Citrus Sinensis ID: 026819

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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--
Protein Sequence
MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYLRY
Secondary Structure (PSIPRED)
ccEEEEEccccccccEEEcccccEEEEcccccccccccccccHHHHHHHHHHHccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEEEcccccHHHEEEcccccEEEEEcccccccccHEEEHcHEEEEEHHHHccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHEHHHEEEccccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
meyrcvkcgfriKTLFVqyspgnirlmkceNCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSrsnegqsssmSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILlntsagassFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYLRY
Flexible Loop (DISEMBL)
meyrcvkcgfriktlfvqyspgnirlMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVvqglelrylry
Low Complexity Region (SEG)
MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFllldayrslllsrsNEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYLRY
Disordered region (IsUnstruct)
**YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLS**********SFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYL**
Disordered Region (DISOPRED)
MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLL*************SLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYLRY
Disordered Region (DISEMBL)
MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLS*********MSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYLRY
Disordered Region (DISPRO)
MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYLRY
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooHHHHHHHHHHHHHHHHHHHHiiiHHHHHHHHHHHHHHHHHHHHHHHoooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYLRY
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	232	2.2.26 [Sep-21-2011]
Q54GD9	246	Protein arv1 homolog OS=D	yes	no	0.836	0.788	0.303	1e-23
Q9HDX5	266	Protein arv1 OS=Schizosac	yes	no	0.827	0.721	0.307	2e-17
Q9H2C2	271	Protein ARV1 OS=Homo sapi	yes	no	0.810	0.693	0.328	3e-17
Q9D0U9	266	Protein ARV1 OS=Mus muscu	yes	no	0.814	0.710	0.318	3e-15
Q3SZW3	282	Protein ARV1 OS=Bos tauru	yes	no	0.810	0.666	0.313	9e-15
Q750Q7	299	Protein ARV1 OS=Ashbya go	yes	no	0.284	0.220	0.439	3e-07
Q06541	321	Protein ARV1 OS=Saccharom	yes	no	0.271	0.196	0.396	0.0001

>sp|Q54GD9|ARV1_DICDI Protein arv1 homolog OS=Dictyostelium discoideum GN=arv1 PE=3 SV=1

 Score =  109 bits (273), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 65/214 (30%), Positives = 108/214 (50%), Gaps = 20/214 (9%)

Query: 5   CVKCGFRIKTLFVQYSP---GNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
           C++CG  +  ++ ++     GNIRL +C +C   AD+Y+E + +I+ +DL LHK QAYRH
Sbjct: 3   CIECGRPVNDVYKEFGKAGSGNIRLTRCASCNQTADKYVEYDFIIVFLDLFLHKAQAYRH 62

Query: 62  LLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLK 121
           LL+N        +     K  V ++  ++Y   L  +  E   S  +F  + W       
Sbjct: 63  LLFNRQPYRDFGIPIQYIKVLVVYIFFESYIKWLRFKEYEQHPSGPAFYYIDW-----QD 117

Query: 122 DVVLGNVMFLGVFLHAS------------RILLNTSAGASSFKDFLLAVLISSYFKIFLV 169
           DV      F+ V   A             R +  +      +   ++A+++SS+ K FLV
Sbjct: 118 DVPYDRYWFIFVTAIAEFAVYILSIILSVRFIYESRYPIIKYNYLIMAIILSSFGKGFLV 177

Query: 170 AMMVWNFPSSVIYIIDLFVLSSNTVALKVITESA 203
            MM+W++P S   I+++FVLSSN VA+KV  ++ 
Sbjct: 178 LMMIWDYPFSFGSILNIFVLSSNVVAIKVFLDTT 211

Mediator of sterol homeostasis involved in sterol uptake, trafficking and distribution into membranes. Regulates also the sphingolipid metabolism.
Dictyostelium discoideum (taxid: 44689)

>sp|Q9HDX5|ARV1_SCHPO Protein arv1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=arv1 PE=3 SV=3

 Score = 89.0 bits (219), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/208 (30%), Positives = 120/208 (57%), Gaps = 16/208 (7%)

Query: 4   RCVKCGFRIKTLFVQYSPG--NIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
           +CV+CG  + +L+  Y  G  NIRL +C+NC+  AD+YIE +++++ +D+IL KPQ YRH
Sbjct: 2   KCVECGAEVDSLYTYYGRGTSNIRLAQCKNCKQFADKYIELDVVLISMDVILMKPQVYRH 61

Query: 62  LLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSN-EGQSSSMSFSLLAWIF--QK 118
           LL+N L++ T       +++ V F +L +  ++ L  S  E +++   +   A  F  Q 
Sbjct: 62  LLFNSLSART-------FRNVVNFCILISLFNVFLVWSRLEKRAALFPYFTPAQAFLSQP 114

Query: 119 MLKD---VVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWN 175
           +++    ++L  ++   V+  +  +LL  + G  S+     AV++SS  ++  V M++W+
Sbjct: 115 IIRQYLTLLLICLVETTVYQISVVLLLCLTMGWKSWTSASGAVILSSSTRMLPVFMVIWD 174

Query: 176 FPSSV-IYIIDLFVLSSNTVALKVITES 202
           +  S+   +++  VL SN  AL ++T S
Sbjct: 175 YDLSIAATVVEWVVLFSNVDALCILTGS 202

Mediator of sterol homeostasis involved in sterol uptake, trafficking and distribution into membranes. Regulates also the sphingolipid metabolism.

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

>sp|Q9H2C2|ARV1_HUMAN Protein ARV1 OS=Homo sapiens GN=ARV1 PE=2 SV=1

 Score = 88.6 bits (218), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/204 (32%), Positives = 111/204 (54%), Gaps = 16/204 (7%)

Query: 2   EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
           +YRC++C    K L+  Y+ G +++  C++C+   D+YIE + +I+LI+ IL K QAYRH
Sbjct: 31  QYRCIECNQEAKELYRDYNHGVLKITICKSCQKPVDKYIEYDPVIILINAILCKAQAYRH 90

Query: 62  LLYNVLNSETVNLKGILWKSTVGFLLLDAY-RSLLLSRSNEGQSSSMSFSLL-AWIFQKM 119
           +L+N      +N+ G   K  +  LL +AY R   L  SN+  +          W F +M
Sbjct: 91  ILFNT----QINIHG---KLCIFCLLCEAYLRWWQLQDSNQNTAPDDLIRYAKEWDFYRM 143

Query: 120 LKDVVLGNVM-FLGV--FLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVW-- 174
                L     F+G+  FL   R +  T+    +F   L A+L+SSY K+ L+  ++W  
Sbjct: 144 FAIAALEQTAYFIGIFTFLWVERPM--TAKKKPNFILLLKALLLSSYGKLLLIPAVIWEH 201

Query: 175 NFPSSVIYIIDLFVLSSNTVALKV 198
           ++ S  + +I +FVL+SN  A++V
Sbjct: 202 DYTSVCLKLIKVFVLTSNFQAIRV 225

May act as a mediator of sterol homeostasis.

Homo sapiens (taxid: 9606)

>sp|Q9D0U9|ARV1_MOUSE Protein ARV1 OS=Mus musculus GN=Arv1 PE=2 SV=1

 Score = 82.0 bits (201), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/201 (31%), Positives = 105/201 (52%), Gaps = 12/201 (5%)

Query: 3   YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHL 62
           YRC++C    + L+  YS G +++  C++C+   D+YIE + +I+LI+ IL K QAYRH+
Sbjct: 27  YRCIECNREAQELYRDYSHGVLKITICKSCQKPVDKYIEYDPVIILINAILCKTQAYRHI 86

Query: 63  LYNVLNSETVNLKGILWKSTVGFLLLDAY-RSLLLSRSNEGQSSSMSFSLL-AWIFQKML 120
           L+N      +N+ G L    +  LL +AY R   L  S++  +          W F +M 
Sbjct: 87  LFNT----KINIHGKL---CMFCLLCEAYLRWWQLQDSSQSPAPDDVIRYAKEWDFYRMF 139

Query: 121 KDVVLGNVMFL-GVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVW--NFP 177
                    FL G+F         T+  A  F   L A+L+SSY K+ L+  ++W  ++ 
Sbjct: 140 VIASFEQAAFLTGIFAFLWVQQPMTAKRAPDFVLLLKALLLSSYGKLLLIPAVIWEHDYT 199

Query: 178 SSVIYIIDLFVLSSNTVALKV 198
              + +I +FVL+SN  A++V
Sbjct: 200 PLCLRLIKVFVLTSNFQAVRV 220

May act as a mediator of sterol homeostasis.

Mus musculus (taxid: 10090)

>sp|Q3SZW3|ARV1_BOVIN Protein ARV1 OS=Bos taurus GN=ARV1 PE=2 SV=1

 Score = 80.5 bits (197), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 64/204 (31%), Positives = 107/204 (52%), Gaps = 16/204 (7%)

Query: 2   EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
           +YRC++C    K L+  Y+ G +++  C++C+   D+YIE + +I+LI+ IL K QAYRH
Sbjct: 42  QYRCIECNQEAKELYRDYNHGVLKITICKSCQKPVDKYIEYDPVIILINAILCKAQAYRH 101

Query: 62  LLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLA--WIFQKM 119
           +L+N      +N+ G L    V  LL +AY      + +        F   A  W F +M
Sbjct: 102 ILFNT----KINMHGKL---CVFCLLCEAYLRWWQLQDSSQSIDPDDFIRYAKEWDFYRM 154

Query: 120 LKDVVLGNVM-FLGV--FLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVW-- 174
                L     F+G+  FL   R +   +    +F   L A+L+SSY K+ L+  ++W  
Sbjct: 155 FAIASLEQTAYFIGIFAFLWVERPI--RAKEKLNFTLLLKALLLSSYGKLLLIPAVIWEH 212

Query: 175 NFPSSVIYIIDLFVLSSNTVALKV 198
           ++    + +I +FVL+SN  A++V
Sbjct: 213 DYTPLCLRLIKVFVLTSNFQAIRV 236

May act as a mediator of sterol homeostasis.

Bos taurus (taxid: 9913)

>sp|Q750Q7|ARV1_ASHGO Protein ARV1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=ARV1 PE=3 SV=1

 Score = 55.5 bits (132), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/66 (43%), Positives = 42/66 (63%)

Query: 5  CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLY 64
          C+ C   +++L+V Y   +IRL  C  C  V D Y+E + ++L IDL+L KP AYRHL+Y
Sbjct: 3  CINCCCHVESLYVAYPGDHIRLTDCWQCGEVVDRYVEFDNVLLFIDLLLLKPGAYRHLVY 62

Query: 65 NVLNSE 70
          N L  +
Sbjct: 63 NSLEVD 68

Mediator of sterol homeostasis involved in sterol uptake, trafficking and distribution into membranes. Regulates also the sphingolipid metabolism.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

>sp|Q06541|ARV1_YEAST Protein ARV1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ARV1 PE=1 SV=1

 Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 40/63 (63%)

Query: 5  CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLY 64
          C+ C   + +L+  YS  +I+L  C  C+   D+Y+E + ++L IDL+L K  AYRHL++
Sbjct: 3  CITCMRPVDSLYTVYSNDHIQLTDCPYCQETVDKYVEIDNVLLFIDLLLLKAGAYRHLVF 62

Query: 65 NVL 67
          N L
Sbjct: 63 NAL 65

Mediator of sterol homeostasis involved in sterol uptake, trafficking and distribution into membranes. Regulates also the sphingolipid metabolism. Required for growth during anaerobiosis and sterol uptake.

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	232
225453664	248	PREDICTED: protein arv1 homolog [Vitis v	0.961	0.899	0.708	3e-87
224128085	232	predicted protein [Populus trichocarpa]	0.995	0.995	0.682	7e-86
356504684	250	PREDICTED: protein arv1 homolog [Glycine	0.978	0.908	0.603	2e-69
356570412	247	PREDICTED: protein arv1 homolog [Glycine	0.978	0.919	0.590	1e-67
297843020	245	hypothetical protein ARALYDRAFT_470181 [	0.943	0.893	0.568	4e-66
449431936	277	PREDICTED: protein arv1 homolog [Cucumis	0.943	0.790	0.565	7e-65
255548091	187	arv1, putative [Ricinus communis] gi|223	0.771	0.957	0.668	2e-64
79332834	245	Arv1-like protein [Arabidopsis thaliana]	0.943	0.893	0.555	1e-61
297814177	228	hypothetical protein ARALYDRAFT_490425 [	0.913	0.929	0.570	9e-61
242032783	237	hypothetical protein SORBIDRAFT_01g00613	0.922	0.902	0.536	3e-58

>gi|225453664|ref|XP_002268438.1| PREDICTED: protein arv1 homolog [Vitis vinifera] gi|296089029|emb|CBI38732.3| unnamed protein product [Vitis vinifera]

 Score =  327 bits (838), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 158/223 (70%), Positives = 185/223 (82%)

Query: 1   MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYR 60
           ME RC+ CGF IKTLF+QYSPGNIRLMKCENC+AVADEYIECE MI+LIDLILHKP+AYR
Sbjct: 1   MELRCIHCGFPIKTLFLQYSPGNIRLMKCENCKAVADEYIECESMIVLIDLILHKPKAYR 60

Query: 61  HLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKML 120
           HLL+N+LN +T+N +G+LWKS +GFLLLDAYR L+L+RS E    SMSFS L W F K+L
Sbjct: 61  HLLFNLLNPQTLNFQGLLWKSALGFLLLDAYRILVLTRSEEEWGLSMSFSSLFWRFSKIL 120

Query: 121 KDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSV 180
            DV+ GN+ FL +FL A+R LLNT  GAS +K+ LLA+LISSYFKIFL+AMMVW  PSSV
Sbjct: 121 MDVLFGNLAFLSIFLLATRNLLNTVGGASRYKNLLLAILISSYFKIFLIAMMVWELPSSV 180

Query: 181 IYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQ 223
           I+IID+FVLSSNTVALKV+T S M+R    C VAHAVK FV Q
Sbjct: 181 IFIIDVFVLSSNTVALKVVTGSGMSRCAETCFVAHAVKLFVSQ 223

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128085|ref|XP_002320240.1| predicted protein [Populus trichocarpa] gi|222861013|gb|EEE98555.1| predicted protein [Populus trichocarpa]

 Score =  322 bits (825), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 159/233 (68%), Positives = 187/233 (80%), Gaps = 2/233 (0%)

Query: 1   MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYR 60
           ME RCV+CGF IKTLFVQYSPGNIRLM+CENC+AVADEYIECE MI+LIDLILHK +AYR
Sbjct: 1   MEPRCVECGFPIKTLFVQYSPGNIRLMRCENCKAVADEYIECEFMIILIDLILHKTKAYR 60

Query: 61  HLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQ-SSSMSFSLLAWIFQKM 119
           HLL+NV+N  TVN +G LWKS   FLLLDAYRSLLL R NEG+  SSMSFS + W F+++
Sbjct: 61  HLLFNVINQHTVNFEGSLWKSIFAFLLLDAYRSLLLKR-NEGEWGSSMSFSSIVWTFEEV 119

Query: 120 LKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSS 179
           + DV +GN +F  +FL + R++LNTS   S  KD LLA+L+SSYFKIFL+A MVW FPSS
Sbjct: 120 IVDVFVGNFVFFCIFLLSMRLMLNTSIQISRCKDILLAILVSSYFKIFLIATMVWEFPSS 179

Query: 180 VIYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLELRYLRY 232
           VI+IIDLFVLSSNTVALKVIT+SAMNR +  C  A A+K  V QG   R LR+
Sbjct: 180 VIFIIDLFVLSSNTVALKVITDSAMNRCIAACFCAQALKLLVTQGPARRSLRF 232

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504684|ref|XP_003521125.1| PREDICTED: protein arv1 homolog [Glycine max]

 Score =  268 bits (684), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 137/227 (60%), Positives = 169/227 (74%)

Query: 1   MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYR 60
           M YRC++C   +KTL+VQYSPGNIRLMKCENC+AVADEYIECEIMIL+IDLILHKP+AYR
Sbjct: 1   MGYRCIQCWCPVKTLYVQYSPGNIRLMKCENCKAVADEYIECEIMILVIDLILHKPKAYR 60

Query: 61  HLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKML 120
           HLL+NV+N ET+   G+LWK  V FLL ++YR L+L  S     SS S S L  I  K+L
Sbjct: 61  HLLHNVINQETMKFHGLLWKLAVIFLLFESYRCLILESSKGKLGSSNSVSSLVSICWKVL 120

Query: 121 KDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSV 180
            DV++GN+MFL  F    ++  + S   S   D LL ++ISSYFKIFL+AMMVW+FPSSV
Sbjct: 121 MDVIIGNLMFLLTFFFMVKMFFHVSITISRCIDLLLTLMISSYFKIFLIAMMVWDFPSSV 180

Query: 181 IYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLEL 227
           I+II+LF LSSN  ALKV+TES M R +  C  A+A+KF V + LEL
Sbjct: 181 IFIIELFCLSSNAAALKVMTESTMRRCVWTCFSAYAIKFIVTRILEL 227

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356570412|ref|XP_003553382.1| PREDICTED: protein arv1 homolog [Glycine max]

 Score =  261 bits (668), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 134/227 (59%), Positives = 165/227 (72%)

Query: 1   MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYR 60
           M YRC++CG  +KTL+VQYSPGNIRLMKCENC+AVADEYIECEIMIL IDLILHKP+AYR
Sbjct: 1   MGYRCIQCGCPVKTLYVQYSPGNIRLMKCENCKAVADEYIECEIMILAIDLILHKPKAYR 60

Query: 61  HLLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKML 120
           HLL+NV+N ET+  +G+LWK  V FL  + YR L+L  S     SSMS S    I  K+L
Sbjct: 61  HLLHNVINQETMKFQGLLWKLAVIFLFFEYYRCLILESSKGKLDSSMSVSPSVSICWKVL 120

Query: 121 KDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSV 180
            DV+ GN+MFL  F     +L + S   +   D LLA++ISSYFKIF +AMMVW FPSSV
Sbjct: 121 MDVLFGNLMFLLTFFFMVMMLFHVSITITRCIDLLLALMISSYFKIFFIAMMVWEFPSSV 180

Query: 181 IYIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLEL 227
           I+II+LF LSSN   LKV+T+S M+R +  C  A+A+KF +   LEL
Sbjct: 181 IFIIELFCLSSNAATLKVMTDSTMSRCVWTCFSAYAIKFIITWILEL 227

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843020|ref|XP_002889391.1| hypothetical protein ARALYDRAFT_470181 [Arabidopsis lyrata subsp. lyrata] gi|297335233|gb|EFH65650.1| hypothetical protein ARALYDRAFT_470181 [Arabidopsis lyrata subsp. lyrata]

 Score =  256 bits (655), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 128/225 (56%), Positives = 168/225 (74%), Gaps = 6/225 (2%)

Query: 2   EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
           E+RCV CGFR+K+LF+QYSPGNIRLMKC NC+ VADEYIECE MI+ IDLILH+P+ YRH
Sbjct: 5   EHRCVGCGFRVKSLFIQYSPGNIRLMKCGNCKEVADEYIECERMIIFIDLILHRPKVYRH 64

Query: 62  LLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLK 121
           +LYN +N ETVN++ +LWK    +LLLD+YRSLLL R++E  S S S  L++    K+L 
Sbjct: 65  VLYNAINPETVNIQHLLWKLVFVYLLLDSYRSLLLRRTDEESSFSHSSVLISI---KVLI 121

Query: 122 DVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVI 181
            V+  N  F+  F  A++ LLN     S  ++ +L + ISSYFKIFL+AM+VW FP SVI
Sbjct: 122 GVLSANAAFIFSFAIAAKGLLNE---VSRGREIMLGICISSYFKIFLLAMLVWEFPMSVI 178

Query: 182 YIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLE 226
           +I+D+ VL+SN++ALKV+TES M R + VCL+AH V+F V Q  E
Sbjct: 179 FIVDILVLTSNSMALKVMTESTMTRCIAVCLIAHLVRFSVGQIFE 223

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449431936|ref|XP_004133756.1| PREDICTED: protein arv1 homolog [Cucumis sativus]

 Score =  252 bits (644), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 126/223 (56%), Positives = 161/223 (72%), Gaps = 4/223 (1%)

Query: 4   RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLL 63
           RCV+CGFR   LFV YSPGN+ LMKC+NC++VADEYIECE MI+L+DLILHK QAYRHLL
Sbjct: 56  RCVQCGFRTSQLFVLYSPGNMHLMKCDNCKSVADEYIECEAMIVLVDLILHKRQAYRHLL 115

Query: 64  YNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLKDV 123
           YN  +   ++ K ++WK  + FLLLDAYR +LL  S   +  SMS S    I QK L   
Sbjct: 116 YNQFDRNRLSRKDLMWKLGLSFLLLDAYRYMLLILSE--KPLSMSLSSTIGICQKALMYA 173

Query: 124 VLGNVMFLGVFLHASRILLNTSAGA--SSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVI 181
           +LGN MF+ V    SR+ L +S+G     +++F  A++ISSYFKIFLV+MM+W FPS+VI
Sbjct: 174 LLGNAMFICVLHILSRVFLTSSSGDHRHRYREFFFAIIISSYFKIFLVSMMIWEFPSTVI 233

Query: 182 YIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQG 224
           +I+DLFVLSSN VA+KVITES ++R +G CL AH  KF   + 
Sbjct: 234 FIVDLFVLSSNVVAIKVITESTVSRCIGTCLCAHGAKFLATKA 276

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548091|ref|XP_002515102.1| arv1, putative [Ricinus communis] gi|223545582|gb|EEF47086.1| arv1, putative [Ricinus communis]

 Score =  251 bits (640), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 121/181 (66%), Positives = 147/181 (81%), Gaps = 2/181 (1%)

Query: 3   YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHL 62
           YRCV+CGF +K+L+VQYSPGNIRLMKCENC+AVADEYIECE MI+LIDLILHKP+AYRHL
Sbjct: 2   YRCVECGFGVKSLYVQYSPGNIRLMKCENCKAVADEYIECEFMIMLIDLILHKPKAYRHL 61

Query: 63  LYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLKD 122
           LYNVLN ETVNL+G++WKS + FLLLDAYRS+LL R+ E Q SS+SF  L W  QK+  D
Sbjct: 62  LYNVLNQETVNLEGLIWKSAISFLLLDAYRSILLQRNVEEQVSSLSFPSLFWRSQKIFMD 121

Query: 123 VVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWN--FPSSV 180
           V LGN+ FL VFL A+RILL  S   S  +  L A+L+SSYFKIFL+AMM ++  +P S+
Sbjct: 122 VFLGNLTFLCVFLLATRILLKASVRVSRTRGLLPAILVSSYFKIFLIAMMPYSLLYPCSL 181

Query: 181 I 181
           +
Sbjct: 182 V 182

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79332834|ref|NP_171610.2| Arv1-like protein [Arabidopsis thaliana] gi|56540523|gb|AAV92715.1| ARV1 [Arabidopsis thaliana] gi|332189096|gb|AEE27217.1| Arv1-like protein [Arabidopsis thaliana]

 Score =  242 bits (617), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 125/225 (55%), Positives = 165/225 (73%), Gaps = 6/225 (2%)

Query: 2   EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
           E+RCV CGFR+K+LF+QYSPGNIRLMKC NC+ VADEYIECE MI+ IDLILH+P+ YRH
Sbjct: 5   EHRCVGCGFRVKSLFIQYSPGNIRLMKCGNCKEVADEYIECERMIIFIDLILHRPKVYRH 64

Query: 62  LLYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLK 121
           +LYN +N  TVN++ +LWK    +LLLD YRSLLL +S+E  S S S  LL+    K+L 
Sbjct: 65  VLYNAINPATVNIQHLLWKLVFAYLLLDCYRSLLLRKSDEESSFSDSPVLLSI---KVLI 121

Query: 122 DVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVI 181
            V+  N  F+  F  A++ LLN     S  ++ +L + ISSYFKIFL+AM+VW FP SVI
Sbjct: 122 GVLSANAAFIISFAIATKGLLNE---VSRRREIMLGIFISSYFKIFLLAMLVWEFPMSVI 178

Query: 182 YIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLE 226
           + +D+ +L+SN++ALKV+TES M R + VCL+AH ++F V Q  E
Sbjct: 179 FFVDILLLTSNSMALKVMTESTMTRCIAVCLIAHLIRFLVGQIFE 223

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814177|ref|XP_002874972.1| hypothetical protein ARALYDRAFT_490425 [Arabidopsis lyrata subsp. lyrata] gi|297320809|gb|EFH51231.1| hypothetical protein ARALYDRAFT_490425 [Arabidopsis lyrata subsp. lyrata]

 Score =  239 bits (609), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 125/219 (57%), Positives = 165/219 (75%), Gaps = 7/219 (3%)

Query: 5   CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLY 64
           CV+CG ++K+LF+QYSPGN RLMKCENC  VADEY+ECE++I+ IDLILHK +AYRHLLY
Sbjct: 8   CVECGHKVKSLFIQYSPGNFRLMKCENCNEVADEYVECELLIIFIDLILHKTKAYRHLLY 67

Query: 65  NVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQKMLKDVV 124
           NV N E+VN++ +LWK  + +LLLD YRSLLL R+N+  + SMSF L +    ++L +V+
Sbjct: 68  NVFNQESVNIQHLLWKLVLAYLLLDTYRSLLLRRTNDESNVSMSFVLESL---EVLVNVL 124

Query: 125 LGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYII 184
             N  F+  F  A++++L  S G    K+ LL VLISSY KIFL AM VW FP SVI+I+
Sbjct: 125 SANFAFVLSFALAAKMMLVMSRG----KEILLGVLISSYIKIFLFAMPVWEFPVSVIFIV 180

Query: 185 DLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQ 223
           D+ VL+SN VALKV+TESA +R L VC +AH+++F V Q
Sbjct: 181 DMLVLTSNAVALKVMTESATSRCLAVCFIAHSIRFLVDQ 219

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242032783|ref|XP_002463786.1| hypothetical protein SORBIDRAFT_01g006130 [Sorghum bicolor] gi|241917640|gb|EER90784.1| hypothetical protein SORBIDRAFT_01g006130 [Sorghum bicolor]

 Score =  230 bits (587), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 117/218 (53%), Positives = 159/218 (72%), Gaps = 4/218 (1%)

Query: 4   RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLL 63
           RCV CG R+KTLFVQYSPGNIRLMKC+NC+AVAD YIECE MI+LIDL+LHK +AYRH+L
Sbjct: 12  RCVGCGGRVKTLFVQYSPGNIRLMKCDNCKAVADPYIECEFMIILIDLVLHKTRAYRHVL 71

Query: 64  YNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSN--EGQSSSMSFSLLAWIFQKMLK 121
           +N L+  +   KGIL++ST+  + LDA+R +  S+ N  +G SS   FS ++    +++ 
Sbjct: 72  FNKLSMGSSVDKGILYRSTLIHIALDAFR-ISFSKGNRADGASSRSIFSTISNC-TEVIG 129

Query: 122 DVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVI 181
           D +LGN++F+ + L   R +L  S     ++D L AV+ISSYFK+FL  MMVW FPSSVI
Sbjct: 130 DALLGNIIFMIILLLGVRFILKLSFDVIRYRDVLFAVIISSYFKLFLFTMMVWEFPSSVI 189

Query: 182 YIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKF 219
           +I+++FVLSSN VAL+V+++        VCLVAHA K+
Sbjct: 190 FIVEMFVLSSNVVALRVVSQFPKAHCFAVCLVAHAAKY 227

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	232
TAIR|locus:2117012	228	ARV2 "AT4G01510" [Arabidopsis	0.913	0.929	0.511	1.1e-55
TAIR|locus:2200940	245	ARV1 "AT1G01020" [Arabidopsis	0.943	0.893	0.506	3.7e-55
DICTYBASE|DDB_G0290221	246	arv1 "arv1-like family protein	0.262	0.247	0.437	1.5e-24
POMBASE|SPAPB1A10.15	266	arv1 "Arv1-like family protein	0.293	0.255	0.471	1.8e-22
UNIPROTKB|Q9H2C2	271	ARV1 "Protein ARV1" [Homo sapi	0.875	0.749	0.294	8.3e-19
UNIPROTKB|E2QRS2	281	ARV1 "Uncharacterized protein"	0.818	0.676	0.292	3.6e-18
ZFIN|ZDB-GENE-080204-35	239	arv1 "ARV1 homolog (S. cerevis	0.853	0.828	0.316	7.5e-18
MGI|MGI:1916115	266	Arv1 "ARV1 homolog (yeast)" [M	0.879	0.766	0.285	9.5e-18
RGD|1310264	267	Arv1 "ARV1 homolog (S. cerevis	0.943	0.820	0.269	1.2e-17
UNIPROTKB|F1RGS6	281	ARV1 "Uncharacterized protein"	0.314	0.259	0.389	1.3e-17

TAIR|locus:2117012 ARV2 "AT4G01510" [Arabidopsis thaliana (taxid:3702)]

 Score = 574 (207.1 bits), Expect = 1.1e-55, P = 1.1e-55
 Identities = 112/219 (51%), Positives = 153/219 (69%)

Query:     5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLY 64
             CV+CG ++K+LF+QYSPGN RLMKCENC  VADEY+ECE++I+ IDLILHK +AYRHLLY
Sbjct:     8 CVECGHKVKSLFIQYSPGNFRLMKCENCEEVADEYVECELLIIFIDLILHKTKAYRHLLY 67

Query:    65 NVLNSETVNLKGILWKSTVGFXXXXXXXXXXXXXXNEGQSSSMSFSLLAWIFQKMLKDVV 124
             NV+N E+ N++ +LWK  + +              N+G + SMSF L   +  ++L +V+
Sbjct:    68 NVVNQESANVQHLLWKLVLAYLLLDTYRSLLLRRTNDGSNVSMSF-LFESL--EVLVNVL 124

Query:   125 LGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIYII 184
               N  F+  F  A++++L    G    K+ LL +LISSY KIFL AM VW FP SVI+I+
Sbjct:   125 SANFAFVFSFAFAAKLMLVMPRG----KEILLTILISSYVKIFLFAMPVWEFPVSVIFIV 180

Query:   185 DLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQ 223
             D+ VL+SN VALKV+TESA +R L VC +AH+++F V Q
Sbjct:   181 DMLVLTSNAVALKVMTESATSRCLAVCFIAHSIRFLVDQ 219

GO:0003674 "molecular_function" evidence=ND

GO:0016020 "membrane" evidence=ISS

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0006665 "sphingolipid metabolic process" evidence=IMP

GO:0016125 "sterol metabolic process" evidence=IMP

GO:0006661 "phosphatidylinositol biosynthetic process" evidence=RCA

TAIR|locus:2200940 ARV1 "AT1G01020" [Arabidopsis thaliana (taxid:3702)]

 Score = 569 (205.4 bits), Expect = 3.7e-55, P = 3.7e-55
 Identities = 114/225 (50%), Positives = 153/225 (68%)

Query:     2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
             E+RCV CGFR+K+LF+QYSPGNIRLMKC NC+ VADEYIECE MI+ IDLILH+P+ YRH
Sbjct:     5 EHRCVGCGFRVKSLFIQYSPGNIRLMKCGNCKEVADEYIECERMIIFIDLILHRPKVYRH 64

Query:    62 LLYNVLNSETVNLKGILWKSTVGFXXXXXXXXXXXXXXNEGQSSSMSFSLLAWIFQKMLK 121
             +LYN +N  TVN++ +LWK    +              +E  S S S  LL+    K+L 
Sbjct:    65 VLYNAINPATVNIQHLLWKLVFAYLLLDCYRSLLLRKSDEESSFSDSPVLLSI---KVLI 121

Query:   122 DVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVI 181
              V+  N  F+  F  A++ LLN     S  ++ +L + ISSYFKIFL+AM+VW FP SVI
Sbjct:   122 GVLSANAAFIISFAIATKGLLNE---VSRRREIMLGIFISSYFKIFLLAMLVWEFPMSVI 178

Query:   182 YIIDLFVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGLE 226
             + +D+ +L+SN++ALKV+TES M R + VCL+AH ++F V Q  E
Sbjct:   179 FFVDILLLTSNSMALKVMTESTMTRCIAVCLIAHLIRFLVGQIFE 223

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0016020 "membrane" evidence=ISS

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0006665 "sphingolipid metabolic process" evidence=IMP

GO:0016125 "sterol metabolic process" evidence=IMP

DICTYBASE|DDB_G0290221 arv1 "arv1-like family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 167 (63.8 bits), Expect = 1.5e-24, Sum P(2) = 1.5e-24
 Identities = 28/64 (43%), Positives = 44/64 (68%)

Query:     5 CVKCGFRIKTLFVQYSP---GNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
             C++CG  +  ++ ++     GNIRL +C +C   AD+Y+E + +I+ +DL LHK QAYRH
Sbjct:     3 CIECGRPVNDVYKEFGKAGSGNIRLTRCASCNQTADKYVEYDFIIVFLDLFLHKAQAYRH 62

Query:    62 LLYN 65
             LL+N
Sbjct:    63 LLFN 66

GO:0016021 "integral to membrane" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0006869 "lipid transport" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0006665 "sphingolipid metabolic process" evidence=IEA

GO:0006629 "lipid metabolic process" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0000139 "Golgi membrane" evidence=IEA

POMBASE|SPAPB1A10.15 arv1 "Arv1-like family protein Arv1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 193 (73.0 bits), Expect = 1.8e-22, Sum P(2) = 1.8e-22
 Identities = 33/70 (47%), Positives = 52/70 (74%)

Query:     4 RCVKCGFRIKTLFVQYSPG--NIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
             +CV+CG  + +L+  Y  G  NIRL +C+NC+  AD+YIE +++++ +D+IL KPQ YRH
Sbjct:     2 KCVECGAEVDSLYTYYGRGTSNIRLAQCKNCKQFADKYIELDVVLISMDVILMKPQVYRH 61

Query:    62 LLYNVLNSET 71
             LL+N L++ T
Sbjct:    62 LLFNSLSART 71

GO:0000139 "Golgi membrane" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0005783 "endoplasmic reticulum" evidence=ISO

GO:0005794 "Golgi apparatus" evidence=ISO

GO:0006665 "sphingolipid metabolic process" evidence=ISO

GO:0006696 "ergosterol biosynthetic process" evidence=ISO

GO:0016021 "integral to membrane" evidence=ISO

GO:0030176 "integral to endoplasmic reticulum membrane" evidence=IC

GO:0032366 "intracellular sterol transport" evidence=ISO

UNIPROTKB|Q9H2C2 ARV1 "Protein ARV1" [Homo sapiens (taxid:9606)]

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 64/217 (29%), Positives = 109/217 (50%)

Query:     2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
             +YRC++C    K L+  Y+ G +++  C++C+   D+YIE + +I+LI+ IL K QAYRH
Sbjct:    31 QYRCIECNQEAKELYRDYNHGVLKITICKSCQKPVDKYIEYDPVIILINAILCKAQAYRH 90

Query:    62 LLYNVLNSETVNLKGILWKSTVGFXXXXXXXXXXXXXXNEGQSSSMSFSLLAWIFQKMLK 121
             +L+N      +N+ G L    +                N      + ++   W F +M  
Sbjct:    91 ILFNT----QINIHGKLCIFCLLCEAYLRWWQLQDSNQNTAPDDLIRYAK-EWDFYRMFA 145

Query:   122 DVVLGNVM-FLGVF--LHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVW--NF 176
                L     F+G+F  L   R +  T+    +F   L A+L+SSY K+ L+  ++W  ++
Sbjct:   146 IAALEQTAYFIGIFTFLWVERPM--TAKKKPNFILLLKALLLSSYGKLLLIPAVIWEHDY 203

Query:   177 PSSVIYIIDLFVLSSNTVALKVITESAMNRILGVCLV 213
              S  + +I +FVL+SN  A++V     +NR L    V
Sbjct:   204 TSVCLKLIKVFVLTSNFQAIRVTLN--INRKLSFLAV 238

GO:0006665 "sphingolipid metabolic process" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008206 "bile acid metabolic process" evidence=IEA

GO:0030301 "cholesterol transport" evidence=IEA

GO:0090181 "regulation of cholesterol metabolic process" evidence=IEA

UNIPROTKB|E2QRS2 ARV1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 59/202 (29%), Positives = 104/202 (51%)

Query:     2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
             +YRC++C    K L+  Y+ G +++  C++C+   D+YIE + +I+LI+ IL K QAYRH
Sbjct:    41 QYRCIECNQEAKELYRDYNHGVLKITICKSCQKPVDKYIEYDPVIILINAILCKAQAYRH 100

Query:    62 LLYNVLNSETVNLKGILWKSTVGFXXXXXXXXXXXXXXNEGQSSSMSFSLLAWIFQKMLK 121
             +L+N      +N+ G L    +                N   +  + ++   W F +M  
Sbjct:   101 ILFNT----KINMHGKLCIFCLLCEAYLRWWQLQDSNQNTDPNDFIRYAK-EWDFYRMFA 155

Query:   122 DVVLGNV-MFLGVF--LHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVW--NF 176
                L     F+G+F  L   R +  T+    +F   L A+L+SSY K+ L+  ++W  ++
Sbjct:   156 IASLEQTAFFIGIFTFLWIERPM--TAKKKPNFTLLLKALLLSSYGKLLLIPAVIWEHDY 213

Query:   177 PSSVIYIIDLFVLSSNTVALKV 198
                 + +I +FVL+SN  A++V
Sbjct:   214 TPLCLRLIKVFVLTSNFQAIRV 235

GO:0090181 "regulation of cholesterol metabolic process" evidence=IEA

GO:0030301 "cholesterol transport" evidence=IEA

GO:0008206 "bile acid metabolic process" evidence=IEA

ZFIN|ZDB-GENE-080204-35 arv1 "ARV1 homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 69/218 (31%), Positives = 106/218 (48%)

Query:     3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHL 62
             ++CV+C      L   YS G +++  C +CR   D+YIE + +I+LID  L K QA+RH+
Sbjct:     6 FKCVECNEDANELHRDYSNGILKITICSSCRKPVDKYIEYDPVIILIDATLCKIQAFRHI 65

Query:    63 LYNVLNSETVNLKGILWKSTVGFXXXXXXXXXXXXXXNEGQSSSMSFSLLA----WIFQK 118
             L+N      +N+    WK  V F                 QSSS    ++     W F  
Sbjct:    66 LFNT----EINIH---WKLCV-FCLLCEAYLRWSLLQGS-QSSSDPADIIRYTKEWEFYC 116

Query:   119 MLKDVVLG-NVMFLGVFLHASRILLNTSAGAS-SFKDFLLAVLISSYFKIFLVAMMVW-- 174
             M     L   V F+GV +     +    +GAS  F   L A+L+SS+ K+ L+  ++W  
Sbjct:   117 MFALAALELTVFFIGVLVILW--MAQCFSGASLQFAPLLKALLLSSFGKVLLIPAVIWEH 174

Query:   175 NFPSSVIYIIDLFVLSSNTVALKVITESAMN-RILGVC 211
             +F      +I LFVL+SN+ A++VI   +    +L VC
Sbjct:   175 DFSPLCFSLIRLFVLTSNSQAIRVILNCSRRLSLLAVC 212

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

MGI|MGI:1916115 Arv1 "ARV1 homolog (yeast)" [Mus musculus (taxid:10090)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 61/214 (28%), Positives = 105/214 (49%)

Query:     3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHL 62
             YRC++C    + L+  YS G +++  C++C+   D+YIE + +I+LI+ IL K QAYRH+
Sbjct:    27 YRCIECNREAQELYRDYSHGVLKITICKSCQKPVDKYIEYDPVIILINAILCKTQAYRHI 86

Query:    63 LYNVLNSETVNLKGILWKSTVGFXXXXXXXXXXXXXXNEGQSSSMSFSLLAWIFQKMLKD 122
             L+N      +N+ G L    +                +      + ++   W F +M   
Sbjct:    87 LFNT----KINIHGKLCMFCLLCEAYLRWWQLQDSSQSPAPDDVIRYAK-EWDFYRMFVI 141

Query:   123 VVLGNVMFL-GVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVW--NFPSS 179
                    FL G+F         T+  A  F   L A+L+SSY K+ L+  ++W  ++   
Sbjct:   142 ASFEQAAFLTGIFAFLWVQQPMTAKRAPDFVLLLKALLLSSYGKLLLIPAVIWEHDYTPL 201

Query:   180 VIYIIDLFVLSSNTVALKVITESAMNRILGVCLV 213
              + +I +FVL+SN  A++V   +  NR L + +V
Sbjct:   202 CLRLIKVFVLTSNFQAVRVTLNT--NRRLSLLVV 233

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0006629 "lipid metabolic process" evidence=IEA

GO:0006665 "sphingolipid metabolic process" evidence=IEA

GO:0008206 "bile acid metabolic process" evidence=IMP

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0030301 "cholesterol transport" evidence=ISO

GO:0090181 "regulation of cholesterol metabolic process" evidence=IMP

RGD|1310264 Arv1 "ARV1 homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 215 (80.7 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 62/230 (26%), Positives = 110/230 (47%)

Query:     3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHL 62
             YRC++C    + L+  Y+ G +++  C++C+   D+YIE + +I+LI+ IL K QAYRH+
Sbjct:    28 YRCIECNREARELYRDYNHGVLKITICKSCQKPVDKYIEYDPVIILINAILCKTQAYRHI 87

Query:    63 LYNVLNSETVNLKGILWKSTVGFXXXXXXXXXXXXXXNEGQSSSMSFSLLAWIFQKMLKD 122
             L+N      +N+ G L    +                +      + ++   W F +M   
Sbjct:    88 LFNT----QINIHGKLCMFCLLCEAYLRWWQLQDSSQSPAPDDVIRYAK-EWDFYRMFVI 142

Query:   123 VVLGNVMFL-GVFLHASRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSS-- 179
                    F  G+F         T+ GA  F   L A+L+SSY K+ L+  ++W    +  
Sbjct:   143 ASFEQAAFFTGMFAFLWVQQHMTARGAPDFVLLLKALLLSSYGKLLLIPAVIWEHDHTPL 202

Query:   180 VIYIIDLFVLSSNTVALKV-ITESAMNRILGVC--LVAHAVKFFVVQGLE 226
              + +I +FVL+SN  A++V +  +    +L V   L+  ++  F  Q +E
Sbjct:   203 CLRLIKVFVLTSNFQAIRVTLNTNRRLSLLAVLSGLLLESIMVFFFQRME 252

GO:0008206 "bile acid metabolic process" evidence=IEA;ISO

GO:0030301 "cholesterol transport" evidence=IEA

GO:0090181 "regulation of cholesterol metabolic process" evidence=IEA;ISO

UNIPROTKB|F1RGS6 ARV1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 158 (60.7 bits), Expect = 1.3e-17, Sum P(2) = 1.3e-17
 Identities = 30/77 (38%), Positives = 50/77 (64%)

Query:     2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRH 61
             +YRC++C    K L+  Y+ G +++  C++C+   D+YIE + +I+LI+ IL K QAYRH
Sbjct:    41 QYRCIECNQEAKELYRDYNHGVLKITICKSCQKPVDKYIEYDPVIILINAILCKAQAYRH 100

Query:    62 LLYNVLNSETVNLKGIL 78
             +L+N      +N+ G L
Sbjct:   101 ILFNT----KINMHGKL 113

GO:0090181 "regulation of cholesterol metabolic process" evidence=IEA

GO:0030301 "cholesterol transport" evidence=IEA

GO:0008206 "bile acid metabolic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	232
pfam04161	194	pfam04161, Arv1, Arv1-like family	1e-47
COG5254	239	COG5254, ARV1, Predicted membrane protein [Functio	5e-21

>gnl|CDD|217936 pfam04161, Arv1, Arv1-like family

 Score =  155 bits (393), Expect = 1e-47
 Identities = 76/201 (37%), Positives = 109/201 (54%), Gaps = 14/201 (6%)

Query: 3   YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHL 62
             C++CG  +K+L+ +YS GNI+L  C NC  VAD+YIE + +IL IDL+L K QAYRHL
Sbjct: 1   MICIECGRPVKSLYKKYSSGNIKLTDCPNCNEVADKYIEYDNVILFIDLLLLKKQAYRHL 60

Query: 63  LYNVLNSETVNLKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQK---- 118
           LYNVL     N    LW+  +  +L + Y  L   R  +    S++ ++L+         
Sbjct: 61  LYNVL-----NKYDRLWRLFLLLILFEVY--LTWRREEKKSQHSLTRNVLSQSPYLQYLF 113

Query: 119 MLKDVVLGNVMFLGVFLHASRILLNTSAGASSFKDFLL-AVLISSYFKIFLVAMMVWNFP 177
            L  ++L NV+         R LL    G       LL  VL+S Y K+F + M++W + 
Sbjct: 114 FLAYLLLENVLLHISTAILLRKLLKWGKGLRYRTLILLYTVLLSYYGKLFPILMLIWPYD 173

Query: 178 SSVIY--IIDLFVLSSNTVAL 196
           +++I   IIDL VL SN  AL
Sbjct: 174 TTLISMSIIDLIVLLSNIEAL 194

Arv1 is a transmembrane protein with potential zinc-binding motifs. ARV1 is a novel mediator of eukaryotic sterol homeostasis. Length = 194

>gnl|CDD|227579 COG5254, ARV1, Predicted membrane protein [Function unknown]

 Score = 87.6 bits (217), Expect = 5e-21
 Identities = 56/231 (24%), Positives = 109/231 (47%), Gaps = 21/231 (9%)

Query: 3   YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHL 62
             C++CG R+ +L+ +YS   I+L +C +C    D+Y E + ++ LIDL+L K + YRHL
Sbjct: 1   MVCIECGSRVDSLYTRYSTSAIQLSRCPSCNRKMDKYFELDGVLKLIDLLLLKRRIYRHL 60

Query: 63  LYNVLNSETVN-----LKGILWKSTVGFLLLDAYRSLLLSRSNEGQSSSMSFSLLAWIFQ 117
           L+N L + T       +  +         L +A+  LL     EG S +   ++   + +
Sbjct: 61  LFNSLRARTFTNDVLCMLAVRMFCEPILQLHEAFGLLLSWGPGEGVSIAEMATICRDVPE 120

Query: 118 KMLKDVVLGNVMFLGVFLHASRILLNTSAGASSF---------------KDFLLAVLISS 162
            +++  ++  ++F   +LHA  + L+++   SSF               ++ LL + +S 
Sbjct: 121 SLMETSLILRLVFSMQYLHAGFVCLSSALLLSSFYYLFMFIMTMWKYQCEESLLVIELSC 180

Query: 163 YFKIFLVAMMVWNFPSSV-IYIIDLFVLSSNTVALKVITESAMNRILGVCL 212
                 V M +W + + + +  I     ++  V L+++T   +N  L  C 
Sbjct: 181 VACNSPVIMEIWLYDNEIALGCIYWVKFAAGLVCLRILTTIRLNFFLSGCS 231

Length = 239

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	232
PF04161	208	Arv1: Arv1-like family ; InterPro: IPR007290 Arv1	100.0
KOG3134	225	consensus Predicted membrane protein [Function unk	100.0
COG5254	239	ARV1 Predicted membrane protein [Function unknown]	100.0
KOG3134	225	consensus Predicted membrane protein [Function unk	96.62
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	93.0
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	92.6
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	91.96
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	91.48
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	90.22
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	89.22
PF13248	26	zf-ribbon_3: zinc-ribbon domain	88.77
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	88.65
PF14319	111	Zn_Tnp_IS91: Transposase zinc-binding domain	87.28
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	87.28
PF05180	66	zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc	86.49
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	84.99
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	82.54
PF01286	34	XPA_N: XPA protein N-terminal; InterPro: IPR022652	81.22
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	80.5
PF12773	50	DZR: Double zinc ribbon	80.47
PF12647	92	RNHCP: RNHCP domain; InterPro: IPR024439 This doma	80.34

>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis

Probab=100.00  E-value=8.5e-58  Score=395.89  Aligned_cols=194  Identities=41%  Similarity=0.643  Sum_probs=166.9

Q ss_pred             ccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHHHHHhcCcchhheeeccccccccc--------hh
Q 026819            3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETV--------NL   74 (232)
Q Consensus         3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayrHllfN~~~~~~~--------~~   74 (232)
                      ++|||||+||++||++|||||||+|+|++||++||||||+|+++++||++|+|||||||++||+.+++.+        +.
T Consensus         1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYiE~d~vil~IDLlLlK~~AYRHllfN~~~~~~~~~~~~~~~~~   80 (208)
T PF04161_consen    1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYIEYDNVILFIDLLLLKPQAYRHLLFNRLEPELSKFQVKNWFSK   80 (208)
T ss_pred             CEeccCCCcchhhhhccCCCcEEEeeccccCCcccceeccccHHHHHHHHHcchhhHHHhhccCCccccccchhhhhhhh
Confidence            5899999999999999999999999999999999999999999999999999999999999999887765        44


Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhhccCCCCCC---chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-CCChh
Q 026819           75 KGILWKSTVGFLLLDAYRSLLLSRSNEGQSS---SMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTS-AGASS  150 (232)
Q Consensus        75 ~~~l~kl~vl~lL~eay~~~~~~~~~~~~~~---s~~~~~~~~~~~~~l~~~~l~~~~f~~~~~l~~~~~l~~~-~~~~~  150 (232)
                      .+.+||++++++++|||+.|..++++.+...   .....+...++..++...++++++|+..+.+..+...+++ ....+
T Consensus        81 ~~~~~rl~il~ll~eayl~w~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (208)
T PF04161_consen   81 FKSLWRLVILLLLFEAYLRWASEEKSSQSSQLMSSILSQSIYMQYLFFLIYCLLENLLFHLFIALLIRFWLKWGQQYKYR  160 (208)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhccccccchhhhhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchh
Confidence            5689999999999999999987666543221   0111233455556778888899999988888888888887 55678


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccCCCchh--HHHHHHHHHHHHHHH
Q 026819          151 FKDFLLAVLISSYFKIFLVAMMVWNFPSSVI--YIIDLFVLSSNTVAL  196 (232)
Q Consensus       151 ~~~ll~alllSS~~KLf~ilmlIW~~~~s~~--~li~~~vl~snv~Al  196 (232)
                      ++.+++|+++||++|+|+++|+||+||.+..  .++++++++||+|||
T Consensus       161 ~~~l~~alllSs~~Klf~ilmlIW~~~~~~~~~~ii~~~v~~~~~~aL  208 (208)
T PF04161_consen  161 FRVLLTALLLSSYGKLFPILMLIWPYDSSPISLSIIDWFVLLSNIEAL  208 (208)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999996544  599999999999996

Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].

>KOG3134 consensus Predicted membrane protein [Function unknown]

Probab=100.00  E-value=1.6e-41  Score=293.28  Aligned_cols=200  Identities=37%  Similarity=0.601  Sum_probs=148.5

Q ss_pred             ccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHHHHHhcCcchhheeeccccccccchhhhHHHHHH
Q 026819            3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKST   82 (232)
Q Consensus         3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayrHllfN~~~~~~~~~~~~l~kl~   82 (232)
                      ++|||||+++++||++||+||+|+|+||||+++||||||+|+||++||++|+|||||||+|||..++++.+....+||+.
T Consensus         1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkYiE~d~vii~IDliL~k~qaYRHlLfN~~~~~~~~~~~~l~~~~   80 (225)
T KOG3134|consen    1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKYIELDVVIIFIDLILLKAQAYRHLLFNSLIQRTKNVFCLLWKLV   80 (225)
T ss_pred             CcccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhHeehhhHHHHHHHHHHhHHHHHHHHHHhhhHHhHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999988888899988


Q ss_pred             HHHHHHHHHHHHHhhcc-CCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc--------CCChhHHH
Q 026819           83 VGFLLLDAYRSLLLSRS-NEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTS--------AGASSFKD  153 (232)
Q Consensus        83 vl~lL~eay~~~~~~~~-~~~~~~s~~~~~~~~~~~~~l~~~~l~~~~f~~~~~l~~~~~l~~~--------~~~~~~~~  153 (232)
                      ...++++-+.....+.+ ++|+.+++++.   ....+++......+++|.+.+...-..+.+..        ..+..+..
T Consensus        81 ~~~~lL~~~~~~l~~~~~~~e~~~~~~~~---~~~~~~~~~~i~~~~l~~f~~~~~~~~~~~l~~~~lLl~~~~~~syi~  157 (225)
T KOG3134|consen   81 FAWLLLQDFESLLLWLSEDDEWVFYRSFA---LPALEVLSSLIERQYLFVFLWCNRETTFVQLSSALLLLKTLLLKSYIS  157 (225)
T ss_pred             HHHHHHHHhHhhcccccCCCcchhhhhHH---HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHH
Confidence            88888887766555555 45555555431   11112222211113333322211111111110        01123333


Q ss_pred             -HHHHHHHHHHHHHHHHHHhhccCCCc--hhHHHHHHHHHHHHHHHHHHhhcchh
Q 026819          154 -FLLAVLISSYFKIFLVAMMVWNFPSS--VIYIIDLFVLSSNTVALKVITESAMN  205 (232)
Q Consensus       154 -ll~alllSS~~KLf~ilmlIW~~~~s--~~~li~~~vl~snv~Al~vv~~~~~~  205 (232)
                       +......||+.|.++|.|++|++|.+  +...+.|..++++++|++++++.++.
T Consensus       158 ~i~~~~~~s~~~~v~~Ifml~~~~~~~~v~~~~v~~~~~~a~l~~l~i~s~~~~~  212 (225)
T KOG3134|consen  158 VISLLVILSSCVKVNPIFMLISCYQTSRVALGIVYWVSFLAVLLALKILSTSRYF  212 (225)
T ss_pred             HHHHHHHHHHhhhhhheeeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             67778888888899999999999975  45789999999999999999877764

>COG5254 ARV1 Predicted membrane protein [Function unknown]

Probab=100.00  E-value=3.3e-38  Score=269.86  Aligned_cols=194  Identities=21%  Similarity=0.321  Sum_probs=134.3

Q ss_pred             ccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHHHHHhcCcchhheeeccccccccchhhhHHHH--
Q 026819            3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWK--   80 (232)
Q Consensus         3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayrHllfN~~~~~~~~~~~~l~k--   80 (232)
                      ++|||||.||++||++||.++||+++||+|++.+|||+|.|+|+++||++|+|||+|||++||+++.++...+....|  
T Consensus         1 mvCIeCg~~vdsLyt~ysts~iqls~Cp~C~~~~DkY~Eld~vl~~iDllLlK~~iyRHllFNsl~artf~nd~~c~~~v   80 (239)
T COG5254           1 MVCIECGSRVDSLYTRYSTSAIQLSRCPSCNRKMDKYFELDGVLKLIDLLLLKRRIYRHLLFNSLRARTFTNDVLCMLAV   80 (239)
T ss_pred             CeeeEcCCccceeeeeccCcceehhcCchHHHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHhhHhHHHHHhHHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999999999999999988554221111111  


Q ss_pred             ------HHHHHHHHHHHHHHHhhccCCCCCCchhh-----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026819           81 ------STVGFLLLDAYRSLLLSRSNEGQSSSMSF-----------------SLLAWIFQKMLKDVVLGNVMFLGVFLHA  137 (232)
Q Consensus        81 ------l~vl~lL~eay~~~~~~~~~~~~~~s~~~-----------------~~~~~~~~~~l~~~~l~~~~f~~~~~l~  137 (232)
                            +..+...++.|.+|-..++.  +...+.+                 .....++......++.+..+|.....+-
T Consensus        81 ~~Fc~~~~~l~~~f~~~L~w~~~E~~--~~~~~a~~~~~~pes~~~~s~ilr~~~s~qyl~~~~vcl~~~~l~~~f~~lf  158 (239)
T COG5254          81 RMFCEPILQLHEAFGLLLSWGPGEGV--SIAEMATICRDVPESLMETSLILRLVFSMQYLHAGFVCLSSALLLSSFYYLF  158 (239)
T ss_pred             HHHHHHHHHHHHHhhhheeecccccc--chHHHHHhhhhhHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                  22344455555555322221  0000100                 0011122333344445555555443333


Q ss_pred             HHHHhhccCCChhHHHHHHHHHHHHHHHHHHHHHhhccCCCc-hhHHHHHHHHHHHHHHHHHHhh
Q 026819          138 SRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSS-VIYIIDLFVLSSNTVALKVITE  201 (232)
Q Consensus       138 ~~~~l~~~~~~~~~~~ll~alllSS~~KLf~ilmlIW~~~~s-~~~li~~~vl~snv~Al~vv~~  201 (232)
                      ....++|..   ....-..++.+|+.+|.+|++|+||+||.+ ++..|+|.++.+|+++++++|.
T Consensus       159 ~~~~~~Wk~---~~~~s~~~I~ls~~a~~~pV~m~Iw~yd~~Ia~~~I~wv~~~~~~~~l~Ilt~  220 (239)
T COG5254         159 MFIMTMWKY---QCEESLLVIELSCVACNSPVIMEIWLYDNEIALGCIYWVKFAAGLVCLRILTT  220 (239)
T ss_pred             HHHHHHHHH---HhhhcchheeeecchhcchhheeehhcchHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            333333321   112233589999999999999999999974 4679999999999999999996

>KOG3134 consensus Predicted membrane protein [Function unknown]

Probab=96.62  E-value=0.0084  Score=52.96  Aligned_cols=114  Identities=17%  Similarity=0.101  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHhhcc---CCChhHHHHHHHHHHHHHHH-HHHHHHhhccCCCchhHHHHH
Q 026819          112 LAWIFQKMLKDVVLGNVMFLGVFLHASR-ILLNTS---AGASSFKDFLLAVLISSYFK-IFLVAMMVWNFPSSVIYIIDL  186 (232)
Q Consensus       112 ~~~~~~~~l~~~~l~~~~f~~~~~l~~~-~~l~~~---~~~~~~~~ll~alllSS~~K-Lf~ilmlIW~~~~s~~~li~~  186 (232)
                      .+|.++..+.....+...+.+.-.+... .+....   .+.++...+++++.++||+| .+...+..|..+...+++++|
T Consensus       100 ~e~~~~~~~~~~~~~~~~~~i~~~~l~~f~~~~~~~~~~~l~~~~lLl~~~~~~syi~~i~~~~~~s~~~~v~~Ifml~~  179 (225)
T KOG3134|consen  100 DEWVFYRSFALPALEVLSSLIERQYLFVFLWCNRETTFVQLSSALLLLKTLLLKSYISVISLLVILSSCVKVNPIFMLIS  179 (225)
T ss_pred             CcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhheeeeeh
Confidence            3677888777777777776654333332 222222   23567788999999999999 788888888777666677777


Q ss_pred             HHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHhhh
Q 026819          187 FVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGL  225 (232)
Q Consensus       187 ~vl~snv~Al~vv~~~~~~~~~~~~~~a~~~r~~~~~~~  225 (232)
                      -..++++.+-.+-.-.--....+.+++++..|+++..+.
T Consensus       180 ~~~~~~v~~~~v~~~~~~a~l~~l~i~s~~~~~l~~s~~  218 (225)
T KOG3134|consen  180 CYQTSRVALGIVYWVSFLAVLLALKILSTSRYFLFDSIC  218 (225)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            766666655554443333356677788999999887653

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=93.00  E-value=0.037  Score=35.36  Aligned_cols=34  Identities=32%  Similarity=0.640  Sum_probs=23.7

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCccccccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE   38 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk   38 (232)
                      +|+|.+||+..+.+... + + -....||+||.-+.|
T Consensus         5 ~y~C~~Cg~~fe~~~~~-~-~-~~~~~CP~Cg~~~~r   38 (41)
T smart00834        5 EYRCEDCGHTFEVLQKI-S-D-DPLATCPECGGDVRR   38 (41)
T ss_pred             EEEcCCCCCEEEEEEec-C-C-CCCCCCCCCCCccee
Confidence            47999999987765322 1 1 367789999985443

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

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

Probab=92.60  E-value=0.086  Score=34.65  Aligned_cols=33  Identities=30%  Similarity=0.729  Sum_probs=23.4

Q ss_pred             ccccccCcccccceeeccCCceEeecCCCccccccccc
Q 026819            3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYI   40 (232)
Q Consensus         3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYi   40 (232)
                      ++|.+||...  +..++..+.+   .|++||.+.|..+
T Consensus         1 m~Cp~Cg~~~--~~~D~~~g~~---vC~~CG~Vl~e~~   33 (43)
T PF08271_consen    1 MKCPNCGSKE--IVFDPERGEL---VCPNCGLVLEENI   33 (43)
T ss_dssp             ESBTTTSSSE--EEEETTTTEE---EETTT-BBEE-TT
T ss_pred             CCCcCCcCCc--eEEcCCCCeE---ECCCCCCEeeccc
Confidence            5799999965  6666766653   8999998877554

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

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

Probab=91.96  E-value=0.074  Score=35.41  Aligned_cols=31  Identities=23%  Similarity=0.573  Sum_probs=22.7

Q ss_pred             CCccccccCcccccceeeccCCceEeecCCCcccccc
Q 026819            1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD   37 (232)
Q Consensus         1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D   37 (232)
                      ++|+|.+||..++-     .++. ....||+||...+
T Consensus         2 ~~y~C~~CG~~~~~-----~~~~-~~~~Cp~CG~~~~   32 (46)
T PRK00398          2 AEYKCARCGREVEL-----DEYG-TGVRCPYCGYRIL   32 (46)
T ss_pred             CEEECCCCCCEEEE-----CCCC-CceECCCCCCeEE
Confidence            46899999998643     2222 2679999998766

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=91.48  E-value=0.11  Score=34.75  Aligned_cols=28  Identities=29%  Similarity=0.647  Sum_probs=20.4

Q ss_pred             CCccccccCcccccceeeccCCceEeecCCCcccc
Q 026819            1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV   35 (232)
Q Consensus         1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~   35 (232)
                      +.|+|-+||+.++.-    +.+   .-+|++||.-
T Consensus         1 ~~Y~C~~Cg~~~~~~----~~~---~irC~~CG~r   28 (44)
T smart00659        1 MIYICGECGRENEIK----SKD---VVRCRECGYR   28 (44)
T ss_pred             CEEECCCCCCEeecC----CCC---ceECCCCCce
Confidence            579999999987642    232   3479999963

present in RNA polymerase I, II and III

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=90.22  E-value=0.11  Score=34.16  Aligned_cols=34  Identities=29%  Similarity=0.641  Sum_probs=24.7

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCccc-cccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA-VADE   38 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~-~~Dk   38 (232)
                      +|+|-+||+.-+.+.. .+.  -....||+||. -+.|
T Consensus         5 ey~C~~Cg~~fe~~~~-~~~--~~~~~CP~Cg~~~~~r   39 (42)
T PF09723_consen    5 EYRCEECGHEFEVLQS-ISE--DDPVPCPECGSTEVRR   39 (42)
T ss_pred             EEEeCCCCCEEEEEEE-cCC--CCCCcCCCCCCCceEE
Confidence            5899999998877643 222  46779999998 4443

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=89.22  E-value=0.16  Score=34.32  Aligned_cols=30  Identities=40%  Similarity=0.877  Sum_probs=22.3

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA   34 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~   34 (232)
                      +|+|-+||+..+.+ ...+.  -....||+||.
T Consensus         5 ey~C~~Cg~~fe~~-~~~~~--~~~~~CP~Cg~   34 (52)
T TIGR02605         5 EYRCTACGHRFEVL-QKMSD--DPLATCPECGG   34 (52)
T ss_pred             EEEeCCCCCEeEEE-EecCC--CCCCCCCCCCC
Confidence            58999999987765 33332  25678999997

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=88.77  E-value=0.19  Score=29.75  Aligned_cols=24  Identities=42%  Similarity=0.796  Sum_probs=17.7

Q ss_pred             CCccccccCcccccceeeccCCceEeecCCCccc
Q 026819            1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA   34 (232)
Q Consensus         1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~   34 (232)
                      |+..|.+||++++.          .-.-|++||+
T Consensus         1 m~~~Cp~Cg~~~~~----------~~~fC~~CG~   24 (26)
T PF13248_consen    1 MEMFCPNCGAEIDP----------DAKFCPNCGA   24 (26)
T ss_pred             CcCCCcccCCcCCc----------ccccChhhCC
Confidence            56789999997643          2347999986

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

Probab=88.65  E-value=0.27  Score=30.87  Aligned_cols=25  Identities=28%  Similarity=0.826  Sum_probs=17.0

Q ss_pred             ccccccCcccccceeeccCCceEeecCCCccc
Q 026819            3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA   34 (232)
Q Consensus         3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~   34 (232)
                      |+|-+||+.++ +   -..+.   .+|++||.
T Consensus         1 Y~C~~Cg~~~~-~---~~~~~---irC~~CG~   25 (32)
T PF03604_consen    1 YICGECGAEVE-L---KPGDP---IRCPECGH   25 (32)
T ss_dssp             EBESSSSSSE--B---STSST---SSBSSSS-
T ss_pred             CCCCcCCCeeE-c---CCCCc---EECCcCCC
Confidence            68999999998 2   22333   38999985

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

>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain

Probab=87.28  E-value=0.46  Score=37.61  Aligned_cols=52  Identities=29%  Similarity=0.623  Sum_probs=34.1

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHHHHHhcC--cchhheeecccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHK--PQAYRHLLYNVL   67 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k--~~ayrHllfN~~   67 (232)
                      .+.|.+||+.-..    |.+..-|  .||+|+..+        .-.++|-...+  |-.|||++|=..
T Consensus        42 ~~~C~~Cg~~~~~----~~SCk~R--~CP~C~~~~--------~~~W~~~~~~~ll~~~y~HvVFTlP   95 (111)
T PF14319_consen   42 RYRCEDCGHEKIV----YNSCKNR--HCPSCQAKA--------TEQWIEKQREDLLPVPYFHVVFTLP   95 (111)
T ss_pred             eeecCCCCceEEe----cCcccCc--CCCCCCChH--------HHHHHHHHHhhCCCCCeEEEEEcCc
Confidence            5789999987522    4444334  899999753        33444443333  588999999763

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=87.28  E-value=0.2  Score=34.46  Aligned_cols=28  Identities=32%  Similarity=0.860  Sum_probs=19.9

Q ss_pred             CCccccccCcccccceeeccCCceEeecCCCccc
Q 026819            1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA   34 (232)
Q Consensus         1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~   34 (232)
                      ++|+|..||..++.+   .   .-+--.||.||.
T Consensus         5 ~~Y~C~~Cg~~~~~~---~---~~~~irCp~Cg~   32 (49)
T COG1996           5 MEYKCARCGREVELD---Q---ETRGIRCPYCGS   32 (49)
T ss_pred             EEEEhhhcCCeeehh---h---ccCceeCCCCCc
Confidence            469999999999543   1   123348999985

>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.49  E-value=0.33  Score=35.40  Aligned_cols=36  Identities=33%  Similarity=0.905  Sum_probs=24.7

Q ss_pred             CccccccCcccccceee--ccCCceEeecCCCccc---cccc
Q 026819            2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENCRA---VADE   38 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~--y~~~~i~l~~C~~C~~---~~Dk   38 (232)
                      .+-|-.|+++....+.+  |.+|. .+.+||+|++   +||.
T Consensus         4 ~FTC~~C~~Rs~~~~sk~aY~~Gv-Viv~C~gC~~~HlIaDn   44 (66)
T PF05180_consen    4 TFTCNKCGTRSAKMFSKQAYHKGV-VIVQCPGCKNRHLIADN   44 (66)
T ss_dssp             EEEETTTTEEEEEEEEHHHHHTSE-EEEE-TTS--EEES--S
T ss_pred             EEEcCCCCCccceeeCHHHHhCCe-EEEECCCCcceeeehhh
Confidence            46799999998887766  66654 8999999986   5664

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.

>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase

Probab=84.99  E-value=0.35  Score=30.51  Aligned_cols=32  Identities=25%  Similarity=0.544  Sum_probs=23.5

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCcccccccccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE   41 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE   41 (232)
                      .++|..||+-.+.        .-....||.|+...+++.+
T Consensus         2 ~~~C~~CG~i~~g--------~~~p~~CP~Cg~~~~~F~~   33 (34)
T cd00729           2 VWVCPVCGYIHEG--------EEAPEKCPICGAPKEKFEE   33 (34)
T ss_pred             eEECCCCCCEeEC--------CcCCCcCcCCCCchHHcEE
Confidence            4789999976432        1134589999999888765

In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

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

Probab=82.54  E-value=0.77  Score=32.57  Aligned_cols=30  Identities=33%  Similarity=0.688  Sum_probs=24.0

Q ss_pred             ccccccCcccccceeeccCCceEeecCCCccccccc
Q 026819            3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE   38 (232)
Q Consensus         3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk   38 (232)
                      -.|-.||++.+.      +.+-+.-.|++||...|.
T Consensus        29 q~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~r   58 (69)
T PF07282_consen   29 QTCPRCGHRNKK------RRSGRVFTCPNCGFEMDR   58 (69)
T ss_pred             cCccCccccccc------ccccceEEcCCCCCEECc
Confidence            469999999877      335588899999988775

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

>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer

Probab=81.22  E-value=0.57  Score=29.88  Aligned_cols=28  Identities=32%  Similarity=0.669  Sum_probs=13.2

Q ss_pred             CCccccccCccc--ccceeeccCCceEeecCCCcc
Q 026819            1 MEYRCVKCGFRI--KTLFVQYSPGNIRLMKCENCR   33 (232)
Q Consensus         1 ~~~~Ci~C~~~v--~~l~~~y~~~~i~l~~C~~C~   33 (232)
                      +.+.|.|||.+-  +-|++     +..+..|.+|.
T Consensus         2 ~~~~C~eC~~~f~dSyL~~-----~F~~~VCD~CR   31 (34)
T PF01286_consen    2 DYPKCDECGKPFMDSYLLN-----NFDLPVCDKCR   31 (34)
T ss_dssp             S-EE-TTT--EES-SSCCC-----CTS-S--TTT-
T ss_pred             CCchHhHhCCHHHHHHHHH-----hCCcccccccc
Confidence            358999999984  34433     44566888885

Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=80.50  E-value=1.4  Score=39.94  Aligned_cols=35  Identities=23%  Similarity=0.525  Sum_probs=20.2

Q ss_pred             ccccccCcccccceeec---cCCceEeecCCCccc---ccc
Q 026819            3 YRCVKCGFRIKTLFVQY---SPGNIRLMKCENCRA---VAD   37 (232)
Q Consensus         3 ~~Ci~C~~~v~~l~~~y---~~~~i~l~~C~~C~~---~~D   37 (232)
                      -.|..||+.-..-+.-+   ..+..|++.|++||.   ..|
T Consensus       212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd  252 (290)
T PF04216_consen  212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD  252 (290)
T ss_dssp             TS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred             CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence            46999999876666555   456899999999994   555

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>PF12773 DZR: Double zinc ribbon

Probab=80.47  E-value=0.85  Score=30.36  Aligned_cols=31  Identities=26%  Similarity=0.491  Sum_probs=21.4

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCcccccccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY   39 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY   39 (232)
                      .-.|.+||++++       ........|++|++..++-
T Consensus        12 ~~fC~~CG~~l~-------~~~~~~~~C~~Cg~~~~~~   42 (50)
T PF12773_consen   12 AKFCPHCGTPLP-------PPDQSKKICPNCGAENPPN   42 (50)
T ss_pred             ccCChhhcCChh-------hccCCCCCCcCCcCCCcCC
Confidence            346889999887       2222455799999876654

>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins

Probab=80.34  E-value=0.89  Score=35.24  Aligned_cols=29  Identities=24%  Similarity=0.780  Sum_probs=23.0

Q ss_pred             CCccccccCcccccceeeccCCceEeecCCCcc
Q 026819            1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCR   33 (232)
Q Consensus         1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~   33 (232)
                      +.+.|.+||..|.-    .++|+-.-..||+|-
T Consensus         3 ~~F~C~~CG~~V~p----~~~g~~~RNHCP~CL   31 (92)
T PF12647_consen    3 ESFTCVHCGLTVSP----LAAGSAHRNHCPSCL   31 (92)
T ss_pred             cccCccccCCCccc----CCCCCCccCcCcccc
Confidence            46899999999976    356666667999995

It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	232
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	89.49
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	85.77

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

Probab=89.49  E-value=0.14  Score=36.54  Aligned_cols=27  Identities=19%  Similarity=0.785  Sum_probs=20.3

Q ss_pred             CCccccccCcccccceeeccCCceEeecCCCccc
Q 026819            1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA   34 (232)
Q Consensus         1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~   34 (232)
                      .+|+|-+||..++..    ..+.+   .|++||.
T Consensus        27 v~Y~C~~CG~~~e~~----~~d~i---rCp~CG~   53 (70)
T 1twf_L           27 LKYICAECSSKLSLS----RTDAV---RCKDCGH   53 (70)
T ss_dssp             CCEECSSSCCEECCC----TTSTT---CCSSSCC
T ss_pred             EEEECCCCCCcceeC----CCCCc---cCCCCCc
Confidence            368999999997654    33333   7999997

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

Probab=85.77  E-value=0.39  Score=33.69  Aligned_cols=27  Identities=30%  Similarity=0.806  Sum_probs=19.3

Q ss_pred             CCccccccCcccccceeeccCCceEeecCCCccc
Q 026819            1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA   34 (232)
Q Consensus         1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~   34 (232)
                      +.|+|-+||+.++-=    ..   .--+|++||.
T Consensus        20 v~Y~C~~Cg~~~~l~----~~---~~iRC~~CG~   46 (63)
T 3h0g_L           20 MIYLCADCGARNTIQ----AK---EVIRCRECGH   46 (63)
T ss_dssp             CCCBCSSSCCBCCCC----SS---SCCCCSSSCC
T ss_pred             eEEECCCCCCeeecC----CC---CceECCCCCc
Confidence            469999999998621    12   2247999985

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	232
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	93.43
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	84.87
d1d4ua2	36	DNA repair factor XPA DNA- and RPA-binding domain,	83.73
d1y0ja1	39	Erythroid transcription factor GATA-1 {Mouse (Mus	82.11
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	81.51
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	80.14

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.43  E-value=0.014  Score=35.38  Aligned_cols=33  Identities=27%  Similarity=0.667  Sum_probs=26.0

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCccccccccccch
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE   43 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d   43 (232)
                      .++|..||+-...    -.|     .+||-|+...|+|.++|
T Consensus         5 ~~~C~vCG~i~~g----~~P-----~~CPvCg~~~~~F~~~e   37 (37)
T d1nnqa2           5 VYICPICGYTAVD----EAP-----EYCPVCGAPKEKFVVFE   37 (37)
T ss_dssp             EEECTTTCCEEES----CCC-----SBCTTTCCBGGGSEEEC
T ss_pred             EEECCCCCCEecC----CCC-----CcCCCCCCcHHHcEEcC
Confidence            3689999987643    134     37999999999999876

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=84.87  E-value=0.2  Score=29.96  Aligned_cols=32  Identities=25%  Similarity=0.392  Sum_probs=24.1

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCccccccccccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIEC   42 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~   42 (232)
                      -++|..||+-...    -.|     .+||-|+...++|-+|
T Consensus         5 ~~vC~vCGyi~~g----~~P-----e~CPvCg~~~~~F~~f   36 (36)
T d1yuza2           5 FHLCPICGYIHKG----EDF-----EKCPICFRPKDTFTAY   36 (36)
T ss_dssp             EEECSSSCCEEES----SCC-----SBCTTTCCBGGGCEEC
T ss_pred             EEECCCCCCEeeC----CCC-----CcCCCCCCcHHHcCcC
Confidence            3689999987542    123     4799999999998764

>d1d4ua2 g.39.1.5 (A:1-36) DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain
domain: DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.73  E-value=0.15  Score=30.29  Aligned_cols=28  Identities=29%  Similarity=0.771  Sum_probs=20.6

Q ss_pred             ccccccCccc-ccceeeccCCceEeecCCCccc
Q 026819            3 YRCVKCGFRI-KTLFVQYSPGNIRLMKCENCRA   34 (232)
Q Consensus         3 ~~Ci~C~~~v-~~l~~~y~~~~i~l~~C~~C~~   34 (232)
                      -+|.|||.+- ++    |=..+.-+..|.+|.-
T Consensus         6 ~~C~eCg~~F~DS----YL~~~Fd~~vCD~CRD   34 (36)
T d1d4ua2           6 VICEECGKEFMDS----YLMDHFDLPTCDDCRD   34 (36)
T ss_dssp             EECTTTCCEESCS----SSTTTTSCCCCTTTCS
T ss_pred             HHHHHhCcHHHHH----HHHHcCCchhcccccC
Confidence            4799999984 33    5455667788999963

>d1y0ja1 g.39.1.1 (A:200-238) Erythroid transcription factor GATA-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Erythroid transcription factor GATA-1
domain: Erythroid transcription factor GATA-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.11  E-value=0.31  Score=29.59  Aligned_cols=31  Identities=26%  Similarity=0.628  Sum_probs=25.5

Q ss_pred             CCccccccCcccccceeeccCCceEeecCCCccc
Q 026819            1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA   34 (232)
Q Consensus         1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~   34 (232)
                      |...|.+||.....++++-.++.   +.|..||-
T Consensus         1 e~r~C~~Cgtt~Tp~WR~gp~G~---~LCNACGl   31 (39)
T d1y0ja1           1 EARECVNCGATATPLWRRDRTGH---YLCNACGL   31 (39)
T ss_dssp             CCCCCSSSCCCCCSCCEECTTSC---EECSSHHH
T ss_pred             CcCCCCCCCCCCCcccccCCCCC---EeeHHhHH
Confidence            46789999999999999876662   58999974

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.51  E-value=0.44  Score=31.06  Aligned_cols=36  Identities=28%  Similarity=0.541  Sum_probs=25.8

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCccccc-cccccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA-DEYIEC   42 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~-DkYiE~   42 (232)
                      ...|.+||.+  .+-..++.|.   ..|.+||-+. |+-|..
T Consensus        11 ~~~Cp~Cgs~--~ii~D~~~Ge---~vC~~CG~Vlee~~ID~   47 (58)
T d1dl6a_          11 RVTCPNHPDA--ILVEDYRAGD---MICPECGLVVGDRVIDV   47 (58)
T ss_dssp             CCSBTTBSSS--CCEECSSSCC---EECTTTCCEECCSCCCC
T ss_pred             ccCCCCCCCC--CEEEECCCCc---EecccCCCEeccccccC
Confidence            5689999976  4556676664   5899999975 555543

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=80.14  E-value=0.54  Score=29.65  Aligned_cols=36  Identities=22%  Similarity=0.479  Sum_probs=26.1

Q ss_pred             CccccccCcccccceeeccCCceEeecCCCccccc-cccccc
Q 026819            2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA-DEYIEC   42 (232)
Q Consensus         2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~-DkYiE~   42 (232)
                      +-+|.+||..  .+-..+..|   -..|.+||-+. |+.|+.
T Consensus         5 ~~~Cp~Cgs~--~iv~D~~~G---e~vC~~CG~Viee~~iD~   41 (50)
T d1pfta_           5 QKVCPACESA--ELIYDPERG---EIVCAKCGYVIEENIIDM   41 (50)
T ss_dssp             CCSCTTTSCC--CEEEETTTT---EEEESSSCCBCCCCCCCC
T ss_pred             cccCcCCCCC--cEEEECCCC---eEecccCCcEeccccccC
Confidence            4589999864  477777776   35799999865 556654