            477899999999999999654432210                                        01 2467889999


Q ss_pred             HHHHhhhhhhhhHHHHHHHHHHHHHhhc--ccccccc
Q 011020          425 LEKASHDTLSLDFQKYNQKLRQLLFNLK--RAWVGPG  459 (495)
Q Consensus       425 le~~~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~~  459 (495)
                      +|.|+|+.++....+|++|+|+|+||||  +|+.|..
T Consensus        47 IE~~lf~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~Lr~   83 (120)
T 2dme_A           47 IEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFK   83 (120)
T ss_dssp             HHHHHHHHHCSCSHHHHHHHHHHTHHHHSSSCCSHHH
T ss_pred             HHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            9999999999988999999999999999  7877654

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

Probab=98.30  E-value=4.8e-07  Score=79.31  Aligned_cols=72  Identities=22%  Similarity=0.178  Sum_probs=55.4

Q ss_pred             ccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHHH
Q 011020          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTAL  425 (495)
Q Consensus       346 ~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~al  425 (495)
                      +|||.-|||+.+-|.+++..   .++.. ..                                      ..++..+..++
T Consensus         7 ~t~D~vRdk~~e~L~~aL~~---~~~~~-~~--------------------------------------~~~~~~~A~~I   44 (113)
T 2lw4_A            7 VTCDAVRNKCREMLTAALQT---DHDHV-AI--------------------------------------GADCERLSAQI   44 (113)
T ss_dssp             CCCSTTHHHHHHHHHHHHHS---STHHH-HH--------------------------------------TCCHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHHHc---CCCcc-cc--------------------------------------cchHHHHHHHH
Confidence            59999999999999988852   11000 00                                      01455678899


Q ss_pred             HHHhhhhhhhhHHHHHHHHHHHHHhhc--ccccccc
Q 011020          426 EKASHDTLSLDFQKYNQKLRQLLFNLK--RAWVGPG  459 (495)
Q Consensus       426 e~~~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~~  459 (495)
                      |.+.|+.++..-.+|.+|+|+|.||||  +|+-|..
T Consensus        45 E~~~f~~~~~~~~~Yk~k~Rsl~~NLkd~~Np~Lr~   80 (113)
T 2lw4_A           45 EECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRR   80 (113)
T ss_dssp             HHHHHHHHTCTTTHHHHHHHHHHHHHHCSSSSHHHH
T ss_pred             HHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            999999999999999999999999999  5665543

>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=98.24  E-value=7.7e-07  Score=83.48  Aligned_cols=70  Identities=16%  Similarity=0.136  Sum_probs=54.6

Q ss_pred             ccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHHH
Q 011020          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTAL  425 (495)
Q Consensus       346 ~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~al  425 (495)
                      +|||.-|||+.+-|.+++......                                           . |..++.++.+|
T Consensus        12 ~~~d~vRdk~~~lL~~aL~~~~~~-------------------------------------------~-~~~~~~~A~~I   47 (178)
T 3po3_S           12 IYHHKLRDQVLKALYDVLAKESEH-------------------------------------------P-PQSILHTAKAI   47 (178)
T ss_dssp             ---CHHHHHHHHHHHHHTTSSSSC-------------------------------------------S-TTHHHHHHHHH
T ss_pred             cCCChHHHHHHHHHHHHHhcCCCC-------------------------------------------c-hhhHHHHHHHH
Confidence            599999999999999888642110                                           0 45788999999


Q ss_pred             HHHhhhhhhh--hHHHHHHHHHHHHHhhc--ccccccc
Q 011020          426 EKASHDTLSL--DFQKYNQKLRQLLFNLK--RAWVGPG  459 (495)
Q Consensus       426 e~~~~~~~~~--d~~kyn~k~~~l~~n~k--~~~~~~~  459 (495)
                      |.|+|+.++.  +..+|++|+|+|+||||  +|+.|..
T Consensus        48 E~~if~~~~~~~~~k~Yk~k~Rsl~~NLKd~~N~~Lr~   85 (178)
T 3po3_S           48 ESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKH   85 (178)
T ss_dssp             HHHHHHHTSCSSSSTHHHHHHHHHHHHHHSSSCSHHHH
T ss_pred             HHHHHHHhcCCCchhhhhhhhhHHHHHcCCCCCHHHHH
Confidence            9999999986  55689999999999999  7766643

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

Probab=98.19  E-value=9.2e-07  Score=76.92  Aligned_cols=71  Identities=21%  Similarity=0.082  Sum_probs=55.7

Q ss_pred             ccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHHH
Q 011020          346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTAL  425 (495)
Q Consensus       346 ~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~al  425 (495)
                      +|||.-|||+.+-|-+++..-.   +  +..                               .      -..+..+...+
T Consensus        11 ~t~d~vR~k~~~lL~~aL~~~~---d--~~~-------------------------------~------~~~~~~lA~~I   48 (108)
T 3ndq_A           11 STSDSVRLKCREMLAAALRTGD---D--YIA-------------------------------I------GADEEELGSQI   48 (108)
T ss_dssp             CCCCHHHHHHHHHHHHHTTGGG---H--HHH-------------------------------H------TCCHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHcCC---C--CCc-------------------------------c------cccHHHHHHHH
Confidence            4999999999999998886521   0  000                               0      01456788999


Q ss_pred             HHHhhhhhhhhHHHHHHHHHHHHHhhc--cccccc
Q 011020          426 EKASHDTLSLDFQKYNQKLRQLLFNLK--RAWVGP  458 (495)
Q Consensus       426 e~~~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~  458 (495)
                      |.|.|+.++..-.+|.+|+|+|+||||  +|+-|.
T Consensus        49 E~~if~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~Lr   83 (108)
T 3ndq_A           49 EEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLR   83 (108)
T ss_dssp             HHHHHHHHCSSSHHHHHHHHHHHHHHTCTTCHHHH
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHHHH
Confidence            999999999888899999999999999  776553

>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=98.03  E-value=4.1e-06  Score=84.37  Aligned_cols=70  Identities=20%  Similarity=0.216  Sum_probs=57.5

Q ss_pred             cccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHH
Q 011020          345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA  424 (495)
Q Consensus       345 ~~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~a  424 (495)
                      ..|||..||+|++.|.++++....     +                                      . |++++.+..+
T Consensus       142 ~~~~d~~R~k~r~~L~~aL~~~~~-----~--------------------------------------~-~~~~~~~A~~  177 (309)
T 1pqv_S          142 AIYHHKLRDQVLKALYDVLAKESE-----H--------------------------------------P-PQSILHTAKA  177 (309)
T ss_pred             CcCChHHHHHHHHHHHHHHhcCCC-----c--------------------------------------c-chhHHHHHHH
Confidence            458999999999999999963100     0                                      0 3478899999


Q ss_pred             HHHHhhhhhhhhHHH--HHHHHHHHHHhhc--cccccc
Q 011020          425 LEKASHDTLSLDFQK--YNQKLRQLLFNLK--RAWVGP  458 (495)
Q Consensus       425 le~~~~~~~~~d~~k--yn~k~~~l~~n~k--~~~~~~  458 (495)
                      ||.|+|+.++.+..+  |++|+|+|+||||  +|+.|.
T Consensus       178 IE~al~~~~~~~~~~~~Yk~k~Rsl~~NLKd~~N~~Lr  215 (309)
T 1pqv_S          178 IESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLK  215 (309)
T ss_pred             HHHHHHHHhCCCchhHHHHHHHHHHHHHcCcCCChHHH
Confidence            999999999888888  9999999999999  777554

---

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	495
d1m4za_	217	b.34.12.1 (A:) Origin-recognition complex protein	5e-18

>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 = 80.8 bits (199), Expect = 5e-18
 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

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	495
d1m4za_	217	Origin-recognition complex protein 120kDa subunit,	99.71
d1enwa_	114	Elongation factor TFIIS domain 2 {Baker's yeast (S	97.98

>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=99.71  E-value=1.1e-19  Score=173.01  Aligned_cols=135  Identities=16%  Similarity=0.126  Sum_probs=101.9

Q ss_pred             CCCCcceeeeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCC-ceEEEEEEeecccccccCC----------
Q 011020          113 KGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDG-SMMVTGQWFYRPEEADRKG----------  181 (495)
Q Consensus       113 KGkk~R~~Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG-~~~VrVqWFYRPEET~~~~----------  181 (495)
                      ++++....|-....||.+|++||+|||.++. ++++|||+|.+|..+..+ ...+-+.||+|..|..-..          
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            4444455666667799999999999999776 678999999999877554 3566666777766643110          


Q ss_pred             ----------CCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEeecC
Q 011020          182 ----------GGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLT  248 (495)
Q Consensus       182 ----------~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~~L~  248 (495)
                                .+......+||||+|.+++++|+++|+|||+|+...+|..+. .....++|||+++||+...+|..+.
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 3345789999999999999998764

>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=97.98  E-value=3.2e-06  Score=72.03  Aligned_cols=69  Identities=19%  Similarity=0.160  Sum_probs=54.2

Q ss_pred             cccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHH
Q 011020          345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA  424 (495)
Q Consensus       345 ~~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~a  424 (495)
                      .+|+|..||++++.|.+.+..-...                                            .|+.+..+..+
T Consensus        16 ~~~~d~~R~~~~~~L~~aL~~~~~~--------------------------------------------~~~~~~~la~~   51 (114)
T d1enwa_          16 AIYHHKLRDQVLKALYDVLAKESEH--------------------------------------------PPQSILHTAKA   51 (114)
T ss_dssp             CSSTTTTHHHHHHHHHHHHHHHCSS--------------------------------------------SCSCHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhCcCcc--------------------------------------------chhHHHHHHHH
Confidence            6799999999999999988521100                                            14567888899


Q ss_pred             HHHHhhhhhhhh--HHHHHHHHHHHHHhhc--ccccc
Q 011020          425 LEKASHDTLSLD--FQKYNQKLRQLLFNLK--RAWVG  457 (495)
Q Consensus       425 le~~~~~~~~~d--~~kyn~k~~~l~~n~k--~~~~~  457 (495)
                      +|+++|..+..+  -++|.+|+|+|.||||  +|+-|
T Consensus        52 IE~~lf~~~~~~~~~~~Y~~k~rsi~~NLkd~~N~~L   88 (114)
T d1enwa_          52 IESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDL   88 (114)
T ss_dssp             HTTTTTSSCTTTTTHHHHHHHHHHHHHHHTTSCCCCT
T ss_pred             HHHHHHHHhcccCCcHHHHHHHHHHHHHcCccchHHH
Confidence            999999999754  3689999999999998  45433