Citrus Sinensis ID: 043474

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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
Protein Sequence
MDHTLQNTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVVNKS
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHcccccccccEEEccEEEEEEEEEEEEEEEEEccccEEEEEEEccccEEEEEEEcccccccccccccccHHHHHccccHHHHHccccccEEEEEEEEcEEccEEEEEEEEEEEcccHHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHccccccccEEEEccccEEEEEEEEEEEEEccccccEEEEEEcccccEEEEEEEEccccccccccccccHHHHHHHHHHHHcccEEEccEEEEEEEEEEEccEEEEEEEEEEEccccHHHHHHHHHHHHHHHHHcccEEccc
Coil and Loop (DISEMBL)
MDHTLQNTHVKLLAFDllsltptpdpatfsrsgkllSRAEIVGtitsrdhkpskfikftvddgtgcvpcvlwlnhltslylprrdpstVRLIAGVATDFAAKIKIGLVARVRGRIasyrgdvqitvsdvviekdpnmevlHWLDCLRLARKRYDVVVNKS
Flexible Loop (DISEMBL)
MDHTLQNTHVKLLAFDLLSLTPTPDPatfsrsgkllsRAEIVgtitsrdhkpskfIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATdfaakikiglvarvrgriasyrgdvqitvsdvviekdpnmevlhwldclrlarkrydvvvnks
Low Complexity Region (SEG)
MDHTLQNTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVVNKS
Disordered region (IsUnstruct)
********HVKLLAFDLLSLT*************LLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVV***
Disordered Region (DISOPRED)
***TLQNTHVKLLAFDLLSLTPT*DPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLN****************************IKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVV***
Disordered Region (DISEMBL)
********HVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVVNKS
Disordered Region (DISPRO)
**HTLQNTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHL*********PSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVVN**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDHTLQNTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVVNKS
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	160	2.2.26 [Sep-21-2011]
Q9LMK5	160	CST complex subunit STN1	yes	no	0.981	0.981	0.562	4e-45
D2GXY4	367	CST complex subunit STN1	yes	no	0.9	0.392	0.272	2e-08
Q8K2X3	378	CST complex subunit STN1	yes	no	0.9	0.380	0.273	9e-08
Q08DB2	370	CST complex subunit STN1	yes	no	0.9	0.389	0.288	4e-07
Q6AYD2	408	CST complex subunit STN1	yes	no	0.893	0.350	0.269	2e-06
Q9H668	368	CST complex subunit STN1	yes	no	0.9	0.391	0.272	2e-06
Q4R804	368	CST complex subunit STN1	N/A	no	0.9	0.391	0.272	3e-06
Q8LFJ8	278	Replication protein A 32	no	no	0.718	0.413	0.268	2e-05
Q9ZQ19	279	Replication protein A 32	no	no	0.618	0.354	0.247	0.0001
Q6DJ48	368	CST complex subunit STN1	yes	no	0.875	0.380	0.254	0.0001

>sp|Q9LMK5|STN1_ARATH CST complex subunit STN1 OS=Arabidopsis thaliana GN=STN1 PE=1 SV=1

 Score =  180 bits (456), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 90/160 (56%), Positives = 114/160 (71%), Gaps = 3/160 (1%)

Query: 1   MDHTLQNTHVKLLAFDLLSLTPTP-DPATFSR-SGKLLSRAEIVGTITSRDHKPSKFIKF 58
           MD +LQ+TH KL+A D+  LT +P +  +FS   G  +SR EIVGTI SRD  P KF+KF
Sbjct: 1   MDRSLQSTHAKLVARDIQRLTQSPTESNSFSLLGGACVSRVEIVGTIVSRDLTP-KFLKF 59

Query: 59  TVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY 118
            VDDGTGCV CV+WLN LTS Y  R DP+T+ L+A  A   AA+I+IG VARVRGR+ SY
Sbjct: 60  GVDDGTGCVTCVMWLNQLTSSYFSRWDPATILLLASAARKQAAQIRIGAVARVRGRVGSY 119

Query: 119 RGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVVN 158
           RG +QIT +  V E+DPN E+LHWL+CL+L +  Y V + 
Sbjct: 120 RGVMQITANVAVAERDPNAEILHWLECLKLGQSCYRVRIQ 159

Component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves.
Arabidopsis thaliana (taxid: 3702)

>sp|D2GXY4|STN1_AILME CST complex subunit STN1 OS=Ailuropoda melanoleuca GN=OBFC1 PE=3 SV=2

 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 70/154 (45%), Gaps = 10/154 (6%)

Query: 10  VKLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVP 68
            KL   D+L L  +   P  F  +G  + + EI+GT+  R  K + F  + VDDGTG + 
Sbjct: 26  AKLYIGDILDLKESRQVPGVFFYNGHPIKQVEILGTVIGRREKDA-FYSYGVDDGTGVIN 84

Query: 69  CVLWLNHLTSLYLPRRDPSTVRLIAGV------ATDFAAKIKIGLVARVRGRIASYRGDV 122
           C+ W     +          V  +           +   KI+IG + ++RG + +YR + 
Sbjct: 85  CICWKKSNNAAPSSAAPALGVLNLTSQLKKLQETIEQKTKIEIGDIVQIRGYVHTYREER 144

Query: 123 QITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
           +I V+      DP  N+++   L+   + RK YD
Sbjct: 145 EIRVTTYYKVDDPVCNIQIARMLELPSIYRKVYD 178

Component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites.

Ailuropoda melanoleuca (taxid: 9646)

>sp|Q8K2X3|STN1_MOUSE CST complex subunit STN1 OS=Mus musculus GN=Obfc1 PE=1 SV=2

 Score = 56.2 bits (134), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 43/157 (27%), Positives = 74/157 (47%), Gaps = 13/157 (8%)

Query: 10  VKLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVP 68
            KL   D+L +  +   P T+  +G  + R +I+G + S   + + F  + VDD TG + 
Sbjct: 34  AKLYIKDILEMKESQQVPGTYFYNGHPIRRVDIMGAVISVKERET-FYSYGVDDATGVIN 92

Query: 69  CVLW--LNHLTSLYLP-----RRDPSTVRLIAGVATDFAAKIKIGL--VARVRGRIASYR 119
           CV W  L++  S   P      R+ S    +  +      K +IG+  + RVRG +  +R
Sbjct: 93  CVCWKKLSNAESSSDPAILSTARELSMTSQLKKLQETIEQKTRIGIGDIIRVRGSVRMFR 152

Query: 120 GDVQITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
            + +I  +      DP  NM++   L+  +L +K YD
Sbjct: 153 EEREICANIYYKVDDPVWNMQIARMLELPKLYQKVYD 189

Component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites.

Mus musculus (taxid: 10090)

>sp|Q08DB2|STN1_BOVIN CST complex subunit STN1 OS=Bos taurus GN=OBFC1 PE=2 SV=1

 Score = 53.9 bits (128), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/156 (28%), Positives = 73/156 (46%), Gaps = 12/156 (7%)

Query: 10  VKLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVP 68
            KL   D+L L  +      F  +G  + + +I+GT+     K + F  + VDD TG + 
Sbjct: 27  AKLYIRDILDLKESGQVQGVFFYNGHPIKQVDILGTVIGVREKDA-FYSYGVDDSTGVIN 85

Query: 69  CVLW--LNHLTSLYL----PRRDPSTVRLIAGVATDFA--AKIKIGLVARVRGRIASYRG 120
           C+ W  LN+  S         R+ S    +  +    A  AK++IG + RVRG I  +RG
Sbjct: 86  CICWKRLNNTKSSSATATPSARELSLTSQLKKLQETIAQRAKLEIGDIIRVRGHIRMFRG 145

Query: 121 DVQITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
           + +I  +      DP  N+++   L+   + RK YD
Sbjct: 146 EREIHATTYYKVDDPVCNVQIARMLELPAIYRKVYD 181

Component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites.

Bos taurus (taxid: 9913)

>sp|Q6AYD2|STN1_RAT CST complex subunit STN1 OS=Rattus norvegicus GN=Obfc1 PE=2 SV=1

 Score = 52.0 bits (123), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 42/156 (26%), Positives = 71/156 (45%), Gaps = 13/156 (8%)

Query: 11  KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
           KL   D+L +  +   P  +  +G  + R +I+G + S   + + F  + VDD TG + C
Sbjct: 35  KLYIKDILEMKESQQVPGMYFYNGHPIRRVDIMGAVISVKERET-FYSYGVDDATGVINC 93

Query: 70  VLWL---NHLTS----LYLPRRDPSTVRLIAGVATDFAAKIKIGL--VARVRGRIASYRG 120
           V W    N  +S    +    R+ S    +  +      K KIG+  + RVRG +  +R 
Sbjct: 94  VCWKRPSNAESSSDPAILSTSRELSMTSQLKKLQETIEQKTKIGIGDIIRVRGYVRMFRE 153

Query: 121 DVQITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
           + +I  +      DP  NM++   L+   L +K YD
Sbjct: 154 EREICATIYYKVDDPVWNMQIARMLELPELYKKVYD 189

Component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites.

Rattus norvegicus (taxid: 10116)

>sp|Q9H668|STN1_HUMAN CST complex subunit STN1 OS=Homo sapiens GN=OBFC1 PE=1 SV=2

 Score = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 72/154 (46%), Gaps = 10/154 (6%)

Query: 10  VKLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVP 68
            KL   D+L +  +   P  F  +G  + + +++GT+     + + F  + VDD TG + 
Sbjct: 27  AKLYIRDILDMKESRQVPGVFLYNGHPIKQVDVLGTVIGVRERDA-FYSYGVDDSTGVIN 85

Query: 69  CVLW--LNHLTSLYLPR--RDPSTVRLIAGVAT--DFAAKIKIGLVARVRGRIASYRGDV 122
           C+ W  LN  +    P   R+ S    +  +    +   KI+IG   RVRG I +YR + 
Sbjct: 86  CICWKKLNTESVSAAPSAARELSLTSQLKKLQETIEQKTKIEIGDTIRVRGSIRTYREER 145

Query: 123 QITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
           +I  +      DP  N+++   L+   + RK YD
Sbjct: 146 EIHATTYYKVDDPVWNIQIARMLELPTIYRKVYD 179

Component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites.

Homo sapiens (taxid: 9606)

>sp|Q4R804|STN1_MACFA CST complex subunit STN1 OS=Macaca fascicularis GN=OBFC1 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 71/154 (46%), Gaps = 10/154 (6%)

Query: 10  VKLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVP 68
            KL   D+L +  +   P  F  +G  + + +++GT+     + + F  + VDD TG + 
Sbjct: 27  AKLYIRDILDMKESRQVPGVFLYNGHPIKQVDVLGTVVGVRERDA-FYSYGVDDSTGVIN 85

Query: 69  CVLW--LNHLTSLYLPR--RDPSTVRLIAGVATDFA--AKIKIGLVARVRGRIASYRGDV 122
           C+ W  LN  +    P   R+ S    +  +        KI+IG   RVRG I +YR + 
Sbjct: 86  CICWKKLNTESVSAAPSAARELSLTSQLKKLQETIERRTKIEIGDTIRVRGSIRTYREER 145

Query: 123 QITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
           +I  +      DP  N+++   L+   + RK YD
Sbjct: 146 EIHATAYYKVDDPVWNIQIARMLELPTIYRKIYD 179

Component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites.

Macaca fascicularis (taxid: 9541)

>sp|Q8LFJ8|RFA2B_ARATH Replication protein A 32 kDa subunit B OS=Arabidopsis thaliana GN=RPA2B PE=2 SV=1

 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 36/134 (26%), Positives = 58/134 (43%), Gaps = 19/134 (14%)

Query: 13  LAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLW 72
           L    LS   T   + FS  G  +    IVG I+  +++ ++ + F VDDGTG V CV W
Sbjct: 44  LTLKQLSSASTTGESNFSIDGVDIKTVVIVGRISRMENRITQ-VDFVVDDGTGWVDCVRW 102

Query: 73  LNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIE 132
            +                  A   T+    +K+G+  R+ G +  ++G   + V  V   
Sbjct: 103 CH------------------ARQETEEMEAVKLGMYVRLHGHLKIFQGKRSVNVFSVRPV 144

Query: 133 KDPNMEVLHWLDCL 146
            D N  V H+ +C+
Sbjct: 145 TDFNEIVHHFTECM 158

Component of the replication protein A complex (RP-A) required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required fo cell division in meristems. Involved in the maintenance of transcriptional epigenetic gene silencing (TGS) at specific loci (including some transposons) by regulating histone H3 acetylation, 'Lys-4' and 'Lys-9' methylation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZQ19|RFA2A_ARATH Replication protein A 32 kDa subunit A OS=Arabidopsis thaliana GN=RPA2A PE=1 SV=2

 Score = 46.2 bits (108), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 18/117 (15%)

Query: 32  SGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRL 91
           +G  L+   +VG +  +D      ++FT+DDGTG + C  W+    S     R+  +VR 
Sbjct: 66  NGISLTNVSLVGLVCDKDESKVTEVRFTLDDGTGRIDCKRWV----SETFDAREMESVR- 120

Query: 92  IAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRL 148
                         G   R+ G + +++G  Q+ V  V    D N    H+++C+  
Sbjct: 121 -------------DGTYVRLSGHLKTFQGKTQLLVFSVRPIMDFNEVTFHYIECIHF 164

Component of the replication protein A complex (RP-A) required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required fo cell division in meristems. Involved in the maintenance of transcriptional epigenetic gene silencing (TGS) at specific loci (including some transposons) by regulating histone H3 acetylation, 'Lys-4' and 'Lys-9' methylation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6DJ48|STN1_XENTR CST complex subunit STN1 OS=Xenopus tropicalis GN=obfc1 PE=2 SV=1

 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/161 (25%), Positives = 67/161 (41%), Gaps = 21/161 (13%)

Query: 11  KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
           KL   D+L L  +   P  F   G  + + +++GT+     K + F  + VDD TG + C
Sbjct: 25  KLYIKDILELKESQQVPGIFFYRGHPIKQVDVLGTVVFVREKEN-FYSYGVDDSTGVISC 83

Query: 70  VLWLNHL-TSLYLPRRDPSTVRLIAGVATDF-------------AAKIKIGLVARVRGRI 115
             W +   T +  P    ++ R ++  + D               AK+ IG   RVRG I
Sbjct: 84  TCWKSTAPTEVSSP---GTSARHVSSSSKDLDVMMRELYKEESKKAKLDIGDTIRVRGSI 140

Query: 116 ASYRGDVQITVSDVVIEKDPNMEV--LHWLDCLRLARKRYD 154
             +R   +I  S     +DP +++      D   + R  YD
Sbjct: 141 KVFRDQREIVASVFYKVEDPKLDIQMARMFDLPYMYRNVYD 181

Component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves.

Xenopus tropicalis (taxid: 8364)

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	160
255567532	166	conserved hypothetical protein [Ricinus	0.968	0.933	0.65	4e-54
359479657	165	PREDICTED: CST complex subunit STN1-like	0.975	0.945	0.652	4e-53
224085511	166	predicted protein [Populus trichocarpa]	0.981	0.945	0.679	6e-53
357483465	185	CST complex subunit STN1 [Medicago trunc	0.956	0.827	0.587	5e-47
388505562	179	unknown [Medicago truncatula]	0.95	0.849	0.590	5e-46
400180216	154	CST complex subunit STN1-like protein [C	0.887	0.922	0.598	2e-44
449455286	168	PREDICTED: CST complex subunit STN1-like	0.95	0.904	0.584	6e-44
18390729	160	CST complex subunit STN1 [Arabidopsis th	0.981	0.981	0.562	2e-43
297843504	158	OB-fold nucleic acid binding domain-cont	0.968	0.981	0.575	3e-43
242035657	164	hypothetical protein SORBIDRAFT_01g03449	0.931	0.908	0.521	3e-39

>gi|255567532|ref|XP_002524745.1| conserved hypothetical protein [Ricinus communis] gi|223535929|gb|EEF37588.1| conserved hypothetical protein [Ricinus communis]

 Score =  215 bits (548), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 104/160 (65%), Positives = 119/160 (74%), Gaps = 5/160 (3%)

Query: 1   MDHTLQNTHVKLLAFDLLSLTPTP-----DPATFSRSGKLLSRAEIVGTITSRDHKPSKF 55
           MD   QN HVKLLA DL+SLT TP     DP +FS + K  SRAEI+G +TS +HKP KF
Sbjct: 1   MDQKFQNIHVKLLALDLVSLTQTPPFSPSDPISFSHANKSFSRAEILGIVTSCEHKPHKF 60

Query: 56  IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI 115
           +KFT+DDGTGCV C+LWLN LTS Y  RR    VRLIA  AT FA+ IKIG+VARVRGRI
Sbjct: 61  LKFTIDDGTGCVSCILWLNQLTSPYFSRRSTPAVRLIASTATHFASLIKIGVVARVRGRI 120

Query: 116 ASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDV 155
            SYRG VQIT SDVVIE+DPN E+ HWL C++LAR  Y V
Sbjct: 121 TSYRGTVQITASDVVIERDPNAEIFHWLQCVKLARSCYHV 160

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359479657|ref|XP_003632321.1| PREDICTED: CST complex subunit STN1-like [Vitis vinifera] gi|147810449|emb|CAN65336.1| hypothetical protein VITISV_023849 [Vitis vinifera]

 Score =  212 bits (539), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 105/161 (65%), Positives = 131/161 (81%), Gaps = 5/161 (3%)

Query: 1   MDHTLQNTHVKLLAFDLLSLTPTPDPATFS-----RSGKLLSRAEIVGTITSRDHKPSKF 55
           M + L NTHVKLLAFDLLSLT TP P++       R G  LSRAE +GT+TSR+ KP KF
Sbjct: 1   MSNQLYNTHVKLLAFDLLSLTQTPSPSSSDPISFSRRGTPLSRAETLGTVTSRELKPHKF 60

Query: 56  IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI 115
           +KFTVDDGTGCVPCVLWLNHL+S Y  RR+P+ VRLIA +A   A+++K+G++ RVRGRI
Sbjct: 61  LKFTVDDGTGCVPCVLWLNHLSSPYFSRRNPADVRLIADLAEYQASEVKLGVLVRVRGRI 120

Query: 116 ASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVV 156
            +YRG VQITVS+V++E+DPNME+LHWLDC++LARK YDV+
Sbjct: 121 TAYRGTVQITVSNVIVERDPNMEILHWLDCIKLARKCYDVM 161

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224085511|ref|XP_002307601.1| predicted protein [Populus trichocarpa] gi|222857050|gb|EEE94597.1| predicted protein [Populus trichocarpa]

 Score =  211 bits (538), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 110/162 (67%), Positives = 129/162 (79%), Gaps = 5/162 (3%)

Query: 1   MDHTLQNTHVKLLAFDLLSLTPTP-----DPATFSRSGKLLSRAEIVGTITSRDHKPSKF 55
           MD  LQNTHVKLLAFDLLSL  TP     DP TF+R    +SR EI+G ITSR+ KP+KF
Sbjct: 1   MDQRLQNTHVKLLAFDLLSLAQTPSFSTYDPITFTRKNTTISRTEILGVITSRELKPNKF 60

Query: 56  IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI 115
           +KFT+DDGTGCV CVLWLN LTS Y  RR+P+ V+LIA +A  FA++IKIGLVARVRGRI
Sbjct: 61  LKFTIDDGTGCVTCVLWLNQLTSPYFSRRNPANVKLIADMAAHFASEIKIGLVARVRGRI 120

Query: 116 ASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVV 157
           A YRG VQ+TVSDVV+E+DPN+E  HWLDC+RLAR  Y+VV 
Sbjct: 121 AGYRGAVQVTVSDVVVERDPNVEAFHWLDCIRLARNCYNVVA 162

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357483465|ref|XP_003612019.1| CST complex subunit STN1 [Medicago truncatula] gi|355513354|gb|AES94977.1| CST complex subunit STN1 [Medicago truncatula]

 Score =  192 bits (487), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 91/155 (58%), Positives = 120/155 (77%), Gaps = 2/155 (1%)

Query: 4   TLQNTHVKLLAFDLLSLTPTPDPA-TFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDD 62
           +L NTHVKLLAFDLL+LTP   P  +F+R+   ++RAE VGTIT RDHKP KF++F +DD
Sbjct: 11  SLHNTHVKLLAFDLLTLTPPISPNHSFTRNSIPITRAETVGTITLRDHKPFKFLRFAIDD 70

Query: 63  GTGCVPCVLWLNHLTSLYLPRR-DPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGD 121
           GTGC+PC+LWLNH+TS +L RR  P  + L+A  A   A  +K+G VARVRGR+  Y+G 
Sbjct: 71  GTGCIPCILWLNHMTSPHLARRRSPQDLCLLADAAARSAEVVKVGNVARVRGRVTEYKGG 130

Query: 122 VQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVV 156
           VQITV+DV+ E+DPN+EVLHW++C+ LAR  Y++V
Sbjct: 131 VQITVTDVISERDPNVEVLHWVECVNLARNCYNLV 165

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388505562|gb|AFK40847.1| unknown [Medicago truncatula]

 Score =  189 bits (479), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 91/154 (59%), Positives = 117/154 (75%), Gaps = 2/154 (1%)

Query: 4   TLQNTHVKLLAFDLLSLTPTPDPA-TFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDD 62
           +L NTHVKLLAFDLL+LTP   P  +F+R+   ++RAE VGTIT RDHKP KF++F +DD
Sbjct: 11  SLHNTHVKLLAFDLLTLTPPISPNHSFTRNSISITRAETVGTITLRDHKPFKFLRFAIDD 70

Query: 63  GTGCVPCVLWLNHLTSLYLP-RRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGD 121
           GTGC+PC+LWLNH+TS +L  RR P  + L+A  A   A   K G VARVRGR+  Y+G 
Sbjct: 71  GTGCIPCILWLNHMTSPHLARRRSPQDLCLLADAAARSAEVAKFGNVARVRGRVTEYKGG 130

Query: 122 VQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDV 155
           VQITV+DVV E+DPN+EVLHW++C+ LAR  Y++
Sbjct: 131 VQITVTDVVSERDPNVEVLHWVECVNLARNCYNL 164

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|400180216|gb|AFP73237.1| CST complex subunit STN1-like protein [Carica papaya]

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 88/147 (59%), Positives = 112/147 (76%), Gaps = 5/147 (3%)

Query: 9   HVKLLAFDLLSLTPT-PDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCV 67
           H+KLLAFD  SLT T     +F+R G  +SR E +GT+ SRD KPS+F+KF +DDGTGC+
Sbjct: 9   HMKLLAFDFTSLTQTRSHSKSFTRKGIPISRVESLGTVVSRDLKPSRFLKFKLDDGTGCI 68

Query: 68  PCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVS 127
            C+LWLN L+S     ++PSTVRLIA VA   A +IK+G VARVRGR+  YRG +QITVS
Sbjct: 69  ACILWLNQLSS----NQNPSTVRLIAQVANHLAEEIKMGRVARVRGRVTGYRGRIQITVS 124

Query: 128 DVVIEKDPNMEVLHWLDCLRLARKRYD 154
           D+VIE+DPN ++LHWL+C+RLARK  D
Sbjct: 125 DIVIERDPNAQILHWLECIRLARKVLD 151

Source: Carica papaya

Species: Carica papaya

Genus: Carica

Family: Caricaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455286|ref|XP_004145384.1| PREDICTED: CST complex subunit STN1-like [Cucumis sativus] gi|449474220|ref|XP_004154109.1| PREDICTED: CST complex subunit STN1-like [Cucumis sativus] gi|449526303|ref|XP_004170153.1| PREDICTED: CST complex subunit STN1-like [Cucumis sativus]

 Score =  181 bits (460), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 90/154 (58%), Positives = 113/154 (73%), Gaps = 2/154 (1%)

Query: 4   TLQNTHVKLLAFDLLSLTPTPDPATFS--RSGKLLSRAEIVGTITSRDHKPSKFIKFTVD 61
           +L  THVKLLAFDL SL  T    + S  R G  +S  EIVG +  RD KP++F+KF+VD
Sbjct: 10  SLYQTHVKLLAFDLNSLNQTSSSDSVSFSRKGYAVSCTEIVGVVVFRDLKPNRFLKFSVD 69

Query: 62  DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGD 121
           DGT CV C+LWLNHLTS Y   R    VR++  +AT FAA+I++G+V RVRG+++SYRG 
Sbjct: 70  DGTACVGCILWLNHLTSSYFASRHHQDVRILGDMATHFAAQIRVGIVVRVRGKLSSYRGM 129

Query: 122 VQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDV 155
           VQITVSDVV+E DPN E+LHWLD +RLA K YD+
Sbjct: 130 VQITVSDVVVEDDPNAEILHWLDSMRLAMKCYDL 163

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18390729|ref|NP_563781.1| CST complex subunit STN1 [Arabidopsis thaliana] gi|75335200|sp|Q9LMK5.1|STN1_ARATH RecName: Full=CST complex subunit STN1; AltName: Full=Suppressor of cdc thirteen homolog; Short=AtSTN1 gi|8954034|gb|AAF82208.1|AC067971_16 F10K1.17 [Arabidopsis thaliana] gi|21554324|gb|AAM63429.1| unknown [Arabidopsis thaliana] gi|26452561|dbj|BAC43365.1| unknown protein [Arabidopsis thaliana] gi|28827422|gb|AAO50555.1| unknown protein [Arabidopsis thaliana] gi|332189958|gb|AEE28079.1| CST complex subunit STN1 [Arabidopsis thaliana]

 Score =  180 bits (456), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 90/160 (56%), Positives = 114/160 (71%), Gaps = 3/160 (1%)

Query: 1   MDHTLQNTHVKLLAFDLLSLTPTP-DPATFSR-SGKLLSRAEIVGTITSRDHKPSKFIKF 58
           MD +LQ+TH KL+A D+  LT +P +  +FS   G  +SR EIVGTI SRD  P KF+KF
Sbjct: 1   MDRSLQSTHAKLVARDIQRLTQSPTESNSFSLLGGACVSRVEIVGTIVSRDLTP-KFLKF 59

Query: 59  TVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY 118
            VDDGTGCV CV+WLN LTS Y  R DP+T+ L+A  A   AA+I+IG VARVRGR+ SY
Sbjct: 60  GVDDGTGCVTCVMWLNQLTSSYFSRWDPATILLLASAARKQAAQIRIGAVARVRGRVGSY 119

Query: 119 RGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVVN 158
           RG +QIT +  V E+DPN E+LHWL+CL+L +  Y V + 
Sbjct: 120 RGVMQITANVAVAERDPNAEILHWLECLKLGQSCYRVRIQ 159

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843504|ref|XP_002889633.1| OB-fold nucleic acid binding domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297335475|gb|EFH65892.1| OB-fold nucleic acid binding domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  179 bits (454), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 91/158 (57%), Positives = 113/158 (71%), Gaps = 3/158 (1%)

Query: 1   MDHTLQNTHVKLLAFDLLSLTPTP-DPATFSR-SGKLLSRAEIVGTITSRDHKPSKFIKF 58
           MD +LQNTH KL+A D+  LT +P +  +FS   G  +SR E VGTI SRD  P KF+KF
Sbjct: 1   MDRSLQNTHAKLVARDIQRLTQSPTESNSFSLLGGACVSRVETVGTIISRDLTP-KFLKF 59

Query: 59  TVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY 118
            VDDGTGCV CVLWLN LTS Y  R  P T+ L+A  A   AA+I+IG VARVRGR+ SY
Sbjct: 60  GVDDGTGCVTCVLWLNQLTSSYFSRWHPDTILLLASAARKQAAEIRIGSVARVRGRVGSY 119

Query: 119 RGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVV 156
           RG +QIT + VV+E+DPN E+LHWL+CLRL +  Y ++
Sbjct: 120 RGVMQITATVVVVERDPNAEILHWLECLRLGQSCYRIL 157

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242035657|ref|XP_002465223.1| hypothetical protein SORBIDRAFT_01g034490 [Sorghum bicolor] gi|241919077|gb|EER92221.1| hypothetical protein SORBIDRAFT_01g034490 [Sorghum bicolor]

 Score =  166 bits (421), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 84/161 (52%), Positives = 111/161 (68%), Gaps = 12/161 (7%)

Query: 1   MDHTLQNTHVKLLAFDLLSLT-PTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFT 59
           MDH L   HVK+LA DLLSLT     P  F R G+ ++RAE+VG + SRD +  KF++F 
Sbjct: 1   MDHLLHLVHVKILAADLLSLTIQHTSPPAFLRCGRTVARAELVGIVVSRDRR-EKFLRFV 59

Query: 60  VDDGTGCVPCVLWLNHL-----TSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGR 114
           +DDGTGCVPC+LWLNH      TS  L   DP+     A +A   + ++++G + RVRG+
Sbjct: 60  IDDGTGCVPCILWLNHQYLNASTSSGLSESDPT-----AEIALKMSEEVRLGTLLRVRGK 114

Query: 115 IASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDV 155
           I +YRG +QITV DVV+EKDPN EVLHWL C+RLA++ YD+
Sbjct: 115 ITTYRGAIQITVRDVVVEKDPNSEVLHWLQCVRLAKECYDL 155

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	160
TAIR|locus:2007352	160	STN1 [Arabidopsis thaliana (ta	0.962	0.962	0.573	1.1e-41
UNIPROTKB|D2GXY4	367	OBFC1 "CST complex subunit STN	0.893	0.389	0.307	7.6e-10
UNIPROTKB|Q08DB2	370	OBFC1 "CST complex subunit STN	0.893	0.386	0.296	4.5e-09
UNIPROTKB|F1PJS4	374	OBFC1 "Uncharacterized protein	0.893	0.382	0.278	1.6e-08
UNIPROTKB|J9PA40	368	OBFC1 "Uncharacterized protein	0.893	0.388	0.269	2e-08
MGI|MGI:1915581	378	Obfc1 "oligonucleotide/oligosa	0.893	0.378	0.275	2.1e-08
UNIPROTKB|Q9H668	368	OBFC1 "CST complex subunit STN	0.893	0.388	0.274	4.3e-08
UNIPROTKB|Q4R804	368	OBFC1 "CST complex subunit STN	0.893	0.388	0.274	4.3e-08
UNIPROTKB|F1S835	371	OBFC1 "Uncharacterized protein	0.893	0.385	0.283	7.2e-08
RGD|1305637	408	Obfc1 "oligonucleotide/oligosa	0.893	0.350	0.269	3e-07

TAIR|locus:2007352 STN1 [Arabidopsis thaliana (taxid:3702)]

 Score = 442 (160.7 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 90/157 (57%), Positives = 113/157 (71%)

Query:     1 MDHTLQNTHVKLLAFDLLSLTPTPDPA-TFSR-SGKLLSRAEIVGTITSRDHKPSKFIKF 58
             MD +LQ+TH KL+A D+  LT +P  + +FS   G  +SR EIVGTI SRD  P KF+KF
Sbjct:     1 MDRSLQSTHAKLVARDIQRLTQSPTESNSFSLLGGACVSRVEIVGTIVSRDLTP-KFLKF 59

Query:    59 TVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY 118
              VDDGTGCV CV+WLN LTS Y  R DP+T+ L+A  A   AA+I+IG VARVRGR+ SY
Sbjct:    60 GVDDGTGCVTCVMWLNQLTSSYFSRWDPATILLLASAARKQAAQIRIGAVARVRGRVGSY 119

Query:   119 RGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDV 155
             RG +QIT +  V E+DPN E+LHWL+CL+L +  Y V
Sbjct:   120 RGVMQITANVAVAERDPNAEILHWLECLKLGQSCYRV 156

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0000784 "nuclear chromosome, telomeric region" evidence=IDA

GO:0016233 "telomere capping" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

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

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

UNIPROTKB|D2GXY4 OBFC1 "CST complex subunit STN1" [Ailuropoda melanoleuca (taxid:9646)]

 Score = 148 (57.2 bits), Expect = 7.6e-10, P = 7.6e-10
 Identities = 47/153 (30%), Positives = 74/153 (48%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L L  +   P  F  +G  + + EI+GT+  R  K + F  + VDDGTG + C
Sbjct:    27 KLYIGDILDLKESRQVPGVFFYNGHPIKQVEILGTVIGRREKDA-FYSYGVDDGTGVINC 85

Query:    70 VLWL---NHLTSLYLPRRDPS--TVRLIAGVAT-DFAAKIKIGLVARVRGRIASYRGDVQ 123
             + W    N   S   P       T +L     T +   KI+IG + ++RG + +YR + +
Sbjct:    86 ICWKKSNNAAPSSAAPALGVLNLTSQLKKLQETIEQKTKIEIGDIVQIRGYVHTYREERE 145

Query:   124 ITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
             I V+      DP  N+++   L+   + RK YD
Sbjct:   146 IRVTTYYKVDDPVCNIQIARMLELPSIYRKVYD 178

GO:0000723 "telomere maintenance" evidence=ISS

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0010833 "telomere maintenance via telomere lengthening" evidence=ISS

GO:0043047 "single-stranded telomeric DNA binding" evidence=ISS

UNIPROTKB|Q08DB2 OBFC1 "CST complex subunit STN1" [Bos taurus (taxid:9913)]

 Score = 141 (54.7 bits), Expect = 4.5e-09, P = 4.5e-09
 Identities = 46/155 (29%), Positives = 74/155 (47%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L L  +      F  +G  + + +I+GT+     K + F  + VDD TG + C
Sbjct:    28 KLYIRDILDLKESGQVQGVFFYNGHPIKQVDILGTVIGVREKDA-FYSYGVDDSTGVINC 86

Query:    70 VLW--LNHLTS---LYLPR-RDPSTVRLIAGVATDFA--AKIKIGLVARVRGRIASYRGD 121
             + W  LN+  S      P  R+ S    +  +    A  AK++IG + RVRG I  +RG+
Sbjct:    87 ICWKRLNNTKSSSATATPSARELSLTSQLKKLQETIAQRAKLEIGDIIRVRGHIRMFRGE 146

Query:   122 VQITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
              +I  +      DP  N+++   L+   + RK YD
Sbjct:   147 REIHATTYYKVDDPVCNVQIARMLELPAIYRKVYD 181

GO:0043047 "single-stranded telomeric DNA binding" evidence=ISS

GO:0000723 "telomere maintenance" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0010833 "telomere maintenance via telomere lengthening" evidence=ISS

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISS

GO:0070188 "Stn1-Ten1 complex" evidence=IEA

GO:0045740 "positive regulation of DNA replication" evidence=IEA

GO:0045111 "intermediate filament cytoskeleton" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|F1PJS4 OBFC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 136 (52.9 bits), Expect = 1.6e-08, P = 1.6e-08
 Identities = 44/158 (27%), Positives = 78/158 (49%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L+L  +      F  +G  + + EI+GT+  R  K + F  + VDD TG + C
Sbjct:    28 KLYIRDILNLKESRQVQGVFFYNGHPIKQVEILGTVIGRREKDA-FYSYGVDDSTGVINC 86

Query:    70 VLWL--NHL-TSLYLPRRDPSTVRLIAGVAT--------DFAAKIKIGLVARVRGRIASY 118
             + W   N++ +S  L     ST  +++  +         +   KI+IG + ++RG + +Y
Sbjct:    87 ICWKKSNNIESSSALVTTAASTAGVLSLTSQLKKLQETIEQKTKIEIGDIIQIRGYVHTY 146

Query:   119 RGDVQITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
             R + +I V+      DP  N+++   L+   + RK YD
Sbjct:   147 REEREIRVTTFYKVDDPVCNIQIARMLELPSIYRKVYD 184

GO:0043047 "single-stranded telomeric DNA binding" evidence=IEA

GO:0010833 "telomere maintenance via telomere lengthening" evidence=IEA

UNIPROTKB|J9PA40 OBFC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 135 (52.6 bits), Expect = 2.0e-08, P = 2.0e-08
 Identities = 42/156 (26%), Positives = 76/156 (48%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L+L  +      F  +G  + + EI+GT+  R  K + F  + VDD TG + C
Sbjct:    28 KLYIRDILNLKESRQVQGVFFYNGHPIKQVEILGTVIGRREKDA-FYSYGVDDSTGVINC 86

Query:    70 VLWL--NHL--TSLYLPRRDPSTVRLIAGV-----ATDFAAKIKIGLVARVRGRIASYRG 120
             + W   N++  +S+         + L + +       +   KI+IG + ++RG + +YR 
Sbjct:    87 ICWKKSNNIESSSVTTAASTAGVLSLTSQLKKLQETIEQKTKIEIGDIIQIRGYVHTYRE 146

Query:   121 DVQITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
             + +I V+      DP  N+++   L+   + RK YD
Sbjct:   147 EREIRVTTFYKVDDPVCNIQIARMLELPSIYRKVYD 182

GO:0043047 "single-stranded telomeric DNA binding" evidence=IEA

GO:0010833 "telomere maintenance via telomere lengthening" evidence=IEA

MGI|MGI:1915581 Obfc1 "oligonucleotide/oligosaccharide-binding fold containing 1" [Mus musculus (taxid:10090)]

 Score = 135 (52.6 bits), Expect = 2.1e-08, P = 2.1e-08
 Identities = 43/156 (27%), Positives = 74/156 (47%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L +  +   P T+  +G  + R +I+G + S   + + F  + VDD TG + C
Sbjct:    35 KLYIKDILEMKESQQVPGTYFYNGHPIRRVDIMGAVISVKERET-FYSYGVDDATGVINC 93

Query:    70 VLW--LNHLTSLYLPR-----RDPSTVRLIAGVATDFAAKIKIGL--VARVRGRIASYRG 120
             V W  L++  S   P      R+ S    +  +      K +IG+  + RVRG +  +R 
Sbjct:    94 VCWKKLSNAESSSDPAILSTARELSMTSQLKKLQETIEQKTRIGIGDIIRVRGSVRMFRE 153

Query:   121 DVQITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
             + +I  +      DP  NM++   L+  +L +K YD
Sbjct:   154 EREICANIYYKVDDPVWNMQIARMLELPKLYQKVYD 189

GO:0000723 "telomere maintenance" evidence=ISO

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISO;IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005694 "chromosome" evidence=IEA

GO:0010833 "telomere maintenance via telomere lengthening" evidence=ISO

GO:0043047 "single-stranded telomeric DNA binding" evidence=ISO

GO:0045740 "positive regulation of DNA replication" evidence=IDA

GO:0070188 "Stn1-Ten1 complex" evidence=IDA

UNIPROTKB|Q9H668 OBFC1 "CST complex subunit STN1" [Homo sapiens (taxid:9606)]

 Score = 132 (51.5 bits), Expect = 4.3e-08, P = 4.3e-08
 Identities = 42/153 (27%), Positives = 72/153 (47%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L +  +   P  F  +G  + + +++GT+     + + F  + VDD TG + C
Sbjct:    28 KLYIRDILDMKESRQVPGVFLYNGHPIKQVDVLGTVIGVRERDA-FYSYGVDDSTGVINC 86

Query:    70 VLW--LNHLTSLYLPR--RDPSTVRLIAGV--ATDFAAKIKIGLVARVRGRIASYRGDVQ 123
             + W  LN  +    P   R+ S    +  +    +   KI+IG   RVRG I +YR + +
Sbjct:    87 ICWKKLNTESVSAAPSAARELSLTSQLKKLQETIEQKTKIEIGDTIRVRGSIRTYREERE 146

Query:   124 ITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
             I  +      DP  N+++   L+   + RK YD
Sbjct:   147 IHATTYYKVDDPVWNIQIARMLELPTIYRKVYD 179

GO:0070188 "Stn1-Ten1 complex" evidence=IEA

GO:0005634 "nucleus" evidence=ISS;IDA

GO:0000784 "nuclear chromosome, telomeric region" evidence=IDA

GO:0000723 "telomere maintenance" evidence=IMP

GO:0043047 "single-stranded telomeric DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0010833 "telomere maintenance via telomere lengthening" evidence=IMP

GO:0045740 "positive regulation of DNA replication" evidence=ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

GO:0045111 "intermediate filament cytoskeleton" evidence=IDA

UNIPROTKB|Q4R804 OBFC1 "CST complex subunit STN1" [Macaca fascicularis (taxid:9541)]

 Score = 132 (51.5 bits), Expect = 4.3e-08, P = 4.3e-08
 Identities = 42/153 (27%), Positives = 72/153 (47%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L +  +   P  F  +G  + + +++GT+     + + F  + VDD TG + C
Sbjct:    28 KLYIRDILDMKESRQVPGVFLYNGHPIKQVDVLGTVVGVRERDA-FYSYGVDDSTGVINC 86

Query:    70 VLW--LNHLTSLYLPR--RDPSTVRLIAGV--ATDFAAKIKIGLVARVRGRIASYRGDVQ 123
             + W  LN  +    P   R+ S    +  +    +   KI+IG   RVRG I +YR + +
Sbjct:    87 ICWKKLNTESVSAAPSAARELSLTSQLKKLQETIERRTKIEIGDTIRVRGSIRTYREERE 146

Query:   124 ITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
             I  +      DP  N+++   L+   + RK YD
Sbjct:   147 IHATAYYKVDDPVWNIQIARMLELPTIYRKIYD 179

GO:0000723 "telomere maintenance" evidence=ISS

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0010833 "telomere maintenance via telomere lengthening" evidence=ISS

GO:0043047 "single-stranded telomeric DNA binding" evidence=ISS

UNIPROTKB|F1S835 OBFC1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 130 (50.8 bits), Expect = 7.2e-08, P = 7.2e-08
 Identities = 44/155 (28%), Positives = 74/155 (47%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L L  +   P  F  +G  + + +I+GT+     + + F  + VDD TG + C
Sbjct:    28 KLYIRDILDLKESRQVPGVFFYNGHPIKQVDILGTVIGVRERDA-FYSYGVDDSTGVINC 86

Query:    70 VLW--LNHLTSLYLPR----RDPSTVRLIAGVATDFAA--KIKIGLVARVRGRIASYRGD 121
             + W  LN+  S         R+ S    +  +    A   KI+IG + ++RG I +YR +
Sbjct:    87 ICWKKLNNTDSSSATAATNARELSLTSQLKKLQETIAQRLKIEIGDLVQIRGHIRTYREE 146

Query:   122 VQI--TVSDVVIEKDPNMEVLHWLDCLRLARKRYD 154
              +I  TV   V +   N+++   L+   + RK YD
Sbjct:   147 REIHATVYHKVDDPVCNIQIARMLELPTIYRKVYD 181

GO:0070188 "Stn1-Ten1 complex" evidence=IEA

GO:0045740 "positive regulation of DNA replication" evidence=IEA

GO:0045111 "intermediate filament cytoskeleton" evidence=IEA

GO:0043047 "single-stranded telomeric DNA binding" evidence=IEA

GO:0010833 "telomere maintenance via telomere lengthening" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

RGD|1305637 Obfc1 "oligonucleotide/oligosaccharide-binding fold containing 1" [Rattus norvegicus (taxid:10116)]

 Score = 125 (49.1 bits), Expect = 3.0e-07, P = 3.0e-07
 Identities = 42/156 (26%), Positives = 71/156 (45%)

Query:    11 KLLAFDLLSLTPTPD-PATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPC 69
             KL   D+L +  +   P  +  +G  + R +I+G + S   + + F  + VDD TG + C
Sbjct:    35 KLYIKDILEMKESQQVPGMYFYNGHPIRRVDIMGAVISVKERET-FYSYGVDDATGVINC 93

Query:    70 VLWL---NHLTS----LYLPRRDPSTVRLIAGVATDFAAKIKIGL--VARVRGRIASYRG 120
             V W    N  +S    +    R+ S    +  +      K KIG+  + RVRG +  +R 
Sbjct:    94 VCWKRPSNAESSSDPAILSTSRELSMTSQLKKLQETIEQKTKIGIGDIIRVRGYVRMFRE 153

Query:   121 DVQITVSDVVIEKDP--NMEVLHWLDCLRLARKRYD 154
             + +I  +      DP  NM++   L+   L +K YD
Sbjct:   154 EREICATIYYKVDDPVWNMQIARMLELPELYKKVYD 189

GO:0000723 "telomere maintenance" evidence=ISO;ISS

GO:0000784 "nuclear chromosome, telomeric region" evidence=ISO;ISS

GO:0003697 "single-stranded DNA binding" evidence=ISO;ISS

GO:0005634 "nucleus" evidence=ISO;ISS

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0010833 "telomere maintenance via telomere lengthening" evidence=ISO;ISS

GO:0043047 "single-stranded telomeric DNA binding" evidence=ISO;ISS

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0045111 "intermediate filament cytoskeleton" evidence=IEA;ISO

GO:0045740 "positive regulation of DNA replication" evidence=ISO;ISS

GO:0070188 "Stn1-Ten1 complex" evidence=IEA;ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9LMK5	STN1_ARATH	No assigned EC number	0.5625	0.9812	0.9812	yes	no

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: GSVIVG00023760001 SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (206 aa) (Vitis vinifera)

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	160
cd04483	92	cd04483, hOBFC1_like, hOBFC1_like: A subfamily of	4e-24
pfam01336	75	pfam01336, tRNA_anti, OB-fold nucleic acid binding	6e-07
cd03524	75	cd03524, RPA2_OBF_family, RPA2_OBF_family: A famil	9e-07
cd04492	83	cd04492, YhaM_OBF_like, YhaM_OBF_like: A subfamily	6e-05
cd04478	95	cd04478, RPA2_DBD_D, RPA2_DBD_D: A subfamily of OB	2e-04
COG3390	196	COG3390, COG3390, Uncharacterized protein conserve	5e-04

>gnl|CDD|239929 cd04483, hOBFC1_like, hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1)

 Score = 89.4 bits (222), Expect = 4e-24
 Identities = 36/93 (38%), Positives = 50/93 (53%), Gaps = 1/93 (1%)

Query: 40  EIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF 99
           +I+GT+ SR  +   F  F VDDGTG V CV W N   +    R D + +   A +A   
Sbjct: 1   DILGTVVSRRERE-TFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQ 59

Query: 100 AAKIKIGLVARVRGRIASYRGDVQITVSDVVIE 132
           A  ++IG + RVRG I +YRG+ +I  S V   
Sbjct: 60  AKVLEIGDLLRVRGSIRTYRGEREINASVVYKV 92

Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization. Length = 92

>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain

 Score = 44.6 bits (106), Expect = 6e-07
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 21/92 (22%)

Query: 41  IVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFA 100
           + G +TS      K    T+ DGTG +  VL+                       A   A
Sbjct: 3   VAGRVTSVRRSGGKVAFLTLRDGTGSIQVVLF--------------------KEEAEKLA 42

Query: 101 AKIKIGLVARVRGRI-ASYRGDVQITVSDVVI 131
            K+K G V  V G++     G++++ V ++ +
Sbjct: 43  KKLKEGDVVLVTGKVKKRPGGELELVVEEIEV 74

This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. Length = 75

>gnl|CDD|239601 cd03524, RPA2_OBF_family, RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

 Score = 43.9 bits (104), Expect = 9e-07
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 23/94 (24%)

Query: 40  EIVGTITSRDHKP--SKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA 96
            IVG + + +      K + FT+ DGTG  +   L+                       A
Sbjct: 1   TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGEL--------------------A 40

Query: 97  TDFAAKIKIGLVARVRGRIASYRGDVQITVSDVV 130
            +    +K G V  ++G++  +RG +Q+ V  + 
Sbjct: 41  EELENLLKEGQVVYIKGKVKKFRGRLQLIVESIE 74

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1). Length = 75

>gnl|CDD|239938 cd04492, YhaM_OBF_like, YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1)

 Score = 39.1 bits (92), Expect = 6e-05
 Identities = 21/102 (20%), Positives = 42/102 (41%), Gaps = 26/102 (25%)

Query: 35  LLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAG 94
           L+   E+    T+++ KP  ++  T+ D TG +   LW                      
Sbjct: 5   LIKSKELR---TAKNGKP--YLALTLQDKTGEIEAKLWDA-------------------- 39

Query: 95  VATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPN 136
            + +   K K G +  V+GR+  YRG +Q+ +  + +  + +
Sbjct: 40  -SEEDEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIRLVTEED 80

Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases. Length = 83

>gnl|CDD|239924 cd04478, RPA2_DBD_D, RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 23/107 (21%), Positives = 40/107 (37%), Gaps = 20/107 (18%)

Query: 41  IVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFA 100
           +VG + + + + +  I +T+DDGTG +    WL+                          
Sbjct: 4   LVGVVRNVEEQSTN-ITYTIDDGTGTIEVRQWLD------------------DDNDDSSE 44

Query: 101 A-KIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCL 146
              I+ G   RV G + S++G   I    +    D N    H L+ +
Sbjct: 45  VEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTDFNEVTYHLLEVI 91

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro. Length = 95

>gnl|CDD|225925 COG3390, COG3390, Uncharacterized protein conserved in archaea [Function unknown]

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 28/140 (20%), Positives = 51/140 (36%), Gaps = 33/140 (23%)

Query: 20  LTPTPDPATFSRSGKLLSRAEIVGTITSR--DHKPSKFIKFTVDDGTGCVPCVLWLNHLT 77
           +TP          G  ++R  IVGT+T +    +  ++ +  V D TG      ++    
Sbjct: 38  ITPL---------GLKVNRIFIVGTLTEKEGIGEDREYWRIRVVDPTG----SFYV--YA 82

Query: 78  SLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGD----VQITVSDVVIEK 133
             Y P             A  F   +++  +  V G+I +YR D    +     ++V + 
Sbjct: 83  GQYQPE------------AKAFLEDVEVPDLVAVIGKIRTYRTDEGVVLFSIRPELVSKV 130

Query: 134 DPNMEVLHWLDCLRLARKRY 153
           D     L  L+      +R 
Sbjct: 131 DEEARDLWVLETAEQTLERI 150

Length = 196

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	160
COG5235	258	RFA2 Single-stranded DNA-binding replication prote	99.93
cd04478	95	RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor	99.92
PF10451	256	Stn1: Telomere regulation protein Stn1; InterPro:	99.9
KOG3108	265	consensus Single-stranded DNA-binding replication	99.88
cd04483	92	hOBFC1_like hOBFC1_like: A subfamily of OB folds s	99.85
PF01336	75	tRNA_anti-codon: OB-fold nucleic acid binding doma	99.44
PRK13480	314	3'-5' exoribonuclease YhaM; Provisional	99.37
cd04492	83	YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol	99.2
cd03524	75	RPA2_OBF_family RPA2_OBF_family: A family of oligo	99.04
cd04485	84	DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp	99.0
cd04489	78	ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol	98.95
cd04491	82	SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil	98.93
PRK06461	129	single-stranded DNA-binding protein; Reviewed	98.93
cd04487	73	RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f	98.7
cd04482	91	RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara	98.64
cd04488	75	RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f	98.59
PF13742	99	tRNA_anti_2: OB-fold nucleic acid binding domain	98.52
COG3390	196	Uncharacterized protein conserved in archaea [Func	98.43
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	98.4
cd04490	79	PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds	98.3
COG4085	204	Predicted RNA-binding protein, contains TRAM domai	98.27
cd04484	82	polC_OBF polC_OBF: A subfamily of OB folds corresp	98.13
COG1570	440	XseA Exonuclease VII, large subunit [DNA replicati	98.12
TIGR00237	432	xseA exodeoxyribonuclease VII, large subunit. This	98.03
cd04321	86	ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, a	98.02
PRK00286	438	xseA exodeoxyribonuclease VII large subunit; Revie	98.0
PRK05673	1135	dnaE DNA polymerase III subunit alpha; Validated	97.98
cd04100	85	Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant	97.95
cd04316	108	ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a	97.93
KOG3416	134	consensus Predicted nucleic acid binding protein [	97.92
cd04323	84	AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, a	97.92
PRK07373	449	DNA polymerase III subunit alpha; Reviewed	97.89
cd04320	102	AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r	97.88
COG3481	287	Predicted HD-superfamily hydrolase [General functi	97.83
cd04322	108	LysRS_N LysRS_N: N-terminal, anticodon recognition	97.79
cd04317	135	EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod	97.79
PRK07217	311	replication factor A; Reviewed	97.77
PF04076	103	BOF: Bacterial OB fold (BOF) protein; InterPro: IP	97.75
cd04319	103	PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticod	97.74
PRK07211	485	replication factor A; Reviewed	97.67
PRK07218	423	replication factor A; Provisional	97.66
cd04318	82	EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticod	97.65
PRK14699	484	replication factor A; Provisional	97.63
TIGR00156	126	conserved hypothetical protein TIGR00156. As of th	97.51
PRK07211	485	replication factor A; Reviewed	97.5
PRK07218	423	replication factor A; Provisional	97.39
PRK07374	1170	dnaE DNA polymerase III subunit alpha; Validated	97.38
PRK06920	1107	dnaE DNA polymerase III DnaE; Reviewed	97.38
PRK05672	1046	dnaE2 error-prone DNA polymerase; Validated	97.33
PRK12366	637	replication factor A; Reviewed	97.32
TIGR00458	428	aspS_arch aspartyl-tRNA synthetase, archaeal type.	97.32
PRK06826	1151	dnaE DNA polymerase III DnaE; Reviewed	97.31
PRK08402	355	replication factor A; Reviewed	97.3
PRK05159	437	aspC aspartyl-tRNA synthetase; Provisional	97.26
PRK15491	374	replication factor A; Provisional	97.23
COG0017	435	AsnS Aspartyl/asparaginyl-tRNA synthetases [Transl	97.21
PRK00484	491	lysS lysyl-tRNA synthetase; Reviewed	97.2
PRK03932	450	asnC asparaginyl-tRNA synthetase; Validated	97.16
TIGR00457	453	asnS asparaginyl-tRNA synthetase. In a multiple se	97.11
PRK07279	1034	dnaE DNA polymerase III DnaE; Reviewed	97.07
PRK12445	505	lysyl-tRNA synthetase; Reviewed	97.06
PRK14699	484	replication factor A; Provisional	97.04
PRK06386	358	replication factor A; Reviewed	97.03
TIGR00499	496	lysS_bact lysyl-tRNA synthetase, eukaryotic and no	97.02
PLN02903	652	aminoacyl-tRNA ligase	97.0
PRK15491	374	replication factor A; Provisional	96.98
PRK10053	130	hypothetical protein; Provisional	96.91
PLN02221	572	asparaginyl-tRNA synthetase	96.88
PLN02502	553	lysyl-tRNA synthetase	96.85
PRK06386	358	replication factor A; Reviewed	96.82
PRK12366	637	replication factor A; Reviewed	96.82
TIGR00459	583	aspS_bact aspartyl-tRNA synthetase, bacterial type	96.8
COG3111	128	Periplasmic protein with OB-fold [Function unknown	96.75
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.74
PRK12820	706	bifunctional aspartyl-tRNA synthetase/aspartyl/glu	96.73
PTZ00385	659	lysyl-tRNA synthetase; Provisional	96.69
PTZ00401	550	aspartyl-tRNA synthetase; Provisional	96.68
PRK00476	588	aspS aspartyl-tRNA synthetase; Validated	96.68
cd04497	138	hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f	96.64
cd04479	101	RPA3 RPA3: A subfamily of OB folds similar to huma	96.62
PLN02850	530	aspartate-tRNA ligase	96.62
cd04474	104	RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor	96.59
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	96.58
PRK02983	1094	lysS lysyl-tRNA synthetase; Provisional	96.48
PTZ00425	586	asparagine-tRNA ligase; Provisional	96.45
TIGR01405	1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	96.44
PRK05813	219	single-stranded DNA-binding protein; Provisional	96.42
PRK00448	1437	polC DNA polymerase III PolC; Validated	96.42
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.37
PLN02603	565	asparaginyl-tRNA synthetase	96.31
PF08661	109	Rep_fac-A_3: Replication factor A protein 3; Inter	96.28
cd04475	101	RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor	96.17
COG1190	502	LysU Lysyl-tRNA synthetase (class II) [Translation	95.94
PRK08402	355	replication factor A; Reviewed	95.89
PRK07275	162	single-stranded DNA-binding protein; Provisional	95.75
PRK02801	101	primosomal replication protein N; Provisional	95.73
PRK08486	182	single-stranded DNA-binding protein; Provisional	95.7
cd04481	106	RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc	95.66
PRK06751	173	single-stranded DNA-binding protein; Provisional	95.57
PRK08763	164	single-stranded DNA-binding protein; Provisional	95.49
PF02765	146	POT1: Telomeric single stranded DNA binding POT1/C	95.46
COG1571	421	Predicted DNA-binding protein containing a Zn-ribb	95.45
PTZ00417	585	lysine-tRNA ligase; Provisional	95.38
PRK07459	121	single-stranded DNA-binding protein; Provisional	95.33
COG2176	1444	PolC DNA polymerase III, alpha subunit (gram-posit	95.17
PRK08182	148	single-stranded DNA-binding protein; Provisional	95.17
PRK06752	112	single-stranded DNA-binding protein; Validated	95.16
PRK06293	161	single-stranded DNA-binding protein; Provisional	95.07
cd04486	78	YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fol	94.71
PRK05813	219	single-stranded DNA-binding protein; Provisional	94.31
PF00436	104	SSB: Single-strand binding protein family; InterPr	94.27
PF03100	131	CcmE: CcmE; InterPro: IPR004329 CcmE is the produc	94.18
PRK06863	168	single-stranded DNA-binding protein; Provisional	93.9
PF02760	170	HIN: HIN-200/IF120x domain; InterPro: IPR004021 Th	93.7
TIGR00621	164	ssb single stranded DNA-binding protein (ssb). Thi	93.35
PRK06958	182	single-stranded DNA-binding protein; Provisional	93.32
COG0587	1139	DnaE DNA polymerase III, alpha subunit [DNA replic	93.3
PF15072	86	DUF4539: Domain of unknown function (DUF4539)	92.91
PRK07135	973	dnaE DNA polymerase III DnaE; Validated	92.89
PRK07274	131	single-stranded DNA-binding protein; Provisional	92.83
TIGR00617	608	rpa1 replication factor-a protein 1 (rpa1). This f	92.68
PF08646	146	Rep_fac-A_C: Replication factor-A C terminal domai	92.59
KOG1885	560	consensus Lysyl-tRNA synthetase (class II) [Transl	92.29
PRK05733	172	single-stranded DNA-binding protein; Provisional	91.87
PRK07217	311	replication factor A; Reviewed	91.84
PRK13254	148	cytochrome c-type biogenesis protein CcmE; Reviewe	91.64
PRK06642	152	single-stranded DNA-binding protein; Provisional	91.33
cd04496	100	SSB_OBF SSB_OBF: A subfamily of OB folds similar t	90.97
PRK13732	175	single-stranded DNA-binding protein; Provisional	90.87
PRK13159	155	cytochrome c-type biogenesis protein CcmE; Reviewe	90.38
KOG0555	545	consensus Asparaginyl-tRNA synthetase [Translation	89.85
PLN02532	633	asparagine-tRNA synthetase	89.51
COG0173	585	AspS Aspartyl-tRNA synthetase [Translation, riboso	89.25
PF12869	144	tRNA_anti-like: tRNA_anti-like; InterPro: IPR02442	89.18
KOG0554	446	consensus Asparaginyl-tRNA synthetase (mitochondri	88.36
cd04476	166	RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor	88.35
PRK13165	160	cytochrome c-type biogenesis protein CcmE; Reviewe	88.33
PRK09010	177	single-stranded DNA-binding protein; Provisional	87.78
TIGR00617	608	rpa1 replication factor-a protein 1 (rpa1). This f	87.11
PRK04036	504	DNA polymerase II small subunit; Validated	85.96
PRK06341	166	single-stranded DNA-binding protein; Provisional	85.57
PRK13150	159	cytochrome c-type biogenesis protein CcmE; Reviewe	85.34
TIGR00594	1022	polc DNA-directed DNA polymerase III (polc). This	84.33
TIGR00644	539	recJ single-stranded-DNA-specific exonuclease RecJ	84.1
KOG2411	628	consensus Aspartyl-tRNA synthetase, mitochondrial	83.41
PRK07772	186	single-stranded DNA-binding protein; Provisional	82.38

>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]

Probab=99.93  E-value=3e-25  Score=169.15  Aligned_cols=125  Identities=19%  Similarity=0.344  Sum_probs=112.7

Q ss_pred             ccccceehhhhhccCCCCCCCceEECCeEeeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCC
Q 043474            7 NTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDP   86 (160)
Q Consensus         7 ~~~~~l~i~~i~~l~~~~~~~~~~~~~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~   86 (160)
                      +..-|+.||||++.++...++.|++++.++.+|.+||.|+++.... ....|+|+||||.|+|+.|...+..        
T Consensus        37 ntLrpvTIKQIl~~~qd~~d~~f~vd~~Ev~~V~fVGvvrni~~~t-tn~~~~iEDGTG~Ievr~W~~~~~~--------  107 (258)
T COG5235          37 NTLRPVTIKQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKTST-TNSMFVIEDGTGSIEVRFWPGNSYE--------  107 (258)
T ss_pred             eeeeeeEHHHhhcccccccCCceeecceEEeeEEEEEEEEeeeecc-cceEEEEecCCceEEEEecCCCchH--------
Confidence            4556899999999999888899999999999999999999999877 5589999999999999999876542        


Q ss_pred             CccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCChhHHHHHHHHHHHHHH
Q 043474           87 STVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLAR  150 (160)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~~~  150 (160)
                                .++....+.|.||+|.|.++.|+||+.|....|++++|.||..+|||||+..|-
T Consensus       108 ----------~e~~~d~~~~~yvkV~G~lk~F~GK~~I~~~~i~~I~d~NeV~~HfLe~I~~Hl  161 (258)
T COG5235         108 ----------EEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHL  161 (258)
T ss_pred             ----------HHhccccccccEEEEecceeeeCCeeEEehhheeeccccchhHHHHHHHHHHHH
Confidence                      235567788999999999999999999999999999999999999999998764

>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=99.92  E-value=4.7e-24  Score=146.35  Aligned_cols=94  Identities=24%  Similarity=0.413  Sum_probs=83.5

Q ss_pred             EEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           38 RAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        38 ~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      .|++||.|++++..+ .|+.|+|+|+||+|+|++|...+...                 ....+.++.|++|+|.|+++.
T Consensus         1 ~v~~vG~V~~~~~~~-~~~~~tL~D~TG~I~~~~W~~~~~~~-----------------~~~~~~~~~g~~v~v~G~v~~   62 (95)
T cd04478           1 QVTLVGVVRNVEEQS-TNITYTIDDGTGTIEVRQWLDDDNDD-----------------SSEVEPIEEGTYVRVFGNLKS   62 (95)
T ss_pred             CEEEEEEEEeeeEcc-cEEEEEEECCCCcEEEEEeCCCCCcc-----------------cccccccccCCEEEEEEEEcc
Confidence            378999999999887 88999999999999999998765310                 013467999999999999999


Q ss_pred             eCCceEEEEEEEEEcCChhHHHHHHHHHHHHH
Q 043474          118 YRGDVQITVSDVVIEKDPNMEVLHWLDCLRLA  149 (160)
Q Consensus       118 f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~~  149 (160)
                      |+|++||.+..++|++|+||.++|+|+|+++|
T Consensus        63 ~~g~~ql~i~~i~~v~d~ne~~~h~l~~~~~~   94 (95)
T cd04478          63 FQGKKSIMAFSIRPVTDFNEVTYHLLEVIYVH   94 (95)
T ss_pred             cCCeeEEEEEEEEEeCCccHHHHhHhhhhhhh
Confidence            99999999999999999999999999999875

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam

>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA

Probab=99.90  E-value=1e-22  Score=162.43  Aligned_cols=134  Identities=21%  Similarity=0.342  Sum_probs=105.4

Q ss_pred             CCcccccc-ceehhhhhc-cCCC----------CCCCceEECCeEeeEEEEEEEEEEeecc----CCceEEEEEeCCCc-
Q 043474            3 HTLQNTHV-KLLAFDLLS-LTPT----------PDPATFSRSGKLLSRAEIVGTITSRDHK----PSKFIKFTVDDGTG-   65 (160)
Q Consensus         3 ~p~~~~~~-~l~i~~i~~-l~~~----------~~~~~~~~~~~~i~~v~ivG~V~~~~~~----~~~~~~~~IdDgTG-   65 (160)
                      +|++..++ ||||+||+. +..+          ..++.|+++|+||+.|+|+|.|++++.+    . +|+.|+|||+|| 
T Consensus        21 ~~~~~~~~~PlfI~DI~~~~~~Sr~~~~~y~~~~~~~~~f~~NhPI~~v~i~G~Vv~~~~~~~~~~-~~~~l~iDD~Sg~   99 (256)
T PF10451_consen   21 SPTYGKVTVPLFISDIHKRLKQSRKVCENYYAPQQQNIYFYNNHPIRWVRIVGVVVGIDYKWIENE-DRIILTIDDSSGA   99 (256)
T ss_dssp             STTTTSEE-E--HHHHCT----C--THHHHGGGG-TT-EEETTEEE-EEEEEEEEEEEEEEE-BBT-CEEEEEEE-SSCS
T ss_pred             ccccccccCcEEHHHhhhhcccccchhhhhhhhccCCEEEECCcccEEEEEEEEEEEEEEEeeccc-ceEEEEEeCCCCc
Confidence            68888777 999999998 5454          2468999999999999999999999865    4 889999999999 


Q ss_pred             -eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCChhHHHHHHHH
Q 043474           66 -CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLD  144 (160)
Q Consensus        66 -~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~n~~~~h~le  144 (160)
                       .|+|++|.......                .. ..... +|+.|+|+|.++  ++.+||.+..|..+.+.+.|+.||.+
T Consensus       100 ~~i~~~~~~~~~~~~----------------~l-~~~~~-~G~~V~VkG~vs--r~~~ql~ve~i~~~~~l~~Ei~fW~~  159 (256)
T PF10451_consen  100 NTIECKCSKSSYLSM----------------GL-PINDL-IGKVVEVKGTVS--RNERQLDVERIELVRDLNAEIEFWKE  159 (256)
T ss_dssp             -EEEEEEEHHHHHCC----------------CH-HCTT--TT-EEEEEEEEE--SSSEEEEEEEEEEETSCCHHHHHHHH
T ss_pred             eeEEEEEEccccccc----------------CC-CccCC-CCcEEEEEEEEc--cCcEEEEEEEEEccCChHHHHHHHHH
Confidence             89999997653210                00 12334 999999999999  89999999999999999999999999


Q ss_pred             HHHHHHhhcccCCC
Q 043474          145 CLRLARKRYDVVVN  158 (160)
Q Consensus       145 ~~~~~~~~~~~p~~  158 (160)
                      ++++++. +++||.
T Consensus       160 ~~~~R~~-L~~PW~  172 (256)
T PF10451_consen  160 RMRFRKE-LSKPWV  172 (256)
T ss_dssp             HHHHHHH-CCCHHH
T ss_pred             HHHHHHH-cCCCcC
Confidence            9999765 899984

Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.

>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]

Probab=99.88  E-value=2.3e-22  Score=160.39  Aligned_cols=127  Identities=21%  Similarity=0.352  Sum_probs=111.0

Q ss_pred             cccccceehhhhhccCCCCCCCceEECCeEeeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCC
Q 043474            6 QNTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRD   85 (160)
Q Consensus         6 ~~~~~~l~i~~i~~l~~~~~~~~~~~~~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~   85 (160)
                      ....+++.++||.+.+..... .|.++|.++.+|.+||+|++++... ..+.|+|+|+||.|+|+.|......       
T Consensus        39 ~~~v~~~ti~qi~s~~~~~~~-~~~i~~~~v~~v~~VGivr~~e~~~-t~i~y~I~D~tg~id~r~W~~~~~~-------  109 (265)
T KOG3108|consen   39 VQGVVPLTIKQILSSTQDDDS-VFKIGGVEVSAVSIVGIVRNIEKSA-TNITYEIEDGTGQIDVRQWFHDNAE-------  109 (265)
T ss_pred             eccccccceeeeccccccccc-cEEEccEEEEEEEEEEEEEeceecC-cceEEEEecCcccEEEEEeccccch-------
Confidence            345668899999987765433 9999999999999999999999987 5589999999999999999887642       


Q ss_pred             CCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCChhHHHHHHHHHHHHHHhh
Q 043474           86 PSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKR  152 (160)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~~~~~  152 (160)
                                 ..+...++.|.|||+.|.++.|+|++.|.+++|+|+.|+||.+.|+|||++.|.-.
T Consensus       110 -----------~~e~~~l~~~~yVkv~G~Lk~f~Gk~sl~~fkI~pv~D~Nevt~h~LE~i~~hl~~  165 (265)
T KOG3108|consen  110 -----------SEEMPALETGTYVKVYGHLKPFQGKKSLQVFKIRPVEDFNEVTTHFLEVINAHLSL  165 (265)
T ss_pred             -----------hhhCcccccCcEEEeeecccCCCCceeEEEEeeeeeecCCceeEEeehhhHHHHHh
Confidence                       12346899999999999999999999999999999999999999999999986543

>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1)

Probab=99.85  E-value=1.8e-20  Score=128.43  Aligned_cols=91  Identities=40%  Similarity=0.584  Sum_probs=68.5

Q ss_pred             EEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeC
Q 043474           40 EIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYR  119 (160)
Q Consensus        40 ~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~  119 (160)
                      .|||.|++++.++ +|+.|+||||||+|+|++|........++..+.......+.++.+....+++|+||+|+|+++.|+
T Consensus         1 ~ivG~V~sv~~~~-~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~~fr   79 (92)
T cd04483           1 DILGTVVSRRERE-TFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYR   79 (92)
T ss_pred             CeEEEEEEEEecC-CeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEeccC
Confidence            4899999999998 889999999999999999987653321111111111112223334557899999999999999999


Q ss_pred             CceEEEEEEEEE
Q 043474          120 GDVQITVSDVVI  131 (160)
Q Consensus       120 ~~~qi~~~~i~~  131 (160)
                      +++||+++.+.-
T Consensus        80 g~~ql~i~~~~~   91 (92)
T cd04483          80 GEREINASVVYK   91 (92)
T ss_pred             CeeEEEEEEEEe
Confidence            999999998863

Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.

>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands

Probab=99.44  E-value=1e-12  Score=85.22  Aligned_cols=74  Identities=31%  Similarity=0.591  Sum_probs=61.7

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      |.|.|+|.++....++++.++|+|+||.|+|++|.....                    .....+++|+.|+|.|+++.|
T Consensus         1 V~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~--------------------~~~~~l~~g~~v~v~G~v~~~   60 (75)
T PF01336_consen    1 VTVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYE--------------------RFREKLKEGDIVRVRGKVKRY   60 (75)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHH--------------------HHHHTS-TTSEEEEEEEEEEE
T ss_pred             CEEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhh--------------------HHhhcCCCCeEEEEEEEEEEE
Confidence            679999999954344899999999999999999982221                    244689999999999999999


Q ss_pred             CCc-eEEEEEEEEEc
Q 043474          119 RGD-VQITVSDVVIE  132 (160)
Q Consensus       119 ~~~-~qi~~~~i~~v  132 (160)
                      ++. .||.+.+++++
T Consensus        61 ~~~~~~l~~~~i~~l   75 (75)
T PF01336_consen   61 NGGELELIVPKIEIL   75 (75)
T ss_dssp             TTSSEEEEEEEEEEE
T ss_pred             CCccEEEEECEEEEC
Confidence            997 99999999864

The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....

>PRK13480 3'-5' exoribonuclease YhaM; Provisional

Probab=99.37  E-value=1.4e-12  Score=107.16  Aligned_cols=87  Identities=17%  Similarity=0.246  Sum_probs=67.3

Q ss_pred             hhhccCCCC-CCCceEECCeEeeEEEEEEEEEEeeccC-CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCcccccc
Q 043474           16 DLLSLTPTP-DPATFSRSGKLLSRAEIVGTITSRDHKP-SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIA   93 (160)
Q Consensus        16 ~i~~l~~~~-~~~~~~~~~~~i~~v~ivG~V~~~~~~~-~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~   93 (160)
                      .|.+++++. ++++|++....++.           .++ .+|+.++|.|+||+|+|++|....+                
T Consensus         4 ~i~~l~~g~~v~~~~lv~~~~~~~-----------~knG~~yl~l~l~D~tG~I~ak~W~~~~~----------------   56 (314)
T PRK13480          4 GIEELEVGEQVDHFLLIKSATKGV-----------ASNGKPFLTLILQDKSGDIEAKLWDVSPE----------------   56 (314)
T ss_pred             hHhhcCCCCEeeEEEEEEEceeee-----------cCCCCeEEEEEEEcCCcEEEEEeCCCChh----------------
Confidence            455555544 44555555444433           333 3799999999999999999987643                


Q ss_pred             ccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCC
Q 043474           94 GVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus        94 ~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d  134 (160)
                           ....++.|++|+|.|++..|+|+.|+++..++++++
T Consensus        57 -----~~~~~~~g~vv~v~G~v~~y~g~~Ql~i~~i~~~~~   92 (314)
T PRK13480         57 -----DEATYVPETIVHVKGDIINYRGRKQLKVNQIRLATE   92 (314)
T ss_pred             -----hHhhcCCCCEEEEEEEEEEECCcceEEEEEeEECCC
Confidence                 346799999999999999999999999999998765

>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1)

Probab=99.20  E-value=2.9e-10  Score=74.94  Aligned_cols=63  Identities=25%  Similarity=0.507  Sum_probs=55.3

Q ss_pred             ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcC
Q 043474           54 KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEK  133 (160)
Q Consensus        54 ~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~  133 (160)
                      +|+.++|+|+||.|+|++|.+...                     ....++.|.+|.|.|+++.|++..|+.+..+.+++
T Consensus        19 ~~~~~~l~D~tg~i~~~~f~~~~~---------------------~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~i~~l~   77 (83)
T cd04492          19 PYLALTLQDKTGEIEAKLWDASEE---------------------DEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIRLVT   77 (83)
T ss_pred             cEEEEEEEcCCCeEEEEEcCCChh---------------------hHhhCCCCCEEEEEEEEEEeCCceeEEEEEEEECC
Confidence            789999999999999999964432                     23578899999999999999999999999999999


Q ss_pred             ChhH
Q 043474          134 DPNM  137 (160)
Q Consensus       134 d~n~  137 (160)
                      ++|.
T Consensus        78 ~~~~   81 (83)
T cd04492          78 EEDG   81 (83)
T ss_pred             cccC
Confidence            8874

Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.

>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=99.04  E-value=1.5e-09  Score=68.88  Aligned_cols=71  Identities=27%  Similarity=0.518  Sum_probs=59.1

Q ss_pred             EEEEEEEEeeccC--CceEEEEEeCCC-ceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           40 EIVGTITSRDHKP--SKFIKFTVDDGT-GCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        40 ~ivG~V~~~~~~~--~~~~~~~IdDgT-G~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      +++|.|.++..+.  ..+..++|+|+| |.++|++|.+....                    ....++.|..+.+.|+++
T Consensus         1 ~v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~~--------------------~~~~~~~g~~v~v~g~v~   60 (75)
T cd03524           1 TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEE--------------------LENLLKEGQVVYIKGKVK   60 (75)
T ss_pred             CeEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHHH--------------------HHhhccCCCEEEEEEEEE
Confidence            3789999998765  478999999999 99999999765431                    225688999999999999


Q ss_pred             eeCCceEEEEEEEE
Q 043474          117 SYRGDVQITVSDVV  130 (160)
Q Consensus       117 ~f~~~~qi~~~~i~  130 (160)
                      .|+++.++.+..+.
T Consensus        61 ~~~~~~~l~~~~~~   74 (75)
T cd03524          61 KFRGRLQLIVESIE   74 (75)
T ss_pred             ecCCeEEEEeeeec
Confidence            99999999988665

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco

>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE)

Probab=99.00  E-value=9.8e-10  Score=71.99  Aligned_cols=73  Identities=18%  Similarity=0.316  Sum_probs=57.9

Q ss_pred             EEEEEEEeec---cC-CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           41 IVGTITSRDH---KP-SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        41 ivG~V~~~~~---~~-~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ++|.|.++..   +. .+++.++|+|+||.++|++|.....                    +....+++|.+|.+.|++.
T Consensus         2 i~g~v~~~~~~~~k~g~~~~~~~l~D~tg~~~~~~f~~~~~--------------------~~~~~l~~g~~v~v~G~v~   61 (84)
T cd04485           2 VAGLVTSVRRRRTKKGKRMAFVTLEDLTGSIEVVVFPETYE--------------------KYRDLLKEDALLLVEGKVE   61 (84)
T ss_pred             EEEEEEEeEEEEcCCCCEEEEEEEEeCCCeEEEEECHHHHH--------------------HHHHHhcCCCEEEEEEEEE
Confidence            5677766543   22 2589999999999999999965421                    1235788999999999999


Q ss_pred             eeCCceEEEEEEEEEcC
Q 043474          117 SYRGDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~~~~qi~~~~i~~v~  133 (160)
                      .|++..|+.+..+.++.
T Consensus        62 ~~~~~~~l~~~~i~~~~   78 (84)
T cd04485          62 RRDGGLRLIAERIEDLE   78 (84)
T ss_pred             ecCCceEEEeeccccHH
Confidence            99999999999888765

The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.

>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit

Probab=98.95  E-value=1.7e-08  Score=66.10  Aligned_cols=73  Identities=22%  Similarity=0.486  Sum_probs=60.4

Q ss_pred             EEEEEEEEEeec-cCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           39 AEIVGTITSRDH-KPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        39 v~ivG~V~~~~~-~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      +.+.|.|.+++. +. .+..++|+|.||.|+|++|.+....                    ....++.|+.|.|.|++..
T Consensus         2 ~~v~g~v~~i~~tk~-g~~~~~L~D~~~~i~~~~f~~~~~~--------------------~~~~l~~g~~v~v~g~v~~   60 (78)
T cd04489           2 VWVEGEISNLKRPSS-GHLYFTLKDEDASIRCVMWRSNARR--------------------LGFPLEEGMEVLVRGKVSF   60 (78)
T ss_pred             EEEEEEEecCEECCC-cEEEEEEEeCCeEEEEEEEcchhhh--------------------CCCCCCCCCEEEEEEEEEE
Confidence            468899999875 44 4899999999999999999865431                    2367899999999999998


Q ss_pred             eC--CceEEEEEEEEEc
Q 043474          118 YR--GDVQITVSDVVIE  132 (160)
Q Consensus       118 f~--~~~qi~~~~i~~v  132 (160)
                      +.  +..++.+.+|.+.
T Consensus        61 ~~~~~~~~l~v~~i~~~   77 (78)
T cd04489          61 YEPRGGYQLIVEEIEPA   77 (78)
T ss_pred             ECCCCEEEEEEEEEEEC
Confidence            74  7899999999874

E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.

>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB)

Probab=98.93  E-value=7.6e-09  Score=68.89  Aligned_cols=57  Identities=21%  Similarity=0.384  Sum_probs=49.0

Q ss_pred             cCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE-EEeceeCCceEEEEEEE
Q 043474           51 KPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR-GRIASYRGDVQITVSDV  129 (160)
Q Consensus        51 ~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~-G~v~~f~~~~qi~~~~i  129 (160)
                      ++++|..++|.|.||+|.+++|.....                       ..+++|++|++. |+++.|++..||.+..-
T Consensus        20 ~~~~~~~~~l~D~TG~i~~~~W~~~~~-----------------------~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~   76 (82)
T cd04491          20 SEGKVQSGLVGDETGTIRFTLWDEKAA-----------------------DDLEPGDVVRIENAYVREFNGRLELSVGKN   76 (82)
T ss_pred             CeeEEEEEEEECCCCEEEEEEECchhc-----------------------ccCCCCCEEEEEeEEEEecCCcEEEEeCCc
Confidence            335899999999999999999976531                       468899999999 99999999999998764


Q ss_pred             E
Q 043474          130 V  130 (160)
Q Consensus       130 ~  130 (160)
                      .
T Consensus        77 ~   77 (82)
T cd04491          77 S   77 (82)
T ss_pred             e
Confidence            3

SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating

>PRK06461 single-stranded DNA-binding protein; Reviewed

Probab=98.93  E-value=3.6e-09  Score=76.64  Aligned_cols=87  Identities=22%  Similarity=0.295  Sum_probs=65.2

Q ss_pred             eEEEEEEEEEEeec------cC--CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcE
Q 043474           37 SRAEIVGTITSRDH------KP--SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLV  108 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~~--~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~  108 (160)
                      ..|.+.|.|.++..      +.  ..+..++|.|.||+|.+++|.+..                        ..+++|++
T Consensus        15 ~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~a------------------------~~l~~Gdv   70 (129)
T PRK06461         15 ERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQA------------------------GSLKEGEV   70 (129)
T ss_pred             CceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCcc------------------------ccCCCCCE
Confidence            45677777775432      22  258899999999999999998632                        35789999


Q ss_pred             EEEE-EEeceeCCceEEEEE---EEEEcCChhHHHHHHHHHHH
Q 043474          109 ARVR-GRIASYRGDVQITVS---DVVIEKDPNMEVLHWLDCLR  147 (160)
Q Consensus       109 V~V~-G~v~~f~~~~qi~~~---~i~~v~d~n~~~~h~le~~~  147 (160)
                      |+|. |.++.|+|+.||++.   .|+++++.......++.+.+
T Consensus        71 V~I~na~v~~f~G~lqL~i~~~~~i~~~~~~~v~~~~~i~~~~  113 (129)
T PRK06461         71 VEIENAWTTLYRGKVQLNVGKYGSISESDDEEVPEAEEIPEET  113 (129)
T ss_pred             EEEECcEEeeeCCEEEEEECCCEEEEECCccccCCCCccCccC
Confidence            9999 889999999999999   58888764434444444443

>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ

Probab=98.70  E-value=2.5e-07  Score=60.59  Aligned_cols=72  Identities=24%  Similarity=0.342  Sum_probs=58.1

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      +.+-|.|.+... .+..+-|+|.|.++.|.|++|......                    ....++.|+-|.+.|++...
T Consensus         1 v~v~GeVs~~~~-~~GHvyfsLkD~~a~i~cv~f~~~~~~--------------------~~~~l~~Gd~V~v~G~v~~~   59 (73)
T cd04487           1 VHIEGEVVQIKQ-TSGPTIFTLRDETGTVWAAAFEEAGVR--------------------AYPEVEVGDIVRVTGEVEPR   59 (73)
T ss_pred             CEEEEEEecccc-CCCCEEEEEEcCCEEEEEEEEchhccC--------------------CcCCCCCCCEEEEEEEEecC
Confidence            356788887665 434589999999999999999765421                    23568999999999999998


Q ss_pred             CCceEEEEEEEEE
Q 043474          119 RGDVQITVSDVVI  131 (160)
Q Consensus       119 ~~~~qi~~~~i~~  131 (160)
                      +|+.|+.+..|+.
T Consensus        60 ~G~~ql~v~~i~~   72 (73)
T cd04487          60 DGQLQIEVESLEV   72 (73)
T ss_pred             CeEEEEEEeeEEE
Confidence            8999999999874

RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.

>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=98.64  E-value=4.7e-07  Score=61.73  Aligned_cols=74  Identities=15%  Similarity=0.274  Sum_probs=58.3

Q ss_pred             EEEEEEEEeecc-CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           40 EIVGTITSRDHK-PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        40 ~ivG~V~~~~~~-~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      .+.|.|.+.... .+..+.|+|.|.++.|.|.+|......                  ......++.|+.|.|.|.++.|
T Consensus         2 ~v~GeVs~~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~------------------~~~~~~l~~Gd~V~v~G~v~~y   63 (91)
T cd04482           2 RVTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTKEF------------------RDVVRLLIPGDEVTVYGSVRPG   63 (91)
T ss_pred             EEEEEEeCCeecCCCCCEEEEEECCCcEEEEEEECccccc------------------ccccCCCCCCCEEEEEEEEecC
Confidence            477888887653 334489999999999999999766210                  0123578999999999999999


Q ss_pred             CCceEEEEEEEEEcCC
Q 043474          119 RGDVQITVSDVVIEKD  134 (160)
Q Consensus       119 ~~~~qi~~~~i~~v~d  134 (160)
                      .   ||.++++++...
T Consensus        64 ~---ql~ve~l~~~gl   76 (91)
T cd04482          64 T---TLNLEKLRVIRL   76 (91)
T ss_pred             C---EEEEEEEEECCC
Confidence            7   999999998764

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende

>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG

Probab=98.59  E-value=5.2e-07  Score=57.76  Aligned_cols=67  Identities=27%  Similarity=0.463  Sum_probs=50.1

Q ss_pred             EEEEEEEeecc---CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           41 IVGTITSRDHK---PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        41 ivG~V~~~~~~---~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      +.|.|.+....   ..+++.+++.|+||.|+|+.|.....                     ....++.|+.+.+.|+++.
T Consensus         2 i~~~V~~~~~~~~~~~~~~~~~~~D~~g~i~~~~F~~~~~---------------------~~~~~~~G~~~~v~Gkv~~   60 (75)
T cd04488           2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQPY---------------------LKKQLPPGTRVRVSGKVKR   60 (75)
T ss_pred             EEEEEEEEEeccCCCccEEEEEEEcCCCEEEEEEECCCHH---------------------HHhcCCCCCEEEEEEEEee
Confidence            45666655422   23689999999999999999963221                     2256899999999999999


Q ss_pred             eCCceEEEEEE
Q 043474          118 YRGDVQITVSD  128 (160)
Q Consensus       118 f~~~~qi~~~~  128 (160)
                      |++.+|+.--.
T Consensus        61 ~~~~~qi~~P~   71 (75)
T cd04488          61 FRGGLQIVHPE   71 (75)
T ss_pred             cCCeeEEeCCc
Confidence            99988876433

RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha

>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain

Probab=98.52  E-value=1.2e-06  Score=60.57  Aligned_cols=76  Identities=25%  Similarity=0.444  Sum_probs=64.3

Q ss_pred             eeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccc-cccccCcEEEEEEE
Q 043474           36 LSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFA-AKIKIGLVARVRGR  114 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~G~~V~V~G~  114 (160)
                      +..+.|.|.|.+.+.+.+..+-|+|-|+.+.|.|++|......                    .. ..++.|+-|.+.|+
T Consensus        21 ~~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~~--------------------i~~~~l~~G~~V~v~g~   80 (99)
T PF13742_consen   21 LPNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRARR--------------------IRGFDLKDGDKVLVRGR   80 (99)
T ss_pred             cCCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHhh--------------------CCCCCCCCCCEEEEEEE
Confidence            5889999999999985446789999999999999999876531                    12 46899999999999


Q ss_pred             eceeC--CceEEEEEEEEE
Q 043474          115 IASYR--GDVQITVSDVVI  131 (160)
Q Consensus       115 v~~f~--~~~qi~~~~i~~  131 (160)
                      +..|.  |+.|+.+..|+|
T Consensus        81 ~~~y~~~G~~sl~v~~i~P   99 (99)
T PF13742_consen   81 VSFYEPRGSLSLIVEDIDP   99 (99)
T ss_pred             EEEECCCcEEEEEEEEeEC
Confidence            99987  578999999986

>COG3390 Uncharacterized protein conserved in archaea [Function unknown]

Probab=98.43  E-value=2.6e-06  Score=64.70  Aligned_cols=120  Identities=22%  Similarity=0.309  Sum_probs=83.5

Q ss_pred             cceehhhhhccCCCC---C---CCce--EECCeEeeEEEEEEEEEEeeccC--CceEEEEEeCCCceEEEEEeecCccCC
Q 043474           10 VKLLAFDLLSLTPTP---D---PATF--SRSGKLLSRAEIVGTITSRDHKP--SKFIKFTVDDGTGCVPCVLWLNHLTSL   79 (160)
Q Consensus        10 ~~l~i~~i~~l~~~~---~---~~~~--~~~~~~i~~v~ivG~V~~~~~~~--~~~~~~~IdDgTG~I~~~~w~~~~~~~   79 (160)
                      .++|++++.+++-+.   .   .-.|  .-.|..++++.|+|.++..+..+  ..|...+++|+||++-+  +....+  
T Consensus        11 ~rVFa~El~e~~~s~~e~~e~~sp~yliTPlG~k~nRifivGtltek~~i~ed~~~~R~rVvDpTGsF~V--yag~yq--   86 (196)
T COG3390          11 YRVFAKELRESKFSKKEEDEERSPNYLITPLGLKVNRIFIVGTLTEKEGIGEDREYWRIRVVDPTGSFYV--YAGQYQ--   86 (196)
T ss_pred             HHHHHHHHhhcceeccccccccCCcEEechhhhheeEEEEEEEEEeccCcCCcccEEEEEEecCCceEEE--EcCCCC--
Confidence            478899998877432   1   1123  34678899999999999988765  47899999999997544  222211  


Q ss_pred             CCCCCCCCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEc----CChhHHHHHHHHHHH
Q 043474           80 YLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIE----KDPNMEVLHWLDCLR  147 (160)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v----~d~n~~~~h~le~~~  147 (160)
                                    .++......++.+++|.|.|+++.|++.--....+|||.    .|++.-.+|-+++..
T Consensus        87 --------------PEa~a~l~~ve~~~~VaViGKi~~y~~d~g~~~~siRpE~vs~vde~~r~~Wv~eta~  144 (196)
T COG3390          87 --------------PEAKAFLEDVEVPDLVAVIGKIRTYRTDEGVVLFSIRPELVSKVDEEARDLWVLETAE  144 (196)
T ss_pred             --------------hHHHHHHHhccCCceEEEecccceeecCCCceEEEechhhhhhcCHHHHHHHHHHHHH
Confidence                          112234467889999999999999998744555555543    346666677777665

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=98.40  E-value=1.3e-06  Score=76.18  Aligned_cols=78  Identities=19%  Similarity=0.273  Sum_probs=65.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      +.|+|-|.|++++..+++ +.|||-|+||.|.|-.+.....-                    --..+++|++|+|.|.|.
T Consensus       214 ~tV~I~GeV~qikqT~GP-TVFtltDetg~i~aAAFe~aGvR--------------------AyP~IevGdiV~ViG~V~  272 (715)
T COG1107         214 KTVRIEGEVTQIKQTSGP-TVFTLTDETGAIWAAAFEEAGVR--------------------AYPEIEVGDIVEVIGEVT  272 (715)
T ss_pred             ceEEEEEEEEEEEEcCCC-EEEEEecCCCceehhhhccCCcc--------------------cCCCCCCCceEEEEEEEe
Confidence            689999999999998877 79999999998877766544321                    125789999999999999


Q ss_pred             eeCCceEEEEEEEEEcCCh
Q 043474          117 SYRGDVQITVSDVVIEKDP  135 (160)
Q Consensus       117 ~f~~~~qi~~~~i~~v~d~  135 (160)
                      ...|+.||-+..|..+...
T Consensus       273 ~r~g~lQiE~~~me~L~G~  291 (715)
T COG1107         273 RRDGRLQIEIEAMEKLTGD  291 (715)
T ss_pred             ecCCcEEEeehhhHHhhCc
Confidence            9999999999999977655

>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit

Probab=98.30  E-value=1.1e-05  Score=53.51  Aligned_cols=71  Identities=20%  Similarity=0.254  Sum_probs=52.4

Q ss_pred             EEEEEEEEEee-ccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           39 AEIVGTITSRD-HKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        39 v~ivG~V~~~~-~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      +.++|+|.++. .+.++. .++|+|.||+++|.+|.+.-..                  -+....++.|..|-|.|++..
T Consensus         2 v~i~GiI~~v~~TK~g~~-~~~leD~~G~~Ev~~F~~~~~~------------------~~~~~~l~~d~~v~v~g~v~~   62 (79)
T cd04490           2 VSIIGMVNDVRSTKNGHR-IVELEDTTGRITVLLTKDKEEL------------------FEEAEDILPDEVIGVSGTVSK   62 (79)
T ss_pred             EEEEEEEeEEEEcCCCCE-EEEEECCCCEEEEEEeCchhhh------------------hhhhhhccCCCEEEEEEEEec
Confidence            57889998885 233354 9999999999999999654320                  012357889999999999966


Q ss_pred             eCCceEEEEEEEE
Q 043474          118 YRGDVQITVSDVV  130 (160)
Q Consensus       118 f~~~~qi~~~~i~  130 (160)
                       ++. ++.+..|-
T Consensus        63 -~~~-~l~~~~I~   73 (79)
T cd04490          63 -DGG-LIFADEIF   73 (79)
T ss_pred             -CCC-EEEEEEeE
Confidence             444 77777765

PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.

>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]

Probab=98.27  E-value=4.9e-06  Score=63.49  Aligned_cols=92  Identities=21%  Similarity=0.302  Sum_probs=68.0

Q ss_pred             CCeEeeEEEEEEEEEEeeccC-CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEE
Q 043474           32 SGKLLSRAEIVGTITSRDHKP-SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVAR  110 (160)
Q Consensus        32 ~~~~i~~v~ivG~V~~~~~~~-~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~  110 (160)
                      +|.-.+.+.+=|.|.+.+... ..-..+.|+||||+|+++......+...               .......+..|++|.
T Consensus        47 ~G~l~e~v~vkg~V~~~~n~~~~gi~~l~lndgtGti~vva~~~tee~l~---------------~n~~~p~~~eGe~ve  111 (204)
T COG4085          47 DGRLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRSTEETLE---------------LNEGMPVTVEGEIVE  111 (204)
T ss_pred             CceeeccceeeeEEEeeecccccceEEEEEECCCCcEEEEEecChhHhHh---------------hcCCCCccccCcEEE
Confidence            455667788889998887443 2557899999999999999877765321               111235678999999


Q ss_pred             EEEEeceeCCceEEEEEE---EEEcCChhHH
Q 043474          111 VRGRIASYRGDVQITVSD---VVIEKDPNME  138 (160)
Q Consensus       111 V~G~v~~f~~~~qi~~~~---i~~v~d~n~~  138 (160)
                      |+|++..|||+.+++++.   ++|....+.|
T Consensus       112 VtGrv~~yrG~~eVkvnq~~d~~~l~k~~~e  142 (204)
T COG4085         112 VTGRVEEYRGSSEVKVNQPNDSRPLPKHLTE  142 (204)
T ss_pred             EEEEEEEeCCCceeeccCcccccccccccch
Confidence            999999999999998876   4555444433

>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC)

Probab=98.13  E-value=3.7e-05  Score=51.30  Aligned_cols=73  Identities=19%  Similarity=0.352  Sum_probs=55.3

Q ss_pred             EEEEEEEEEeeccC---C-ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccc-cCcEEEEEE
Q 043474           39 AEIVGTITSRDHKP---S-KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIK-IGLVARVRG  113 (160)
Q Consensus        39 v~ivG~V~~~~~~~---~-~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~G~~V~V~G  113 (160)
                      |.|-|.|-+.+.++   + ..++|.|-|.|++|.|+.|.....                    +....++ .|+.|+++|
T Consensus         2 v~i~G~Vf~~e~re~k~g~~i~~~~itD~t~Si~~K~F~~~~~--------------------~~~~~ik~~G~~v~v~G   61 (82)
T cd04484           2 VVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRKDE--------------------KDKEELKSKGDWVRVRG   61 (82)
T ss_pred             EEEEEEEEEEEEEEecCCCEEEEEEEEcCCCCEEEEEeccCCh--------------------hHHhhcccCCCEEEEEE
Confidence            66888888887533   3 345899999999999999985111                    1235688 999999999


Q ss_pred             Eec--eeCCceEEEEEEEEE
Q 043474          114 RIA--SYRGDVQITVSDVVI  131 (160)
Q Consensus       114 ~v~--~f~~~~qi~~~~i~~  131 (160)
                      +++  .|.+...+.+..|..
T Consensus        62 ~v~~D~f~~e~~~~i~~i~~   81 (82)
T cd04484          62 KVQYDTFSKELVLMINDIEE   81 (82)
T ss_pred             EEEEccCCCceEEEeeeEEE
Confidence            987  577888888877654

Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.

>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]

Probab=98.12  E-value=3.3e-05  Score=65.98  Aligned_cols=81  Identities=23%  Similarity=0.363  Sum_probs=68.8

Q ss_pred             eeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           36 LSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      +..|.|-|-|.+.+...+..+-|+|-|..+.|.|++|......                    ....++.|+-|-|.|++
T Consensus        23 ~~~V~v~GEISn~t~~~sgH~YFtLKD~~A~i~c~mf~~~~~~--------------------l~f~p~eG~~V~v~G~i   82 (440)
T COG1570          23 LGQVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNNRR--------------------LKFRPEEGMQVLVRGKI   82 (440)
T ss_pred             CCeEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCcccc--------------------cCCCccCCCEEEEEEEE
Confidence            7889999999999965544689999999999999999877641                    33568899999999999


Q ss_pred             ceeC--CceEEEEEEEEEcCChh
Q 043474          116 ASYR--GDVQITVSDVVIEKDPN  136 (160)
Q Consensus       116 ~~f~--~~~qi~~~~i~~v~d~n  136 (160)
                      ..|-  |.-||.++.|+|....+
T Consensus        83 s~Y~~rG~YQi~~~~~~p~G~G~  105 (440)
T COG1570          83 SLYEPRGDYQIVAESMEPAGLGA  105 (440)
T ss_pred             EEEcCCCceEEEEecCCcCChhH
Confidence            9996  67899999999877554

>TIGR00237 xseA exodeoxyribonuclease VII, large subunit

Probab=98.03  E-value=0.00011  Score=63.04  Aligned_cols=79  Identities=25%  Similarity=0.343  Sum_probs=66.0

Q ss_pred             eeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           36 LSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      +..+.|.|-|.+.....+..+-|+|-|..+.|.|++|......                    ....++.|+-|.|.|++
T Consensus        17 ~~~v~V~GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~~~--------------------l~f~~~~G~~V~v~g~v   76 (432)
T TIGR00237        17 FLQVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNNR--------------------LKFRPQNGQQVLVRGGI   76 (432)
T ss_pred             CCcEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhhC--------------------CCCCCCCCCEEEEEEEE
Confidence            6789999999998865545689999999999999999876531                    23568899999999999


Q ss_pred             ceeC--CceEEEEEEEEEcCC
Q 043474          116 ASYR--GDVQITVSDVVIEKD  134 (160)
Q Consensus       116 ~~f~--~~~qi~~~~i~~v~d  134 (160)
                      ..|.  |..||.+..|.|...
T Consensus        77 ~~y~~~G~~ql~v~~i~~~G~   97 (432)
T TIGR00237        77 SVYEPRGDYQIICFEMQPAGE   97 (432)
T ss_pred             EEECCCCcEEEEEEEeccCCh
Confidence            9987  668999999998763

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.

>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS)

Probab=98.02  E-value=0.0001  Score=49.38  Aligned_cols=76  Identities=17%  Similarity=0.196  Sum_probs=55.2

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      |++.|+|.++....++...+.|.|+|| .++|++ .....                  .......+..|+.|.|.|.+..
T Consensus         2 V~v~Gwv~~~R~~~~~~~Fi~LrD~~g~~iQvv~-~~~~~------------------~~~~~~~l~~~s~V~V~G~v~~   62 (86)
T cd04321           2 VTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLVS-TAKKD------------------AFSLLKSITAESPVQVRGKLQL   62 (86)
T ss_pred             EEEEEeEeeEeCCCCceEEEEEECCCCCEEEEEE-CCCHH------------------HHHHHhcCCCCcEEEEEEEEEe
Confidence            689999999887333667889999999 699865 22111                  0012246889999999999986


Q ss_pred             eC-------CceEEEEEEEEEcC
Q 043474          118 YR-------GDVQITVSDVVIEK  133 (160)
Q Consensus       118 f~-------~~~qi~~~~i~~v~  133 (160)
                      -.       +...|.+.++..+.
T Consensus        63 ~~~~~~~~~~~~Ei~~~~i~il~   85 (86)
T cd04321          63 KEAKSSEKNDEWELVVDDIQTLN   85 (86)
T ss_pred             CCCcCCCCCCCEEEEEEEEEEec
Confidence            43       56789998888654

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for

>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed

Probab=98.00  E-value=0.00016  Score=62.10  Aligned_cols=80  Identities=24%  Similarity=0.375  Sum_probs=66.9

Q ss_pred             eeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           36 LSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      ...+.|.|.|.+.....+..+-|+|-|.++.|.|++|......                    ....++.|+-|.|.|++
T Consensus        23 ~~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~~--------------------~~~~~~~G~~v~v~g~~   82 (438)
T PRK00286         23 LGQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSARR--------------------LKFKPEEGMKVLVRGKV   82 (438)
T ss_pred             CCcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhhc--------------------CCCCCCCCCEEEEEEEE
Confidence            6889999999998876545689999999999999999865431                    23568899999999999


Q ss_pred             ceeC--CceEEEEEEEEEcCCh
Q 043474          116 ASYR--GDVQITVSDVVIEKDP  135 (160)
Q Consensus       116 ~~f~--~~~qi~~~~i~~v~d~  135 (160)
                      ..|.  |..||.+..|.|....
T Consensus        83 ~~y~~~g~~ql~v~~i~~~g~G  104 (438)
T PRK00286         83 SLYEPRGDYQLIVEEIEPAGIG  104 (438)
T ss_pred             EEECCCCCEEEEEEEeeeCCcc
Confidence            9887  5689999999987753

>PRK05673 dnaE DNA polymerase III subunit alpha; Validated

Probab=97.98  E-value=1.6e-05  Score=75.27  Aligned_cols=78  Identities=18%  Similarity=0.338  Sum_probs=64.0

Q ss_pred             eEEEEEEEEEEeeccC----CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTITSRDHKP----SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~----~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ..+.++|.|.+++.+.    .++..++|+|.||++++++|.+.-.                    +....++.|.+|.|.
T Consensus       978 ~~V~v~G~I~~vk~~~TKkG~~mafltLeD~TG~iEvviFp~~ye--------------------~~~~~L~~g~iV~V~ 1037 (1135)
T PRK05673        978 SVVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSEALE--------------------KYRDLLEEDRIVVVK 1037 (1135)
T ss_pred             ceEEEEEEEEEEEecccCCCCeEEEEEEEeCCCcEEEEECHHHHH--------------------HHHHHhccCCEEEEE
Confidence            4688999999988533    2688999999999999999965422                    133578899999999


Q ss_pred             EEeceeCCceEEEEEEEEEcCC
Q 043474          113 GRIASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~d  134 (160)
                      |+++.+++..|+.+.++.++.+
T Consensus      1038 GkVe~~~~~~qlii~~I~~L~~ 1059 (1135)
T PRK05673       1038 GQVSFDDGGLRLTAREVMDLEE 1059 (1135)
T ss_pred             EEEEecCCeEEEEEeecccHHH
Confidence            9999988889999999988753

>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs)

Probab=97.95  E-value=0.00014  Score=48.42  Aligned_cols=77  Identities=21%  Similarity=0.343  Sum_probs=56.6

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      |.|.|+|.++.... +...+.|.|+||.++|++-.....                . .......++.|++|.|.|.+..=
T Consensus         2 V~i~Gwv~~~R~~g-~~~Fi~Lrd~~~~iQ~v~~~~~~~----------------~-~~~~~~~l~~~s~V~v~G~~~~~   63 (85)
T cd04100           2 VTLAGWVHSRRDHG-GLIFIDLRDGSGIVQVVVNKEELG----------------E-FFEEAEKLRTESVVGVTGTVVKR   63 (85)
T ss_pred             EEEEEEEehhccCC-CEEEEEEEeCCeeEEEEEECCcCh----------------H-HHHHHhCCCCCCEEEEEeEEEEC
Confidence            78999999988765 678899999999999976332211                0 01123578999999999998763


Q ss_pred             ------CCceEEEEEEEEEcC
Q 043474          119 ------RGDVQITVSDVVIEK  133 (160)
Q Consensus       119 ------~~~~qi~~~~i~~v~  133 (160)
                            .+...|.+..+..+.
T Consensus        64 ~~~~~~~~~~El~~~~i~il~   84 (85)
T cd04100          64 PEGNLATGEIELQAEELEVLS   84 (85)
T ss_pred             CCCCCCCCCEEEEEeEEEEEC
Confidence                  445788888887653

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A

>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS)

Probab=97.93  E-value=0.00019  Score=50.01  Aligned_cols=82  Identities=12%  Similarity=0.106  Sum_probs=60.0

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|++.|+|.++.... +...+.|.|+||.++|++-......                +.......+..|+.|.|.|.+.
T Consensus        13 ~~V~v~Gwv~~~R~~g-~~~Fi~LrD~~g~iQ~v~~~~~~~~----------------~~~~~~~~l~~es~V~V~G~v~   75 (108)
T cd04316          13 EEVTVAGWVHEIRDLG-GIKFVILRDREGIVQVTAPKKKVDK----------------ELFKTVRKLSRESVISVTGTVK   75 (108)
T ss_pred             CEEEEEEEEEeeeccC-CeEEEEEecCCeeEEEEEeCCCCCH----------------HHHHHHhCCCCcCEEEEEEEEE
Confidence            4689999999988766 6788999999999999774221110                0011335688999999999987


Q ss_pred             eeCC---ceEEEEEEEEEcCCh
Q 043474          117 SYRG---DVQITVSDVVIEKDP  135 (160)
Q Consensus       117 ~f~~---~~qi~~~~i~~v~d~  135 (160)
                      .=..   ...|.+..+..+...
T Consensus        76 ~~~~~~~~~Ei~~~~i~il~~~   97 (108)
T cd04316          76 AEPKAPNGVEIIPEEIEVLSEA   97 (108)
T ss_pred             eCCCCCCCEEEEEeEEEEEeCC
Confidence            6433   478999999877654

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.

>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]

Probab=97.92  E-value=7.6e-05  Score=53.35  Aligned_cols=50  Identities=22%  Similarity=0.379  Sum_probs=40.7

Q ss_pred             ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe-ceeCCceEEEEE
Q 043474           54 KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI-ASYRGDVQITVS  127 (160)
Q Consensus        54 ~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v-~~f~~~~qi~~~  127 (160)
                      ++.++.+.|.||+|+..+|++..                        ..+++||+||..|-. +.|||.+.|.+-
T Consensus        37 ~v~~~kVaD~TgsI~isvW~e~~------------------------~~~~PGDIirLt~Gy~Si~qg~LtL~~G   87 (134)
T KOG3416|consen   37 EVRSCKVADETGSINISVWDEEG------------------------CLIQPGDIIRLTGGYASIFQGCLTLYVG   87 (134)
T ss_pred             EEEEEEEecccceEEEEEecCcC------------------------cccCCccEEEecccchhhhcCceEEEec
Confidence            78899999999999999998432                        468999999998776 458887666543

>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs

Probab=97.92  E-value=0.00025  Score=47.15  Aligned_cols=76  Identities=20%  Similarity=0.244  Sum_probs=55.5

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      |.+.|+|.++.... +...+.|.|+||.++|++-.+...                 . ......+..|+.|.|.|.+..-
T Consensus         2 V~v~Gwv~~~R~~g-~~~Fi~LrD~~~~iQ~v~~~~~~~-----------------~-~~~~~~l~~es~V~V~G~v~~~   62 (84)
T cd04323           2 VKVFGWVHRLRSQK-KLMFLVLRDGTGFLQCVLSKKLVT-----------------E-FYDAKSLTQESSVEVTGEVKED   62 (84)
T ss_pred             EEEEEEEEEEecCC-CcEEEEEEcCCeEEEEEEcCCcch-----------------h-HHHHhcCCCcCEEEEEEEEEEC
Confidence            78999999988764 778899999999999976222110                 0 1123468899999999999875


Q ss_pred             CCc------eEEEEEEEEEcC
Q 043474          119 RGD------VQITVSDVVIEK  133 (160)
Q Consensus       119 ~~~------~qi~~~~i~~v~  133 (160)
                      ...      ..|.+.++..+.
T Consensus        63 ~~~~~~~~~~Ei~~~~i~vl~   83 (84)
T cd04323          63 PRAKQAPGGYELQVDYLEIIG   83 (84)
T ss_pred             CcccCCCCCEEEEEEEEEEEc
Confidence            333      678888877653

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with

>PRK07373 DNA polymerase III subunit alpha; Reviewed

Probab=97.89  E-value=5.1e-05  Score=65.49  Aligned_cols=78  Identities=12%  Similarity=0.190  Sum_probs=62.4

Q ss_pred             eEEEEEEEEEEeeccC----CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTITSRDHKP----SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~----~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ..|+++|+|.+++...    ..+..++|+|.||.++|++|-+.-.                    +....++.|..|-|.
T Consensus       281 ~~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~~y~--------------------~~~~~l~~~~~v~v~  340 (449)
T PRK07373        281 TKVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYE--------------------RISELLQVDARLIIW  340 (449)
T ss_pred             CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHH--------------------HHHHHhccCCEEEEE
Confidence            4688999999988533    3678999999999999999965432                    134678899999999


Q ss_pred             EEeceeCCceEEEEEEEEEcCC
Q 043474          113 GRIASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~d  134 (160)
                      |+++.-.+..++.+.+|.++.+
T Consensus       341 G~v~~~~~~~~liv~~i~~l~~  362 (449)
T PRK07373        341 GKVDRRDDQVQLIVEDAEPIEE  362 (449)
T ss_pred             EEEEecCCeEEEEEeEeecHhh
Confidence            9998744678999999887754

>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS)

Probab=97.88  E-value=0.00025  Score=48.85  Aligned_cols=82  Identities=12%  Similarity=0.172  Sum_probs=58.8

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCc-cCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHL-TSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      |++.|+|.++.....+...+.|.|+||.|+|++-.... ..               ++.......++.|+.|.|.|.+..
T Consensus         2 V~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~---------------~~~~~~~~~l~~es~V~V~G~v~~   66 (102)
T cd04320           2 VLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVS---------------KQMVKWAGSLSKESIVDVEGTVKK   66 (102)
T ss_pred             EEEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCC---------------HHHHHHHhcCCCccEEEEEEEEEC
Confidence            78999999988654367889999999999999843321 00               000112346889999999999876


Q ss_pred             e-C-------CceEEEEEEEEEcCCh
Q 043474          118 Y-R-------GDVQITVSDVVIEKDP  135 (160)
Q Consensus       118 f-~-------~~~qi~~~~i~~v~d~  135 (160)
                      - +       +...|.+.+++.+...
T Consensus        67 ~~~~~~~~~~~~~El~~~~i~il~~~   92 (102)
T cd04320          67 PEEPIKSCTQQDVELHIEKIYVVSEA   92 (102)
T ss_pred             CCCcccCCCcCcEEEEEEEEEEEecC
Confidence            2 1       4578999999877643

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.

>COG3481 Predicted HD-superfamily hydrolase [General function prediction only]

Probab=97.83  E-value=1.1e-05  Score=65.47  Aligned_cols=63  Identities=27%  Similarity=0.377  Sum_probs=55.6

Q ss_pred             CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEE
Q 043474           52 PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVI  131 (160)
Q Consensus        52 ~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~  131 (160)
                      ...|+.++++|.||.|++++|.....                     ....+..|.+|.+.|....|++.+|+++..+++
T Consensus        19 ~~~~l~l~~~d~~gei~~~~wd~~~~---------------------~~~~~~~~~Vv~~~g~~~~~~~~~q~ki~~~r~   77 (287)
T COG3481          19 GKDKLKLTLQDKTGEIEAKLWDALKN---------------------DEEAFKPGMVVHVEGVKEVYRGRKQHKIIRIRL   77 (287)
T ss_pred             CChhheeeeccccceecccccccccc---------------------cHhhhCcCceeccccceecccccchheeeeccc
Confidence            34889999999999999999987764                     236799999999999999999999999999998


Q ss_pred             cCCh
Q 043474          132 EKDP  135 (160)
Q Consensus       132 v~d~  135 (160)
                      +++.
T Consensus        78 ~~~~   81 (287)
T COG3481          78 ITDS   81 (287)
T ss_pred             cccc
Confidence            7664

>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS)

Probab=97.79  E-value=0.00033  Score=48.80  Aligned_cols=80  Identities=19%  Similarity=0.271  Sum_probs=56.4

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      |++.|+|.++.... +.+.+.|-|+||.++|++-......               .........+..|+.|.|.|.+..=
T Consensus         2 v~v~GwV~~~R~~g-~~~Fi~lrd~~~~lQ~v~~~~~~~~---------------~~~~~~~~~l~~g~~V~v~G~v~~~   65 (108)
T cd04322           2 VSVAGRIMSKRGSG-KLSFADLQDESGKIQVYVNKDDLGE---------------EEFEDFKKLLDLGDIIGVTGTPFKT   65 (108)
T ss_pred             EEEEEEEEEEecCC-CeEEEEEEECCeEEEEEEECCCCCH---------------HHHHHHHhcCCCCCEEEEEEEEEec
Confidence            68999999998876 6789999999999999873221100               0000111238899999999998643


Q ss_pred             -CCceEEEEEEEEEcCC
Q 043474          119 -RGDVQITVSDVVIEKD  134 (160)
Q Consensus       119 -~~~~qi~~~~i~~v~d  134 (160)
                       ++...|.+..+..+..
T Consensus        66 ~~g~~El~~~~~~ils~   82 (108)
T cd04322          66 KTGELSIFVKEFTLLSK   82 (108)
T ss_pred             CCCCEEEEeCEeEEeec
Confidence             3567888888876653

These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein

>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS

Probab=97.79  E-value=0.00026  Score=51.26  Aligned_cols=80  Identities=18%  Similarity=0.318  Sum_probs=59.2

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|.++.... +...+.|.|+||.++|++-.....                  +.+....++.|++|.|.|.+.
T Consensus        15 ~~V~i~Gwv~~~R~~g-k~~Fi~LrD~~g~~Q~v~~~~~~~------------------~~~~~~~l~~gs~V~V~G~~~   75 (135)
T cd04317          15 QEVTLCGWVQRRRDHG-GLIFIDLRDRYGIVQVVFDPEEAP------------------EFELAEKLRNESVIQVTGKVR   75 (135)
T ss_pred             CEEEEEEeEehhcccC-CEEEEEEecCCeeEEEEEeCCchh------------------HHHHHhCCCCccEEEEEEEEE
Confidence            4599999999988765 678899999999999987322111                  011235688999999999987


Q ss_pred             ee----------CCceEEEEEEEEEcCCh
Q 043474          117 SY----------RGDVQITVSDVVIEKDP  135 (160)
Q Consensus       117 ~f----------~~~~qi~~~~i~~v~d~  135 (160)
                      .=          .+...|.+..+..+...
T Consensus        76 ~~~~~~~~~~~~~~~~El~~~~i~vl~~~  104 (135)
T cd04317          76 ARPEGTVNPKLPTGEIEVVASELEVLNKA  104 (135)
T ss_pred             CCCccccCCCCCCCcEEEEEeEEEEEECC
Confidence            52          24578999998877643

These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh

>PRK07217 replication factor A; Reviewed

Probab=97.77  E-value=0.00013  Score=59.80  Aligned_cols=77  Identities=12%  Similarity=0.177  Sum_probs=60.3

Q ss_pred             EeeEEEEEEEEEEeeccCCceEE--EEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           35 LLSRAEIVGTITSRDHKPSKFIK--FTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~~~~~~~~--~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      +-.+|.|-|+|+++......-+.  =.|.|.||+|....|.++..                       ..++.|+.+++.
T Consensus        81 ~~~~VsV~aKVl~l~e~~~~si~qvGllgDETG~IkfT~W~~s~~-----------------------~~leeGd~~rI~  137 (311)
T PRK07217         81 PEQWVDVTAKVVQLWEPSSDSIAQVGLLGDETGTIKFTKWAKSDL-----------------------PELEEGKSYLLK  137 (311)
T ss_pred             CCCcEEEEEEEEEecCCCCCceEEEEEEEcCCceEEEEEccCCCC-----------------------CcccCCCEEEEE
Confidence            35789999999998754432222  37999999999999987542                       458899999999


Q ss_pred             EE-eceeCCceEEEEEEEEEcCC
Q 043474          113 GR-IASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       113 G~-v~~f~~~~qi~~~~i~~v~d  134 (160)
                      +- ++.|+|..+|++.+-..+..
T Consensus       138 na~v~ey~G~~~lnlg~~t~I~~  160 (311)
T PRK07217        138 NVVTDEYQGRFSVKLNRTTSIEE  160 (311)
T ss_pred             eEEEeeECCEEEEEeCCceEEEe
Confidence            87 57899999999987665543

>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif)

Probab=97.75  E-value=0.00083  Score=46.80  Aligned_cols=68  Identities=15%  Similarity=0.200  Sum_probs=49.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+-|.|+..-..+    .|...|+||+|.+-+=.+.-.                      -..+.+++.|+|.|.|.
T Consensus        35 ~~V~L~G~Iv~~l~~d----~Y~F~D~TG~I~VeId~~~w~----------------------g~~vt~~~~Vri~GeVD   88 (103)
T PF04076_consen   35 TPVTLEGNIVKQLGDD----KYLFRDATGEIEVEIDDDVWR----------------------GQTVTPDDKVRISGEVD   88 (103)
T ss_dssp             EEEEEEEEEEEEEETT----EEEEEETTEEEEEE--GGGST----------------------T----TTSEEEEEEEEE
T ss_pred             CeEEEEEEEEEEecCC----EEEEECCCCcEEEEEChhhcC----------------------CcccCCCCEEEEEEEEe
Confidence            6788889988877665    689999999999987332211                      13567889999999999


Q ss_pred             eeCCceEEEEEEEE
Q 043474          117 SYRGDVQITVSDVV  130 (160)
Q Consensus       117 ~f~~~~qi~~~~i~  130 (160)
                      ..-+...|.+.+|+
T Consensus        89 k~~~~~~IdV~~I~  102 (103)
T PF04076_consen   89 KDWNKTEIDVDRIE  102 (103)
T ss_dssp             EETTEEEEEEEEEE
T ss_pred             CCCCceEEEEEEEE
Confidence            76678899998886

Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.

>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS)

Probab=97.74  E-value=0.0006  Score=47.11  Aligned_cols=79  Identities=16%  Similarity=0.133  Sum_probs=57.3

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      |++.|+|.++.... +...+.|.|+||.++|++-.+...                +. ......+..|+.|.|.|.+..=
T Consensus         2 V~v~Gwv~~~R~~g-k~~Fi~lrD~~g~iQ~v~~~~~~~----------------~~-~~~~~~l~~~s~v~V~G~v~~~   63 (103)
T cd04319           2 VTLAGWVYRKREVG-KKAFIVLRDSTGIVQAVFSKDLNE----------------EA-YREAKKVGIESSVIVEGAVKAD   63 (103)
T ss_pred             EEEEEEEEeEEcCC-CeEEEEEecCCeeEEEEEeCCCCH----------------HH-HHHHhCCCCCCEEEEEEEEEEC
Confidence            78999999988765 668899999999999987332111                00 1122468899999999998763


Q ss_pred             CC---ceEEEEEEEEEcCCh
Q 043474          119 RG---DVQITVSDVVIEKDP  135 (160)
Q Consensus       119 ~~---~~qi~~~~i~~v~d~  135 (160)
                      .+   ...|.+..+..+...
T Consensus        64 ~~~~~~~Ei~~~~i~vl~~a   83 (103)
T cd04319          64 PRAPGGAEVHGEKLEIIQNV   83 (103)
T ss_pred             CCCCCCEEEEEEEEEEEecC
Confidence            32   367888998877654

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.

>PRK07211 replication factor A; Reviewed

Probab=97.67  E-value=0.00038  Score=60.49  Aligned_cols=77  Identities=23%  Similarity=0.413  Sum_probs=60.9

Q ss_pred             eEEEEEEEEEEeec------c---CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH------K---PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~---~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..+.|.|+|.++..      +   +++...++|-|.||.|.+.+|.+...                     ....+++|+
T Consensus       172 ~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG~IR~TlW~d~Ad---------------------~~~~le~G~  230 (485)
T PRK07211        172 SDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGRVRVTLWDDRAD---------------------LAEELDAGE  230 (485)
T ss_pred             CceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCCeEEEEEechhhh---------------------hhccCCCCC
Confidence            56778888886553      1   23667999999999999999987643                     225688999


Q ss_pred             EEEEE-EEeceeCCceEEEEE---EEEEcCC
Q 043474          108 VARVR-GRIASYRGDVQITVS---DVVIEKD  134 (160)
Q Consensus       108 ~V~V~-G~v~~f~~~~qi~~~---~i~~v~d  134 (160)
                      +|+|. |+++.|++.++|++.   .|.++.+
T Consensus       231 Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~d  261 (485)
T PRK07211        231 SVEIVDGYVRERDGSLELHVGDRGAVEEVDE  261 (485)
T ss_pred             EEEEEeeEEEecCCcEEEEECCCceEEECCc
Confidence            99996 889999999999887   6777655

>PRK07218 replication factor A; Provisional

Probab=97.66  E-value=0.00046  Score=59.14  Aligned_cols=72  Identities=21%  Similarity=0.370  Sum_probs=58.3

Q ss_pred             eEEEEEEEEEEeeccC-------CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEE
Q 043474           37 SRAEIVGTITSRDHKP-------SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVA  109 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~-------~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V  109 (160)
                      ..|.|.|.|.++..++       +......|.|.||+|...+|.+.                         +.+++|+.|
T Consensus       173 ~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG~Ir~tlW~~~-------------------------~~l~~Gd~v  227 (423)
T PRK07218        173 RGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPL-------------------------PEIEIGASI  227 (423)
T ss_pred             CceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCceEEEEEeccc-------------------------ccCCCCCEE
Confidence            5688999999885532       24567899999999999999853                         237899999


Q ss_pred             EEEE-EeceeCCceEEEEE---EEEEcC
Q 043474          110 RVRG-RIASYRGDVQITVS---DVVIEK  133 (160)
Q Consensus       110 ~V~G-~v~~f~~~~qi~~~---~i~~v~  133 (160)
                      +|.| .++.|+|..+|++.   .|..++
T Consensus       228 ~I~na~v~e~~G~~elnv~~~t~I~~~d  255 (423)
T PRK07218        228 RIEDAYVREFRGVPSVNVSEFTTVEALD  255 (423)
T ss_pred             EEeeeEEeccCCeEEEEECCceEEEECC
Confidence            9999 57899999999999   676654

>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS

Probab=97.65  E-value=0.0015  Score=43.16  Aligned_cols=74  Identities=15%  Similarity=0.168  Sum_probs=54.4

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCce--EEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGC--VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~--I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      +++.|+|.++.... +...+.|.||||.  ++|++-.+...                   ......++.|+.|.|.|.+.
T Consensus         2 v~v~Gwv~~~R~~g-~~~Fi~LrD~s~~~~lQvv~~~~~~~-------------------~~~~~~l~~gs~V~v~G~v~   61 (82)
T cd04318           2 VTVNGWVRSVRDSK-KISFIELNDGSCLKNLQVVVDKELTN-------------------FKEILKLSTGSSIRVEGVLV   61 (82)
T ss_pred             EEEEEeEEEEEcCC-cEEEEEEECCCCccCEEEEEeCcccC-------------------HHHHhcCCCceEEEEEEEEE
Confidence            68999999998765 6678889999994  99986322110                   01235688999999999987


Q ss_pred             eeC---CceEEEEEEEEEc
Q 043474          117 SYR---GDVQITVSDVVIE  132 (160)
Q Consensus       117 ~f~---~~~qi~~~~i~~v  132 (160)
                      .-.   +...|.+.++..+
T Consensus        62 ~~~~~~~~~El~~~~i~il   80 (82)
T cd04318          62 KSPGAKQPFELQAEKIEVL   80 (82)
T ss_pred             eCCCCCCCEEEEEEEEEEe
Confidence            643   3477888888754

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial

>PRK14699 replication factor A; Provisional

Probab=97.63  E-value=0.00021  Score=62.28  Aligned_cols=74  Identities=22%  Similarity=0.291  Sum_probs=56.2

Q ss_pred             eeEEEEEEEEEEee-cc--------CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccC
Q 043474           36 LSRAEIVGTITSRD-HK--------PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIG  106 (160)
Q Consensus        36 i~~v~ivG~V~~~~-~~--------~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G  106 (160)
                      -..|.+.|+|.++. .+        .+.+..++|.|.||+|...+|.+....                .   ....+++|
T Consensus        67 ~~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~iaDeTG~ir~tlW~~~a~~----------------~---~~g~l~~G  127 (484)
T PRK14699         67 SGPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMADL----------------I---KAGKIKAG  127 (484)
T ss_pred             CceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccch----------------h---hhcCCCCC
Confidence            36788999999885 22        246678899999999999999865421                0   11258999


Q ss_pred             cEEEEEEEeceeCCceEEEEEE
Q 043474          107 LVARVRGRIASYRGDVQITVSD  128 (160)
Q Consensus       107 ~~V~V~G~v~~f~~~~qi~~~~  128 (160)
                      ++|+|.|.++.+.+..+|++..
T Consensus       128 Dvv~I~~~~r~~~~g~el~~~~  149 (484)
T PRK14699        128 QTLQISGYAKQGYSGVEVNIGN  149 (484)
T ss_pred             CEEEEcceeccCCCCceEEeCC
Confidence            9999999997766667888873

>TIGR00156 conserved hypothetical protein TIGR00156

Probab=97.51  E-value=0.0018  Score=46.63  Aligned_cols=68  Identities=12%  Similarity=0.231  Sum_probs=49.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+-|.|+..-..+    .|...|+||+|.+.+=.+.-.                      -..+.+++-|+|.|.|.
T Consensus        58 t~V~L~G~Iv~~l~~d----~Y~F~D~TG~I~VeId~~~w~----------------------G~~v~p~d~V~I~GeVD  111 (126)
T TIGR00156        58 ASVTLRGNIISHIGDD----RYVFRDKSGEINVVIPAAVWN----------------------GREVQPKDMVNISGSLD  111 (126)
T ss_pred             CEEEEEEEEEEEeCCc----eEEEECCCCCEEEEECHHHcC----------------------CCcCCCCCEEEEEEEEC
Confidence            6788888888866554    689999999988877222111                      13567899999999998


Q ss_pred             eeCCceEEEEEEEE
Q 043474          117 SYRGDVQITVSDVV  130 (160)
Q Consensus       117 ~f~~~~qi~~~~i~  130 (160)
                      .--+...|.+.+|+
T Consensus       112 k~~~~~~IdV~~I~  125 (126)
T TIGR00156       112 KKSAPAEVDVTHIQ  125 (126)
T ss_pred             CCCCCeEEEEEEEE
Confidence            64346788888775

As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.

>PRK07211 replication factor A; Reviewed

Probab=97.50  E-value=0.00072  Score=58.81  Aligned_cols=79  Identities=20%  Similarity=0.399  Sum_probs=61.2

Q ss_pred             eEEEEEEEEEEeec------c----CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccC
Q 043474           37 SRAEIVGTITSRDH------K----PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIG  106 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~----~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G  106 (160)
                      .++.|.|+|.++..      +    +++...+.|-|.||.|.+.+|.+....                    ....+++|
T Consensus        64 ~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG~Ir~TlW~d~ad~--------------------~~~~Le~G  123 (485)
T PRK07211         64 DEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETGSVRVAFWDEQAVA--------------------AEEELEVG  123 (485)
T ss_pred             CceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCCeEEEEEechHhHh--------------------hhcccCCC
Confidence            66888888887653      2    357789999999999999999865421                    23578999


Q ss_pred             cEEEEEEEeceeCCceEEEEEEEEEcCCh
Q 043474          107 LVARVRGRIASYRGDVQITVSDVVIEKDP  135 (160)
Q Consensus       107 ~~V~V~G~v~~f~~~~qi~~~~i~~v~d~  135 (160)
                      ++++|.|+++...+..+|.+..+.+..+.
T Consensus       124 dV~~I~~~~~~~ys~~El~i~~ve~~~d~  152 (485)
T PRK07211        124 QVLRIKGRPKDGYNGLEVSVDKVEPDPDA  152 (485)
T ss_pred             CEEEEeceEeccccceEEEEeeEEEcccc
Confidence            99999999865555679999988876553

>PRK07218 replication factor A; Provisional

Probab=97.39  E-value=0.001  Score=57.01  Aligned_cols=67  Identities=10%  Similarity=0.293  Sum_probs=55.4

Q ss_pred             eeEEEEEEEEEEeecc-------CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcE
Q 043474           36 LSRAEIVGTITSRDHK-------PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLV  108 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~-------~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~  108 (160)
                      -.+|.+.|+|.++..+       ++......|.|.||+|...+|.+.                          .+++|+.
T Consensus        68 ~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~~--------------------------~l~~Gdv  121 (423)
T PRK07218         68 DKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKDF--------------------------GLSPGDT  121 (423)
T ss_pred             CceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEECCC--------------------------CCCCCCE
Confidence            3789999999998643       246678999999999999999721                          2889999


Q ss_pred             EEEEE-EeceeCCceEEEEEE
Q 043474          109 ARVRG-RIASYRGDVQITVSD  128 (160)
Q Consensus       109 V~V~G-~v~~f~~~~qi~~~~  128 (160)
                      |+|.+ .++.|+|..+|++..
T Consensus       122 v~I~na~vre~~g~~el~ig~  142 (423)
T PRK07218        122 VTIGNAGVREWDGRPELNIGE  142 (423)
T ss_pred             EEEeccEeeccCCceEEeccC
Confidence            99995 789999999999744

>PRK07374 dnaE DNA polymerase III subunit alpha; Validated

Probab=97.38  E-value=0.00055  Score=65.21  Aligned_cols=78  Identities=13%  Similarity=0.219  Sum_probs=62.4

Q ss_pred             eEEEEEEEEEEeeccC----CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTITSRDHKP----SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~----~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ..|+++|.|.+++...    .++..++|+|.||.+++++|-+.-.                    +....+..|..+-|.
T Consensus      1001 ~~v~v~g~i~~~k~~~Tk~G~~maf~~leD~tg~~e~vvFp~~y~--------------------~~~~~l~~~~~~~v~ 1060 (1170)
T PRK07374       1001 AKVSAIAMIPEMKQVTTRKGDRMAILQLEDLTGSCEAVVFPKSYE--------------------RLSDHLMTDTRLLVW 1060 (1170)
T ss_pred             CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHH--------------------HHHHHhccCCEEEEE
Confidence            4689999999987433    2578899999999999999966543                    133568899999999


Q ss_pred             EEeceeCCceEEEEEEEEEcCC
Q 043474          113 GRIASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~d  134 (160)
                      |+++.-.+..++.+.++.++.+
T Consensus      1061 g~v~~~~~~~~~~~~~i~~l~~ 1082 (1170)
T PRK07374       1061 AKVDRRDDRVQLIIDDCREIDD 1082 (1170)
T ss_pred             EEEEecCCeEEEEEeeeecHhh
Confidence            9998755778999999887653

>PRK06920 dnaE DNA polymerase III DnaE; Reviewed

Probab=97.38  E-value=0.00058  Score=64.71  Aligned_cols=78  Identities=19%  Similarity=0.183  Sum_probs=62.4

Q ss_pred             eEEEEEEEEEEeeccC----CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTITSRDHKP----SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~----~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ..++++|.|.+++...    .++..++|+|.||.+++++|-+.-.                    .....+..|..|.|.
T Consensus       944 ~~v~v~g~i~~~~~~~tk~g~~maf~~leD~tg~~e~~vFp~~y~--------------------~~~~~l~~~~~~~v~ 1003 (1107)
T PRK06920        944 KVQRAIVYITSVKVIRTKKGQKMAFITFCDQNDEMEAVVFPETYI--------------------HFSDKLQEGAIVLVD 1003 (1107)
T ss_pred             CEEEEEEEEEEeEeecCCCCCeEEEEEEeeCCCcEEEEECHHHHH--------------------HHHHHhccCCEEEEE
Confidence            3689999999986422    3678899999999999999965432                    133568899999999


Q ss_pred             EEeceeCCceEEEEEEEEEcCC
Q 043474          113 GRIASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~d  134 (160)
                      |+++.-++..++.+.++.++.+
T Consensus      1004 G~v~~~~~~~~~~~~~i~~l~~ 1025 (1107)
T PRK06920       1004 GTIELRNHKLQWIVNGLYPLEE 1025 (1107)
T ss_pred             EEEEecCCcEEEEEeecccHHH
Confidence            9998766778999999987753

>PRK05672 dnaE2 error-prone DNA polymerase; Validated

Probab=97.33  E-value=0.00068  Score=64.01  Aligned_cols=78  Identities=21%  Similarity=0.282  Sum_probs=62.3

Q ss_pred             eEEEEEEEEEEeeccCC--ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEE
Q 043474           37 SRAEIVGTITSRDHKPS--KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGR  114 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~--~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~  114 (160)
                      ..|.++|+|..++...+  .+..++|+|.||.++|++|.+.-.                    +....++.|.++.|+|+
T Consensus       954 ~~v~v~g~i~~~~~~~TkkGmaf~~leD~~g~~e~~ifp~~~~--------------------~~~~~l~~~~~~~v~g~ 1013 (1046)
T PRK05672        954 RRVRVAGVVTHRQRPGTASGVTFLTLEDETGMVNVVVWPGLWE--------------------RQRREALGARLLLVRGR 1013 (1046)
T ss_pred             CEEEEEEEEEEEEEecCCCceEEEEEecCCCCEEEEECHHHHH--------------------HHHHHhccCCEEEEEEE
Confidence            35889999998876432  267899999999999999976543                    12356889999999999


Q ss_pred             eceeCCceEEEEEEEEEcCC
Q 043474          115 IASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       115 v~~f~~~~qi~~~~i~~v~d  134 (160)
                      ++.-++..++.+.++.++.+
T Consensus      1014 v~~~~~~~~~~~~~i~~~~~ 1033 (1046)
T PRK05672       1014 VQNAEGVRHLVADRLEDLSP 1033 (1046)
T ss_pred             EEecCCeEEEEEeeeechHH
Confidence            99766778999999987753

>PRK12366 replication factor A; Reviewed

Probab=97.32  E-value=0.0011  Score=59.54  Aligned_cols=75  Identities=25%  Similarity=0.466  Sum_probs=59.8

Q ss_pred             eEEEEEEEEEEeecc---------CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDHK---------PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~---------~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..|.|.|.|.++...         ++....++|.|.||+|.+.+|.+...                       ..++.|+
T Consensus       185 ~~v~v~G~V~~~~~~~~f~rkdg~~~~~r~~~l~D~TG~irvTlW~~~a~-----------------------~~~~~g~  241 (637)
T PRK12366        185 LSATIEGEVTKAYPIKEFTRKDGSEGKLKSFILKDDTGSIRVTLWNDLTD-----------------------IEVNKGD  241 (637)
T ss_pred             CeEEEEEEEEEccCcEEEEEcCCCeeEEEEEEEEcCCCcEEEEEEChhhc-----------------------ccCCCCC
Confidence            378999999987641         13557899999999999999987653                       2478999


Q ss_pred             EEEEEEEe-ceeCCceEEEEEEEEEcCC
Q 043474          108 VARVRGRI-ASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       108 ~V~V~G~v-~~f~~~~qi~~~~i~~v~d  134 (160)
                      +|+|.|.+ ..|+|.+.|.+.+...+..
T Consensus       242 vv~i~g~~~~~~~~~~el~~~~~~~i~~  269 (637)
T PRK12366        242 IVRVKGYVKQGYRTGLEISANNIEILEK  269 (637)
T ss_pred             EEEEEeEEecCcCCceEEEeCCceeecc
Confidence            99999984 5688899999888776654

>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type

Probab=97.32  E-value=0.0022  Score=55.13  Aligned_cols=81  Identities=15%  Similarity=0.238  Sum_probs=60.0

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|.++.... +.+.+.|.|+||.|+|++-.+....               +. .+....+..|+.|.|.|.+.
T Consensus        13 ~~v~i~G~v~~~R~~g-~~~Fi~lrd~~g~iQ~v~~~~~~~~---------------~~-~~~~~~l~~~s~v~v~G~v~   75 (428)
T TIGR00458        13 QEVTFMGWVHEIRDLG-GLIFVLLRDREGLIQITAPAKKVSK---------------NL-FKWAKKLNLESVVAVRGIVK   75 (428)
T ss_pred             CEEEEEEEEEEEecCC-CcEEEEEEeCCeeEEEEEECCcCCH---------------HH-HHHHhCCCCCcEEEEEEEEE
Confidence            5689999999998776 5678999999999999874322110               00 11235689999999999998


Q ss_pred             eeC---CceEEEEEEEEEcCC
Q 043474          117 SYR---GDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f~---~~~qi~~~~i~~v~d  134 (160)
                      .-+   +...|.+.++..+..
T Consensus        76 ~~~~~~~~~el~~~~i~vl~~   96 (428)
T TIGR00458        76 IKEKAPGGFEIIPTKIEVINE   96 (428)
T ss_pred             ecCCCCCcEEEEEeEEEEEec
Confidence            543   567888888887654

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).

>PRK06826 dnaE DNA polymerase III DnaE; Reviewed

Probab=97.31  E-value=0.00073  Score=64.31  Aligned_cols=77  Identities=14%  Similarity=0.239  Sum_probs=61.3

Q ss_pred             eEEEEEEEEEEeeccC----CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTITSRDHKP----SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~----~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ..++++|.|.+++...    .++..++|+|.||.+++++|.+.-.                    .....++.|..|.|.
T Consensus       992 ~~v~v~g~i~~~~~~~tk~G~~maf~~leD~~g~~e~~vfp~~~~--------------------~~~~~l~~~~~~~v~ 1051 (1151)
T PRK06826        992 DKVIIGGIITEVKRKTTRNNEMMAFLTLEDLYGTVEVIVFPKVYE--------------------KYRSLLNEDNIVLIK 1051 (1151)
T ss_pred             cEEEEEEEEEEeEeeccCCCCeEEEEEEEECCCcEEEEECHHHHH--------------------HHHHHhccCCEEEEE
Confidence            4688999999988533    2578899999999999999965432                    123568899999999


Q ss_pred             EEecee-CCceEEEEEEEEEcC
Q 043474          113 GRIASY-RGDVQITVSDVVIEK  133 (160)
Q Consensus       113 G~v~~f-~~~~qi~~~~i~~v~  133 (160)
                      |+++.. ++..++.+.++.++.
T Consensus      1052 g~v~~~~~~~~~~~~~~~~~l~ 1073 (1151)
T PRK06826       1052 GRVSLREDEEPKLICEEIEPLV 1073 (1151)
T ss_pred             EEEEecCCCceEEEEeeeecHh
Confidence            999865 466899999988765

>PRK08402 replication factor A; Reviewed

Probab=97.30  E-value=0.0017  Score=54.52  Aligned_cols=72  Identities=21%  Similarity=0.377  Sum_probs=55.4

Q ss_pred             eEEEEEEEEEEeec-c-----C---CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH-K-----P---SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-~-----~---~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..|.+.|.|.++.. +     .   +....++|.|.||.|...+|.+....                    ....+++|+
T Consensus        73 ~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~ir~TlW~~~a~~--------------------~~~~l~~Gd  132 (355)
T PRK08402         73 RGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVAK--------------------YYNKINVGD  132 (355)
T ss_pred             ceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechhhhh--------------------hcccCCCCC
Confidence            68999999999753 2     1   23445899999999999999876431                    124588999


Q ss_pred             EEEEE-EEecee-CCceEEEEEE
Q 043474          108 VARVR-GRIASY-RGDVQITVSD  128 (160)
Q Consensus       108 ~V~V~-G~v~~f-~~~~qi~~~~  128 (160)
                      +|+|. ++++.| +|..+|++..
T Consensus       133 vi~I~~a~V~e~~~G~~eLsvg~  155 (355)
T PRK08402        133 VIKVIDAQVRESLSGLPELHINF  155 (355)
T ss_pred             EEEEECCEEeecCCCcEEEEECC
Confidence            99997 788875 8888998863

>PRK05159 aspC aspartyl-tRNA synthetase; Provisional

Probab=97.26  E-value=0.0027  Score=54.72  Aligned_cols=81  Identities=14%  Similarity=0.171  Sum_probs=59.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|.++.... +.+-+.|.|++|.|+|++=.+...                 ...+....+..|++|.|.|.+.
T Consensus        17 ~~V~i~GrV~~~R~~g-k~~Fl~LrD~~g~iQ~v~~~~~~~-----------------~~~~~~~~L~~gs~V~v~G~v~   78 (437)
T PRK05159         17 EEVTLAGWVHEIRDLG-GIAFLILRDRSGIIQVVVKKKVDE-----------------ELFETIKKLKRESVVSVTGTVK   78 (437)
T ss_pred             CEEEEEEEeEeeecCC-CeEEEEEEcCCcEEEEEEeCCccH-----------------HHHHHHhCCCCCcEEEEEEEEE
Confidence            5688999999998765 667899999999999987322110                 0011235688999999999998


Q ss_pred             eeC---CceEEEEEEEEEcCCh
Q 043474          117 SYR---GDVQITVSDVVIEKDP  135 (160)
Q Consensus       117 ~f~---~~~qi~~~~i~~v~d~  135 (160)
                      .-+   +...|.+.++..+...
T Consensus        79 ~~~~~~~~~el~~~~i~vls~a  100 (437)
T PRK05159         79 ANPKAPGGVEVIPEEIEVLNKA  100 (437)
T ss_pred             cCCCCCCCEEEEEeEEEEEeCC
Confidence            654   4577999888876544

>PRK15491 replication factor A; Provisional

Probab=97.23  E-value=0.0031  Score=53.33  Aligned_cols=77  Identities=22%  Similarity=0.363  Sum_probs=57.1

Q ss_pred             eEEEEEEEEEEeec------cC---CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH------KP---SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~~---~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..|.|.|+|.++..      +.   ++...+.|-|.||.|.+.+|.+...                     ....+++|+
T Consensus       177 ~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG~Ir~t~W~~~a~---------------------~~~~l~~Gd  235 (374)
T PRK15491        177 SDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKTD---------------------LADKLENGD  235 (374)
T ss_pred             ccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCCeEEEEEecchhc---------------------ccccCCCCC
Confidence            35888999998763      11   2566899999999999999987543                     224688999


Q ss_pred             EEEEEE-Eec--eeCCceEEEEE---EEEEcCC
Q 043474          108 VARVRG-RIA--SYRGDVQITVS---DVVIEKD  134 (160)
Q Consensus       108 ~V~V~G-~v~--~f~~~~qi~~~---~i~~v~d  134 (160)
                      .|++.+ .++  .|+|..+|++.   .|.++++
T Consensus       236 ~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~  268 (374)
T PRK15491        236 SVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR  268 (374)
T ss_pred             EEEEEeceEEEeccCCCEEEEeCCCceEEECCc
Confidence            999966 355  56788888876   4666554

>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]

Probab=97.21  E-value=0.0043  Score=53.25  Aligned_cols=79  Identities=16%  Similarity=0.244  Sum_probs=59.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      +.|+|.|+|.++.... +..-+.|-||||.|+|++-.+....                .... ...+..+..|.|.|.|.
T Consensus        17 ~~V~v~GWV~~~R~~g-~i~Fi~lrDgsg~iQ~v~~~~~~~~----------------~~~~-~~~L~~es~v~V~G~v~   78 (435)
T COG0017          17 QEVTVRGWVHNKRDLG-KIIFLVLRDGSGFIQAVVPKNKVYE----------------ELFK-AKKLTLESSVVVTGIVK   78 (435)
T ss_pred             cEEEEEEEeeeecccC-CeEEEEEEcCCcEEEEEEECCCCcH----------------HHhh-hhcCCCccEEEEEEEEE
Confidence            8999999999988776 6788899999999999986432210                0011 34788999999999998


Q ss_pred             eeC---CceEEEEEEEEEcC
Q 043474          117 SYR---GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~---~~~qi~~~~i~~v~  133 (160)
                      .-.   +...|.+.+|..+.
T Consensus        79 ~~~~a~~g~El~v~~i~Vl~   98 (435)
T COG0017          79 ASPKAPQGFELQVEKIEVLG   98 (435)
T ss_pred             cCCCCCCCEEEEEEEEEEee
Confidence            755   34568888877554

>PRK00484 lysS lysyl-tRNA synthetase; Reviewed

Probab=97.20  E-value=0.0033  Score=54.99  Aligned_cols=81  Identities=15%  Similarity=0.253  Sum_probs=59.2

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|.++.... +..-+.|.|+||.|+|++=.+...                .........+..|++|.|.|.+.
T Consensus        55 ~~v~v~G~v~~~R~~g-~~~Fi~lrD~~g~iQ~v~~~~~~~----------------~~~~~~~~~l~~g~~v~v~G~v~  117 (491)
T PRK00484         55 IEVSVAGRVMLKRVMG-KASFATLQDGSGRIQLYVSKDDVG----------------EEALEAFKKLDLGDIIGVEGTLF  117 (491)
T ss_pred             cEEEEEEEEEEEecCC-ceEEEEEEcCCccEEEEEECCcCC----------------HHHHHHHhcCCCCCEEEEEEEEE
Confidence            5699999999998776 678899999999999986322111                00011223489999999999987


Q ss_pred             e-eCCceEEEEEEEEEcCC
Q 043474          117 S-YRGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~-f~~~~qi~~~~i~~v~d  134 (160)
                      . -.|...|.+.++..+..
T Consensus       118 ~t~~ge~el~~~~~~vls~  136 (491)
T PRK00484        118 KTKTGELSVKATELTLLTK  136 (491)
T ss_pred             EcCCCcEEEEEeEEEEEec
Confidence            4 34678888888876653

>PRK03932 asnC asparaginyl-tRNA synthetase; Validated

Probab=97.16  E-value=0.0043  Score=53.69  Aligned_cols=80  Identities=10%  Similarity=0.132  Sum_probs=60.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|.++.... +..-+.|.|+||.|++++-.+...                 ...+....+..|++|.|.|.+.
T Consensus        17 ~~V~i~G~v~~~R~~g-~~~Fi~lrD~~g~iq~~~~~~~~~-----------------~~~~~~~~l~~~s~v~v~G~v~   78 (450)
T PRK03932         17 QEVTVRGWVRTKRDSG-KIAFLQLRDGSCFKQLQVVKDNGE-----------------EYFEEIKKLTTGSSVIVTGTVV   78 (450)
T ss_pred             CEEEEEEEEEEEEeCC-CeEEEEEECCCCcEEEEEEcCCCh-----------------HHHHHHhcCCCCcEEEEEEEEE
Confidence            6799999999998774 768899999999988877433211                 0011234689999999999998


Q ss_pred             eeC---CceEEEEEEEEEcCC
Q 043474          117 SYR---GDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f~---~~~qi~~~~i~~v~d  134 (160)
                      .-.   +...|.+.++..+..
T Consensus        79 ~~~~~~~~~el~~~~i~vl~~   99 (450)
T PRK03932         79 ESPRAGQGYELQATKIEVIGE   99 (450)
T ss_pred             cCCCCCCCEEEEEEEEEEccC
Confidence            643   357899999987764

>TIGR00457 asnS asparaginyl-tRNA synthetase

Probab=97.11  E-value=0.0045  Score=53.65  Aligned_cols=80  Identities=15%  Similarity=0.290  Sum_probs=58.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCC--ceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEE
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGT--GCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGR  114 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgT--G~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~  114 (160)
                      ..|.|.|+|.++.... +..-+.|.|+|  |.|+|++-.....                 ........+..|+.|.|.|.
T Consensus        17 ~~v~v~Gwv~~~R~~~-~~~F~~lrD~~~~g~iQ~v~~~~~~~-----------------~~~~~~~~l~~gs~V~v~G~   78 (453)
T TIGR00457        17 DEVTVSGWVRTKRSSK-KIIFLELNDGSSLGPIQAVINGEDNP-----------------YLFQLLKSLTTGSSVSVTGK   78 (453)
T ss_pred             CEEEEEEEeEEEEcCC-CeEEEEEECCCCCccEEEEEeCCcCh-----------------HHHHHHHcCCCCcEEEEEEE
Confidence            6799999999998554 66788999999  9999987332111                 00112356899999999999


Q ss_pred             ecee---CCceEEEEEEEEEcCC
Q 043474          115 IASY---RGDVQITVSDVVIEKD  134 (160)
Q Consensus       115 v~~f---~~~~qi~~~~i~~v~d  134 (160)
                      +..-   .+...|.+..+..+..
T Consensus        79 v~~~~~~~~~~El~~~~i~vl~~  101 (453)
T TIGR00457        79 VVESPGKGQPVELQVKKIEVVGE  101 (453)
T ss_pred             EEcCCCCCCCEEEEEeEEEEEec
Confidence            8752   2457788888887664

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.

>PRK07279 dnaE DNA polymerase III DnaE; Reviewed

Probab=97.07  E-value=0.0015  Score=61.45  Aligned_cols=76  Identities=18%  Similarity=0.275  Sum_probs=59.1

Q ss_pred             EEEEEEEEEEeec---c--CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           38 RAEIVGTITSRDH---K--PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        38 ~v~ivG~V~~~~~---~--~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      .+.++|.|.++..   +  +..+..++|+|.||.++|++|.+.-.                    +....+..|..|.|.
T Consensus       886 ~~~~~~~i~~~~~~~tk~~g~~maf~~leD~~g~ie~~vFp~~y~--------------------~~~~~l~~~~~~~v~  945 (1034)
T PRK07279        886 EATILVQIQSIRVIRTKTKGQQMAFLSVTDTKKKLDVTLFPETYR--------------------QYKDELKEGKFYYLK  945 (1034)
T ss_pred             cceEEEEEEEEEEEEEcCCCCeEEEEEEeeCCCcEEEEECHHHHH--------------------HHHHHhccCCEEEEE
Confidence            3567777776552   2  33678999999999999999965432                    133568899999999


Q ss_pred             EEeceeCCceEEEEEEEEEcC
Q 043474          113 GRIASYRGDVQITVSDVVIEK  133 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~  133 (160)
                      |+++.-++..++.+.++.++.
T Consensus       946 G~v~~~~~~~~l~~~~i~~l~  966 (1034)
T PRK07279        946 GKIQERDGRLQMVLQQIQEAS  966 (1034)
T ss_pred             EEEEecCCeeEEEEeeeeccc
Confidence            999976777899999998764

>PRK12445 lysyl-tRNA synthetase; Reviewed

Probab=97.06  E-value=0.0053  Score=53.91  Aligned_cols=82  Identities=20%  Similarity=0.267  Sum_probs=58.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|.++.... +..-+.|.|+||.|+|++-.+....               +........+..|++|.|.|.+.
T Consensus        66 ~~v~v~Grv~~~R~~G-k~~F~~lrD~~g~iQ~~~~~~~~~~---------------~~~~~~~~~l~~Gd~V~v~G~~~  129 (505)
T PRK12445         66 IEVSVAGRMMTRRIMG-KASFVTLQDVGGRIQLYVARDSLPE---------------GVYNDQFKKWDLGDIIGARGTLF  129 (505)
T ss_pred             CEEEEEEEEEEEecCC-CcEEEEEEeCCccEEEEEECCccch---------------hhHHHHHhcCCCCCEEEEEEEEE
Confidence            3599999999998776 6688999999999999774222110               00001124588999999999986


Q ss_pred             e-eCCceEEEEEEEEEcCC
Q 043474          117 S-YRGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~-f~~~~qi~~~~i~~v~d  134 (160)
                      . -.|...|.+.++..+..
T Consensus       130 ~t~~gelel~~~~~~llsk  148 (505)
T PRK12445        130 KTQTGELSIHCTELRLLTK  148 (505)
T ss_pred             ecCCCcEEEEEeEEEEEec
Confidence            4 34778888888876654

>PRK14699 replication factor A; Provisional

Probab=97.04  E-value=0.0034  Score=54.79  Aligned_cols=78  Identities=17%  Similarity=0.336  Sum_probs=58.0

Q ss_pred             eEEEEEEEEEEeec-cC--------CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH-KP--------SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-~~--------~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..|.|.|+|.++.. +.        ++...+.|.|.||.|.+.+|.+...                     ....+++|+
T Consensus       177 ~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG~ir~tlW~~~a~---------------------~~~~l~~Gd  235 (484)
T PRK14699        177 GDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETGTLRVTLWDDKTD---------------------FLNQIEYGD  235 (484)
T ss_pred             CceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCceEEEEEECcccc---------------------cccccCCCC
Confidence            45889999988765 21        2455689999999999999987432                     224688999


Q ss_pred             EEEEEEE-e--ceeCCceEEEEEEEEEcCCh
Q 043474          108 VARVRGR-I--ASYRGDVQITVSDVVIEKDP  135 (160)
Q Consensus       108 ~V~V~G~-v--~~f~~~~qi~~~~i~~v~d~  135 (160)
                      +|+|.+. +  +.|++..+|++.....+...
T Consensus       236 ~v~I~~a~vr~~~~~~~~el~~~~~s~i~~~  266 (484)
T PRK14699        236 TVELINAYARENAFTQKVELQVGNRSIIRKS  266 (484)
T ss_pred             EEEEecceEeecccCCceEEEecCceEeecc
Confidence            9998744 4  45889999999876665543

>PRK06386 replication factor A; Reviewed

Probab=97.03  E-value=0.0032  Score=52.94  Aligned_cols=71  Identities=18%  Similarity=0.299  Sum_probs=55.7

Q ss_pred             eEEEEEEEEEEeeccC-------CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEE
Q 043474           37 SRAEIVGTITSRDHKP-------SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVA  109 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~-------~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V  109 (160)
                      ..+.+.|.|.++..++       +......|.|.||+|...+|.+                           .++.|+.+
T Consensus       118 ~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGrIr~TlW~~---------------------------~l~eGd~v  170 (358)
T PRK06386        118 PYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTARVRISSFGK---------------------------PLEDNRFV  170 (358)
T ss_pred             CceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCeEEEEEccc---------------------------cccCCCEE
Confidence            4677888888875421       2445899999999999999964                           25689999


Q ss_pred             EEEEE-eceeCCceEEEEEEEEEcCC
Q 043474          110 RVRGR-IASYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       110 ~V~G~-v~~f~~~~qi~~~~i~~v~d  134 (160)
                      ++.+- ++.|+|..+|++.+...+..
T Consensus       171 ~i~na~v~e~~G~~el~v~~~t~I~~  196 (358)
T PRK06386        171 RIENARVSQYNGYIEISVGNKSVIKE  196 (358)
T ss_pred             EEeeeEEEccCCeEEEEeCCeEEEEE
Confidence            99987 56899999999988766654

>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial

Probab=97.02  E-value=0.0061  Score=53.39  Aligned_cols=82  Identities=18%  Similarity=0.220  Sum_probs=57.1

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +..-+.|.|+||.|+|++-.+....               +........+..|++|.|.|.+.
T Consensus        54 ~~v~v~Grv~~~R~~g-k~~F~~l~D~~g~iQ~~~~~~~~~~---------------~~~~~~~~~l~~gd~V~v~G~~~  117 (496)
T TIGR00499        54 IEVSIAGRIMARRSMG-KATFITLQDESGQIQLYVNKDDLPE---------------DFYEFDEYLLDLGDIIGVTGYPF  117 (496)
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEEcCCccEEEEEECCcCcH---------------HHHHHHHhcCCCCCEEEEEEEEE
Confidence            3589999999998554 7788999999999999873222110               00000112478999999999986


Q ss_pred             eeC-CceEEEEEEEEEcCC
Q 043474          117 SYR-GDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f~-~~~qi~~~~i~~v~d  134 (160)
                      .=+ |...|.+.++..+..
T Consensus       118 ~t~~gelel~~~~i~ilsk  136 (496)
T TIGR00499       118 KTKTGELSVHVTELQILTK  136 (496)
T ss_pred             ECCCCcEEEEeeEEEEEec
Confidence            544 557888888776553

This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.

>PLN02903 aminoacyl-tRNA ligase

Probab=97.00  E-value=0.0057  Score=55.11  Aligned_cols=80  Identities=24%  Similarity=0.284  Sum_probs=59.3

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      +.|.|.|+|.++.... +.+-+.|.|+||.++|++-.....                 ........++.|++|.|.|.|.
T Consensus        73 k~V~l~GWV~~~R~~G-~l~FidLRD~~G~iQvV~~~~~~~-----------------~~~~~~~~L~~esvV~V~G~V~  134 (652)
T PLN02903         73 SRVTLCGWVDLHRDMG-GLTFLDVRDHTGIVQVVTLPDEFP-----------------EAHRTANRLRNEYVVAVEGTVR  134 (652)
T ss_pred             CEEEEEEEEEEEecCC-CcEEEEEEcCCccEEEEEeCCccH-----------------HHHHHHhcCCCCCEEEEEEEEE
Confidence            5699999999998776 668899999999999987322111                 0011235789999999999998


Q ss_pred             ee----------CCceEEEEEEEEEcCC
Q 043474          117 SY----------RGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f----------~~~~qi~~~~i~~v~d  134 (160)
                      .-          .|...|.+.++..+..
T Consensus       135 ~r~~~~~n~~~~tGeiEl~~~~i~VL~~  162 (652)
T PLN02903        135 SRPQESPNKKMKTGSVEVVAESVDILNV  162 (652)
T ss_pred             eCCCcCcCCCCCCCCEEEEEeEEEEEec
Confidence            53          1457888888887654

>PRK15491 replication factor A; Provisional

Probab=96.98  E-value=0.006  Score=51.62  Aligned_cols=77  Identities=17%  Similarity=0.334  Sum_probs=57.5

Q ss_pred             eEEEEEEEEEEeec---------cCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH---------KPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~---------~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      .++.|.|+|.++..         .+++...+.|-|.||+|.+.+|.+.....                   ....+++|+
T Consensus        68 ~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~a~~~-------------------~~~~le~G~  128 (374)
T PRK15491         68 SNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLADLI-------------------KTGDIEVGK  128 (374)
T ss_pred             CceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECchhhhh-------------------ccCCcCCCC
Confidence            77889999998732         12466788999999999999998654310                   114588999


Q ss_pred             EEEEEEEec-eeCCceEEEEEE---EEEcC
Q 043474          108 VARVRGRIA-SYRGDVQITVSD---VVIEK  133 (160)
Q Consensus       108 ~V~V~G~v~-~f~~~~qi~~~~---i~~v~  133 (160)
                      +++|.|..+ .|++ .+|++..   +.+++
T Consensus       129 v~~I~~~~~~~y~g-~Ei~i~~~~~i~~~~  157 (374)
T PRK15491        129 SLNISGYAKEGYSG-IEVNIGRYGGISESD  157 (374)
T ss_pred             EEEEeeeeccCccc-EEEEeCCCceeeecc
Confidence            999999987 5666 7888884   55443

>PRK10053 hypothetical protein; Provisional

Probab=96.91  E-value=0.013  Score=42.46  Aligned_cols=68  Identities=7%  Similarity=0.232  Sum_probs=49.3

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+-|.|+..-..+    .|...|+||+|++-+=.+.-.                      -..+.+.+.|++.|.|.
T Consensus        62 ~~V~L~G~Iv~~lg~d----~Y~F~D~tG~I~VeID~~~w~----------------------G~~v~p~~kV~I~GevD  115 (130)
T PRK10053         62 ATVSLRGNLIDHKGDD----RYVFRDKSGEINVIIPAAVFD----------------------GREVQPDQMININGSLD  115 (130)
T ss_pred             CeEEEEEEEEEEeCCc----eEEEECCCCcEEEEeCHHHcC----------------------CCcCCCCCEEEEEEEEC
Confidence            5677888888765554    678899999988876222211                      13567899999999998


Q ss_pred             eeCCceEEEEEEEE
Q 043474          117 SYRGDVQITVSDVV  130 (160)
Q Consensus       117 ~f~~~~qi~~~~i~  130 (160)
                      .=.....|.+.+|+
T Consensus       116 k~~~~~~IdV~~i~  129 (130)
T PRK10053        116 KKSAPPVVRVTHLQ  129 (130)
T ss_pred             CCCCCeEEEEEEEe
Confidence            54456788888775

>PLN02221 asparaginyl-tRNA synthetase

Probab=96.88  E-value=0.011  Score=52.60  Aligned_cols=98  Identities=14%  Similarity=0.198  Sum_probs=65.9

Q ss_pred             cccceehhhhhccCCCCCCCceEECCeEeeEEEEEEEEEEeeccCC-ceEEEEEeCCC--ceEEEEEeecCccCCCCCCC
Q 043474            8 THVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPS-KFIKFTVDDGT--GCVPCVLWLNHLTSLYLPRR   84 (160)
Q Consensus         8 ~~~~l~i~~i~~l~~~~~~~~~~~~~~~i~~v~ivG~V~~~~~~~~-~~~~~~IdDgT--G~I~~~~w~~~~~~~~~~~~   84 (160)
                      ...+..|++|+..+.+.       ..+.-..|+|.|+|.++..... +...+.|.|||  |.|+|++-.....       
T Consensus        29 ~~~~~~~~~~~~~~~~~-------~~~~g~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~~-------   94 (572)
T PLN02221         29 FSDRVLIRSILDRPDGG-------AGLAGQKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLYD-------   94 (572)
T ss_pred             ccCceEHHHHhccccCC-------hhcCCCEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchhh-------
Confidence            33566788887433221       0112256999999999987653 35678999999  8999987321110       


Q ss_pred             CCCccccccccccccccccccCcEEEEEEEeceeC------CceEEEEEEEEEcC
Q 043474           85 DPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYR------GDVQITVSDVVIEK  133 (160)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~------~~~qi~~~~i~~v~  133 (160)
                                    ....+..|..|.|.|.|..-.      +...|.+..+..+.
T Consensus        95 --------------~~~~L~~ES~V~V~G~V~~~~~~~~~~~~iEl~v~~i~vl~  135 (572)
T PLN02221         95 --------------LSTLVATGTCVTVDGVLKVPPEGKGTKQKIELSVEKVIDVG  135 (572)
T ss_pred             --------------HHhcCCCceEEEEEEEEEeCCccCCCCccEEEEEeEEEEEe
Confidence                          112477999999999997532      25788888887665

>PLN02502 lysyl-tRNA synthetase

Probab=96.85  E-value=0.011  Score=52.41  Aligned_cols=84  Identities=13%  Similarity=0.171  Sum_probs=58.7

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +...+.|.|+||.|+|++-.+....         +    ..........+..|++|.|.|.+.
T Consensus       109 ~~V~v~GrV~~~R~~G-k~~F~~LrD~~g~iQv~~~~~~~~~---------~----~~~~~~~~~~l~~gdiV~V~G~~~  174 (553)
T PLN02502        109 VSVSVAGRIMAKRAFG-KLAFYDLRDDGGKIQLYADKKRLDL---------D----EEEFEKLHSLVDRGDIVGVTGTPG  174 (553)
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEecCCccEEEEEECccccc---------h----hHHHHHHHhCCCCCcEEEEEEEEE
Confidence            4699999999998776 7789999999999999763222110         0    000001123588999999999986


Q ss_pred             ee-CCceEEEEEEEEEcCC
Q 043474          117 SY-RGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f-~~~~qi~~~~i~~v~d  134 (160)
                      .- .+...|.+.++..+..
T Consensus       175 ~t~~gelel~~~~i~vLs~  193 (553)
T PLN02502        175 KTKKGELSIFPTSFEVLTK  193 (553)
T ss_pred             ecCCCCEEEEEeEEEEEec
Confidence            43 3677888888776553

>PRK06386 replication factor A; Reviewed

Probab=96.82  E-value=0.01  Score=49.86  Aligned_cols=68  Identities=19%  Similarity=0.311  Sum_probs=52.4

Q ss_pred             eeEEEEEEEEEEeecc-----C--CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcE
Q 043474           36 LSRAEIVGTITSRDHK-----P--SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLV  108 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~-----~--~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~  108 (160)
                      -.+|.+.|+|+++..+     .  +....-.|.|.||.|....|...                         ..++.|+.
T Consensus        12 ~~~V~v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG~I~fT~W~~~-------------------------~~l~~Gd~   66 (358)
T PRK06386         12 RQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEFP-------------------------DAVKSGDV   66 (358)
T ss_pred             CCcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcceEEEEecCCc-------------------------ccCCCCCE
Confidence            3667888888876532     2  24456679999999999999732                         24789999


Q ss_pred             EEEEEE-eceeCCceEEEEEE
Q 043474          109 ARVRGR-IASYRGDVQITVSD  128 (160)
Q Consensus       109 V~V~G~-v~~f~~~~qi~~~~  128 (160)
                      +++.+- ++.|+|+.+|++..
T Consensus        67 v~i~na~v~~~~G~~~Lnv~~   87 (358)
T PRK06386         67 IEIKYCYSKEYNGKIRIYFDS   87 (358)
T ss_pred             EEEEeEEEeeECCEEEEEEcC
Confidence            999976 67999999999964

>PRK12366 replication factor A; Reviewed

Probab=96.82  E-value=0.0048  Score=55.57  Aligned_cols=76  Identities=22%  Similarity=0.389  Sum_probs=58.5

Q ss_pred             eEEEEEEEEEEeec------c---CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH------K---PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~---~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      .++.|.|+|.++..      +   +++...+.|-|.||+|.+++|.+...                     ....++.|+
T Consensus        74 ~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG~Ir~t~W~~~~~---------------------~~~~le~G~  132 (637)
T PRK12366         74 INVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTIRLTLWNDNAK---------------------LLKGLKEGD  132 (637)
T ss_pred             cceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCCEEEEEEEchhhh---------------------hhccCCCCC
Confidence            56888888887642      1   34678999999999999999986532                     225789999


Q ss_pred             EEEEEEE-eceeCCceEEEEEE---EEEcC
Q 043474          108 VARVRGR-IASYRGDVQITVSD---VVIEK  133 (160)
Q Consensus       108 ~V~V~G~-v~~f~~~~qi~~~~---i~~v~  133 (160)
                      ++++.|. ++.|++..+|++..   |.+++
T Consensus       133 v~~i~~~~v~~~~~~~el~~~~~t~I~~~~  162 (637)
T PRK12366        133 VIKIENARSRKWNNDVELNSGSETRIDKLE  162 (637)
T ss_pred             EEEEeccEecccCCceEEEcCCcceEEEcc
Confidence            9999887 78999999887653   55554

>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type

Probab=96.80  E-value=0.0087  Score=53.38  Aligned_cols=78  Identities=18%  Similarity=0.305  Sum_probs=58.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|.++.... +.+-+.|.|+||.|+|++-.+ ..                  ..+....++.|++|.|.|.+.
T Consensus        16 ~~V~l~GwV~~~R~~G-kl~Fi~LrD~sg~iQvv~~~~-~~------------------~~~~~~~L~~esvV~V~G~v~   75 (583)
T TIGR00459        16 QTVTLAGWVNRRRDLG-GLIFIDLRDRSGIVQVVCDPD-AD------------------ALKLAKGLRNEDVVQVKGKVS   75 (583)
T ss_pred             CEEEEEEEEEEEEcCC-CcEEEEEEeCCccEEEEEeCC-HH------------------HHHHHhcCCCCCEEEEEEEEE
Confidence            4799999999998776 668899999999999986322 11                  011235688999999999997


Q ss_pred             e----------eCCceEEEEEEEEEcCC
Q 043474          117 S----------YRGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~----------f~~~~qi~~~~i~~v~d  134 (160)
                      .          =.+...|.+..+..+..
T Consensus        76 ~r~~~~~n~~~~tg~iEl~~~~i~iL~~  103 (583)
T TIGR00459        76 ARPEGNINRNLDTGEIEILAESITLLNK  103 (583)
T ss_pred             eCCccccCccCCCCcEEEEEeEEEEeec
Confidence            4          23567889998887543

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.

>COG3111 Periplasmic protein with OB-fold [Function unknown]

Probab=96.75  E-value=0.016  Score=41.40  Aligned_cols=71  Identities=13%  Similarity=0.154  Sum_probs=52.2

Q ss_pred             eeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           36 LSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      =..|.+.|-|+..-...    .|..-|+||+|.+-+=...-.                      -..+.+.+.|++.|.+
T Consensus        57 da~V~l~GnIv~qi~~D----~y~FrD~sGeI~VeIdd~~w~----------------------g~tv~P~dkV~I~Gev  110 (128)
T COG3111          57 DAWVSLEGNIVRQIGDD----RYVFRDASGEINVDIDDKVWN----------------------GQTVTPKDKVRIQGEV  110 (128)
T ss_pred             CCeEEEEeeEEEeeCCc----eEEEEcCCccEEEEecccccC----------------------CcccCcccEEEEEeEE
Confidence            36788889888865553    788999999988765322221                      1356788999999999


Q ss_pred             ceeCCceEEEEEEEEEc
Q 043474          116 ASYRGDVQITVSDVVIE  132 (160)
Q Consensus       116 ~~f~~~~qi~~~~i~~v  132 (160)
                      ..=-++..|.+.+|+.+
T Consensus       111 Dk~~~~~eIdV~~I~k~  127 (128)
T COG3111         111 DKDWNSVEIDVKHIEKL  127 (128)
T ss_pred             cCCCccceeEhhheEec
Confidence            87556778888888754

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.74  E-value=0.012  Score=53.33  Aligned_cols=68  Identities=18%  Similarity=0.308  Sum_probs=52.0

Q ss_pred             eEEEEEEEEEEeecc--CCceEEEEEeCCCceEEEEEeec-CccCCCCCCCCCCccccccccccccccccccCcEEEEEE
Q 043474           37 SRAEIVGTITSRDHK--PSKFIKFTVDDGTGCVPCVLWLN-HLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRG  113 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~--~~~~~~~~IdDgTG~I~~~~w~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G  113 (160)
                      ..+.+.|.|++....  ..+.+.+++.|+||.+.++.|.. ..-                     ....+++|+.+.|.|
T Consensus        60 ~~vtv~g~V~~~~~~~~~~~~~~v~l~D~tg~i~l~~F~~n~~~---------------------~~~~l~~G~~~~v~G  118 (681)
T PRK10917         60 EKVTVEGEVLSAEVVFGKRRRLTVTVSDGTGNLTLRFFNFNQPY---------------------LKKQLKVGKRVAVYG  118 (681)
T ss_pred             CEEEEEEEEEEEEEccCCceEEEEEEEECCeEEEEEEEccCcHH---------------------HHhhCCCCCEEEEEE
Confidence            578899998887533  22568999999999999987731 111                     235799999999999


Q ss_pred             EeceeCCceEEE
Q 043474          114 RIASYRGDVQIT  125 (160)
Q Consensus       114 ~v~~f~~~~qi~  125 (160)
                      +++.+++.+|+.
T Consensus       119 kv~~~~~~~qm~  130 (681)
T PRK10917        119 KVKRGKYGLEMV  130 (681)
T ss_pred             EEEecCCeEEEE
Confidence            999988877763

>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional

Probab=96.73  E-value=0.012  Score=53.48  Aligned_cols=81  Identities=14%  Similarity=0.279  Sum_probs=59.3

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      +.|+|.|+|.++.... +.+-+.|.|+||.|+|++-......                ...+....++.|+.|.|.|.|.
T Consensus        19 ~~V~l~GWV~~~R~~G-~l~FidLRD~~G~iQvV~~~~~~~~----------------~~~~~~~~L~~EsvV~V~G~v~   81 (706)
T PRK12820         19 REVCLAGWVDAFRDHG-ELLFIHLRDRNGFIQAVFSPEAAPA----------------DVYELAASLRAEFCVALQGEVQ   81 (706)
T ss_pred             CEEEEEEEEEEEEcCC-CcEEEEEEeCCccEEEEEeCCcCCH----------------HHHHHHhcCCCCCEEEEEeEEe
Confidence            5699999999998776 6688999999999999873221110                0011235789999999999998


Q ss_pred             ee----------CCceEEEEEEEEEcCC
Q 043474          117 SY----------RGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f----------~~~~qi~~~~i~~v~d  134 (160)
                      .-          .+...|.+.++..+..
T Consensus        82 ~r~~~~~n~~~~tg~iEl~~~~i~iL~~  109 (706)
T PRK12820         82 KRLEETENPHIETGDIEVFVRELSILAA  109 (706)
T ss_pred             ccCccccCCCCCCCcEEEEeeEEEEEec
Confidence            73          1557888888886644

>PTZ00385 lysyl-tRNA synthetase; Provisional

Probab=96.69  E-value=0.016  Score=52.35  Aligned_cols=82  Identities=16%  Similarity=0.223  Sum_probs=59.6

Q ss_pred             EEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           38 RAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        38 ~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      .|+|.|+|.++...+ +-..+.|.|+||.|+|++-.+...+              .+........+..|++|.|.|.+..
T Consensus       109 ~V~vaGrV~~~R~~G-k~~F~~LrD~~G~IQvv~~~~~~~~--------------~~~~~~~~~~l~~gdiV~V~G~v~~  173 (659)
T PTZ00385        109 TVRVAGRVTSVRDIG-KIIFVTIRSNGNELQVVGQVGEHFT--------------REDLKKLKVSLRVGDIIGADGVPCR  173 (659)
T ss_pred             EEEEEEEEEeeeccC-CeEEEEEEECCceEEEEEECCccCC--------------HHHHHHHHhCCCCCCEEEEEEEEEe
Confidence            499999999988776 6678899999999999985432100              0000011235889999999999876


Q ss_pred             e-CCceEEEEEEEEEcCC
Q 043474          118 Y-RGDVQITVSDVVIEKD  134 (160)
Q Consensus       118 f-~~~~qi~~~~i~~v~d  134 (160)
                      - .|...|.+..+..+..
T Consensus       174 t~~GeleI~~~~i~lLsk  191 (659)
T PTZ00385        174 MQRGELSVAASRMLILSP  191 (659)
T ss_pred             cCCceEEEEeeEEEEech
Confidence            5 4778888899887663

>PTZ00401 aspartyl-tRNA synthetase; Provisional

Probab=96.68  E-value=0.015  Score=51.51  Aligned_cols=82  Identities=15%  Similarity=0.259  Sum_probs=60.1

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +.+.+.|.|+||.|+|++-.....+              .++ .+....+..|++|.|.|.|.
T Consensus        79 ~~V~v~Grv~~~R~~G-k~~Fl~LRd~~~~iQ~v~~~~~~~~--------------~~~-~~~~~~l~~esiV~V~G~v~  142 (550)
T PTZ00401         79 KTVLIRARVSTTRKKG-KMAFMVLRDGSDSVQAMAAVEGDVP--------------KEM-IDFIGQIPTESIVDVEATVC  142 (550)
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEEeCCcCEEEEEECCCccC--------------HHH-HHHHhcCCCCCEEEEEEEEE
Confidence            5699999999998876 6688999999999999974322110              001 12335789999999999987


Q ss_pred             ee--------CCceEEEEEEEEEcCC
Q 043474          117 SY--------RGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f--------~~~~qi~~~~i~~v~d  134 (160)
                      .-        .+...|.+.++..+..
T Consensus       143 ~~~~~~~~~~~~~~El~v~~i~vls~  168 (550)
T PTZ00401        143 KVEQPITSTSHSDIELKVKKIHTVTE  168 (550)
T ss_pred             ecCccCCCCCCccEEEEeeEEEEEeC
Confidence            52        3457888888876643

>PRK00476 aspS aspartyl-tRNA synthetase; Validated

Probab=96.68  E-value=0.014  Score=52.13  Aligned_cols=78  Identities=17%  Similarity=0.308  Sum_probs=58.7

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+.|+|.++.... +.+-+.|.|+||.++|++-. . ..                . .+....+..|++|.|.|.|.
T Consensus        18 ~~V~l~GwV~~~R~~g-~l~Fi~LrD~~g~iQ~v~~~-~-~~----------------~-~~~~~~l~~es~V~V~G~v~   77 (588)
T PRK00476         18 QTVTLCGWVHRRRDHG-GLIFIDLRDREGIVQVVFDP-D-AE----------------A-FEVAESLRSEYVIQVTGTVR   77 (588)
T ss_pred             CEEEEEEEEEEEEeCC-CeEEEEEEeCCceEEEEEeC-C-HH----------------H-HHHHhCCCCCCEEEEEEEEE
Confidence            4599999999998776 67889999999999998732 1 10                0 11235688999999999998


Q ss_pred             ee----------CCceEEEEEEEEEcCC
Q 043474          117 SY----------RGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f----------~~~~qi~~~~i~~v~d  134 (160)
                      .-          .|...|.+.++..+..
T Consensus        78 ~~~~~~~n~~~~~g~~El~~~~i~il~~  105 (588)
T PRK00476         78 ARPEGTVNPNLPTGEIEVLASELEVLNK  105 (588)
T ss_pred             ecCCcccCccCCCCcEEEEEeEEEEEec
Confidence            63          3457888888876654

>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP)

Probab=96.64  E-value=0.022  Score=41.48  Aligned_cols=71  Identities=20%  Similarity=0.273  Sum_probs=53.9

Q ss_pred             eEEEEEEEEEEeec----cCC-ceEEEEEeCCCce----EEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH----KPS-KFIKFTVDDGTGC----VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~----~~~-~~~~~~IdDgTG~----I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..|.++|.|++...    +.+ -...|+|-|.|+.    +.+.+|.+..+                     ....+..|+
T Consensus        15 ~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~---------------------~LP~v~~GD   73 (138)
T cd04497          15 GSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEE---------------------SLPIVKVGD   73 (138)
T ss_pred             CeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChh---------------------hCCCCCCCC
Confidence            66778999998763    111 4478999999873    99999988754                     224458999


Q ss_pred             EEEEEEE-eceeCCceEEEEEE
Q 043474          108 VARVRGR-IASYRGDVQITVSD  128 (160)
Q Consensus       108 ~V~V~G~-v~~f~~~~qi~~~~  128 (160)
                      +|.+++- |+.|+|+.+.....
T Consensus        74 VIll~~~kv~~~~g~~~~~~~~   95 (138)
T cd04497          74 IILLRRVKIQSYNGKPQGISND   95 (138)
T ss_pred             EEEEEEEEEEEECCceEEEECC
Confidence            9999984 78999998876665

POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB

>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14)

Probab=96.62  E-value=0.081  Score=36.50  Aligned_cols=69  Identities=23%  Similarity=0.301  Sum_probs=47.2

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      +.|+++|.|.+....     .+++.+.-| .++|.+-.+.                          ....+.+|.|.|++
T Consensus        16 k~V~ivGkV~~~~~~-----~~~~~~~Dg~~v~v~l~~~~--------------------------~~~~~~~vEViG~V   64 (101)
T cd04479          16 KTVRIVGKVEKVDGD-----SLTLISSDGVNVTVELNRPL--------------------------DLPISGYVEVIGKV   64 (101)
T ss_pred             CEEEEEEEEEEecCC-----eEEEEcCCCCEEEEEeCCCC--------------------------CcccCCEEEEEEEE
Confidence            789999999997543     344555444 7888753221                          34578999999999


Q ss_pred             ceeCCceEEEEEEEEEcCCh-hHHH
Q 043474          116 ASYRGDVQITVSDVVIEKDP-NMEV  139 (160)
Q Consensus       116 ~~f~~~~qi~~~~i~~v~d~-n~~~  139 (160)
                      ..   ...|.+.......+. +.++
T Consensus        65 ~~---~~~I~~~~~~~~g~~~D~~~   86 (101)
T cd04479          65 SP---DLTIRVLSYIDFGDDFDMDL   86 (101)
T ss_pred             CC---CCeEEEEEEEECCCccCHHH
Confidence            85   456777777766653 4443

RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.

>PLN02850 aspartate-tRNA ligase

Probab=96.62  E-value=0.017  Score=51.00  Aligned_cols=83  Identities=20%  Similarity=0.291  Sum_probs=59.8

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +...+.|.|++|.|+|++-......             ..++ .+....+..|++|.|.|.|.
T Consensus        82 ~~V~v~Grv~~~R~~g-k~~Fl~Lrd~~~~iQ~v~~~~~~~~-------------~~~~-~~~~~~l~~es~V~V~G~v~  146 (530)
T PLN02850         82 SEVLIRGRVHTIRGKG-KSAFLVLRQSGFTVQCVVFVSEVTV-------------SKGM-VKYAKQLSRESVVDVEGVVS  146 (530)
T ss_pred             CEEEEEEEEEEEccCC-CeEEEEEEeCCcCEEEEEECCcccc-------------CHHH-HHHHhCCCCCCEEEEEEEEE
Confidence            6799999999998877 5678999999999999884332110             0011 12235789999999999998


Q ss_pred             e-------eCCceEEEEEEEEEcCC
Q 043474          117 S-------YRGDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~-------f~~~~qi~~~~i~~v~d  134 (160)
                      .       -.+...|.+.++..+..
T Consensus       147 ~~~~~~~~~t~~~El~~~~i~vls~  171 (530)
T PLN02850        147 VPKKPVKGTTQQVEIQVRKIYCVSK  171 (530)
T ss_pred             ccCcCCCCCCccEEEEEeEEEEEeC
Confidence            3       12347888888886654

>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70)

Probab=96.59  E-value=0.0064  Score=42.12  Aligned_cols=58  Identities=16%  Similarity=0.305  Sum_probs=42.8

Q ss_pred             eEEEEEEEEEEeec------c--CCceEEEEEeCC-CceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH------K--PSKFIKFTVDDG-TGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~--~~~~~~~~IdDg-TG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ...+|.|+|++...      .  +++.+.+.|-|. +|+|.|.+|.+...                    ...+.++.|+
T Consensus        10 ~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~--------------------~f~~~l~eG~   69 (104)
T cd04474          10 NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVD--------------------KFYDLLEVGK   69 (104)
T ss_pred             CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHH--------------------Hhhccccccc
Confidence            46788888886432      1  246679999999 88999999986532                    2446789999


Q ss_pred             EEEEEEE
Q 043474          108 VARVRGR  114 (160)
Q Consensus       108 ~V~V~G~  114 (160)
                      ++.+.|-
T Consensus        70 vy~i~~~   76 (104)
T cd04474          70 VYYISKG   76 (104)
T ss_pred             EEEEecc
Confidence            8888754

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]

Probab=96.58  E-value=0.02  Score=51.48  Aligned_cols=76  Identities=28%  Similarity=0.439  Sum_probs=60.6

Q ss_pred             EeeEEEEEEEEEEeecc---CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEE
Q 043474           35 LLSRAEIVGTITSRDHK---PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARV  111 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~~---~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V  111 (160)
                      +-..+.++|.|.+....   ..+.+.+++.|+||.|.++.++.+..                     ....++.|.-|.+
T Consensus        59 ~g~~vti~g~V~~~~~~~~~~~~~l~v~~~d~~~~l~l~fFn~~~~---------------------l~~~~~~G~~v~v  117 (677)
T COG1200          59 PGEIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPAY---------------------LKKKLKVGERVIV  117 (677)
T ss_pred             CCceEEEEEEEEeeeccCCCCCceEEEEEecCcEEEEEEEECccHH---------------------HHhhCCCCCEEEE
Confidence            34688999999888765   34668999999999999998876632                     2367899999999


Q ss_pred             EEEeceeCCceEEEEEEEEE
Q 043474          112 RGRIASYRGDVQITVSDVVI  131 (160)
Q Consensus       112 ~G~v~~f~~~~qi~~~~i~~  131 (160)
                      .|+++.|++..|+.--.+..
T Consensus       118 ~Gk~~~~~~~~~~~hpe~~~  137 (677)
T COG1200         118 YGKVKRFKGGLQITHPEYIV  137 (677)
T ss_pred             EEEEeeccCceEEEcceEEe
Confidence            99999999888776555444

>PRK02983 lysS lysyl-tRNA synthetase; Provisional

Probab=96.48  E-value=0.024  Score=54.11  Aligned_cols=81  Identities=17%  Similarity=0.288  Sum_probs=57.4

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|.++.... +..-+.|.|+||.|+|++=.+....               .........+..|++|.|+|.+.
T Consensus       652 ~~V~v~Grv~~~R~~G-~~~F~~lrD~~g~iQ~v~~~~~~~~---------------~~~~~~~~~l~~gd~V~v~G~v~  715 (1094)
T PRK02983        652 EEVSVSGRVLRIRDYG-GVLFADLRDWSGELQVLLDASRLEQ---------------GSLADFRAAVDLGDLVEVTGTMG  715 (1094)
T ss_pred             CEEEEEEEEEEEeeCC-CeEEEEEEeCCeeEEEEEECCccch---------------hhHHHHHhcCCCCCEEEEEEEEE
Confidence            4699999999998776 6788999999999999873322110               00001123578999999999986


Q ss_pred             ee-CCceEEEEEEEEEcC
Q 043474          117 SY-RGDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f-~~~~qi~~~~i~~v~  133 (160)
                      .- ++...|.+.+++.+.
T Consensus       716 ~t~~ge~ei~~~~i~ll~  733 (1094)
T PRK02983        716 TSRNGTLSLLVTSWRLAG  733 (1094)
T ss_pred             EcCCCCEEEEEeEEEEEe
Confidence            43 366778888776554

>PTZ00425 asparagine-tRNA ligase; Provisional

Probab=96.45  E-value=0.023  Score=50.76  Aligned_cols=95  Identities=9%  Similarity=0.136  Sum_probs=59.9

Q ss_pred             ccccccceehhhhhccCCCC--CCCceEECCeEeeEEEEEEEEEEeeccCC-ceEEEEEeCCCc--eEEEEEeecCccCC
Q 043474            5 LQNTHVKLLAFDLLSLTPTP--DPATFSRSGKLLSRAEIVGTITSRDHKPS-KFIKFTVDDGTG--CVPCVLWLNHLTSL   79 (160)
Q Consensus         5 ~~~~~~~l~i~~i~~l~~~~--~~~~~~~~~~~i~~v~ivG~V~~~~~~~~-~~~~~~IdDgTG--~I~~~~w~~~~~~~   79 (160)
                      ++.+-.++-|..++....++  ..+--......-..|+|.|+|.++....+ +.+.+.|.||||  .++|++- ....  
T Consensus        48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~Vtl~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv~-~~~~--  124 (586)
T PTZ00425         48 DRGCRSRIRICNVLNVPKSEKEFNDNSRKNKYIDQIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVD-QSIE--  124 (586)
T ss_pred             ccccccceeeehhccCccccccccccccccccCCCEEEEEEEEeehhhcCCceEEEEEEECCCCCcceEEEEC-CchH--
Confidence            34444566777777665444  11111111222357999999999987553 467889999999  4998762 1110  


Q ss_pred             CCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           80 YLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                                      .......+..|..|+|.|++..-
T Consensus       125 ----------------~~~~l~~l~~gs~v~v~G~v~~~  147 (586)
T PTZ00425        125 ----------------NYEKLLKCGVGCCFRFTGKLIIS  147 (586)
T ss_pred             ----------------HHHHHhcCCCccEEEEEEEEEcC
Confidence                            00122457899999999999753

>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type

Probab=96.44  E-value=0.022  Score=54.82  Aligned_cols=81  Identities=26%  Similarity=0.321  Sum_probs=62.7

Q ss_pred             EeeEEEEEEEEEEeeccC---C-ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEE
Q 043474           35 LLSRAEIVGTITSRDHKP---S-KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVAR  110 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~~~---~-~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~  110 (160)
                      +..+|.|.|.|-.++.++   + ..++|.|.|.|++|.|+.|......                  .+....++.|+.|+
T Consensus         6 ~~~~~~~~g~i~~~~~~~~~~~~~~~~~~~~d~~~s~~~k~f~~~~~~------------------~~~~~~~~~g~~~~   67 (1213)
T TIGR01405         6 EENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEED------------------PEKFDGIKIGKWVR   67 (1213)
T ss_pred             cCCeEEEEEEEEEEEeEeccCCCEEEEEEEEcCCCCEEEEEecccccc------------------hHHHhhcCCCcEEE
Confidence            346788999998887643   3 4458999999999999999865431                  12346789999999


Q ss_pred             EEEEec--eeCCceEEEEEEEEEcC
Q 043474          111 VRGRIA--SYRGDVQITVSDVVIEK  133 (160)
Q Consensus       111 V~G~v~--~f~~~~qi~~~~i~~v~  133 (160)
                      ++|++.  .|.+...+.+..|..+.
T Consensus        68 ~~g~~~~d~~~~~~~~~~~~~~~~~   92 (1213)
T TIGR01405        68 ARGKIELDNFSRDLQMIIKDIEEIP   92 (1213)
T ss_pred             EEEEEeccCCCCceEEEeeeeeecC
Confidence            999987  67788888888887653

The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.

>PRK05813 single-stranded DNA-binding protein; Provisional

Probab=96.42  E-value=0.05  Score=42.82  Aligned_cols=79  Identities=18%  Similarity=0.314  Sum_probs=57.3

Q ss_pred             EeeEEEEEEEEEEee-----ccCCceEEEEEe-----CCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccc
Q 043474           35 LLSRAEIVGTITSRD-----HKPSKFIKFTVD-----DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIK  104 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~-----~~~~~~~~~~Id-----DgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (160)
                      +..+|.++|.+++--     .....|..|+|.     |.+--|+|++|....+                     . ..+.
T Consensus         7 ~~NkV~L~Grl~~d~e~~~~~~G~~~~~f~laV~R~s~~~D~i~v~v~~rlae---------------------~-~~l~   64 (219)
T PRK05813          7 ENNKVYLEGKVVSELEFSHEMYGEGFYNFKLEVPRLSDSKDILPVTVSERLLA---------------------G-MDLK   64 (219)
T ss_pred             hcCEEEEEEEEcCCceEEEEeCCeEEEEEEEEeeccCCCccEEEEEEEhhhhh---------------------h-hccc
Confidence            457888899887622     222366677765     7788899999987754                     1 2389


Q ss_pred             cCcEEEEEEEeceeC----Cc----eEEEEEEEEEcCCh
Q 043474          105 IGLVARVRGRIASYR----GD----VQITVSDVVIEKDP  135 (160)
Q Consensus       105 ~G~~V~V~G~v~~f~----~~----~qi~~~~i~~v~d~  135 (160)
                      .|+.|.|.|++++|+    |+    ..+.+..|..++..
T Consensus        65 kG~~v~VeGqlrsy~~~~~G~~R~vl~V~a~~i~~l~~~  103 (219)
T PRK05813         65 VGTLVIVEGQLRSYNKFIDGKNRLILTVFARNIEYCDER  103 (219)
T ss_pred             CCCEEEEEEEEEEeccCCCCcEEEEEEEEEEEEEEccCC
Confidence            999999999999994    32    35677778877754

>PRK00448 polC DNA polymerase III PolC; Validated

Probab=96.42  E-value=0.023  Score=55.49  Aligned_cols=82  Identities=20%  Similarity=0.282  Sum_probs=63.4

Q ss_pred             eeEEEEEEEEEEeeccC---C-ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEE
Q 043474           36 LSRAEIVGTITSRDHKP---S-KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARV  111 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~~---~-~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V  111 (160)
                      ..+|.|-|.|-.++.++   + ..++|.|.|.|++|.|+.|......                  .+....++.|++|+|
T Consensus       236 ~~~v~i~G~if~~e~~~~k~~~~~~~~~~td~~~s~~~k~f~~~~~~------------------~~~~~~~~~g~~v~~  297 (1437)
T PRK00448        236 ERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKED------------------LKKFDEIKKGDWVKV  297 (1437)
T ss_pred             CCeEEEEEEEEEEEEEeccCCCEEEEEEEEcCCCCEEEEEEecCcch------------------hHHHhcCCCCCEEEE
Confidence            36889999999988644   2 3468999999999999999855431                  123467999999999


Q ss_pred             EEEec--eeCCceEEEEEEEEEcCCh
Q 043474          112 RGRIA--SYRGDVQITVSDVVIEKDP  135 (160)
Q Consensus       112 ~G~v~--~f~~~~qi~~~~i~~v~d~  135 (160)
                      +|++.  .|.+...+.+..|..+..+
T Consensus       298 ~g~~~~d~~~~~~~~~~~~~~~~~~~  323 (1437)
T PRK00448        298 RGSVQNDTFTRDLVMNAQDINEIKHP  323 (1437)
T ss_pred             EEEEeccCCCCceEEEeeeeeecCCc
Confidence            99997  4777888888888766544

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.37  E-value=0.023  Score=51.10  Aligned_cols=67  Identities=25%  Similarity=0.341  Sum_probs=50.3

Q ss_pred             eEEEEEEEEEEeec---cCCceEEEEEeC-CCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTITSRDH---KPSKFIKFTVDD-GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~~~~---~~~~~~~~~IdD-gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ..+.+.|.|.+...   +..+.+.+.+.| +||.+.++.|....                      ....+++|+.+.+.
T Consensus        33 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~F~~~~----------------------~~~~~~~g~~~~~~   90 (630)
T TIGR00643        33 ERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNRAF----------------------LKKKFKVGSKVVVY   90 (630)
T ss_pred             CEEEEEEEEEEeEeccCCCCceEEEEEEECCCCEEEEEEECCHH----------------------HHhhCCCCCEEEEE
Confidence            56778888776431   112458999999 99999998875221                      23578999999999


Q ss_pred             EEeceeCCceEEE
Q 043474          113 GRIASYRGDVQIT  125 (160)
Q Consensus       113 G~v~~f~~~~qi~  125 (160)
                      |+++.|++..|+.
T Consensus        91 Gk~~~~~~~~~~~  103 (630)
T TIGR00643        91 GKVKSSKFKAYLI  103 (630)
T ss_pred             EEEEeeCCEEEEE
Confidence            9999998877653

>PLN02603 asparaginyl-tRNA synthetase

Probab=96.31  E-value=0.032  Score=49.71  Aligned_cols=78  Identities=22%  Similarity=0.365  Sum_probs=56.0

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCc--eEEEEEeecCccCCCCCCCCCCcccccccccccccc--ccccCcEEEEE
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTG--CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAA--KIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG--~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~G~~V~V~  112 (160)
                      ..|+|.|+|.++.... +..-+.|.||||  .|+|++= .....                  .....  .+..|+.|.|.
T Consensus       108 ~~V~v~GwV~~iR~~g-~~~Fi~l~Dgs~~~~lQ~v~~-~~~~~------------------~~~l~~~~l~~gs~V~V~  167 (565)
T PLN02603        108 KTLNVMGWVRTLRAQS-SVTFIEVNDGSCLSNMQCVMT-PDAEG------------------YDQVESGLITTGASVLVQ  167 (565)
T ss_pred             CEEEEEEEEEEEEeCC-CeEEEEEECCCCCEeEEEEEE-CcHHH------------------HHHHhhcCCCCCCEEEEE
Confidence            6799999999998665 667899999997  4999872 21110                  00111  38899999999


Q ss_pred             EEeceeCC---ceEEEEEEEEEcCC
Q 043474          113 GRIASYRG---DVQITVSDVVIEKD  134 (160)
Q Consensus       113 G~v~~f~~---~~qi~~~~i~~v~d  134 (160)
                      |.+..=.+   ...|.+.++..+..
T Consensus       168 G~v~~~~~~~~~~EL~v~~i~vlg~  192 (565)
T PLN02603        168 GTVVSSQGGKQKVELKVSKIVVVGK  192 (565)
T ss_pred             EEEEecCCCCccEEEEEeEEEEEEC
Confidence            99976433   26788888876654

>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair

Probab=96.28  E-value=0.11  Score=36.26  Aligned_cols=82  Identities=17%  Similarity=0.175  Sum_probs=46.7

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      +.|+|+|.|.+....+ .  .++++-+.| .+.|..-.+                          .....+.+|.|.|++
T Consensus        19 k~VrivGkv~~~~~~g-~--~~~l~~~d~~~V~v~l~~~--------------------------~~~~~~~~vEviG~V   69 (109)
T PF08661_consen   19 KTVRIVGKVESVDPDG-G--SATLSTSDGGQVTVSLNPP--------------------------SDEELSKYVEVIGKV   69 (109)
T ss_dssp             SEEEEEEEEEEE-TTS-S--EEEEE-TTS-EEEEEESS----------------------------SS---SEEEEEEEE
T ss_pred             CeEEEEEEEeeEcCCC-C--EEEEEcCCCCEEEEEeCCC--------------------------CCCCCCCEEEEEEEE
Confidence            6899999999987444 3  567775553 577765211                          123468999999999


Q ss_pred             ceeCCceEEEEEEEEEcCChhHHHHHHHHHHHH
Q 043474          116 ASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRL  148 (160)
Q Consensus       116 ~~f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~  148 (160)
                      ..-.+-..|.........+ +.++.-+-+++.+
T Consensus        70 ~~~~~~~~i~~~~~~~~g~-~~D~~~y~~lv~l  101 (109)
T PF08661_consen   70 NDDGTVLSIRYFSFTDFGD-DFDMDLYNELVQL  101 (109)
T ss_dssp             -TTS-EEEEEEEE---SSS----HHHHHHHHHH
T ss_pred             cCCCCceEEEEEEeccCCC-CcCHHHHHHHHHH
Confidence            9876656788877776664 4444455555554

; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.

>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70)

Probab=96.17  E-value=0.048  Score=37.17  Aligned_cols=66  Identities=17%  Similarity=0.337  Sum_probs=42.7

Q ss_pred             EEEEEEEEEeec----------cCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           39 AEIVGTITSRDH----------KPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        39 v~ivG~V~~~~~----------~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      |-++|.|.++..          +......++|.|.|| .|+|.+|.+....                    .  ..+.|+
T Consensus         2 vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~--------------------~--~~~~~~   59 (101)
T cd04475           2 VDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAEL--------------------F--DGSENP   59 (101)
T ss_pred             EeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhh--------------------c--ccCCCC
Confidence            345666666542          223457899999999 8999999876541                    0  111288


Q ss_pred             EEEEEEE-eceeCCceEEEEE
Q 043474          108 VARVRGR-IASYRGDVQITVS  127 (160)
Q Consensus       108 ~V~V~G~-v~~f~~~~qi~~~  127 (160)
                      ++.+.|- ++.|+ .+.+...
T Consensus        60 vv~~~~~~i~~~~-~~~l~~~   79 (101)
T cd04475          60 VIAIKGVKVSEFN-GKSLSTG   79 (101)
T ss_pred             EEEEEeeEEEecC-CeEEeec
Confidence            8887774 56777 4566553

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona

>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]

Probab=95.94  E-value=0.056  Score=47.14  Aligned_cols=79  Identities=16%  Similarity=0.290  Sum_probs=58.5

Q ss_pred             EEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           39 AEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        39 v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      |.+.|+|..+...+ +-..++|+|.+|.|+.-+-.+....               .........+.+||+|.|.|.+-.-
T Consensus        64 v~vAGRi~~~R~~G-K~~F~~i~d~~gkiQ~yi~k~~~~~---------------~~~~~~~~~~dlGDiigv~G~~~~T  127 (502)
T COG1190          64 VSVAGRIMTIRNMG-KASFADLQDGSGKIQLYVNKDEVGE---------------EVFEALFKKLDLGDIIGVEGPLFKT  127 (502)
T ss_pred             eEEecceeeecccC-ceeEEEEecCCceEEEEEeccccch---------------hhHHHHHhccccCCEEeeeeeeeec
Confidence            99999999988776 6678999999999998775443211               0001123456799999999998765


Q ss_pred             C-CceEEEEEEEEEcC
Q 043474          119 R-GDVQITVSDVVIEK  133 (160)
Q Consensus       119 ~-~~~qi~~~~i~~v~  133 (160)
                      + |...+.+..++.++
T Consensus       128 ~~GelSv~v~~~~lLs  143 (502)
T COG1190         128 KTGELSVSVEELRLLS  143 (502)
T ss_pred             CCCceEEEEEEEeeec
Confidence            5 88888888877554

>PRK08402 replication factor A; Reviewed

Probab=95.89  E-value=0.024  Score=47.75  Aligned_cols=88  Identities=20%  Similarity=0.248  Sum_probs=54.6

Q ss_pred             EEEEEeCCCceEEEEEeecCccCCCCCCCCCCccc-ccc---cc--ccc--------cccccccCcEEEEEEEec--eeC
Q 043474           56 IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVR-LIA---GV--ATD--------FAAKIKIGLVARVRGRIA--SYR  119 (160)
Q Consensus        56 ~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~-~~~---~~--~~~--------~~~~~~~G~~V~V~G~v~--~f~  119 (160)
                      +.+.|+|+||.+.|.+|.+.......  -+.-.+. +..   +.  ..+        ....--.|....++|+++  .|+
T Consensus       247 l~~~l~D~TG~~~vt~f~e~ae~llG--~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~  324 (355)
T PRK08402        247 LDFGLDDGTGYIRVTLFGDDAAELLG--VEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFL  324 (355)
T ss_pred             EEEEEEcCCCcEEEEEecHHHHHHhC--CCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccC
Confidence            57889999999999999887643110  0000000 000   00  000        000123589999999987  587


Q ss_pred             CceEEEEEEEEEcCChhHHHHHHHHHHH
Q 043474          120 GDVQITVSDVVIEKDPNMEVLHWLDCLR  147 (160)
Q Consensus       120 ~~~qi~~~~i~~v~d~n~~~~h~le~~~  147 (160)
                      +.. +.+..+.|++ +..|+.+.++-+.
T Consensus       325 ~~~-~~v~~~~~vd-~~~e~~~l~~~i~  350 (355)
T PRK08402        325 GLI-LKASSWDEVD-YKREIERVRAELE  350 (355)
T ss_pred             CeE-EEEEEcccCC-HHHHHHHHHHHHH
Confidence            754 8888899866 8888888887775

>PRK07275 single-stranded DNA-binding protein; Provisional

Probab=95.75  E-value=0.083  Score=39.68  Aligned_cols=80  Identities=21%  Similarity=0.447  Sum_probs=53.0

Q ss_pred             eeEEEEEEEEEE-ee----ccCCceEEEEEe------C--C---CceEEEEEeecCccCCCCCCCCCCcccccccccccc
Q 043474           36 LSRAEIVGTITS-RD----HKPSKFIKFTVD------D--G---TGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF   99 (160)
Q Consensus        36 i~~v~ivG~V~~-~~----~~~~~~~~~~Id------D--g---TG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (160)
                      +..|.|+|.+.. .+    ........|+|.      +  |   |--|.|++|.+..+.                    .
T Consensus         2 ~N~v~LiGrL~~DPElr~t~sG~~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae~--------------------~   61 (162)
T PRK07275          2 INNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAEN--------------------L   61 (162)
T ss_pred             eeEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHH--------------------H
Confidence            456778887775 11    112255666663      2  2   334999999876431                    3


Q ss_pred             ccccccCcEEEEEEEec--eeCC-------ceEEEEEEEEEcCCh
Q 043474          100 AAKIKIGLVARVRGRIA--SYRG-------DVQITVSDVVIEKDP  135 (160)
Q Consensus       100 ~~~~~~G~~V~V~G~v~--~f~~-------~~qi~~~~i~~v~d~  135 (160)
                      ...++.|+.|-|.|+++  .|.+       ..+|.+.+|..+...
T Consensus        62 ~~~l~KG~~V~VeGrl~~r~y~dkdG~k~~~~evva~~i~~l~~~  106 (162)
T PRK07275         62 ANWAKKGALIGVTGRIQTRNYENQQGQRVYVTEVVADNFQMLESR  106 (162)
T ss_pred             HHHcCCCCEEEEEEEEEeceEECCCCCEEEEEEEEEeEEEECCCC
Confidence            46789999999999996  4644       246888888877644

>PRK02801 primosomal replication protein N; Provisional

Probab=95.73  E-value=0.1  Score=36.00  Aligned_cols=63  Identities=19%  Similarity=0.353  Sum_probs=40.8

Q ss_pred             eEEEEEEEEEEeec-----cCCceEEEEEeC-----CCce-------EEEEEeecCccCCCCCCCCCCcccccccccccc
Q 043474           37 SRAEIVGTITSRDH-----KPSKFIKFTVDD-----GTGC-------VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF   99 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-----~~~~~~~~~IdD-----gTG~-------I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (160)
                      .++.++|.++.-.+     ...+++.|+|.=     .+|-       |+|+.|.+..+.                    .
T Consensus         3 N~v~L~Grl~~dpelr~Tp~G~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~--------------------~   62 (101)
T PRK02801          3 NRLVLSGTVCRTPKRKVSPSGIPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQA--------------------I   62 (101)
T ss_pred             cEEEEEEEECcCcceEECCCCCeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHH--------------------H
Confidence            56777777766321     112455555542     2233       889999866541                    2


Q ss_pred             ccccccCcEEEEEEEeceeC
Q 043474          100 AAKIKIGLVARVRGRIASYR  119 (160)
Q Consensus       100 ~~~~~~G~~V~V~G~v~~f~  119 (160)
                      ...++.|..|.|.|+++.|.
T Consensus        63 ~~~l~kGs~v~V~G~L~~~~   82 (101)
T PRK02801         63 TQSITVGSKITVQGFISCHQ   82 (101)
T ss_pred             HhhcCCCCEEEEEEEEEEeE
Confidence            34689999999999999854

>PRK08486 single-stranded DNA-binding protein; Provisional

Probab=95.70  E-value=0.1  Score=39.94  Aligned_cols=79  Identities=14%  Similarity=0.188  Sum_probs=51.2

Q ss_pred             eeEEEEEEEEEEee-----ccCCceEEEEEe-------------CCCceEEEEEeecCccCCCCCCCCCCcccccccccc
Q 043474           36 LSRAEIVGTITSRD-----HKPSKFIKFTVD-------------DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        36 i~~v~ivG~V~~~~-----~~~~~~~~~~Id-------------DgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      +..|.|+|.+..--     .....++.|+|.             +.|--|+|++|....+.                   
T Consensus         2 ~N~V~LvGrL~~DPElr~t~sG~~va~fslAv~r~~~~~~Ge~~e~t~fi~v~~fg~~AE~-------------------   62 (182)
T PRK08486          2 FNKVILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEI-------------------   62 (182)
T ss_pred             eeEEEEEEEecCCCEEEECCCCCEEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHHH-------------------
Confidence            35677777776521     111255666662             23445899999765431                   


Q ss_pred             ccccccccCcEEEEEEEec--eeCCc-------eEEEEEEEEEcCC
Q 043474           98 DFAAKIKIGLVARVRGRIA--SYRGD-------VQITVSDVVIEKD  134 (160)
Q Consensus        98 ~~~~~~~~G~~V~V~G~v~--~f~~~-------~qi~~~~i~~v~d  134 (160)
                       ....++.|+.|-|.|+|+  .|.++       ..|.+..|..+..
T Consensus        63 -~~~~l~KG~~V~VeGrL~~~~y~dkdG~~r~~~eI~a~~v~~L~~  107 (182)
T PRK08486         63 -ANQYLSKGSKVLIEGRLTFESWMDQNGQKRSKHTITAESMQMLDS  107 (182)
T ss_pred             -HHHHcCCCCEEEEEEEEEeCcEECCCCcEEEEEEEEEeEEEECCC
Confidence             235789999999999996  46442       4688888887654

>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70)

Probab=95.66  E-value=0.058  Score=37.25  Aligned_cols=63  Identities=25%  Similarity=0.396  Sum_probs=39.9

Q ss_pred             CceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEE-E-EEeceeCCceEE----E
Q 043474           53 SKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARV-R-GRIASYRGDVQI----T  125 (160)
Q Consensus        53 ~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V-~-G~v~~f~~~~qi----~  125 (160)
                      +....|+|.|.+| .++|.+|.+....          .      ..........+-+|-+ . .+|+.|+|.+-+    .
T Consensus        22 ~~kr~~~i~D~~~~~l~~tlwG~~A~~----------f------~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls~~~~   85 (106)
T cd04481          22 SRKLDFEIRDLSDERLKCTLWGEYAEE----------F------DAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLSNSFG   85 (106)
T ss_pred             ceEEEEEEEeCCCCEEEEEEEHHHHHH----------H------HHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEEcCCC
Confidence            3568999999998 5999999876531          0      0000002345666655 3 689999986544    4


Q ss_pred             EEEEEE
Q 043474          126 VSDVVI  131 (160)
Q Consensus       126 ~~~i~~  131 (160)
                      +.++..
T Consensus        86 ~s~v~i   91 (106)
T cd04481          86 ASKVYI   91 (106)
T ss_pred             ceEEEE
Confidence            455553

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.

>PRK06751 single-stranded DNA-binding protein; Provisional

Probab=95.57  E-value=0.11  Score=39.55  Aligned_cols=79  Identities=27%  Similarity=0.522  Sum_probs=51.4

Q ss_pred             eeEEEEEEEEEE-ee----ccCCceEEEEEe------CCCc-----eEEEEEeecCccCCCCCCCCCCcccccccccccc
Q 043474           36 LSRAEIVGTITS-RD----HKPSKFIKFTVD------DGTG-----CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF   99 (160)
Q Consensus        36 i~~v~ivG~V~~-~~----~~~~~~~~~~Id------DgTG-----~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (160)
                      +..|.|+|+|.. .+    .....++.|+|.      +..|     -+.|++|.+..+                    ..
T Consensus         2 mN~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae--------------------~~   61 (173)
T PRK06751          2 MNRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAE--------------------NV   61 (173)
T ss_pred             ceEEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHH--------------------HH
Confidence            356778888775 11    111256677773      3323     499999987543                    13


Q ss_pred             ccccccCcEEEEEEEece--eCC-------ceEEEEEEEEEcCC
Q 043474          100 AAKIKIGLVARVRGRIAS--YRG-------DVQITVSDVVIEKD  134 (160)
Q Consensus       100 ~~~~~~G~~V~V~G~v~~--f~~-------~~qi~~~~i~~v~d  134 (160)
                      ...++.|+.|.|.|+|+.  |.+       ..+|.+..|..++.
T Consensus        62 ~~~l~KG~~V~VeGrL~~r~yedkdG~~~~~~eVva~~i~~l~~  105 (173)
T PRK06751         62 ANYLKKGSLAGVDGRLQTRNYEGQDGKRVYVTEVLAESVQFLEP  105 (173)
T ss_pred             HHHcCCCCEEEEEEEEEeCccCCCCCcEEEEEEEEEEEEEeCcC
Confidence            457899999999999975  643       24677777776653

>PRK08763 single-stranded DNA-binding protein; Provisional

Probab=95.49  E-value=0.14  Score=38.59  Aligned_cols=79  Identities=11%  Similarity=0.216  Sum_probs=51.7

Q ss_pred             eeEEEEEEEEEEe---e--ccCCceEEEEEe------CCCc-------eEEEEEeecCccCCCCCCCCCCcccccccccc
Q 043474           36 LSRAEIVGTITSR---D--HKPSKFIKFTVD------DGTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        36 i~~v~ivG~V~~~---~--~~~~~~~~~~Id------DgTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      +..|.|+|.+.+-   .  .....++.|+|.      |..|       -+.|++|....+                    
T Consensus         5 ~Nkv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae--------------------   64 (164)
T PRK08763          5 INKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGE--------------------   64 (164)
T ss_pred             ceEEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHH--------------------
Confidence            6788888988772   1  112366667665      2222       288899975432                    


Q ss_pred             ccccccccCcEEEEEEEece--eCC-------ceEEEEEEEEEcCC
Q 043474           98 DFAAKIKIGLVARVRGRIAS--YRG-------DVQITVSDVVIEKD  134 (160)
Q Consensus        98 ~~~~~~~~G~~V~V~G~v~~--f~~-------~~qi~~~~i~~v~d  134 (160)
                      .....++.|+.|.|.|+|+.  |.+       ..+|.+..|..+..
T Consensus        65 ~v~~~L~KGs~V~VeGrL~~~~y~dkdG~kr~~~eIva~~i~~L~~  110 (164)
T PRK08763         65 IAGEYLRKGSQCYIEGSIRYDKFTGQDGQERYVTEIVADEMQMLGG  110 (164)
T ss_pred             HHHHhcCCCCEEEEEEEEEeceeECCCCCEEEEEEEEEeEEEECCC
Confidence            12356899999999999875  633       24677788876653

>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []

Probab=95.46  E-value=0.32  Score=35.60  Aligned_cols=74  Identities=16%  Similarity=0.245  Sum_probs=53.9

Q ss_pred             EeeEEEEEEEEEEeecc------CCc-eEEEEEeCCCc--------eEEEEEeecCccCCCCCCCCCCcccccccccccc
Q 043474           35 LLSRAEIVGTITSRDHK------PSK-FIKFTVDDGTG--------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF   99 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~~------~~~-~~~~~IdDgTG--------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (160)
                      .-..+.++|.|+....-      .+. .++++|-|.|-        .|.|.++.+..+                     .
T Consensus        11 ~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~---------------------~   69 (146)
T PF02765_consen   11 FGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKE---------------------S   69 (146)
T ss_dssp             SSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHH---------------------H
T ss_pred             CCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHH---------------------H
Confidence            34678888999887533      222 36899999983        699999977654                     1


Q ss_pred             cccccc-CcEEEEE-EEeceeCCceEEEEEEE
Q 043474          100 AAKIKI-GLVARVR-GRIASYRGDVQITVSDV  129 (160)
Q Consensus       100 ~~~~~~-G~~V~V~-G~v~~f~~~~qi~~~~i  129 (160)
                      ...++. ||+|++. =+|+.|+++.|+....-
T Consensus        70 LP~v~~~GDii~l~r~kv~~~~~~~~~~~~~~  101 (146)
T PF02765_consen   70 LPNVKSVGDIIRLRRVKVQSYNGKPQGLSNST  101 (146)
T ss_dssp             SCTTCSTTHEEEEEEEEEEEETTEEEEEEECE
T ss_pred             CCCCCCCCCEEEEEEEEEEEECCEEEEEecCC
Confidence            234555 9999998 67999999998776544

It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....

>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=95.45  E-value=0.068  Score=45.78  Aligned_cols=76  Identities=16%  Similarity=0.229  Sum_probs=58.1

Q ss_pred             EeeEEEEEEEEEEeecc-CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEE
Q 043474           35 LLSRAEIVGTITSRDHK-PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRG  113 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~~-~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G  113 (160)
                      +.+..+++|.|...-.. ++....+.+.|++|.|.|..+.+....                  ......+.+|+.|.+.|
T Consensus       265 ~~~~~~v~g~v~~~p~~ieGghv~v~i~d~~G~I~~~A~eptk~f------------------r~~a~~L~pGD~i~~~G  326 (421)
T COG1571         265 DYSKYRVVGRVEAEPRAIEGGHVVVEITDGEGEIGAVAFEPTKEF------------------RELARKLIPGDEITVYG  326 (421)
T ss_pred             hccceEEEEEEecccEEeeCCEEEEEecCCCceEEEEEecccccc------------------hHHHHhcCCCCEEEEec
Confidence            45778888888775432 345579999999999999999877541                  23457899999999999


Q ss_pred             EeceeCCceEEEEEEEEEc
Q 043474          114 RIASYRGDVQITVSDVVIE  132 (160)
Q Consensus       114 ~v~~f~~~~qi~~~~i~~v  132 (160)
                      .++...    |++++++.+
T Consensus       327 ~~~~~~----~n~ek~~v~  341 (421)
T COG1571         327 SVKPGT----LNLEKFQVL  341 (421)
T ss_pred             Cccccc----eeEEEEEEE
Confidence            998865    777777654

>PTZ00417 lysine-tRNA ligase; Provisional

Probab=95.38  E-value=0.15  Score=45.73  Aligned_cols=83  Identities=13%  Similarity=0.150  Sum_probs=56.1

Q ss_pred             EEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           38 RAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        38 ~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      .|+|.|+|.++.....+..-+.|.|.+|.|+|++-.+.....        +     +........+..|+.|.|.|.+..
T Consensus       134 ~v~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~--------~-----~~~~~~~~~l~~Gd~V~V~G~~~~  200 (585)
T PTZ00417        134 ILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHT--------K-----SNFAECYDKIRRGDIVGIVGFPGK  200 (585)
T ss_pred             eEEEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCC--------H-----HHHHHHHhcCCCCCEEEEEeEEcC
Confidence            489999999998765344677887888999998743211100        0     000011245889999999999765


Q ss_pred             e-CCceEEEEEEEEEcC
Q 043474          118 Y-RGDVQITVSDVVIEK  133 (160)
Q Consensus       118 f-~~~~qi~~~~i~~v~  133 (160)
                      - .|...|.+.++..+.
T Consensus       201 t~~gel~i~~~~i~lls  217 (585)
T PTZ00417        201 SKKGELSIFPKETIILS  217 (585)
T ss_pred             CCCceEEEEEEEEEEEe
Confidence            4 477888888887655

>PRK07459 single-stranded DNA-binding protein; Provisional

Probab=95.33  E-value=0.064  Score=38.29  Aligned_cols=78  Identities=17%  Similarity=0.246  Sum_probs=52.8

Q ss_pred             eeEEEEEEEEEEe---e--ccCCceEEEEEe-------CCCceEEEEEeecCccCCCCCCCCCCcccccccccccccccc
Q 043474           36 LSRAEIVGTITSR---D--HKPSKFIKFTVD-------DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKI  103 (160)
Q Consensus        36 i~~v~ivG~V~~~---~--~~~~~~~~~~Id-------DgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (160)
                      +..|.|+|.+..-   .  ..+..++.|+|.       +.|-=++|++|.+..+.                    ....+
T Consensus         3 ~N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~--------------------~~~~l   62 (121)
T PRK07459          3 LNSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQV--------------------AADYV   62 (121)
T ss_pred             ccEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHH--------------------HHHHc
Confidence            3567788887762   1  122256777776       45666999999865431                    23568


Q ss_pred             ccCcEEEEEEEec--eeCC----c----eEEEEEEEEEcC
Q 043474          104 KIGLVARVRGRIA--SYRG----D----VQITVSDVVIEK  133 (160)
Q Consensus       104 ~~G~~V~V~G~v~--~f~~----~----~qi~~~~i~~v~  133 (160)
                      +.|+.|.|.|+++  .|.+    +    ..|.+.+|..++
T Consensus        63 ~KG~~V~V~G~l~~~~~~d~d~G~~r~~~ei~a~~i~~L~  102 (121)
T PRK07459         63 KKGSLIGITGSLKFDRWTDRNTGEDRSKPVIRVDRLELLG  102 (121)
T ss_pred             CCCCEEEEEEEEEecceEcCCCCeEEEEEEEEEeEEEECc
Confidence            9999999999987  4643    1    357788888665

>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]

Probab=95.17  E-value=0.049  Score=51.89  Aligned_cols=81  Identities=19%  Similarity=0.257  Sum_probs=64.3

Q ss_pred             EeeEEEEEEEEEEeeccC---C-ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEE
Q 043474           35 LLSRAEIVGTITSRDHKP---S-KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVAR  110 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~~~---~-~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~  110 (160)
                      +..+|.+.|.|=.++.++   + .-+.+.+-|+|-++.|+.|.+..+                  +.+....++.|+.|+
T Consensus       238 ~~~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~Sl~~k~f~~~~e------------------d~~~~~~ik~g~wvk  299 (1444)
T COG2176         238 EETRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTSSLILKKFLRDEE------------------DEKKFDGIKKGMWVK  299 (1444)
T ss_pred             cccceEEEEEEEEEeeeecccCcEEEEEEEecCchheeehhhccccc------------------cHHHHhhcccCcEEE
Confidence            346699999999888544   2 457899999999999999988543                  234567899999999


Q ss_pred             EEEEece--eCCceEEEEEEEEEcC
Q 043474          111 VRGRIAS--YRGDVQITVSDVVIEK  133 (160)
Q Consensus       111 V~G~v~~--f~~~~qi~~~~i~~v~  133 (160)
                      ++|.|+.  |.+..++.+..|.++.
T Consensus       300 ~~g~v~~d~f~~~l~m~i~~I~ei~  324 (1444)
T COG2176         300 ARGNVQLDTFTRDLTMIINDINEIE  324 (1444)
T ss_pred             EEEEEEecccccceEEEhhhhhhhh
Confidence            9999975  6777888888877664

>PRK08182 single-stranded DNA-binding protein; Provisional

Probab=95.17  E-value=0.18  Score=37.29  Aligned_cols=47  Identities=21%  Similarity=0.410  Sum_probs=33.2

Q ss_pred             EEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece--eCCc-------eEEEEEEEEEcC
Q 043474           67 VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS--YRGD-------VQITVSDVVIEK  133 (160)
Q Consensus        67 I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~--f~~~-------~qi~~~~i~~v~  133 (160)
                      ++|++|....+                    .....++.|+.|-|.|+++.  |.++       ..|.+..|..+.
T Consensus        56 ~~V~~wg~~Ae--------------------~v~~~l~KG~~V~V~GrL~~~~w~dkdG~~r~~~eI~a~~i~~l~  111 (148)
T PRK08182         56 APVELWHRDAE--------------------HWARLYQKGMRVLVEGRMERDEWTDNEDNERVTFKVEARRVGILP  111 (148)
T ss_pred             EEEEEEhHHHH--------------------HHHHhcCCCCEEEEEEEEEecccCCCCCCEEEEEEEEEeEEEEcC
Confidence            88999986543                    12356899999999999864  6432       356777777644

>PRK06752 single-stranded DNA-binding protein; Validated

Probab=95.16  E-value=0.19  Score=35.21  Aligned_cols=79  Identities=16%  Similarity=0.447  Sum_probs=49.3

Q ss_pred             eEEEEEEEEEEee-----ccCCceEEEEEe------CC-----CceEEEEEeecCccCCCCCCCCCCccccccccccccc
Q 043474           37 SRAEIVGTITSRD-----HKPSKFIKFTVD------DG-----TGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFA  100 (160)
Q Consensus        37 ~~v~ivG~V~~~~-----~~~~~~~~~~Id------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (160)
                      ..|.|+|.+..--     .....++.|+|.      |.     |--+.|++|....+.                    ..
T Consensus         3 N~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~--------------------~~   62 (112)
T PRK06752          3 NRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAEN--------------------VT   62 (112)
T ss_pred             eEEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHH--------------------HH
Confidence            4566777766511     111255566654      22     234889999865431                    23


Q ss_pred             cccccCcEEEEEEEece--eCCc-------eEEEEEEEEEcCCh
Q 043474          101 AKIKIGLVARVRGRIAS--YRGD-------VQITVSDVVIEKDP  135 (160)
Q Consensus       101 ~~~~~G~~V~V~G~v~~--f~~~-------~qi~~~~i~~v~d~  135 (160)
                      ..++.|+.|-|.|+++.  |.++       .+|.+.+|..++..
T Consensus        63 ~~l~KG~~V~V~G~l~~~~~~~~~G~~~~~~ei~a~~i~~l~~~  106 (112)
T PRK06752         63 EYCTKGSLVGITGRIHTRNYEDDQGKRIYITEVVIESITFLERR  106 (112)
T ss_pred             HhcCCCCEEEEEEEEEeCccCCCCCcEEEEEEEEEEEEEECCCC
Confidence            56899999999999875  5432       35778888766533

>PRK06293 single-stranded DNA-binding protein; Provisional

Probab=95.07  E-value=0.23  Score=37.34  Aligned_cols=79  Identities=19%  Similarity=0.320  Sum_probs=51.6

Q ss_pred             eEEEEEEEEEEe-e----ccCCceEEEEEe--------CCCceEEEEEeecCccCCCCCCCCCCcccccccccccccccc
Q 043474           37 SRAEIVGTITSR-D----HKPSKFIKFTVD--------DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKI  103 (160)
Q Consensus        37 ~~v~ivG~V~~~-~----~~~~~~~~~~Id--------DgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (160)
                      ..|.|+|.+..= +    .....++.|+|.        +.|-=+.|++|.+..+.                    ....+
T Consensus         2 N~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~--------------------v~~yL   61 (161)
T PRK06293          2 MFGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDK--------------------MLPYL   61 (161)
T ss_pred             eEEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHH--------------------HHHhC
Confidence            356777777651 1    112256666665        23445999999864321                    23568


Q ss_pred             ccCcEEEEEEEece--eCC-------ceEEEEEEEEEcCCh
Q 043474          104 KIGLVARVRGRIAS--YRG-------DVQITVSDVVIEKDP  135 (160)
Q Consensus       104 ~~G~~V~V~G~v~~--f~~-------~~qi~~~~i~~v~d~  135 (160)
                      +.|+.|-|.|+++.  |.+       ...|.+..|..+.-+
T Consensus        62 ~KG~~V~VeGrL~~~~y~dkdG~kr~~~eIva~~I~fl~~~  102 (161)
T PRK06293         62 KKGSGVIVAGEMSPESYVDKDGSPQSSLVVSVDTIKFSPFG  102 (161)
T ss_pred             CCCCEEEEEEEEEeCccCCCCCCEEEEEEEEEeEEEECcCC
Confidence            99999999999975  533       246888888877544

>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR

Probab=94.71  E-value=0.051  Score=35.80  Aligned_cols=28  Identities=32%  Similarity=0.567  Sum_probs=24.8

Q ss_pred             cccccCcEEEEEEEeceeCCceEEEEEE
Q 043474          101 AKIKIGLVARVRGRIASYRGDVQITVSD  128 (160)
Q Consensus       101 ~~~~~G~~V~V~G~v~~f~~~~qi~~~~  128 (160)
                      ..+++|+.|+|.|++.+|++..||....
T Consensus        43 ~~~~~Gd~V~vtG~v~ey~g~tql~~~~   70 (78)
T cd04486          43 ADVAVGDLVRVTGTVTEYYGLTQLTAVS   70 (78)
T ss_pred             CCCCCCCEEEEEEEEEeeCCeEEEccCC
Confidence            5678999999999999999988887754

YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.

>PRK05813 single-stranded DNA-binding protein; Provisional

Probab=94.31  E-value=0.51  Score=37.17  Aligned_cols=82  Identities=18%  Similarity=0.346  Sum_probs=56.4

Q ss_pred             eEeeEEEEEEEEEEee-----ccCCceEEEEEeC-----CCceEEEEEeecCccCCCCCCCCCCcccccccccccccccc
Q 043474           34 KLLSRAEIVGTITSRD-----HKPSKFIKFTVDD-----GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKI  103 (160)
Q Consensus        34 ~~i~~v~ivG~V~~~~-----~~~~~~~~~~IdD-----gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (160)
                      .....|.++|.+..--     ..+..+..|+|.=     .|--|+|++|....+                     ....+
T Consensus       107 ~~~N~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~~td~i~~v~wg~~Ae---------------------~~~~l  165 (219)
T PRK05813        107 KNPNEIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYNKSDYIPCIAWGRNAR---------------------FCKTL  165 (219)
T ss_pred             CCccEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCCCceEEEEEEEhHHhH---------------------HHhhC
Confidence            3478888999887621     1223566777762     244699999987543                     22459


Q ss_pred             ccCcEEEEEEEece--eCC-----------ceEEEEEEEEEcCChh
Q 043474          104 KIGLVARVRGRIAS--YRG-----------DVQITVSDVVIEKDPN  136 (160)
Q Consensus       104 ~~G~~V~V~G~v~~--f~~-----------~~qi~~~~i~~v~d~n  136 (160)
                      +.|+.|.|.|+++.  |.+           ...|.+.+|..++..+
T Consensus       166 ~KG~~V~V~GrL~sr~y~~k~g~~~g~kr~~~eV~v~~i~~l~~~~  211 (219)
T PRK05813        166 EVGDNIRVWGRVQSREYQKKLSEGEVVTKVAYEVSISKMEKVEKEE  211 (219)
T ss_pred             CCCCEEEEEEEEEecceEcCCCCccceEEEEEEEEEEEEEEcCChh
Confidence            99999999999975  543           1367888888776553

>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids

Probab=94.27  E-value=0.45  Score=32.04  Aligned_cols=46  Identities=22%  Similarity=0.343  Sum_probs=28.2

Q ss_pred             eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeC--Cc-------eEEEEEEEEE
Q 043474           66 CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYR--GD-------VQITVSDVVI  131 (160)
Q Consensus        66 ~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~--~~-------~qi~~~~i~~  131 (160)
                      -++|.+|.+..+                    .....++.|+.|.|.|+++...  ++       .+|.+..|..
T Consensus        49 ~~~v~~~g~~A~--------------------~~~~~l~kG~~V~V~G~l~~~~~~~~~G~~~~~~~i~a~~i~f  103 (104)
T PF00436_consen   49 WINVVAWGKLAE--------------------NVAEYLKKGDRVYVEGRLRTRTYEDKDGQKRYRVEIIADNIEF  103 (104)
T ss_dssp             EEEEEEEHHHHH--------------------HHHHH--TT-EEEEEEEEEEEEEESTTSSEEEEEEEEEEEEEE
T ss_pred             EEEEEeeeeccc--------------------ccceEEcCCCEEEEEEEEEeeEEECCCCCEEEEEEEEEEEEEe
Confidence            388888877432                    1335699999999999998643  32       3456665543

It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....

>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria

Probab=94.18  E-value=1.3  Score=31.98  Aligned_cols=70  Identities=19%  Similarity=0.267  Sum_probs=46.0

Q ss_pred             EeeEEEEEEEEE--Eeecc-CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEE
Q 043474           35 LLSRAEIVGTIT--SRDHK-PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARV  111 (160)
Q Consensus        35 ~i~~v~ivG~V~--~~~~~-~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V  111 (160)
                      .-+.+++.|.|.  +++.. +..-++|.|.|+...|++++-...                        .+.++.|.-|-|
T Consensus        49 ~~~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~~------------------------Pd~F~eg~~VVv  104 (131)
T PF03100_consen   49 VGRKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGPL------------------------PDLFREGQGVVV  104 (131)
T ss_dssp             TTSEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--------------------------CTT--TTSEEEE
T ss_pred             CCceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCCC------------------------CccccCCCeEEE
Confidence            347888999998  55543 235589999999888988764322                        257899999999


Q ss_pred             EEEeceeCCceEEEEEEEEE
Q 043474          112 RGRIASYRGDVQITVSDVVI  131 (160)
Q Consensus       112 ~G~v~~f~~~~qi~~~~i~~  131 (160)
                      +|++   .+...+.+.+|-.
T Consensus       105 ~G~~---~~~g~F~A~~lL~  121 (131)
T PF03100_consen  105 EGRL---GEDGVFEATELLA  121 (131)
T ss_dssp             EEEE---CCTSEEEEEEEEE
T ss_pred             EEEE---CCCCEEEEEEEEe
Confidence            9986   3334667776653

Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.

>PRK06863 single-stranded DNA-binding protein; Provisional

Probab=93.90  E-value=0.48  Score=35.78  Aligned_cols=81  Identities=17%  Similarity=0.267  Sum_probs=51.1

Q ss_pred             eeEEEEEEEEEEe---ec-cC-CceEEEEEe------C-CCc-------eEEEEEeecCccCCCCCCCCCCccccccccc
Q 043474           36 LSRAEIVGTITSR---DH-KP-SKFIKFTVD------D-GTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA   96 (160)
Q Consensus        36 i~~v~ivG~V~~~---~~-~~-~~~~~~~Id------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~   96 (160)
                      +.+|.|+|.+..-   .. .+ ..++.|+|.      | .+|       -+.|++|....+                   
T Consensus         4 ~N~V~LiGrLg~DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE-------------------   64 (168)
T PRK06863          4 INKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAE-------------------   64 (168)
T ss_pred             ccEEEEEEEcCCCCEEEEcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHH-------------------
Confidence            4677788877762   11 11 244555543      1 122       378888876432                   


Q ss_pred             cccccccccCcEEEEEEEece--eCC-------ceEEEEEEEEEcCChh
Q 043474           97 TDFAAKIKIGLVARVRGRIAS--YRG-------DVQITVSDVVIEKDPN  136 (160)
Q Consensus        97 ~~~~~~~~~G~~V~V~G~v~~--f~~-------~~qi~~~~i~~v~d~n  136 (160)
                       .....++.|+.|.|.|+++.  |.+       ..+|.+.+|..+...+
T Consensus        65 -~v~~~LkKGs~V~VeGrL~~r~w~DkdG~~r~~~eI~a~~i~~L~~r~  112 (168)
T PRK06863         65 -VAGEYLRKGSQVYVEGRLKTRKWQDQNGQDRYTTEIQGDVLQMLGGRN  112 (168)
T ss_pred             -HHHHHCCCCCEEEEEEEEEeCCccCCCCCEEEEEEEEEeEEEECCCCC
Confidence             13457899999999999975  543       2478888888776554

>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function

Probab=93.70  E-value=0.13  Score=38.58  Aligned_cols=22  Identities=23%  Similarity=0.362  Sum_probs=19.1

Q ss_pred             ceEEEEEeCCCceEEEEEeecC
Q 043474           54 KFIKFTVDDGTGCVPCVLWLNH   75 (160)
Q Consensus        54 ~~~~~~IdDgTG~I~~~~w~~~   75 (160)
                      +++.|.|.|.||.|+++....-
T Consensus       130 ~~~~YeI~DnTG~MeVvv~G~~  151 (170)
T PF02760_consen  130 KNTIYEIQDNTGKMEVVVYGKW  151 (170)
T ss_dssp             SEEEEEEEETTEEEEEEEEGGG
T ss_pred             CeEEEEEecCCCcEEEEEeccC
Confidence            6799999999999999986554

It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.

>TIGR00621 ssb single stranded DNA-binding protein (ssb)

Probab=93.35  E-value=0.59  Score=35.01  Aligned_cols=49  Identities=20%  Similarity=0.253  Sum_probs=33.5

Q ss_pred             CceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece--eCC---c----eEEEEEEEEEc
Q 043474           64 TGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS--YRG---D----VQITVSDVVIE  132 (160)
Q Consensus        64 TG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~--f~~---~----~qi~~~~i~~v  132 (160)
                      |.-+.|++|.+..+                    .....++.|+.|.|.|+++.  |.+   +    .+|.+.+|..+
T Consensus        50 t~~~~v~~wg~~Ae--------------------~~~~~l~KG~~V~V~G~L~~~~~~~kdG~~~~~~ev~a~~i~~L  107 (164)
T TIGR00621        50 TEWHDIVIFGRLAE--------------------VAAQYLKKGSLVYVEGRLRTRKWEDQNGQKRSKTEIIADNVQLL  107 (164)
T ss_pred             ceEEEEEEehHHHH--------------------HHHHhCCCCCEEEEEEEEEeceEECCCCcEEEEEEEEEEEEeec
Confidence            45699999987433                    12357899999999999974  533   2    35666666433

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

>PRK06958 single-stranded DNA-binding protein; Provisional

Probab=93.32  E-value=0.77  Score=35.18  Aligned_cols=79  Identities=14%  Similarity=0.258  Sum_probs=50.3

Q ss_pred             eeEEEEEEEEEEeec----cC-CceEEEEEe------C--------CCceEEEEEeecCccCCCCCCCCCCccccccccc
Q 043474           36 LSRAEIVGTITSRDH----KP-SKFIKFTVD------D--------GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA   96 (160)
Q Consensus        36 i~~v~ivG~V~~~~~----~~-~~~~~~~Id------D--------gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~   96 (160)
                      +..|.|+|.+..--+    .+ ..++.|+|.      |        .|--+.|++|....+                   
T Consensus         4 ~N~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE-------------------   64 (182)
T PRK06958          4 VNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAE-------------------   64 (182)
T ss_pred             ccEEEEEEEecCCCeEEEcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHH-------------------
Confidence            567788888776211    11 245566663      1        233477888865432                   


Q ss_pred             cccccccccCcEEEEEEEece--eCC-------ceEEEEEEEEEcCC
Q 043474           97 TDFAAKIKIGLVARVRGRIAS--YRG-------DVQITVSDVVIEKD  134 (160)
Q Consensus        97 ~~~~~~~~~G~~V~V~G~v~~--f~~-------~~qi~~~~i~~v~d  134 (160)
                       .....++.|+.|.|.|+|+.  |.+       ..+|.+..|..+..
T Consensus        65 -~v~~~LkKGs~V~VeGrL~~~~yeDkdG~kr~~~eVvA~~V~fL~s  110 (182)
T PRK06958         65 -IVGEYLKKGSSVYIEGRIRTRKWQGQDGQDRYSTEIVADQMQMLGG  110 (182)
T ss_pred             -HHHHHhCCCCEEEEEEEEEeCceECCCCcEEEEEEEEEeEEEECCC
Confidence             13357899999999999984  542       24688888887654

>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]

Probab=93.30  E-value=0.1  Score=49.96  Aligned_cols=77  Identities=19%  Similarity=0.383  Sum_probs=54.7

Q ss_pred             EEEEEEEEEEeeccCC-----ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           38 RAEIVGTITSRDHKPS-----KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        38 ~v~ivG~V~~~~~~~~-----~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ...++|.|+.+..+.+     ++..++|+|.||.+++++|.....                    .....+..+..+.|.
T Consensus       978 ~~~~~~~i~~vr~~~tk~~G~~~~f~tl~D~~g~~e~v~f~~~~~--------------------~~~~~l~~~~~~~v~ 1037 (1139)
T COG0587         978 RVVLAGGIVAVRQRPTKAKGNKMAFLTLEDETGILEVVVFPSEYE--------------------RYRRLLLEGRLLIVK 1037 (1139)
T ss_pred             eeEEEEEEEEEEEeeccCCCCEEEEEEEecCCCcEEEEEcHHHHH--------------------HHHHHhccCcEEEEE
Confidence            4778888888775443     378999999999999999965432                    133566777999999


Q ss_pred             EEeceeCCce--EEEEEEEEEcCC
Q 043474          113 GRIASYRGDV--QITVSDVVIEKD  134 (160)
Q Consensus       113 G~v~~f~~~~--qi~~~~i~~v~d  134 (160)
                      |+++.-++..  ++.+..++++..
T Consensus      1038 g~v~~~~~~~~~~~~~~~~~~l~~ 1061 (1139)
T COG0587        1038 GKVQRREDGVGHALILEDLSPLEE 1061 (1139)
T ss_pred             EEEEecccccchhhhHHHhhhHHH
Confidence            9998843332  355555554443

>PF15072 DUF4539: Domain of unknown function (DUF4539)

Probab=92.91  E-value=0.68  Score=31.14  Aligned_cols=58  Identities=16%  Similarity=0.216  Sum_probs=42.7

Q ss_pred             EEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeC
Q 043474           40 EIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYR  119 (160)
Q Consensus        40 ~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~  119 (160)
                      .++|.|.++...+.. ...++-|.||+|+|.+=.+-.+                    +....+..|..+-.+ .|..|.
T Consensus         6 ~l~v~Iks~~~~~~D-~~v~l~DpTG~i~~tiH~~v~~--------------------~y~~~l~~GavLlLk-~V~Vf~   63 (86)
T PF15072_consen    6 CLVVIIKSIVPSSED-AFVVLKDPTGEIRGTIHRKVLE--------------------EYGDELSPGAVLLLK-DVTVFS   63 (86)
T ss_pred             EEEEEEEEeeccCCC-eEEEEECCCCcEEEEEeHHHHh--------------------hcCCccccCEEEEEe-eeeEEe
Confidence            578888888876655 6999999999999998655433                    133567888877666 555665

>PRK07135 dnaE DNA polymerase III DnaE; Validated

Probab=92.89  E-value=0.32  Score=46.00  Aligned_cols=60  Identities=10%  Similarity=0.055  Sum_probs=45.6

Q ss_pred             EEEEEEEEEEeec--c-CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEE
Q 043474           38 RAEIVGTITSRDH--K-PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGR  114 (160)
Q Consensus        38 ~v~ivG~V~~~~~--~-~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~  114 (160)
                      .+++.|.|.++..  + +.++..++++|.||.|+|++|.+.-.                     ....+..|+++.+.|+
T Consensus       899 ~~~v~g~i~~~~~~~K~g~~maf~~~eD~~~~~e~~~F~~~~~---------------------~~~~l~~~~~~~~~~~  957 (973)
T PRK07135        899 EYRLAIEVKNVKRLRKANKEYKKVILSDDSVEITIFVNDNDYL---------------------LFETLKKGDIYEFLIS  957 (973)
T ss_pred             eEEEEEEEEEEEEEeeCCCeEEEEEEEECCCcEEEEEcHHHHH---------------------HHHHhhcCCEEEEEEE
Confidence            4678888888664  2 33778899999999999999965432                     1124778889999999


Q ss_pred             ecee
Q 043474          115 IASY  118 (160)
Q Consensus       115 v~~f  118 (160)
                      .+.-
T Consensus       958 ~~~~  961 (973)
T PRK07135        958 KSKN  961 (973)
T ss_pred             EcCC
Confidence            8773

>PRK07274 single-stranded DNA-binding protein; Provisional

Probab=92.83  E-value=0.39  Score=34.62  Aligned_cols=77  Identities=16%  Similarity=0.363  Sum_probs=49.1

Q ss_pred             eEEEEEEEEEEee----cc-CCceEEEEEe------CCCc-----eEEEEEeecCccCCCCCCCCCCccccccccccccc
Q 043474           37 SRAEIVGTITSRD----HK-PSKFIKFTVD------DGTG-----CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFA  100 (160)
Q Consensus        37 ~~v~ivG~V~~~~----~~-~~~~~~~~Id------DgTG-----~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (160)
                      ..|.|+|.+..--    .. +..++.|+|.      |..|     -+.|++|....+                    ...
T Consensus         3 N~v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae--------------------~v~   62 (131)
T PRK07274          3 NKVILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAE--------------------TLA   62 (131)
T ss_pred             eEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHH--------------------HHH
Confidence            5677777776531    11 1256666665      3333     488999975432                    133


Q ss_pred             cccccCcEEEEEEEece--eC--C----ceEEEEEEEEEcC
Q 043474          101 AKIKIGLVARVRGRIAS--YR--G----DVQITVSDVVIEK  133 (160)
Q Consensus       101 ~~~~~G~~V~V~G~v~~--f~--~----~~qi~~~~i~~v~  133 (160)
                      ..++.|+.|.|.|+++.  |.  |    ..+|.+..+..++
T Consensus        63 ~~l~KG~~V~V~Grl~~~~y~kdG~~~~~~eviv~~i~~l~  103 (131)
T PRK07274         63 SYASKGSLISIDGELRTRKYEKDGQTHYVTEVLCQSFQLLE  103 (131)
T ss_pred             HHcCCCCEEEEEEEEEeccCccCCcEEEEEEEEEEEEEECc
Confidence            56899999999999875  62  2    2367778887665

>TIGR00617 rpa1 replication factor-a protein 1 (rpa1)

Probab=92.68  E-value=1.2  Score=40.07  Aligned_cols=66  Identities=20%  Similarity=0.422  Sum_probs=45.4

Q ss_pred             EEEEEEEEEEeec------c----CCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccC
Q 043474           38 RAEIVGTITSRDH------K----PSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIG  106 (160)
Q Consensus        38 ~v~ivG~V~~~~~------~----~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G  106 (160)
                      .|-|+|.|.++..      +    ....-.++|-|.|| +|++.+|.+....                      .....|
T Consensus       312 ~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~----------------------~~~~~~  369 (608)
T TIGR00617       312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATK----------------------FDVSVQ  369 (608)
T ss_pred             CccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhh----------------------cCCCCC
Confidence            6677888877642      1    12346899999999 5999999876531                      114567


Q ss_pred             cEEEEEE-EeceeCCceEEEE
Q 043474          107 LVARVRG-RIASYRGDVQITV  126 (160)
Q Consensus       107 ~~V~V~G-~v~~f~~~~qi~~  126 (160)
                      .+|-++| +|+.|++ +.|..
T Consensus       370 ~Vva~kg~~V~~f~g-~sLs~  389 (608)
T TIGR00617       370 PVIAIKGVRVSDFGG-KSLST  389 (608)
T ss_pred             CEEEEEeEEEEecCC-ceEec
Confidence            8888885 5778955 45653

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

>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing

Probab=92.59  E-value=0.42  Score=34.74  Aligned_cols=80  Identities=20%  Similarity=0.242  Sum_probs=39.4

Q ss_pred             EEEEEeCCCceEEEEEeecCccCCCCCCCCCCcccccccccc-----ccccccccCcEEEEEEEeceeCCc--eEEEEEE
Q 043474           56 IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT-----DFAAKIKIGLVARVRGRIASYRGD--VQITVSD  128 (160)
Q Consensus        56 ~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~G~~V~V~G~v~~f~~~--~qi~~~~  128 (160)
                      +.+.|.|+||++.+.+|.+..+..- .. +..++....+.+.     .....+-..-.++|+++...|+++  ....+.+
T Consensus        56 l~~~i~D~tg~~~~~~F~~~a~~l~-G~-~a~el~~~~~~~~~~~~~~~~~~~~~~~~f~v~~~~~~y~~e~r~~~~v~~  133 (146)
T PF08646_consen   56 LSLKISDGTGSIWVTLFDEEAEQLL-GM-SADELKELKEEDPEEFPKIIKKLLGKEFVFRVRVKKESYNDESRVKYTVVR  133 (146)
T ss_dssp             EEEEEEETTEEEEEEEEHHHHHHHH-CC-HHCCCHHHCCC-HHHHHHHHHCTTT-EEEEEEEEEE--------EEEEEEE
T ss_pred             EEEEEEeCCCeEEEEEEhHHHHHHh-CC-CHHHHHHHHhhchhHHHHHHHHhhCcEEEEEEEEEEhhhCCceEEEEEEEE
Confidence            6889999999999999987643210 00 0000000000000     011233344678899999999875  3577888


Q ss_pred             EEEcCChhHH
Q 043474          129 VVIEKDPNME  138 (160)
Q Consensus       129 i~~v~d~n~~  138 (160)
                      +.|++ ..+|
T Consensus       134 i~~vd-~~~e  142 (146)
T PF08646_consen  134 IEPVD-YAEE  142 (146)
T ss_dssp             EEE---HHHH
T ss_pred             eEeCC-HHHH
Confidence            88876 4333

It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.

>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]

Probab=92.29  E-value=0.53  Score=41.05  Aligned_cols=82  Identities=16%  Similarity=0.236  Sum_probs=58.7

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      -.+.|.|+|.++...+++.+.|.|-++.+.+++..-.+.-.+              .++..+....++.||+|.+.|...
T Consensus       105 ~~~svaGRI~s~R~sGsKL~Fydl~~~g~klQvm~~~~~~~~--------------~~~F~~~~~~lkrGDiig~~G~pg  170 (560)
T KOG1885|consen  105 EIVSVAGRIHSKRESGSKLVFYDLHGDGVKLQVMANAKKITS--------------EEDFEQLHKFLKRGDIIGVSGYPG  170 (560)
T ss_pred             ceeeeeeeEeeeeccCCceEEEEEecCCeEEEEEEehhhcCC--------------HHHHHHHHhhhhccCEEeeecCCC
Confidence            448999999999888778899999999888888764332110              112234457899999999999986


Q ss_pred             eeC-CceEEEEEEEEEc
Q 043474          117 SYR-GDVQITVSDVVIE  132 (160)
Q Consensus       117 ~f~-~~~qi~~~~i~~v  132 (160)
                      .-+ +...|.++.+..+
T Consensus       171 rt~~gELSi~~~~~~lL  187 (560)
T KOG1885|consen  171 RTKSGELSIIPNEIILL  187 (560)
T ss_pred             cCCCceEEEeecchhee
Confidence            543 5666777666433

>PRK05733 single-stranded DNA-binding protein; Provisional

Probab=91.87  E-value=0.61  Score=35.39  Aligned_cols=62  Identities=13%  Similarity=0.228  Sum_probs=40.0

Q ss_pred             eeEEEEEEEEEEeec-----cCCceEEEEEe------C-CCc-------eEEEEEeecCccCCCCCCCCCCccccccccc
Q 043474           36 LSRAEIVGTITSRDH-----KPSKFIKFTVD------D-GTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA   96 (160)
Q Consensus        36 i~~v~ivG~V~~~~~-----~~~~~~~~~Id------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~   96 (160)
                      +..|.|+|.|..--+     ....++.|+|.      | .+|       =+.|++|....+                   
T Consensus         5 mNkV~LiGrlg~DPElr~t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae-------------------   65 (172)
T PRK05733          5 VNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAE-------------------   65 (172)
T ss_pred             ceEEEEEEEecCCCEEEECCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHH-------------------
Confidence            567788888876311     11245555554      1 233       288999976432                   


Q ss_pred             cccccccccCcEEEEEEEece
Q 043474           97 TDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        97 ~~~~~~~~~G~~V~V~G~v~~  117 (160)
                       .....++.|+.|.|.|+++.
T Consensus        66 -~v~~~l~KGs~V~VeGrLr~   85 (172)
T PRK05733         66 -IAGEYLRKGSQVYIEGKLQT   85 (172)
T ss_pred             -HHHHHhCCCCEEEEEEEEEe
Confidence             13467899999999999975

>PRK07217 replication factor A; Reviewed

Probab=91.84  E-value=0.38  Score=39.76  Aligned_cols=70  Identities=19%  Similarity=0.095  Sum_probs=42.4

Q ss_pred             eEEEEEeCCCceEEEEEeecCccCCCCCCCCCCcccccccccc---------ccccccccCcEEEEEEEeceeCCceEEE
Q 043474           55 FIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT---------DFAAKIKIGLVARVRGRIASYRGDVQIT  125 (160)
Q Consensus        55 ~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~G~~V~V~G~v~~f~~~~qi~  125 (160)
                      ++.+.||||||+++|.+-.......+  ..+   ++-..++..         ......-.|.|++|+|.+  |  -+.+.
T Consensus       218 rik~vlDDGt~~~~~~~~~e~te~l~--G~~---l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~--~--g~~l~  288 (311)
T PRK07217        218 RIKGVLDDGEEVQEVIFNREATEELT--GIT---LEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT--L--GRYLL  288 (311)
T ss_pred             EEEEEEECCCCeEEEEEChHHhHHHh--CCC---HHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc--C--CcEEE
Confidence            48999999999999998765543211  000   000000000         011123589999999976  4  35788


Q ss_pred             EEEEEEcC
Q 043474          126 VSDVVIEK  133 (160)
Q Consensus       126 ~~~i~~v~  133 (160)
                      +..+.+..
T Consensus       289 ~~~~~~~~  296 (311)
T PRK07217        289 ADSVEPLT  296 (311)
T ss_pred             eeEeeccc
Confidence            88888774

>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=91.64  E-value=1.4  Score=32.59  Aligned_cols=69  Identities=19%  Similarity=0.249  Sum_probs=48.5

Q ss_pred             eeEEEEEEEEEE--eeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEE
Q 043474           36 LSRAEIVGTITS--RDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRG  113 (160)
Q Consensus        36 i~~v~ivG~V~~--~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G  113 (160)
                      -+.+++.|.|..  +...++..+.|.|.|+...|.+.+-..                        ..+.++.|.-|-++|
T Consensus        51 g~~vrvgG~V~~gSi~~~~~~~~~F~ltD~~~~i~V~Y~G~------------------------lPd~F~eg~~VVv~G  106 (148)
T PRK13254         51 GRRFRLGGLVEKGSVQRGDGLTVRFVVTDGNATVPVVYTGI------------------------LPDLFREGQGVVAEG  106 (148)
T ss_pred             CCeEEEeEEEecCcEEeCCCCEEEEEEEeCCeEEEEEECCC------------------------CCccccCCCEEEEEE
Confidence            478899999964  433233558999999988888776322                        225789999999999


Q ss_pred             EeceeCCceEEEEEEEEE
Q 043474          114 RIASYRGDVQITVSDVVI  131 (160)
Q Consensus       114 ~v~~f~~~~qi~~~~i~~  131 (160)
                      ++..   .--+.+.+|-.
T Consensus       107 ~~~~---~g~F~A~~vLa  121 (148)
T PRK13254        107 RLQD---GGVFVADEVLA  121 (148)
T ss_pred             EECC---CCeEEEEEEEe
Confidence            9752   22466666653

>PRK06642 single-stranded DNA-binding protein; Provisional

Probab=91.33  E-value=0.76  Score=34.07  Aligned_cols=62  Identities=15%  Similarity=0.284  Sum_probs=41.6

Q ss_pred             eeEEEEEEEEEE---eec--cCCceEEEEEe------CC-Cc-------eEEEEEeec-CccCCCCCCCCCCcccccccc
Q 043474           36 LSRAEIVGTITS---RDH--KPSKFIKFTVD------DG-TG-------CVPCVLWLN-HLTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        36 i~~v~ivG~V~~---~~~--~~~~~~~~~Id------Dg-TG-------~I~~~~w~~-~~~~~~~~~~~~~~~~~~~~~   95 (160)
                      +..|.|+|.+..   +..  ....++.|+|.      |. +|       =+.|++|.+ ..+                  
T Consensus         5 ~N~V~LiGrLg~DPElr~t~~G~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae------------------   66 (152)
T PRK06642          5 LNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVS------------------   66 (152)
T ss_pred             ceEEEEEEEccCCceEEECCCCCEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHH------------------
Confidence            578889999886   221  12367778776      21 22       388888875 221                  


Q ss_pred             ccccccccccCcEEEEEEEece
Q 043474           96 ATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                        .....++.|+.|.|.|+++.
T Consensus        67 --~~~~~l~KG~~V~V~GrL~~   86 (152)
T PRK06642         67 --VVERYVTKGSKLYIEGSLQT   86 (152)
T ss_pred             --HHHHhCCCCCEEEEEEEEEe
Confidence              12356899999999999875

>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB)

Probab=90.97  E-value=1.4  Score=29.26  Aligned_cols=36  Identities=22%  Similarity=0.237  Sum_probs=26.4

Q ss_pred             CCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEecee
Q 043474           63 GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASY  118 (160)
Q Consensus        63 gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f  118 (160)
                      .+--++|.+|.+...                    .....++.|+.|.|.|+++..
T Consensus        42 ~~~~~~v~~~g~~a~--------------------~~~~~~~kG~~V~v~G~l~~~   77 (100)
T cd04496          42 ETDWIRVVAFGKLAE--------------------NAAKYLKKGDLVYVEGRLRTR   77 (100)
T ss_pred             ccEEEEEEEEhHHHH--------------------HHHHHhCCCCEEEEEEEEEec
Confidence            444589999987432                    123578999999999999763

SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart

>PRK13732 single-stranded DNA-binding protein; Provisional

Probab=90.87  E-value=0.88  Score=34.61  Aligned_cols=63  Identities=14%  Similarity=0.206  Sum_probs=42.1

Q ss_pred             EeeEEEEEEEEEEee-----ccCCceEEEEEeC-------CCc-------eEEEEEeecCccCCCCCCCCCCcccccccc
Q 043474           35 LLSRAEIVGTITSRD-----HKPSKFIKFTVDD-------GTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~-----~~~~~~~~~~IdD-------gTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~   95 (160)
                      .+..|.|+|.+..--     .....++.|+|.-       .+|       -++|++|....+                  
T Consensus         5 ~mN~V~LiGrLg~DPElR~t~nG~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae------------------   66 (175)
T PRK13732          5 GINKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAE------------------   66 (175)
T ss_pred             CceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHH------------------
Confidence            367888999888621     1122566676652       234       368899976432                  


Q ss_pred             ccccccccccCcEEEEEEEece
Q 043474           96 ATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                        .....++.|+.|.|.|+|+.
T Consensus        67 --~v~~~L~KG~~V~VeGrL~~   86 (175)
T PRK13732         67 --VAGEYLRKGAQVYIEGQLRT   86 (175)
T ss_pred             --HHHHhcCCCCEEEEEEEEEe
Confidence              13356899999999999875

>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=90.38  E-value=6  Score=29.53  Aligned_cols=74  Identities=14%  Similarity=0.143  Sum_probs=52.7

Q ss_pred             eeEEEEEEEEE--EeeccCC-ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           36 LSRAEIVGTIT--SRDHKPS-KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        36 i~~v~ivG~V~--~~~~~~~-~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      -+.+++-|.|.  ++...+. ..+.|+|-|+.++|.+.+-.-                        ..+.|+.|.=|-++
T Consensus        51 ~~~~RlGG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------------------------lPDlFrEGqgVVae  106 (155)
T PRK13159         51 YQQFRLGGMVKAGSIQRAADSLKVSFTVIDKNAATQVEYTGI------------------------LPDLFRDNQSVIAN  106 (155)
T ss_pred             CCeEEEccEEecCcEEEcCCCcEEEEEEEcCCcEEEEEEccC------------------------CCccccCCCeEEEE
Confidence            37788888888  6655432 358999999999998775322                        23578999999999


Q ss_pred             EEeceeCCceEEEEEEEEEcCChhH
Q 043474          113 GRIASYRGDVQITVSDVVIEKDPNM  137 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~d~n~  137 (160)
                      |++.  .  .-+.+..+-.--|.++
T Consensus       107 G~~~--~--g~F~A~~vLAKHde~Y  127 (155)
T PRK13159        107 GRMQ--G--GRFVANEVLAKHDETY  127 (155)
T ss_pred             EEEc--C--CEEEEeEEEecCCCcC
Confidence            9986  2  2567777665555543

>KOG0555 consensus Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=89.85  E-value=0.52  Score=40.42  Aligned_cols=41  Identities=24%  Similarity=0.370  Sum_probs=33.2

Q ss_pred             eEeeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecC
Q 043474           34 KLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNH   75 (160)
Q Consensus        34 ~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~   75 (160)
                      .--.+|++.|+|-...... +.+...|-||||.++|++-.+-
T Consensus       121 ~r~qrVkv~gWVhrlR~qk-~l~FivLrdg~gflqCVl~~kl  161 (545)
T KOG0555|consen  121 NRGQRVKVFGWVHRLRRQK-SLIFIVLRDGTGFLQCVLSDKL  161 (545)
T ss_pred             ccCceEEeehhhHhhhhcC-ceEEEEEecCCceEEEEEcchh
Confidence            3447899999998887664 6678899999999999986544

>PLN02532 asparagine-tRNA synthetase

Probab=89.51  E-value=1.8  Score=39.25  Aligned_cols=60  Identities=10%  Similarity=0.108  Sum_probs=44.2

Q ss_pred             ceEEEEEeCCCce--EEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeC-----CceEEEE
Q 043474           54 KFIKFTVDDGTGC--VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYR-----GDVQITV  126 (160)
Q Consensus        54 ~~~~~~IdDgTG~--I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~-----~~~qi~~  126 (160)
                      +...+.|.||||.  ++|++-.....                     ....+..|..|.|+|.|..-+     +...|.+
T Consensus       134 ~i~FI~LrDGSg~~~lQvVv~~~~~~---------------------~~~~L~~Es~V~V~G~V~~~~~~~~~g~iEl~v  192 (633)
T PLN02532        134 SVAYLLISDGSCVASLQVVVDSALAP---------------------LTQLMATGTCILAEGVLKLPLPAQGKHVIELEV  192 (633)
T ss_pred             CcEEEEEECCCCccceEEEEeCCccc---------------------HhhcCCCceEEEEEEEEEecCCCCCCCcEEEEe
Confidence            5678899999998  99987322111                     114678999999999998752     3468888


Q ss_pred             EEEEEcCC
Q 043474          127 SDVVIEKD  134 (160)
Q Consensus       127 ~~i~~v~d  134 (160)
                      ..+..+..
T Consensus       193 ~~i~VLg~  200 (633)
T PLN02532        193 EKILHIGT  200 (633)
T ss_pred             eEEEEEec
Confidence            88887763

>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=89.25  E-value=2.5  Score=37.65  Aligned_cols=79  Identities=16%  Similarity=0.283  Sum_probs=56.4

Q ss_pred             eeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           36 LSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      -..|++.|+|-.+...+ ..+...|-|.+|.++.++-.+...                 +..+....++...+|+|.|+|
T Consensus        15 G~~V~L~GWV~r~Rd~G-gliFiDLRDr~GivQvv~~~~~~~-----------------~~~~~a~~lr~E~vi~V~G~V   76 (585)
T COG0173          15 GQTVTLSGWVHRRRDHG-GLIFIDLRDREGIVQVVFDPEDSP-----------------EAFEVASRLRNEFVIQVTGTV   76 (585)
T ss_pred             CCEEEEEeeeeeccccC-CeEEEEcccCCCeEEEEECCccCH-----------------HHHHHHHhcCceEEEEEEEEE
Confidence            37899999988877666 567889999999888876332111                 112345678888999999999


Q ss_pred             ceeC----------CceEEEEEEEEEc
Q 043474          116 ASYR----------GDVQITVSDVVIE  132 (160)
Q Consensus       116 ~~f~----------~~~qi~~~~i~~v  132 (160)
                      ....          |...|.+..|..+
T Consensus        77 ~~R~e~~~N~~l~TGeiEv~a~~i~vl  103 (585)
T COG0173          77 RARPEGTINPNLPTGEIEVLAEEIEVL  103 (585)
T ss_pred             EecCccccCCCCCcceEEEEeeeEEEE
Confidence            8752          2457777777654

>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold []

Probab=89.18  E-value=2  Score=30.79  Aligned_cols=64  Identities=22%  Similarity=0.280  Sum_probs=29.8

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeC--CCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEE
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDD--GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGR  114 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdD--gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~  114 (160)
                      +.+++-|.|.++....+++.....++  +.+.+.|.+-.+...                   ......++.|+.|.|.|+
T Consensus        68 K~i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~-------------------~~~~~~l~~G~~Vti~G~  128 (144)
T PF12869_consen   68 KIIEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQEK-------------------RASVAKLKKGQKVTIKGI  128 (144)
T ss_dssp             -EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGG-------------------HHHHHH--TTSEEEEEEE
T ss_pred             CEEEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchhh-------------------hhhHhcCCCCCEEEEEEE
Confidence            66778899999976333333333333  333466765433311                   001235999999999999


Q ss_pred             eceeC
Q 043474          115 IASYR  119 (160)
Q Consensus       115 v~~f~  119 (160)
                      +..|.
T Consensus       129 ~~g~~  133 (144)
T PF12869_consen  129 CTGYS  133 (144)
T ss_dssp             -----
T ss_pred             EEeee
Confidence            99985

; PDB: 3F1Z_I.

>KOG0554 consensus Asparaginyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis]

Probab=88.36  E-value=1.3  Score=37.95  Aligned_cols=77  Identities=13%  Similarity=0.168  Sum_probs=57.0

Q ss_pred             eEeeEEEEEEEEEEeeccCCceEEEEEeCCCc--eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEE
Q 043474           34 KLLSRAEIVGTITSRDHKPSKFIKFTVDDGTG--CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARV  111 (160)
Q Consensus        34 ~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG--~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V  111 (160)
                      +.-..+.|-|+|.++.... ++.-+.|+|||-  .++|++-.  +                      +...+..|..|.+
T Consensus        18 ~~g~~~~i~GWvKsvr~~~-~~~Fl~i~DGs~~~~lQvVv~~--~----------------------~~q~la~Gt~i~~   72 (446)
T KOG0554|consen   18 RAGDTISIGGWVKSVRKLK-KVTFLDINDGSCPSPLQVVVDS--E----------------------QSQLLATGTCISA   72 (446)
T ss_pred             CCCCceeecchhhhccccc-ceEEEEecCCCCCcceEEEech--H----------------------HhhhccccceEEE
Confidence            3457788899999988665 678899999995  38888633  1                      2356889999999


Q ss_pred             EEEeceeCC---ceEEEEEEEEEcCCh
Q 043474          112 RGRIASYRG---DVQITVSDVVIEKDP  135 (160)
Q Consensus       112 ~G~v~~f~~---~~qi~~~~i~~v~d~  135 (160)
                      .|.++.=++   +..+.+.+|..+..-
T Consensus        73 ~g~l~~~~~~~q~iel~~eki~~vG~v   99 (446)
T KOG0554|consen   73 EGVLKVSKGAKQQIELNAEKIKVVGTV   99 (446)
T ss_pred             EeeEEeccchheeeeeeeeEEEEEeec
Confidence            999986553   455777777766533

>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70)

Probab=88.35  E-value=2.1  Score=31.70  Aligned_cols=88  Identities=14%  Similarity=0.144  Sum_probs=45.5

Q ss_pred             EEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccc-c----ccccccccCcEEEEEEEeceeCC--ceEEEEEE
Q 043474           56 IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA-T----DFAAKIKIGLVARVRGRIASYRG--DVQITVSD  128 (160)
Q Consensus        56 ~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~-~----~~~~~~~~G~~V~V~G~v~~f~~--~~qi~~~~  128 (160)
                      +.+.|.|+||++.+.+|.+..+..-..  +..++--..++. .    .....+-.--.+++..+...|++  +....+.+
T Consensus        70 l~~~i~D~Tg~~~~~~F~~~ae~l~G~--sa~el~~~~~~~~~~~~~~i~~~~gk~~~f~v~~~~~~y~~e~~~~~~v~~  147 (166)
T cd04476          70 LSLNVADHTGEAWLTLFDEVAEQIFGK--SAEELLELKEEDPDAFPDAIQDLVGKTFLFRVSVKEETYNDEGRIRYTVVK  147 (166)
T ss_pred             EEEEEEeCCCCEEEEEehHHHHHHhCC--CHHHHHHHhhcCHHHHHHHHHHhhCceEEEEEEEEehhcCCcceEEEEEEE
Confidence            679999999999999997665421100  000000000000 0    00111112235667777788997  44566666


Q ss_pred             EEEcCChhHHHHHHHHHH
Q 043474          129 VVIEKDPNMEVLHWLDCL  146 (160)
Q Consensus       129 i~~v~d~n~~~~h~le~~  146 (160)
                      +.|+. ...+..+.++-+
T Consensus       148 i~~~~-~~~~~~~l~~~i  164 (166)
T cd04476         148 VAPVD-YKKESKRLIQSI  164 (166)
T ss_pred             cccCC-HHHHHHHHHHHh
Confidence            66554 334455555433

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun

>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=88.33  E-value=9  Score=28.75  Aligned_cols=74  Identities=20%  Similarity=0.258  Sum_probs=51.5

Q ss_pred             eeEEEEEEEEE--EeeccCC-ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           36 LSRAEIVGTIT--SRDHKPS-KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        36 i~~v~ivG~V~--~~~~~~~-~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      -+.+++-|.|.  ++...+. -.+.|+|-|+...|.+.+-..                        ..+.|+.|.=|-+.
T Consensus        57 g~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~Gi------------------------lPDlFrEG~gVVve  112 (160)
T PRK13165         57 GQRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGI------------------------LPDLFREGQGIVAQ  112 (160)
T ss_pred             CCEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEccc------------------------CCccccCCCeEEEE
Confidence            47889999998  6665432 247999999999988876321                        23578999999999


Q ss_pred             EEeceeCCceEEEEEEEEEcCChh
Q 043474          113 GRIASYRGDVQITVSDVVIEKDPN  136 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~d~n  136 (160)
                      |++..   .--+.+..|-.--|.+
T Consensus       113 G~~~~---~g~F~A~~vLAKhdek  133 (160)
T PRK13165        113 GVLEE---GNHIEAKEVLAKHDEN  133 (160)
T ss_pred             EEECC---CCeEEEEEEEecCCCC
Confidence            99853   1245566655434443

>PRK09010 single-stranded DNA-binding protein; Provisional

Probab=87.78  E-value=2  Score=32.72  Aligned_cols=66  Identities=15%  Similarity=0.229  Sum_probs=41.3

Q ss_pred             EeeEEEEEEEEEEee---c--cCCceEEEEEe------C-CCc-------eEEEEEeecCccCCCCCCCCCCcccccccc
Q 043474           35 LLSRAEIVGTITSRD---H--KPSKFIKFTVD------D-GTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~---~--~~~~~~~~~Id------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~   95 (160)
                      .+..|.|+|.+..--   .  ....++.|+|.      | .+|       -++|++|....+                  
T Consensus         5 ~~N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae------------------   66 (177)
T PRK09010          5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAE------------------   66 (177)
T ss_pred             CceEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHH------------------
Confidence            367778888876621   1  11245555554      2 133       368888876432                  


Q ss_pred             ccccccccccCcEEEEEEEece--eCC
Q 043474           96 ATDFAAKIKIGLVARVRGRIAS--YRG  120 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~~--f~~  120 (160)
                        .....++.|+.|.|.|+|+.  |.+
T Consensus        67 --~~~~~L~KGs~V~VeGrL~~~~yed   91 (177)
T PRK09010         67 --VAGEYLRKGSQVYIEGQLRTRKWTD   91 (177)
T ss_pred             --HHHHhcCCCCEEEEEEEEEeccccC
Confidence              12357899999999999964  643

>TIGR00617 rpa1 replication factor-a protein 1 (rpa1)

Probab=87.11  E-value=1.6  Score=39.37  Aligned_cols=61  Identities=16%  Similarity=0.290  Sum_probs=44.5

Q ss_pred             eEEEEEEEEEEeec--------cCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcE
Q 043474           37 SRAEIVGTITSRDH--------KPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLV  108 (160)
Q Consensus        37 ~~v~ivG~V~~~~~--------~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~  108 (160)
                      .+.+|.|+|++...        .+++.+.+.|-|.+|.|.|.+|.....                    ...+.++.|++
T Consensus       191 ~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Degg~Irat~f~~~~d--------------------kf~~~l~eG~V  250 (608)
T TIGR00617       191 NKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDESGEIRATAFNEQAD--------------------KFYDIIQEGKV  250 (608)
T ss_pred             CceEEEEEEEeccccceecCCCCCceeeEEEEecCCCeEEEEECchHHH--------------------HHhhhcccCCE
Confidence            45778888876431        124678999999999999999987543                    24467899999


Q ss_pred             EEE-EEEece
Q 043474          109 ARV-RGRIAS  117 (160)
Q Consensus       109 V~V-~G~v~~  117 (160)
                      +.+ .|+|+.
T Consensus       251 Y~Is~~~Vk~  260 (608)
T TIGR00617       251 YYISKGSLKP  260 (608)
T ss_pred             EEECceEEEE
Confidence            988 456654

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

>PRK04036 DNA polymerase II small subunit; Validated

Probab=85.96  E-value=4.3  Score=35.78  Aligned_cols=62  Identities=16%  Similarity=0.325  Sum_probs=40.8

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..+.|+|.|.++.........+.|+|.||.+.+..-.....-                  ......+-.|.+|-|.|+..
T Consensus       154 ~~~~viG~v~~~~~~~~g~~~~~LED~sgrv~l~~~~~~~~~------------------~~~~~~lvtg~vv~v~G~~~  215 (504)
T PRK04036        154 EEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKDREDL------------------AELADELLLDEVIGVEGTLS  215 (504)
T ss_pred             ceEEEEEEEEEeecccCCceEEEEECCCCeEEEEeecchhhh------------------hhhhhcccCceEEEEEEEEc
Confidence            568999999887643323347999999999999763211000                  00113567888888888865

>PRK06341 single-stranded DNA-binding protein; Provisional

Probab=85.57  E-value=2.9  Score=31.56  Aligned_cols=65  Identities=9%  Similarity=0.255  Sum_probs=40.5

Q ss_pred             eeEEEEEEEEEEe---e-ccC-CceEEEEEeCC-------Cc-------eEEEEEeecC-ccCCCCCCCCCCcccccccc
Q 043474           36 LSRAEIVGTITSR---D-HKP-SKFIKFTVDDG-------TG-------CVPCVLWLNH-LTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        36 i~~v~ivG~V~~~---~-~~~-~~~~~~~IdDg-------TG-------~I~~~~w~~~-~~~~~~~~~~~~~~~~~~~~   95 (160)
                      +..|.|+|.+..-   . ..+ .+++.|+|.=.       +|       -+.|++|.+. .+                  
T Consensus         5 mN~V~LiGrLg~DPElR~t~sG~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae------------------   66 (166)
T PRK06341          5 VNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCK------------------   66 (166)
T ss_pred             ceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHH------------------
Confidence            5778888888762   1 111 25556655321       33       2688888742 21                  


Q ss_pred             ccccccccccCcEEEEEEEec--eeCC
Q 043474           96 ATDFAAKIKIGLVARVRGRIA--SYRG  120 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~--~f~~  120 (160)
                        .....++.|+.|.|.|+++  .|.+
T Consensus        67 --~~~~~LkKG~~V~VeGrL~~r~w~d   91 (166)
T PRK06341         67 --VAEQYLKKGAKVYIEGQLQTRKWTD   91 (166)
T ss_pred             --HHHHhcCCCCEEEEEEEEEeCcEEC
Confidence              1235789999999999986  4654

>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=85.34  E-value=14  Score=27.78  Aligned_cols=74  Identities=20%  Similarity=0.273  Sum_probs=52.3

Q ss_pred             eeEEEEEEEEE--EeeccC-CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           36 LSRAEIVGTIT--SRDHKP-SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        36 i~~v~ivG~V~--~~~~~~-~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      -+.+++-|.|.  ++...+ +..+.|+|.|+.++|.+.+-..                        ..+.|+.|.=|-+.
T Consensus        57 g~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------------------------lPDlFrEG~gVVve  112 (159)
T PRK13150         57 GQRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGI------------------------LPDLFREGQGVVVQ  112 (159)
T ss_pred             CCEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEecc------------------------CCccccCCCeEEEE
Confidence            47889999998  565433 3358999999999988876322                        23578999999999


Q ss_pred             EEeceeCCceEEEEEEEEEcCChh
Q 043474          113 GRIASYRGDVQITVSDVVIEKDPN  136 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~d~n  136 (160)
                      |++..   .--+.+..|-.--|.+
T Consensus       113 G~~~~---~g~F~A~evLAKhdek  133 (159)
T PRK13150        113 GTLEK---GNHVLAHEVLAKHDEN  133 (159)
T ss_pred             EEECC---CCEEEEeEEEeCCCCC
Confidence            99853   2246666666444444

>TIGR00594 polc DNA-directed DNA polymerase III (polc)

Probab=84.33  E-value=2.1  Score=40.92  Aligned_cols=36  Identities=22%  Similarity=0.419  Sum_probs=29.3

Q ss_pred             eEEEEEEEEEEeecc-----CCceEEEEEeCCCceEEEEEe
Q 043474           37 SRAEIVGTITSRDHK-----PSKFIKFTVDDGTGCVPCVLW   72 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~-----~~~~~~~~IdDgTG~I~~~~w   72 (160)
                      .+++++|.|.+++.+     +.....++|+|.||.|+|++|
T Consensus       982 ~~v~v~G~i~~~~~~~~tkkG~~maf~tleD~tg~ie~viF 1022 (1022)
T TIGR00594       982 SQVRTLGGLNSVKKKITTKNGKPMAFLQLEDETGSIEVVVF 1022 (1022)
T ss_pred             CEEEEEEEEEEEEEecccCCCCEEEEEEEEECCCcEEEEeC
Confidence            468999999876653     125789999999999999987

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

>TIGR00644 recJ single-stranded-DNA-specific exonuclease RecJ

Probab=84.10  E-value=17  Score=32.31  Aligned_cols=84  Identities=17%  Similarity=0.356  Sum_probs=53.8

Q ss_pred             ehhhhhccCCCC--CC-CceEECCeEeeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCcc
Q 043474           13 LAFDLLSLTPTP--DP-ATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTV   89 (160)
Q Consensus        13 ~i~~i~~l~~~~--~~-~~~~~~~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~   89 (160)
                      ++++|..|.+-+  .+ -.|.+.+..+..++.+|       +  +.+.+.+.++-..++|..|.....            
T Consensus       447 l~~~L~~lePfG~gnp~P~F~~~~~~i~~~~~~g-------~--~h~kl~~~~~~~~~~ai~F~~~~~------------  505 (539)
T TIGR00644       447 LIEQIEKLEPFGQGNPEPLFLLKNLRVEDIKLLG-------E--NHLKLSLKSGGKNIEAIAFNAGDL------------  505 (539)
T ss_pred             HHHHHHhcCCCCCCCCCCEEEecCeEEEEEEEcC-------C--CEEEEEEecCCEEEEEEEEcCccc------------
Confidence            345555566533  23 46777888888777655       2  457888887623599999965432            


Q ss_pred             ccccccccccccccccCcEEEEEEEec--eeCCce--EEEEE
Q 043474           90 RLIAGVATDFAAKIKIGLVARVRGRIA--SYRGDV--QITVS  127 (160)
Q Consensus        90 ~~~~~~~~~~~~~~~~G~~V~V~G~v~--~f~~~~--qi~~~  127 (160)
                                ...+..+..+.+.|+++  .|+|+.  |+.+.
T Consensus       506 ----------~~~~~~~~~~~ii~~l~~n~~~g~~~~ql~I~  537 (539)
T TIGR00644       506 ----------ELELNLGRPLDVAGKLSINEWRGRETPQLIIQ  537 (539)
T ss_pred             ----------cccccCCCEEEEEEEEEEEeeCCcceEEEEEE
Confidence                      12234567899999987  599864  55544

All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair.

>KOG2411 consensus Aspartyl-tRNA synthetase, mitochondrial [Translation, ribosomal structure and biogenesis]

Probab=83.41  E-value=7.1  Score=34.60  Aligned_cols=82  Identities=17%  Similarity=0.235  Sum_probs=55.7

Q ss_pred             eeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           36 LSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      -..|.++|++..-..+. ....|.|-|.+|.|.+.+-.+...                 .+......+...++|+|.|.+
T Consensus        47 g~kv~l~GWl~~~~~~k-~~~F~~LRD~~G~vq~lls~~s~~-----------------l~~~~~~~v~~e~vv~v~gtv  108 (628)
T KOG2411|consen   47 GKKVVLCGWLELHRVHK-MLTFFNLRDAYGIVQQLLSPDSFP-----------------LAQKLENDVPLEDVVQVEGTV  108 (628)
T ss_pred             CCEEEEeeeeeeeeccc-cceEEEeeccCcceEEEecchhhh-----------------HHhcccCCCChhheEeeeeeE
Confidence            37899999999877654 446789999999999987543321                 011123457788999999999


Q ss_pred             ceeC----------CceEEEEEEEEEcCCh
Q 043474          116 ASYR----------GDVQITVSDVVIEKDP  135 (160)
Q Consensus       116 ~~f~----------~~~qi~~~~i~~v~d~  135 (160)
                      ..--          |...+.+.++......
T Consensus       109 v~Rp~~sin~km~tg~vev~~e~~~vln~~  138 (628)
T KOG2411|consen  109 VSRPNESINSKMKTGFVEVVAEKVEVLNPV  138 (628)
T ss_pred             ecccccccCccccccceEEEeeeeEEecCc
Confidence            7751          1235666776655443

>PRK07772 single-stranded DNA-binding protein; Provisional

Probab=82.38  E-value=5.1  Score=30.77  Aligned_cols=32  Identities=22%  Similarity=0.540  Sum_probs=25.0

Q ss_pred             eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece
Q 043474           66 CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        66 ~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                      -|+|.+|....+                    .....++.|+.|.|.|+++.
T Consensus        54 fi~V~~Wg~~Ae--------------------~va~~L~KGd~V~V~GrL~~   85 (186)
T PRK07772         54 FLRCSIWRQAAE--------------------NVAESLTKGMRVIVTGRLKQ   85 (186)
T ss_pred             EEEEEEecHHHH--------------------HHHHhcCCCCEEEEEEEEEc
Confidence            589999987543                    13357999999999999974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	160
3kf6_A	159	Protein STN1; OB fold, chromosomal protein, DNA-bi	3e-27
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	4e-16
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	1e-15

>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe} Length = 159

 Score = 98.8 bits (246), Expect = 3e-27
 Identities = 30/155 (19%), Positives = 52/155 (33%), Gaps = 21/155 (13%)

Query: 7   NTHVKLLAFDLLSLTPTP--DPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGT 64
           +    +   D+  ++  P          G  +   +IVG I + D         TVDD +
Sbjct: 16  SRWNPMFISDVHKISFHPHLQRYIGFWMGFPIRWIQIVGYIAAIDIYE-GKHVLTVDDCS 74

Query: 65  G-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQ 123
           G  +  V  +    S+                       +  G V  V G+I S+R +V+
Sbjct: 75  GMVLRVVFIIQDDFSMSKRAIS-----------------MSPGNVVCVFGKINSFRSEVE 117

Query: 124 ITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVVN 158
           +        +DPN E   W   +R  +    +  N
Sbjct: 118 LIAQSFEELRDPNDEWKAWQKRMRYKKNLTKISKN 152

>2pi2_A Replication protein A 32 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2z6k_A 1dpu_A 1z1d_A Length = 270

 Score = 72.5 bits (177), Expect = 4e-16
 Identities = 20/125 (16%), Positives = 41/125 (32%), Gaps = 20/125 (16%)

Query: 23  TPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYL 81
           T     F      +S+  IVG I   +  P+  I + +DD T   +    W++       
Sbjct: 58  TLVDEVFRIGNVEISQVTIVGIIRHAEKAPT-NIVYKIDDMTAAPMDVRQWVD------- 109

Query: 82  PRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLH 141
                          +     +      +V G + S++    +    ++  +D N    H
Sbjct: 110 -----------TDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTH 158

Query: 142 WLDCL 146
            L+ +
Sbjct: 159 ILEVI 163

>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} PDB: 2pqa_A 1quq_A 1l1o_B Length = 132

 Score = 68.0 bits (166), Expect = 1e-15
 Identities = 20/125 (16%), Positives = 41/125 (32%), Gaps = 20/125 (16%)

Query: 23  TPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYL 81
           T     F      +S+  IVG I   +  P+  I + +DD T   +    W++       
Sbjct: 18  TLVDEVFRIGNVEISQVTIVGIIRHAEKAPT-NIVYKIDDMTAAPMDVRQWVD------- 69

Query: 82  PRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLH 141
                          +     +      +V G + S++    +    ++  +D N    H
Sbjct: 70  -----------TDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTH 118

Query: 142 WLDCL 146
            L+ +
Sbjct: 119 ILEVI 123

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	160
3kf6_A	159	Protein STN1; OB fold, chromosomal protein, DNA-bi	100.0
4gop_B	136	Putative uncharacterized protein; OB fold, ssDNA b	100.0
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	100.0
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	99.95
3kf8_A	220	Protein STN1; OB fold; 2.40A {Candida tropicalis m	99.91
3mxn_B	150	RECQ-mediated genome instability protein 2; bloom	99.1
1o7i_A	119	SSB, SSO2364, single stranded DNA binding protein;	98.99
2kbn_A	109	Conserved protein; nucleic acid binding protein, b	98.96
2k50_A	115	Replication factor A related protein; uncharacteri	98.91
2k75_A	106	Uncharacterized protein TA0387; closed beta barrel	98.84
3e0e_A	97	Replication protein A; structural genomics, PSI-2,	98.76
3dm3_A	105	Replication factor A; probably plays AN essential	98.47
3au7_A	402	TIAS, putative uncharacterized protein; ATP hydrol	97.89
1wjj_A	145	Hypothetical protein F20O9.120; DNA-binding protei	97.64
1nnx_A	109	Protein YGIW; structural genomics, hypothetical pr	97.58
3nem_A	438	Aspartyl-tRNA synthetase; rossmann fold, OB fold,	97.39
1e1o_A	504	Lysyl-tRNA synthetase, heat inducible; ligase, ami	97.37
1wyd_A	429	Hypothetical aspartyl-tRNA synthetase; archaea, LI	97.32
3m4p_A	456	Ehasnrs, asparaginyl-tRNA synthetase, putative; am	97.3
1eov_A	487	ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy	97.2
4ex5_A	529	Lysine--tRNA ligase; structural genomics, niaid, n	97.18
1x54_A	434	Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthe	97.18
3a74_A	493	Lysyl-tRNA synthetase; aminoacyl tRNA synthetase,	97.16
1c0a_A	585	Aspartyl tRNA synthetase; protein-RNA complex, lig	97.14
1l0w_A	580	Aspartyl-tRNA synthetase; space-grown crystal, dim	97.14
3i7f_A	548	Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-bi	97.11
2xgt_A	435	Asparaginyl-tRNA synthetase, cytoplasmic; ligase,	97.11
1n9w_A	422	Aspartyl-tRNA synthetase 2; biosynthetic protein;	97.06
3f2b_A	1041	DNA-directed DNA polymerase III alpha chain; DNA p	97.05
2hpi_A	1220	DNA polymerase III alpha subunit; POL-beta-like nu	96.98
3bju_A	521	Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase,	96.96
4gs3_A	107	Single-stranded DNA-binding protein; primosome, ol	96.95
3kdf_A	121	Replication protein A 14 kDa subunit; wheat GERM c	96.5
2pi2_E	142	Replication protein A 14 kDa subunit; FULL-length	96.37
1ynx_A	114	Replication factor-A protein 1; canonical OB fold,	96.19
1txy_A	104	Primosomal replication protein N; OB fold, dimer,	96.05
3koj_A	108	Uncharacterized protein YCF41; single-strand bindi	95.75
1qzg_A	187	Protection of telomeres protein 1; protrein-DNA co	95.73
4gop_A	114	Putative uncharacterized protein; OB fold, ssDNA b	95.65
1xjv_A	294	Protection of telomeres 1; protein-DNA complex, si	95.52
4ah6_A	617	Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo	95.5
3fhw_A	115	Primosomal replication protein N; PRIB BPR162 X-RA	95.48
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	95.09
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	94.82
3en2_A	101	Probable primosomal replication protein N; PRIB RS	94.53
1v1q_A	134	Primosomal replication protein N; primosome, DNA r	94.33
3k8a_A	103	Putative primosomal replication protein; beta-barr	94.28
3tqy_A	158	Single-stranded DNA-binding protein; DNA replicati	94.01
3vdy_A	116	SSB, single-stranded DNA-binding protein SSBB; OB	93.97
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	93.68
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	93.63
1z9f_A	153	Single-strand binding protein; TM0604, single stra	93.45
2vw9_A	134	Single-stranded DNA binding protein; DNA replicati	93.45
1l1o_C	181	Replication protein A 70 kDa DNA-binding subunit;	93.11
3rn5_A	208	Interferon-inducible protein AIM2; OB fold, DNA bi	93.07
3eiv_A	199	Single-stranded DNA-binding protein 2; DNA damage,	92.34
1se8_A	301	Single-strand binding protein; DNA binding protein	92.27
1sr3_A	136	APO-CCME; OB fold, beta barrel, flexible C-termina	92.2
2fxq_A	264	Single-strand binding protein; strand beta-sheet e	91.96
1qvc_A	145	Single stranded DNA binding protein monomer; beta-	91.52
4dka_C	105	RNA-editing complex protein MP81; krepa1, VHH, sin	91.48
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	91.46
3ull_A	132	DNA binding protein; DNA replication, mitochondrio	91.34
3ulp_A	124	Single-strand binding protein; OB-fold, DNA bindin	91.23
1jb7_A	495	Telomere-binding protein alpha subunit; DNA-protei	91.2
1j6q_A	136	Cytochrome C maturation protein E; all-beta protei	91.08
1se8_A	301	Single-strand binding protein; DNA binding protein	90.93
3rlo_A	204	Gamma-interferon-inducible protein 16; HIN200/OB f	90.28
3lgj_A	169	Single-stranded DNA-binding protein; niaid, CAT sc	89.54
3afp_A	168	Single-stranded DNA-binding protein; OB-fold, quat	89.39
3k7u_C	148	MP18 RNA editing complex protein; OB-fold, RNA-edi	89.16
4dam_A	128	Single-stranded DNA-binding protein 1; OB-fold; 1.	88.32
2fxq_A	264	Single-strand binding protein; strand beta-sheet e	88.32
2oq0_A	206	Gamma-interferon-inducible protein IFI-16; OB fold	87.98
3pgz_A	193	Single-stranded DNA-binding protein; ssgcid, singl	87.47
3stb_C	148	RNA-editing complex protein MP42; editosome, nanob	86.31
1eqq_A	178	Single stranded DNA binding protein; beta barrel,	85.74
2kct_A	94	Cytochrome C-type biogenesis protein CCME; solutio	84.61
4dni_A	257	Fusion protein of RNA-editing complex proteins MP	83.18
1xjv_A	294	Protection of telomeres 1; protein-DNA complex, si	80.48

>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.3e-35  Score=220.51  Aligned_cols=134  Identities=22%  Similarity=0.261  Sum_probs=114.2

Q ss_pred             CCccccccceehhhhhccCCCC-CC--CceEECCeEeeEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccC
Q 043474            3 HTLQNTHVKLLAFDLLSLTPTP-DP--ATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTS   78 (160)
Q Consensus         3 ~p~~~~~~~l~i~~i~~l~~~~-~~--~~~~~~~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~   78 (160)
                      |||+++|+||+|+||+.|++.+ .+  +. +++|+||++|+|||.|++++.++ +++.|+|||+|| +|+|++|.+....
T Consensus        12 sPt~~~~v~L~i~DI~~l~~~~~~~~~~~-f~~n~PI~~V~IvGiVv~~~~~~-~~~~ytIDD~TG~~I~cv~w~~~~~~   89 (159)
T 3kf6_A           12 FPTLSRWNPMFISDVHKISFHPHLQRYIG-FWMGFPIRWIQIVGYIAAIDIYE-GKHVLTVDDCSGMVLRVVFIIQDDFS   89 (159)
T ss_dssp             ----CCCCBCCHHHHTTCBCCCC---CCE-EETTEEECEEEEEEEEEEEEEET-TEEEEEEECSSSCEEEEEEEGGGCHH
T ss_pred             CcchhheecchHHHHHhchhcCCCCCcce-eECCeEEEEEEEEEEEEEEEEeC-CEEEEEEecCCCCeEEEEEEccCCCC
Confidence            8999999999999999999877 33  44 89999999999999999999988 779999999999 5999999886421


Q ss_pred             CCCCCCCCCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCChhHHHHHHHHHHHHHHhhcccCC
Q 043474           79 LYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKRYDVVV  157 (160)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~~~~~~~~p~  157 (160)
                                       .......+++|++|+|+|+|+.|+|++||.+++++++.|+|+|+.||.++++++++ + .||
T Consensus        90 -----------------~~~~~~~l~~G~~VrV~G~v~~fr~~rqI~~~~i~~v~d~n~Ev~~W~~~~r~~~~-l-~pW  149 (159)
T 3kf6_A           90 -----------------MSKRAISMSPGNVVCVFGKINSFRSEVELIAQSFEELRDPNDEWKAWQKRMRYKKN-L-TKI  149 (159)
T ss_dssp             -----------------HHHHHTTCCTTCEEEEEEEEECSSSSCEEEEEEEEEECSTHHHHHHHHHHHHHHHH-H-HHH
T ss_pred             -----------------cccccccCCCCCEEEEEEEEEeeCCEEEEEEEEEEECCCcHHHHHHHHHHHHHHHh-C-CCe
Confidence                             00123457899999999999999999999999999999999999999999999998 5 576

>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=100.00  E-value=9.5e-34  Score=205.94  Aligned_cols=128  Identities=20%  Similarity=0.315  Sum_probs=111.1

Q ss_pred             cccccceehhhhhccCCCCCCCceEECCeEeeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCC
Q 043474            6 QNTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRD   85 (160)
Q Consensus         6 ~~~~~~l~i~~i~~l~~~~~~~~~~~~~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~   85 (160)
                      ..+..|++|+||++++++..++.|.++|+++++|++||.|++++..+ +|+.|+||||||+|+|++|.+.+..       
T Consensus         6 ~~~l~PvtIkqil~a~~~~~~~~f~i~g~~i~~V~iVG~V~~~~~~~-~~~~~~ldD~TG~I~~~~W~~~~~~-------   77 (136)
T 4gop_B            6 NNTLRPVTIRQILNAEQPHPDAEFILDGAELGQLTFVAVVRNISRNA-TNVAYSVEDGTGQIEVRQWLDSSSD-------   77 (136)
T ss_dssp             -CCEEECCHHHHHHCBCCSSSCCCBSSSSBCCEEEEEEEEEEEEECS-SEEEEEEECSSCEEEEEEECC-----------
T ss_pred             CCcEEeEEHHHHhhccccCCCCcEEECCEEEEEEEEEEEEEEEEecC-CeEEEEEECCCCCEEEEEecccCCc-------
Confidence            35678999999999987655688999999999999999999999887 8899999999999999999876531       


Q ss_pred             CCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCChhHHHHHHHHHHHHHHh
Q 043474           86 PSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARK  151 (160)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~~~~  151 (160)
                                +......+++|+||+|.|+++.|+|++||.+..|+|++|+||+++|||||+++|..
T Consensus        78 ----------~~~~~~~~~~g~yVrV~G~v~~f~g~~qi~~~~ir~v~d~Nei~~H~Le~i~~hl~  133 (136)
T 4gop_B           78 ----------DSSKASEIRNNVYVRVLGTLKSFQNRRSISSGHMRPVIDYNEVMFHRLEAVHAHLQ  133 (136)
T ss_dssp             --------------CCSCCTTCEEEEEEEEEEETTEEEEEESEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             ----------ccccccccCCCCEEEEEEEEEEeCCEEEEEEEEEEECCCccHHHHHHHHHHHHHHh
Confidence                      01134678999999999999999999999999999999999999999999998754

>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_A 1quq_A 1l1o_B

Probab=100.00  E-value=1.3e-32  Score=198.99  Aligned_cols=124  Identities=19%  Similarity=0.242  Sum_probs=106.7

Q ss_pred             ccccceehhhhhccCCCCCCCceEECCeEeeEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCC
Q 043474            7 NTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRD   85 (160)
Q Consensus         7 ~~~~~l~i~~i~~l~~~~~~~~~~~~~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~   85 (160)
                      ....|+.|+||+++.+.  ++.|.++|+++++|++||.|++++..+ +|+.|+|||||| +|+|++|.+.+..       
T Consensus         4 ~~l~PvtIkqil~a~~~--~~~f~i~g~~i~~V~iVG~V~~~~~~~-~~~~~~ldD~TG~~I~~~~W~~~~~~-------   73 (132)
T 3kdf_D            4 QHIVPCTISQLLSATLV--DEVFRIGNVEISQVTIVGIIRHAEKAP-TNIVYKIDDMTAAPMDVRQWVDTDDT-------   73 (132)
T ss_dssp             -CCEECCHHHHHTCEES--SSCEEETTEECCEEEEEEEEEEEEECS-SEEEEEEECSSSSCEEEEEEC------------
T ss_pred             CceeeEEHHHHhhCccC--CCcEEECCEEEEEEEEEEEEEEEEEcC-CeEEEEEECCCCCEEEEEEEccCCCc-------
Confidence            35679999999998763  568999999999999999999999887 889999999999 9999999876531       


Q ss_pred             CCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCChhHHHHHHHHHHHHHHh
Q 043474           86 PSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARK  151 (160)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~~~~  151 (160)
                                 ......+++|+||+|.|+++.|+|++||.+..|+|++|+||.++|||||+++|..
T Consensus        74 -----------~~~~~~~~~g~yVrV~G~l~~f~g~~qi~~~~ir~v~d~Nei~~H~Le~i~~hl~  128 (132)
T 3kdf_D           74 -----------SSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMV  128 (132)
T ss_dssp             ---------------CCCCTTCEEEEEEEEEEETTEEEEEEEEEEECSSTHHHHHHHHHHHHHHHH
T ss_pred             -----------ccccccccCCCEEEEEEEEEeECCEEEEEEEEEEEcCCccHHHHHHHHHHHHHHe
Confidence                       0124678999999999999999999999999999999999999999999998753

>2pi2_A Replication protein A 32 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2z6k_A 1dpu_A 1z1d_A

Probab=99.95  E-value=1.3e-27  Score=191.41  Aligned_cols=126  Identities=19%  Similarity=0.224  Sum_probs=108.9

Q ss_pred             cccccceehhhhhccCCCCCCCceEECCeEeeEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCC
Q 043474            6 QNTHVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRR   84 (160)
Q Consensus         6 ~~~~~~l~i~~i~~l~~~~~~~~~~~~~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~   84 (160)
                      .....|++|+||+++..  .++.|.++|+++.+|++||+|++++... +|+.|+|+|+|| +|+|++|.+.+..      
T Consensus        43 ~~~l~PvtIkqil~a~~--~d~~f~i~g~~i~~V~ivG~V~~i~~~~-~~~~~~L~D~TG~~I~~k~W~~~~~~------  113 (270)
T 2pi2_A           43 AQHIVPCTISQLLSATL--VDEVFRIGNVEISQVTIVGIIRHAEKAP-TNIVYKIDDMTAAPMDVRQWVDTDDT------  113 (270)
T ss_dssp             CCCCEECCHHHHHHCEE--ETTEEEETTEEESEEEEEEEEEEEEECS-SEEEEEEECSSSSCEEEEEECC----------
T ss_pred             CCceEEEEHHHHhcCcc--CCCcEEECCEEEEEEEEEEEEEEEEecc-ceEEEEEECCCCCEEEEEEEcCcCcc------
Confidence            34568999999999864  3578999999999999999999998877 899999999999 8999999875431      


Q ss_pred             CCCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCChhHHHHHHHHHHHHHHhh
Q 043474           85 DPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARKR  152 (160)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~~~~~  152 (160)
                                  ......+++|+||+|.|+|+.|++++||.+.+|+|++|+||.++|||||+++|...
T Consensus       114 ------------~~~~~~~~~G~yVrV~G~v~~f~g~~qi~i~~ir~v~d~nEi~~H~Le~i~~hl~~  169 (270)
T 2pi2_A          114 ------------SSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVL  169 (270)
T ss_dssp             ---------------CCCCCTTCEEEEEEEEEEETTEEEEEEEEEEECSCTHHHHHHHHHHHHHHHHH
T ss_pred             ------------cchhhcCCCCCEEEEEEEEEecCCeeEEEEEEEEecCCHhHHHHHHHHHHHHHHHH
Confidence                        01235789999999999999999999999999999999999999999999987754

>3kf8_A Protein STN1; OB fold; 2.40A {Candida tropicalis mya-3404}

Probab=99.91  E-value=1.7e-23  Score=161.44  Aligned_cols=139  Identities=13%  Similarity=0.176  Sum_probs=114.6

Q ss_pred             CCccccccceehhhhhccCCCC---------CCCceEECCeEeeEEEEEEEEEEeeccCC-------ceEEEEEeCCCce
Q 043474            3 HTLQNTHVKLLAFDLLSLTPTP---------DPATFSRSGKLLSRAEIVGTITSRDHKPS-------KFIKFTVDDGTGC   66 (160)
Q Consensus         3 ~p~~~~~~~l~i~~i~~l~~~~---------~~~~~~~~~~~i~~v~ivG~V~~~~~~~~-------~~~~~~IdDgTG~   66 (160)
                      +||+++|+||+|+||+.++...         .++.|+++|+||++|+|+|+|++++.+..       .|+.|+|||+||.
T Consensus        43 sPT~~~~vpL~I~DI~~l~~~~~~yg~~~~~~~~i~f~~NhPI~~V~IvG~VVg~~~k~~r~~~~~~~~~~l~IDDsSG~  122 (220)
T 3kf8_A           43 APTFDKTIPLFISDINNSPNLYGIYNYIADHLRHVVLVNNYPVNQINIFGKIVYEQYKEKEFNGVEESYVILVISDFIGI  122 (220)
T ss_dssp             STTTTSEEECCHHHHHTCCCTHHHHGGGGGGCTTCEEETTEEECEEEEEEEEEEEEEECCBCSSCBCCEEEEEEECCCSS
T ss_pred             CcccCcccceEhHHhhhchhhhcccccccccCccEEEECCcccEEEEEEEEEEEEEEEeccccccccceEEEEEeCCCCC
Confidence            7999999999999999998633         25789999999999999999999986652       5799999999996


Q ss_pred             ---EEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeCC--------ceEEEEEEEEEc---
Q 043474           67 ---VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRG--------DVQITVSDVVIE---  132 (160)
Q Consensus        67 ---I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~--------~~qi~~~~i~~v---  132 (160)
                         |.|++-.....+    .+    +         .......|..|+|+|.++.|++        .+||.+++++.+   
T Consensus       123 ~s~i~~k~~~~~~~~----~g----l---------~l~~~~~G~iV~VkG~i~~~r~~~~~~~~~~rei~ve~i~vl~~~  185 (220)
T 3kf8_A          123 DSKIRVRLSQEQFKE----VG----L---------TLDKKNYGKIVELEGEIYNWYDSINVSKKPDRELKVSKITVLSHR  185 (220)
T ss_dssp             SCEEEEEEEHHHHHT----TT----C---------CTTSCCTTCEEEEEEEEEECCCSTTTTSCCCEEEEEEEEEEEESS
T ss_pred             CceEEEEecHHHhhc----cC----c---------cccccCCCeEEEEEEEEEeeccccccccccceEEEEEEEEEeccC
Confidence               777654332210    00    0         0112448999999999999998        899999999999   


Q ss_pred             -CChhHHHHHHHHHHHHHHhhcccCCC
Q 043474          133 -KDPNMEVLHWLDCLRLARKRYDVVVN  158 (160)
Q Consensus       133 -~d~n~~~~h~le~~~~~~~~~~~p~~  158 (160)
                       .|...|+.||-++++.++++++.||.
T Consensus       186 ~~dl~~Ei~~W~~~~~fR~~vL~~PWv  212 (220)
T 3kf8_A          186 PDGLHFEFEQWKKRMEFRKNNLVEPWV  212 (220)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHTTSCCC
T ss_pred             CCcHHHHHHHHHHHHHHHHHhccCCeE
Confidence             55589999999999999999999995

>3mxn_B RECQ-mediated genome instability protein 2; bloom syndrome, helicase, RMI, topoisomerase, replication PR replication; 1.55A {Homo sapiens} PDB: 4day_B 3nbh_B

Probab=99.10  E-value=3e-09  Score=76.63  Aligned_cols=118  Identities=15%  Similarity=0.063  Sum_probs=90.1

Q ss_pred             cccceehhhhhccCCCCCCCceEEC-------CeEeeEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCC
Q 043474            8 THVKLLAFDLLSLTPTPDPATFSRS-------GKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLY   80 (160)
Q Consensus         8 ~~~~l~i~~i~~l~~~~~~~~~~~~-------~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~   80 (160)
                      -.+|+|+.||.+.+++ ..+.|.+.       .-++..|.+-|.|+.. ..  .  .+.|||+||++...--.+...   
T Consensus        24 PpvK~l~~QLr~~~~~-~~~~w~l~r~~~g~~~l~~s~VWmQG~VV~~-~~--g--~~~LdDgTG~~~v~g~~~vp~---   94 (150)
T 3mxn_B           24 PPLKVLAEQLRRDAEG-GPGAWRLSRAAAGRGPLDLAAVWMQGRVVMA-DR--G--EARLRDPSGDFSVRGLERVPR---   94 (150)
T ss_dssp             CCEECCHHHHHHHEES-CTTCCEECCTTTTCCCEECSEEEEEEEEEEE-ET--T--EEEEEETTEEEEEECGGGSCC---
T ss_pred             CcHHHHHHHHHHHhhC-CCceEEEEecccCCccceeEEEEEEeEEEEe-CC--C--eEEEECCCceEEEeeccccCC---
Confidence            3569999999988663 33344333       2478999999999996 22  2  589999999977643221111   


Q ss_pred             CCCCCCCccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCCh-hHHHHHHHHHHHHHHhh
Q 043474           81 LPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDP-NMEVLHWLDCLRLARKR  152 (160)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~-n~~~~h~le~~~~~~~~  152 (160)
                                        -...++.|+||-|.|.+..-....-|.+.+|.-+++. +-|..+++|++++|+.+
T Consensus        95 ------------------g~p~l~~G~YVMV~G~v~~~s~eP~i~AvKm~DLS~~p~~E~mW~lEV~el~r~i  149 (150)
T 3mxn_B           95 ------------------GRPCLVPGKYVMVMGVVQACSPEPCLQAVKMTDLSDNPIHESMWELEVEDLHRNI  149 (150)
T ss_dssp             ------------------CSCCCSTTCEEEEEEEEEECSSSCEEEEEEEEECCSCHHHHHHHHHHHHHHHTTC
T ss_pred             ------------------CCcccCCCCEEEEEEEEEecCCCceEEEEEeeeCCCCcchHHHHHHHHHHHHhcC
Confidence                              1245889999999999998888889999999988765 89999999999998864

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3

Probab=98.99  E-value=3.6e-09  Score=74.39  Aligned_cols=74  Identities=22%  Similarity=0.386  Sum_probs=58.5

Q ss_pred             EEEEEEEEEEee------ccCC--ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEE
Q 043474           38 RAEIVGTITSRD------HKPS--KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVA  109 (160)
Q Consensus        38 ~v~ivG~V~~~~------~~~~--~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V  109 (160)
                      .+.+.|+|.++.      .+++  +|..++|.|.||+|++++|.+..                        +.++.|++|
T Consensus        14 ~v~~~~~V~~~~~~~~~~~k~G~~~~~~~~l~D~TG~I~~tlW~~~~------------------------~~~~~G~vv   69 (119)
T 1o7i_A           14 SVNVTVRVLEASEARQIQTKNGVRTISEAIVGDETGRVKLTLWGKHA------------------------GSIKEGQVV   69 (119)
T ss_dssp             SEEEEEEEEEECCCEEECCTTCCEEEEEEEEEETTEEEEEEEEGGGT------------------------TCCCTTCEE
T ss_pred             cEEEEEEEEECCCCeeEEecCCCEEEEEEEEEeCCCEEEEEEECChh------------------------hcCCCCCEE
Confidence            355666666653      2233  79999999999999999997643                        247899999


Q ss_pred             EEE-EEeceeCCceEEEEEE---EEEcCCh
Q 043474          110 RVR-GRIASYRGDVQITVSD---VVIEKDP  135 (160)
Q Consensus       110 ~V~-G~v~~f~~~~qi~~~~---i~~v~d~  135 (160)
                      +|. |+++.|+|..||.+.+   |.++.++
T Consensus        70 ~i~~g~v~~~~g~~qL~i~~~~~i~~~~~~   99 (119)
T 1o7i_A           70 KIENAWTTAFKGQVQLNAGSKTKIAEASED   99 (119)
T ss_dssp             EEEEEEEEEETTEEEEEECTTCEEEECCCT
T ss_pred             EEEeEEEEEeCCEEEEEECCCEEEEEcCCc
Confidence            999 9999999999999987   7776653

>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_A

Probab=98.96  E-value=3e-09  Score=73.83  Aligned_cols=73  Identities=16%  Similarity=0.145  Sum_probs=60.2

Q ss_pred             eEEEEEEEEEEeeccC--CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE-E
Q 043474           37 SRAEIVGTITSRDHKP--SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR-G  113 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~--~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~-G  113 (160)
                      ..+.+.|+|.++....  ..+...+|.|.||+|.+++|.+...                       ..+++|++|+|+ |
T Consensus        16 ~~v~v~~~V~~~~~~~~~~~~~~~~l~DeTG~I~~t~W~~~~~-----------------------~~~~~G~~V~i~n~   72 (109)
T 2kbn_A           16 QWANLKAKVIQLWENTHESISQVGLLGDETGIIKFTIWKNAEL-----------------------PLLEQGESYLLRSV   72 (109)
T ss_dssp             CEEEEEEEEEEEEECCCSSEEEEEEEECTTCCEEEEEEGGGCC-----------------------CCCCTTCEEEEEEE
T ss_pred             CcEEEEEEEEEeEcCCCCeEEEEEEEECCCCeEEEEEECcccc-----------------------cccCCCCEEEEEEE
Confidence            5678889999887532  3677899999999999999985432                       468899999999 8


Q ss_pred             EeceeCCceEEEEEEEEEc
Q 043474          114 RIASYRGDVQITVSDVVIE  132 (160)
Q Consensus       114 ~v~~f~~~~qi~~~~i~~v  132 (160)
                      .++.|+|..||++.+...+
T Consensus        73 ~v~~~~G~~~L~v~~~~~I   91 (109)
T 2kbn_A           73 VVGEYNDRFQVQVNKNSSI   91 (109)
T ss_dssp             EEEEETTEEEEEECSSSEE
T ss_pred             EEEEECCEEEEEECCceEE
Confidence            9999999999999875433

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=98.91  E-value=9.3e-09  Score=71.56  Aligned_cols=74  Identities=16%  Similarity=0.354  Sum_probs=58.8

Q ss_pred             eEEEEEEEEEEe-ec-----cC---CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSR-DH-----KP---SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~-~~-----~~---~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..+.++|.|.++ ..     +.   +++..++|.|+||+|++++|.+...                     ....+++|+
T Consensus        17 ~~v~i~~~V~~~~~~~~~~~k~G~~~~~~~~~l~D~TG~I~~t~w~~~~~---------------------~~~~l~~G~   75 (115)
T 2k50_A           17 AETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVFWTENIK---------------------LLKKFREGD   75 (115)
T ss_dssp             CEEEEEEEEEEECCCEECCCTTSSCCEEEEEEEEETTEEEEEEEETTGGG---------------------GGGTCCTTS
T ss_pred             CEeEEEEEEEECCCceEEEcCCCCEEEEEEEEEEeCCCeEEEEEeCchhh---------------------hhhcCCCCC
Confidence            456788888887 22     22   4789999999999999999976532                     225689999


Q ss_pred             EEEEEEEe--ceeCCceEEEEEEEEE
Q 043474          108 VARVRGRI--ASYRGDVQITVSDVVI  131 (160)
Q Consensus       108 ~V~V~G~v--~~f~~~~qi~~~~i~~  131 (160)
                      +|.+.|.+  ..|+|.+||.+.+...
T Consensus        76 vv~i~g~~v~~~f~g~~qL~~~~~~~  101 (115)
T 2k50_A           76 VIRIKDVNIRGGFGGRKEAHLMPRST  101 (115)
T ss_dssp             EEEEEEEEECCCSSSSCEEEECTTCC
T ss_pred             EEEEEeeEEccccCCeEEEEECCCce
Confidence            99999998  6799999999877443

>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum}

Probab=98.84  E-value=2.6e-08  Score=68.78  Aligned_cols=72  Identities=18%  Similarity=0.274  Sum_probs=56.5

Q ss_pred             EEEEEEEEEEeecc----CC---ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEE
Q 043474           38 RAEIVGTITSRDHK----PS---KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVAR  110 (160)
Q Consensus        38 ~v~ivG~V~~~~~~----~~---~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~  110 (160)
                      .+.+.|.|.++...    .+   .+..++|.|.||+|.+++|.+.                           +++|++|+
T Consensus        15 ~v~v~~~V~~~~~~~~~k~G~~~~v~~~~l~DeTG~I~~tlW~~~---------------------------l~~Gdvv~   67 (106)
T 2k75_A           15 YVSVIGKITGIHKKEYESDGTTKSVYQGYIEDDTARIRISSFGKQ---------------------------LQDSDVVR   67 (106)
T ss_dssp             EEEEEEEEEEEEEEEEEETTEEEEEEEEEEECSSCEEEEEEESSC---------------------------CCTTEEEE
T ss_pred             eEEEEEEEEEccccccccCCCeeEEEEEEEEcCCCeEEEEEEcCc---------------------------cCCCCEEE
Confidence            45566666655432    33   3889999999999999999531                           77999999


Q ss_pred             EE-EEeceeCCceEEEEEE---EEEcCChh
Q 043474          111 VR-GRIASYRGDVQITVSD---VVIEKDPN  136 (160)
Q Consensus       111 V~-G~v~~f~~~~qi~~~~---i~~v~d~n  136 (160)
                      +. |.++.|+|+.||.+.+   |.+++++.
T Consensus        68 i~ng~v~~~~g~~~L~v~~~~~I~~~~~~~   97 (106)
T 2k75_A           68 IDNARVAQFNGYLSLSVGDSSRIESVNVNI   97 (106)
T ss_dssp             EEEEEEEEETTEEEEEECTTSEEEECCSCC
T ss_pred             EEeeEEeEECCEEEEEECCcEEEEECCCCC
Confidence            99 9999999999999876   66666553

>3e0e_A Replication protein A; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.60A {Methanococcus maripaludis} PDB: 2k5v_A

Probab=98.76  E-value=8.5e-08  Score=65.06  Aligned_cols=73  Identities=19%  Similarity=0.307  Sum_probs=57.7

Q ss_pred             eEEEEEEEEEEeec-----c-C---CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH-----K-P---SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-----~-~---~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..+.+.|+|.++..     + .   +.+..++|.|.||+|.+.+|.+...                       ..+++|+
T Consensus        12 ~~v~i~~~V~~~~~~r~~~~~~G~~~~v~~~~l~DeTG~I~~tlW~~~~~-----------------------~~i~~Gd   68 (97)
T 3e0e_A           12 LSGTINAEVVTAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNELAD-----------------------FEVKKGD   68 (97)
T ss_dssp             EEEEEEEEEEEECCCEEEC----CCEEEEEEEEEETTEEEEEEEEGGGGG-----------------------CCCCTTC
T ss_pred             CcEEEEEEEEECCCceEEEcCCCCeeEEEEEEEECCCCcEEEEEECCccc-----------------------cccCCCC
Confidence            57888999988762     1 1   2577899999999999999987542                       1689999


Q ss_pred             EEEEEEEeceeCCceEEEEEEEEEc
Q 043474          108 VARVRGRIASYRGDVQITVSDVVIE  132 (160)
Q Consensus       108 ~V~V~G~v~~f~~~~qi~~~~i~~v  132 (160)
                      +|++.|+++.|.+..+|.+.+-..+
T Consensus        69 vv~i~g~v~~~~~~~el~~g~~~~i   93 (97)
T 3e0e_A           69 IAEVSGYVKQGYSGLEISVDNIGII   93 (97)
T ss_dssp             EEEEEEEEEEC--CEEEEEEEEEEE
T ss_pred             EEEEEEEEEEcCCeEEEEECCCcEE
Confidence            9999999999999999998876544

>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii}

Probab=98.47  E-value=2.2e-06  Score=58.90  Aligned_cols=75  Identities=31%  Similarity=0.356  Sum_probs=59.0

Q ss_pred             eEEEEEEEEEEeec------cC---CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH------KP---SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~~---~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      ..+.|.|+|.++..      +.   +....++|.|.||+|.+.+|.+...                       ..+++|+
T Consensus        15 ~~v~v~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D~TG~IrvtlW~~~a~-----------------------~~l~~Gd   71 (105)
T 3dm3_A           15 MTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTD-----------------------IDVGRGD   71 (105)
T ss_dssp             EEEEEEEEEEEEEEEEEEECTTSCEEEEEEEEEEETTEEEEEEEEGGGGG-----------------------SCCCTTC
T ss_pred             CeEEEEEEEEECCCceEEEcCCCCeeEEEEEEEECCCCcEEEEEECcccc-----------------------cccCCCC
Confidence            67888888888762      11   2456899999999999999987643                       1688999


Q ss_pred             EEEEEEEecee-CCceEEEEEEEEEcCC
Q 043474          108 VARVRGRIASY-RGDVQITVSDVVIEKD  134 (160)
Q Consensus       108 ~V~V~G~v~~f-~~~~qi~~~~i~~v~d  134 (160)
                      .|.+.|.++.+ +|.++|.+.+-..+..
T Consensus        72 vv~i~g~vk~~~~g~~eL~~g~~~~i~~   99 (105)
T 3dm3_A           72 YVRVRGYIREGYYGGLECTANYVEILKK   99 (105)
T ss_dssp             EEEEEEEEEECTTSSEEEEEEEEEEEEC
T ss_pred             EEEEEEEEEEccCCCEEEEeCCceEEEe
Confidence            99999999997 4589999887665543

>3au7_A TIAS, putative uncharacterized protein; ATP hydrolysis, RNA binding protein; 2.60A {Archaeoglobus fulgidus} PDB: 3amt_A* 3amu_A*

Probab=97.89  E-value=5.4e-05  Score=63.13  Aligned_cols=78  Identities=17%  Similarity=0.249  Sum_probs=63.3

Q ss_pred             eEeeEEEEEEEEEEe-eccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           34 KLLSRAEIVGTITSR-DHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        34 ~~i~~v~ivG~V~~~-~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      .+.+.+.+-|.|.+. ....+..+.|+|+|++|+|+|..|.+...-                  ......+.+||.|.|.
T Consensus       282 ~~~~~~~v~G~V~~~P~~~~GGHV~f~l~d~~~~i~c~ayeptk~f------------------r~~vr~L~~GD~V~v~  343 (402)
T 3au7_A          282 ENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAAFEPTKQF------------------RNVIRLLRKGDVVEVY  343 (402)
T ss_dssp             CTTCEEEEEEEEEEEEEEETTTEEEEEEEETTEEEEEEECGGGTTH------------------HHHHTTCCTTCEEEEE
T ss_pred             ccCceEEEEEEEecCcEeccCceEEEEEEcCCCEEEEEEEccchHH------------------HHHHhcCCCCCEEEEE
Confidence            467899999999998 555555689999999999999999866431                  1233578899999999


Q ss_pred             EEeceeCCceEEEEEEEEEcC
Q 043474          113 GRIASYRGDVQITVSDVVIEK  133 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~  133 (160)
                      |.++.  +  ||+++++.++.
T Consensus       344 G~v~~--g--tLnvEk~~v~~  360 (402)
T 3au7_A          344 GSMKK--D--TINLEKIQIVE  360 (402)
T ss_dssp             EEEET--T--EEEEEEEEEEE
T ss_pred             EeecC--C--EEEEEEEEEcc
Confidence            99887  3  99999999874

>1wjj_A Hypothetical protein F20O9.120; DNA-binding protein-related, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.40.4.3

Probab=97.64  E-value=0.0003  Score=50.90  Aligned_cols=68  Identities=21%  Similarity=0.435  Sum_probs=52.6

Q ss_pred             eEEEEEEEEEEeec------c------------CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccc
Q 043474           37 SRAEIVGTITSRDH------K------------PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATD   98 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~------------~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (160)
                      ..+.+.|+|.++..      +            .+......|.|.||+|...+|.+..                      
T Consensus        27 ~~v~l~~kVl~~~~v~~~~~~~R~dG~~~~~~r~~~V~~~lVgDeTG~I~ftlW~e~~----------------------   84 (145)
T 1wjj_A           27 TGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFTARNDQV----------------------   84 (145)
T ss_dssp             CCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEEECTTHH----------------------
T ss_pred             CceEEEEEEEEcccccccccccccCCccccccCCceEEEEEEEcCCcEEEEEEecCCc----------------------
Confidence            45666777766541      1            2356789999999999999997532                      


Q ss_pred             cccccccCcEEEEEE-EeceeCCceEEEEEE
Q 043474           99 FAAKIKIGLVARVRG-RIASYRGDVQITVSD  128 (160)
Q Consensus        99 ~~~~~~~G~~V~V~G-~v~~f~~~~qi~~~~  128 (160)
                        +.+++|+.|++.+ .++.|+|..+|.+.+
T Consensus        85 --~~l~~Gd~v~i~na~v~~~~G~~~L~vgk  113 (145)
T 1wjj_A           85 --DLMKPGATVILRNSRIDMFKGTMRLGVDK  113 (145)
T ss_dssp             --HHTCTTCEEEEEEEEEEEETTEEEEEECT
T ss_pred             --CcCCCCCEEEEeccEEEeECCEEEEEECC
Confidence              3478999999987 689999999998875

>1nnx_A Protein YGIW; structural genomics, hypothetical protein, OB-fold, structure 2 function project, S2F, unknown function; 1.45A {Escherichia coli} SCOP: b.40.10.1

Probab=97.58  E-value=0.001  Score=45.75  Aligned_cols=70  Identities=13%  Similarity=0.209  Sum_probs=53.4

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+-|.|+..-..+    .|...|+||+|.+-+=.+.-.                      -..+.+++.|+|.|.|.
T Consensus        38 ~~V~L~G~Iv~~~~~d----~Y~F~D~TG~I~VeId~~~w~----------------------g~~v~p~~~Vri~GevD   91 (109)
T 1nnx_A           38 TWVTLRGNIVERISDD----LYVFKDASGTINVDIDHKRWN----------------------GVTVTPKDTVEIQGEVD   91 (109)
T ss_dssp             EEEEEEEEEEEEEETT----EEEEEETTEEEEEECCGGGST----------------------TCCCCTTSCEEEEEEEE
T ss_pred             CeEEEEEEEEEEeCCC----eEEEECCCccEEEEEChhhcC----------------------CcccCCCCEEEEEEEEC
Confidence            6788889888876654    688999999999876222111                      13577899999999999


Q ss_pred             eeCCceEEEEEEEEEc
Q 043474          117 SYRGDVQITVSDVVIE  132 (160)
Q Consensus       117 ~f~~~~qi~~~~i~~v  132 (160)
                      .--+...|.+.+|+.+
T Consensus        92 kd~~~~eIdV~~i~~~  107 (109)
T 1nnx_A           92 KDWNSVEIDVKQIRKV  107 (109)
T ss_dssp             EETTEEEEEEEEEEEC
T ss_pred             CCCCceEEEEEEEEEc
Confidence            7556789999998865

>3nem_A Aspartyl-tRNA synthetase; rossmann fold, OB fold, ligase; HET: AMO ATP; 1.89A {Thermococcus kodakarensis} PDB: 3nel_A* 3nen_A 1b8a_A*

Probab=97.39  E-value=0.0011  Score=55.85  Aligned_cols=80  Identities=13%  Similarity=0.085  Sum_probs=58.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +...+.|.|+||.|+|++-.+...                .+..+....+..|++|.|.|.+.
T Consensus        17 ~~V~v~Gwv~~~R~~g-~~~Fi~LrD~~g~iQ~v~~~~~~~----------------~~~~~~~~~l~~~~~V~V~G~v~   79 (438)
T 3nem_A           17 QKVKVAGWVWEVKDLG-GIKFLWIRDRDGIVQITAPKKKVD----------------PELFKLIPKLRSEDVVAVEGVVN   79 (438)
T ss_dssp             CEEEEEEEEEEEEEET-TEEEEEEEETTEEEEEEEETTTSC----------------HHHHHHGGGCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEEECCeeEEEEEeCCcCC----------------HHHHHHHhcCCCCCEEEEEEEEE
Confidence            5789999999998765 666779999999999987432211                00011235689999999999997


Q ss_pred             eeC---CceEEEEEEEEEcC
Q 043474          117 SYR---GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~---~~~qi~~~~i~~v~  133 (160)
                      .-.   +...|.+.++..+.
T Consensus        80 ~~~~~~~~~el~~~~i~vl~   99 (438)
T 3nem_A           80 FTPKAKLGFEILPEKIVVLN   99 (438)
T ss_dssp             ECTTSTTSEEEEEEEEEEEE
T ss_pred             eCCCCCCcEEEEEEEEEEEe
Confidence            654   46788888887654

>1e1o_A Lysyl-tRNA synthetase, heat inducible; ligase, aminoacyl-tRNA synthetase, protein biosynthesis; HET: LYS; 2.12A {Escherichia coli} SCOP: b.40.4.1 d.104.1.1 PDB: 1e1t_A* 1e22_A* 1e24_A* 1lyl_A 1bbu_A* 1bbw_A 1krs_A 1krt_A

Probab=97.37  E-value=0.0014  Score=56.17  Aligned_cols=80  Identities=16%  Similarity=0.212  Sum_probs=59.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccc-cccccccCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATD-FAAKIKIGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~G~~V~V~G~v  115 (160)
                      ..|.|.|+|.++.... +..-+.|.|+||.|+|++-.+....                +... ....+..|++|.|.|.|
T Consensus        65 ~~V~v~Gwv~~~R~~g-k~~F~~LrD~sg~iQvv~~~~~~~~----------------~~~~~~~~~l~~g~~V~V~G~v  127 (504)
T 1e1o_A           65 IEVSVAGRMMTRRIMG-KASFVTLQDVGGRIQLYVARDSLPE----------------GVYNDQFKKWDLGDIIGARGTL  127 (504)
T ss_dssp             CEEEEEEEEEEEEEET-TEEEEEEEETTEEEEEEEETTTSST----------------THHHHTGGGCCTTCEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CcEEEEEEECCeeEEEEEECCcCCH----------------HHHHHHHhcCCCCCEEEEEEEE
Confidence            4799999999998776 6688999999999999974332110                0011 23568899999999999


Q ss_pred             ceeC-CceEEEEEEEEEcC
Q 043474          116 ASYR-GDVQITVSDVVIEK  133 (160)
Q Consensus       116 ~~f~-~~~qi~~~~i~~v~  133 (160)
                      ..-. |...|.+..+..+.
T Consensus       128 ~~~~~ge~ei~~~~i~vl~  146 (504)
T 1e1o_A          128 FKTQTGELSIHCTELRLLT  146 (504)
T ss_dssp             EECTTCCEEEEEEEEEEEE
T ss_pred             EecCCceEEEEEEEEEEec
Confidence            7543 67889999887664

>1wyd_A Hypothetical aspartyl-tRNA synthetase; archaea, LIGA; HET: EPE; 2.30A {Sulfolobus tokodaii}

Probab=97.32  E-value=0.0015  Score=54.94  Aligned_cols=77  Identities=13%  Similarity=0.127  Sum_probs=58.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +..-+.|.|+||.|+|++-.+. .                 . .+....+..|++|.|.|.|.
T Consensus        17 ~~V~v~Gwv~~~R~~g-~~~F~~lrD~~g~iQ~v~~~~~-~-----------------~-~~~~~~l~~~~~v~v~G~v~   76 (429)
T 1wyd_A           17 KEVIWAGWVHLLRDLG-GKKFIILRDKTGLGQVVVDKNS-S-----------------A-FGISQELTQESVIQVRGIVK   76 (429)
T ss_dssp             CEEEEEEEEEEEEEET-TEEEEEEEETTEEEEEEECTTS-T-----------------T-HHHHTTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEEECCeeEEEEEeCCh-H-----------------H-HHHHHhCCCCCEEEEEEEEE
Confidence            4699999999998775 6678999999999999974321 1                 0 01225688999999999998


Q ss_pred             eeCC---ceEEEEEEEEEcC
Q 043474          117 SYRG---DVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~~---~~qi~~~~i~~v~  133 (160)
                      .-..   ...|.+.++..+.
T Consensus        77 ~~~~~~~~~el~~~~~~vl~   96 (429)
T 1wyd_A           77 ADKRAPRGIELHAEEITLLS   96 (429)
T ss_dssp             ECSSSGGGEEEEEEEEEEEE
T ss_pred             ecCCCCccEEEEEeEEEEec
Confidence            7653   5788888887654

>3m4p_A Ehasnrs, asparaginyl-tRNA synthetase, putative; aminoacyl-tRNA synthetase, tRNA ligase, AARS, translation, ATP-binding, nucleotide-binding; HET: 4AD; 2.83A {Entamoeba histolytica} PDB: 3m4q_A

Probab=97.30  E-value=0.002  Score=54.59  Aligned_cols=80  Identities=15%  Similarity=0.270  Sum_probs=58.1

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++...+++..-+.|.|+||.|+|++-.+...                 . ......+..|+.|.|.|.|.
T Consensus        31 ~~V~v~Gwv~~~R~~Gk~~~Fi~LrD~sg~iQvv~~~~~~~-----------------~-~~~~~~l~~g~~V~V~G~v~   92 (456)
T 3m4p_A           31 KLVTFKGWAYHIRKARKTLIFVELRDGSGYCQCVIFGKELC-----------------E-PEKVKLLTRECSLEITGRLN   92 (456)
T ss_dssp             SEEEEEEEEEEEECCSSSEEEEEEECSSCEEEEEEESTTTT-----------------C-HHHHTTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCCCceEEEEEEeCCccEEEEEecccch-----------------h-hHHhhcCCCccEEEEEeEEE
Confidence            57899999999887653566789999999999987431111                 0 00123688999999999996


Q ss_pred             eeC-----------CceEEEEEEEEEcCC
Q 043474          117 SYR-----------GDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f~-----------~~~qi~~~~i~~v~d  134 (160)
                      .-.           |...|.+.++..+..
T Consensus        93 ~~~~~~~~~~~~t~g~~El~~~~i~vl~~  121 (456)
T 3m4p_A           93 AYAGKNHPPEIADILNLEMQVTEWKVIGE  121 (456)
T ss_dssp             CCCSSSCCCSCTTBCSSEEEEEEEEEEEC
T ss_pred             ecCCcccCcccCCCCcEEEEEeEEEEEec
Confidence            422           557899999886643

>1eov_A ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA synthetase, tRNA ligase, APO-enzyme, OB-fold,; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.1 d.104.1.1 PDB: 1asy_A* 1asz_A*

Probab=97.20  E-value=0.0017  Score=55.45  Aligned_cols=83  Identities=8%  Similarity=0.160  Sum_probs=59.4

Q ss_pred             eEEEEEEEEEEeeccCCce-EEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKF-IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~-~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      ..|.|.|+|.++.... +. +-+.|.|+||.|+|++-.+.....             .....+....+..|++|.|.|.|
T Consensus        37 ~~V~v~GwV~~~R~~g-~~l~Fi~LrD~~g~iQvv~~~~~~~~~-------------~~~~~~~~~~l~~e~~V~V~G~v  102 (487)
T 1eov_A           37 KEVLFRARVHNTRQQG-ATLAFLTLRQQASLIQGLVKANKEGTI-------------SKNMVKWAGSLNLESIVLVRGIV  102 (487)
T ss_dssp             CEEEEEEEEEEEEECS-SSEEEEEEEETTEEEEEEEECCSSSSS-------------CHHHHHHHTTCCTTCEEEEEEEE
T ss_pred             CEEEEEEEEEEeeccC-CccEEEEEEECCccEEEEEeccccccc-------------cHHHHHHHhcCCCCCEEEEEEEE
Confidence            4699999999998776 54 689999999999999743211000             00001123568999999999999


Q ss_pred             ceeC--------CceEEEEEEEEEcC
Q 043474          116 ASYR--------GDVQITVSDVVIEK  133 (160)
Q Consensus       116 ~~f~--------~~~qi~~~~i~~v~  133 (160)
                      ..-.        |...|.+..+..+.
T Consensus       103 ~~~~~~~~~~~~g~~El~~~~i~vl~  128 (487)
T 1eov_A          103 KKVDEPIKSATVQNLEIHITKIYTIS  128 (487)
T ss_dssp             EECSSCCTTSSEEEEEEEEEEEEEEE
T ss_pred             EeCCCCCcCCCCCcEEEEEEEEEEee
Confidence            8765        45788888887665

>4ex5_A Lysine--tRNA ligase; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: LYS; 2.40A {Burkholderia thailandensis}

Probab=97.18  E-value=0.0013  Score=56.67  Aligned_cols=80  Identities=18%  Similarity=0.226  Sum_probs=58.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +...+.|.|+||.|+|++-.+...                .+..+....+..|++|.|.|.|.
T Consensus        87 ~~V~v~GwV~~~R~~G-k~~Fi~LrD~sg~iQvv~~~~~~~----------------~~~~~~~~~l~~gd~V~V~G~v~  149 (529)
T 4ex5_A           87 LEVAIAGRMMLKRVMG-KASFATVQDGSGQIQFFVTPADVG----------------AETYDAFKKWDLGDIVAARGVLF  149 (529)
T ss_dssp             CEEEEEEEEEEEEEET-TEEEEEEECSSCEEEEEECHHHHC----------------HHHHHHHHTCCTTCEEEEEEEEE
T ss_pred             cEEEEEEEEEeeecCC-CeEEEEEEeCCeeEEEEEECCcCC----------------HHHHHHHhcCCCCCEEEEEEEEE
Confidence            5799999999988765 667789999999999987432111                00011234689999999999997


Q ss_pred             eeC-CceEEEEEEEEEcC
Q 043474          117 SYR-GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~-~~~qi~~~~i~~v~  133 (160)
                      .-. |...|.+..+..+.
T Consensus       150 ~t~~gelel~~~~i~vLs  167 (529)
T 4ex5_A          150 RTNKGELSVKCTQLRLLA  167 (529)
T ss_dssp             ECTTSCEEEEEEEEEEEE
T ss_pred             EcCCCcEEEEEEEEEEEe
Confidence            544 67889999887654

>1x54_A Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthetase, riken structural genomics/proteom initiative, RSGI, structural genomics, ligase; HET: 4AD; 1.45A {Pyrococcus horikoshii} PDB: 1x55_A* 1x56_A

Probab=97.18  E-value=0.0013  Score=55.42  Aligned_cols=80  Identities=18%  Similarity=0.167  Sum_probs=59.5

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +..-+.|.|+||.|+|++-.+...                ....+....+..|++|.|.|.|.
T Consensus        17 ~~V~v~G~v~~~R~~g-~~~F~~lrD~~g~iQ~v~~~~~~~----------------~~~~~~~~~l~~~~~v~v~G~v~   79 (434)
T 1x54_A           17 KKVRLAGWVYTNMRVG-KKIFLWIRDSTGIVQAVVAKNVVG----------------EETFEKAKKLGRESSVIVEGIVK   79 (434)
T ss_dssp             CEEEEEEEEEEEEEET-TEEEEEEEETTEEEEEEECHHHHC----------------HHHHHHHHTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEEECCEEEEEEEECCcCC----------------HHHHHHHhcCCCCCEEEEEEEEE
Confidence            4699999999998775 667899999999999997422110                00011225689999999999998


Q ss_pred             eeCC---ceEEEEEEEEEcC
Q 043474          117 SYRG---DVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~~---~~qi~~~~i~~v~  133 (160)
                      .-..   ...|.+.++..+.
T Consensus        80 ~~~~~~~~~el~~~~~~vl~   99 (434)
T 1x54_A           80 ADERAPGGAEVHVEKLEVIQ   99 (434)
T ss_dssp             ECTTSGGGEEEEEEEEEEEE
T ss_pred             ecCCCCccEEEEEeEEEEee
Confidence            7653   5789998887665

>3a74_A Lysyl-tRNA synthetase; aminoacyl tRNA synthetase, ligase, protein biosynthesis, AMI tRNA synthetase, ATP-binding, magnesium; HET: B4P LYN; 1.80A {Geobacillus stearothermophilus} PDB: 3e9h_A* 3e9i_A*

Probab=97.16  E-value=0.0011  Score=56.72  Aligned_cols=80  Identities=18%  Similarity=0.213  Sum_probs=59.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +..-+.|.|+||.|+|++-.+...                .+..+....+..|++|.|.|.|.
T Consensus        57 ~~V~v~Gwv~~~R~~g-k~~F~~LrD~sg~iQvv~~~~~~~----------------~~~~~~~~~l~~g~~v~V~G~v~  119 (493)
T 3a74_A           57 IEVAVAGRIMTKRGMG-KAGFAHIQDVTGQIQIYVRQDDVG----------------EQQYELFKISDLGDIVGVRGTMF  119 (493)
T ss_dssp             CEEEEEEEEEEEEEET-TEEEEEEEETTEEEEEEEEHHHHH----------------HHHHHHHHHCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CcEEEEEEECCEeEEEEEECCcCC----------------HHHHHHHhcCCCCCEEEEEEEEE
Confidence            4799999999998776 668899999999999997432111                00011224688999999999997


Q ss_pred             eeC-CceEEEEEEEEEcC
Q 043474          117 SYR-GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~-~~~qi~~~~i~~v~  133 (160)
                      .-. |...|.+.++..+.
T Consensus       120 ~~~~ge~ei~~~~i~vl~  137 (493)
T 3a74_A          120 KTKVGELSIKVSSYEFLT  137 (493)
T ss_dssp             ECTTCCEEEEEEEEEEEE
T ss_pred             eCCCCcEEEEEEEEEEcc
Confidence            643 67889999887665

>1c0a_A Aspartyl tRNA synthetase; protein-RNA complex, ligase/RNA complex; HET: 4SU H2U QUO G7M 5MU PSU AMP AMO; 2.40A {Escherichia coli} SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1il2_A* 1eqr_A*

Probab=97.14  E-value=0.0019  Score=56.42  Aligned_cols=78  Identities=17%  Similarity=0.306  Sum_probs=59.4

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +.+-+.|.|+||.|+|++-.+. .                 ...+....+..|++|.|.|.|.
T Consensus        16 ~~V~l~GwV~~~R~~G-~~~Fi~LrD~~g~iQvv~~~~~-~-----------------~~~~~~~~l~~e~~V~V~G~v~   76 (585)
T 1c0a_A           16 QQVTLCGWVNRRRDLG-SLIFIDMRDREGIVQVFFDPDR-A-----------------DALKLASELRNEFCIQVTGTVR   76 (585)
T ss_dssp             CEEEEEEEEEEEEECS-SCEEEEEEETTEEEEEEECGGG-H-----------------HHHHHHTTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CcEEEEEEECCeeEEEEEeCCc-h-----------------HHHHHHhcCCCCCEEEEEeEEE
Confidence            4699999999998776 6688999999999999973211 1                 0011235688999999999997


Q ss_pred             ee----------CCceEEEEEEEEEcC
Q 043474          117 SY----------RGDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f----------~~~~qi~~~~i~~v~  133 (160)
                      .-          .|...|.+.++..+.
T Consensus        77 ~~~~~~~n~~~~~geiEl~~~~i~vl~  103 (585)
T 1c0a_A           77 ARDEKNINRDMATGEIEVLASSLTIIN  103 (585)
T ss_dssp             ECCTTTCCTTSTTTTEEEEEEEEEEEE
T ss_pred             ccCcccccccCCCccEEEEEeEEEEEe
Confidence            65          366889999987665

>1l0w_A Aspartyl-tRNA synthetase; space-grown crystal, dimeric enzyme, flexible domains, ligase; 2.01A {Thermus thermophilus} SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1efw_A* 1g51_A

Probab=97.14  E-value=0.0027  Score=55.39  Aligned_cols=77  Identities=18%  Similarity=0.235  Sum_probs=59.0

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +.+-+.|.|+||.|+|++-.+...                   .+....+..|++|.|.|.|.
T Consensus        17 ~~V~l~GwV~~~R~~G-~~~Fi~LrD~~g~iQvv~~~~~~~-------------------~~~~~~l~~e~~V~V~G~v~   76 (580)
T 1l0w_A           17 EEVVLEGWVNRRRDLG-GLIFLDLRDREGLVQLVAHPASPA-------------------YATAERVRPEWVVRAKGLVR   76 (580)
T ss_dssp             CEEEEEEEEEEEEECS-SCEEEEEEETTEEEEEEECTTSTT-------------------HHHHTTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEEECCeeEEEEEeCChhH-------------------HHHHhcCCCCcEEEEEEEEE
Confidence            4699999999998776 667899999999999997322100                   01235688999999999998


Q ss_pred             ee--------CCceEEEEEEEEEcC
Q 043474          117 SY--------RGDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f--------~~~~qi~~~~i~~v~  133 (160)
                      .-        .|...|.+.++..+.
T Consensus        77 ~~~~~~~~~~~ge~Ei~~~~i~vl~  101 (580)
T 1l0w_A           77 LRPEPNPRLATGRVEVELSALEVLA  101 (580)
T ss_dssp             ECSSCCTTSTTTTEEEEEEEEEEEE
T ss_pred             cCCCcCccCCCccEEEEEeEEEEec
Confidence            74        356889998887654

>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding, aminoacyl-tRNA synthetase, LI nucleotide-binding, protein biosynthesis; 2.80A {Entamoeba histolytica}

Probab=97.11  E-value=0.0031  Score=54.56  Aligned_cols=82  Identities=15%  Similarity=0.225  Sum_probs=60.8

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.... +...+.|.|+||.|+|++-.+...+              .+. ......+..|++|.|.|.|.
T Consensus        63 ~~V~v~Gwv~~~R~~g-kl~Fi~LrD~~g~iQ~v~~~~~~~~--------------~~~-~~~~~~l~~es~V~V~G~v~  126 (548)
T 3i7f_A           63 KTVTIRARVQAVRGKG-NMVFLFLRKGIYTCQALVMKSETIS--------------KEF-VQFCQKISAESICDITGIVK  126 (548)
T ss_dssp             CEEEEEEEEEEEEECS-SEEEEEEEETTEEEEEEEECSSSSC--------------HHH-HHHHHTCCTTEEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEEECCeeEEEEEECCCccC--------------HHH-HHHHhCCCCCCEEEEEEEEE
Confidence            6789999999998776 7677889999999999985422110              000 11235689999999999998


Q ss_pred             eeC--------CceEEEEEEEEEcCC
Q 043474          117 SYR--------GDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f~--------~~~qi~~~~i~~v~d  134 (160)
                      .-.        +...|.+.++..+..
T Consensus       127 ~~~~~~~~~~~~~~El~~~~i~vls~  152 (548)
T 3i7f_A          127 AVEKPIEKATQQDVEIHVTSIAVVSL  152 (548)
T ss_dssp             ECSSCCTTSSSCSEEEEEEEEEEEEC
T ss_pred             eCCcccccCCCCcEEEEEeEEEEEec
Confidence            743        567899999886643

>2xgt_A Asparaginyl-tRNA synthetase, cytoplasmic; ligase, ATP-binding, protein biosynthesis; HET: NSS; 1.90A {Brugia malayi} PDB: 2xti_A*

Probab=97.11  E-value=0.0041  Score=52.35  Aligned_cols=78  Identities=19%  Similarity=0.239  Sum_probs=58.2

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++...+++..-+.|.|+||.|+|++- +....                . ... ..+..|++|.|.|.|.
T Consensus        12 ~~V~v~Gwv~~~R~~Gk~~~Fi~LrD~~g~iQvv~~-~~~~~----------------~-~~~-~~l~~~~~v~v~G~v~   72 (435)
T 2xgt_A           12 ERVCIKGWIHRMRRQGKSLMFFILRDGTGFLQVLLM-DKLCQ----------------T-YDA-LTVNTECTVEIYGAIK   72 (435)
T ss_dssp             SEEEEEEEEEEEEECTTSEEEEEEECSSCEEEEEEE-GGGGS----------------S-HHH-HHCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEecccCCCcEEEEEEECCceEEEEEC-Ccchh----------------H-HHH-hcCCCCCEEEEEEEEE
Confidence            469999999999877535678999999999999974 21110                0 011 2588999999999997


Q ss_pred             eeC------CceEEEEEEEEEcC
Q 043474          117 SYR------GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~------~~~qi~~~~i~~v~  133 (160)
                      .-.      |...|.+..+..+.
T Consensus        73 ~~~~~~~~~g~~El~~~~~~vl~   95 (435)
T 2xgt_A           73 EVPEGKEAPNGHELIADFWKIIG   95 (435)
T ss_dssp             ECC------TTEEEEEEEEEEEE
T ss_pred             ecCCCcCCCCcEEEEEEEEEEee
Confidence            632      56789999988776

>1n9w_A Aspartyl-tRNA synthetase 2; biosynthetic protein; 2.30A {Thermus thermophilus} SCOP: b.40.4.1 d.104.1.1 PDB: 3kfu_A*

Probab=97.06  E-value=0.0052  Score=51.55  Aligned_cols=69  Identities=19%  Similarity=0.241  Sum_probs=56.7

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccc-cCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIK-IGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~G~~V~V~G~v  115 (160)
                      ..|.|.|+|.++.... +..-+.|.|+||.|+|++-.                           ..+. .|++|.|.|.|
T Consensus        14 ~~V~v~Gwv~~~R~~g-~~~F~~lrD~~g~iQ~v~~~---------------------------~~l~~~~~~v~v~G~v   65 (422)
T 1n9w_A           14 QEVELLGFLHWRRDLG-RIQFLLLRDRSGVVQVVTGG---------------------------LKLPLPESALRVRGLV   65 (422)
T ss_dssp             SEEEEEEEEEEEEECS-SEEEEEEEETTEEEEEEEES---------------------------CCCCCTTCEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCC-CeEEEEEEECCEEEEEEEEc---------------------------cccCCCCCEEEEEEEE
Confidence            4699999999998876 67789999999999998632                           2477 89999999999


Q ss_pred             ceeCC---ceEEEEEEEEEcC
Q 043474          116 ASYRG---DVQITVSDVVIEK  133 (160)
Q Consensus       116 ~~f~~---~~qi~~~~i~~v~  133 (160)
                      ..-..   ...|.+.++..+.
T Consensus        66 ~~~~~~~~~~el~~~~~~vl~   86 (422)
T 1n9w_A           66 VENAKAPGGLEVQAKEVEVLS   86 (422)
T ss_dssp             EECTTSTTSEEEEEEEEEEEE
T ss_pred             EecCCCCccEEEEEeEEEEec
Confidence            87653   6789998888665

>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA polymerase III; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A*

Probab=97.05  E-value=0.0029  Score=58.44  Aligned_cols=82  Identities=15%  Similarity=0.277  Sum_probs=63.3

Q ss_pred             EeeEEEEEEEEEEeeccC---C-ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEE
Q 043474           35 LLSRAEIVGTITSRDHKP---S-KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVAR  110 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~~~---~-~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~  110 (160)
                      +..+|.|-|.|-+++.++   + ..+.|.|.|-|++|.|+.|.+..+.                  .+....++.|+.|+
T Consensus        16 ~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~td~~~~~~~k~f~~~~~~------------------~~~~~~~~~g~~~~   77 (1041)
T 3f2b_A           16 EERRVVVQGYVFDAEVSELKSGRTLLTMKITDYTNSILVKMFSRDKED------------------AELMSGVKKGMWVK   77 (1041)
T ss_dssp             CEEEEEEEEEEEEEEEEECTTSCEEEEEEEECSSCEEEEEEECSSHHH------------------HHHHHTCCTTCEEE
T ss_pred             ccceEEEEEEEEEEEEEEccCCCEEEEEEEEeCCCCEEEEEeecccch------------------HHHHhcCCCCCEEE
Confidence            567899999999887642   3 4579999999999999999765431                  12345799999999


Q ss_pred             EEEEec--eeCCceEEEEEEEEEcCC
Q 043474          111 VRGRIA--SYRGDVQITVSDVVIEKD  134 (160)
Q Consensus       111 V~G~v~--~f~~~~qi~~~~i~~v~d  134 (160)
                      |+|+++  .|.+...+.+..|..+..
T Consensus        78 ~~g~~~~d~~~~~~~~~~~~~~~~~~  103 (1041)
T 3f2b_A           78 VRGSVQNDTFVRDLVIIANDLNEIAA  103 (1041)
T ss_dssp             EEEEEEEETTTTEEEEEEEEEEEECC
T ss_pred             EEEEEEeccCCcceEEEeeeeEEecc
Confidence            999987  466777888888876653

>2hpi_A DNA polymerase III alpha subunit; POL-beta-like nucleotidyltransferase fold, transferase; HET: DNA; 3.00A {Thermus aquaticus} PDB: 2hpm_A* 3e0d_A*

Probab=96.98  E-value=0.001  Score=62.36  Aligned_cols=76  Identities=17%  Similarity=0.290  Sum_probs=45.2

Q ss_pred             eEEEEEEEEEEeeccCC----ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTITSRDHKPS----KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~----~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ..+.+.|.|++++...+    ++..++|+|.||.+++++|.+.-.                    +....+..+..|.|.
T Consensus      1043 ~~v~v~G~v~~~~~~~Tk~G~~maf~tleD~tg~~evvvf~~~~~--------------------~~~~~l~~~~~~~v~ 1102 (1220)
T 2hpi_A         1043 PKVLLSGMVEEVVRKPTRSGGMMARFTLSDETGALEVVVFGRAYE--------------------GVSPKLKEDIPLLVL 1102 (1220)
T ss_dssp             CEEEEEEEECCC------------CEEEEETTEEEEEC---------------------------------CTTCEEEEE
T ss_pred             CeEEEEEEEEEEEEeecCCCCeEEEEEEEECCCCEEEEEcHHHHH--------------------HHHHHhccCCEEEEE
Confidence            45779999999885432    467899999999999999977653                    134568899999999


Q ss_pred             EEeceeCCceEEEEEEEEEcC
Q 043474          113 GRIASYRGDVQITVSDVVIEK  133 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~  133 (160)
                      |+++.-. ..+|.+.++.+++
T Consensus      1103 G~v~~~~-~~~l~~~~i~~l~ 1122 (1220)
T 2hpi_A         1103 AEVEKGE-ELRVLAQAVWTLE 1122 (1220)
T ss_dssp             EEEC------CEEEEEEEEHH
T ss_pred             EEEEECC-CcEEEEeeeecHH
Confidence            9998644 5789999988664

>3bju_A Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP- binding, cytoplasm, ligase, nucleotide-binding, phosphoprotein, polymorphism; HET: LYS ATP; 2.31A {Homo sapiens}

Probab=96.96  E-value=0.0042  Score=53.50  Aligned_cols=83  Identities=13%  Similarity=0.205  Sum_probs=59.1

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|.++.....+..-+.|.|+||.|+|++-.+...+              .+........+..|++|.|.|.+.
T Consensus        56 ~~V~v~Grv~~~R~~gkk~~F~~LrD~sg~iQvv~~~~~~~~--------------~~~~~~~~~~l~~gd~V~V~G~v~  121 (521)
T 3bju_A           56 ITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKS--------------EEEFIHINNKLRRGDIIGVQGNPG  121 (521)
T ss_dssp             CCEEEEEEEEEEEESSSSEEEEEEEETTEEEEEEEEGGGSSC--------------HHHHHHHHHHCCTTCEEEEEEEEE
T ss_pred             cEEEEEEEEEEEecCCCCcEEEEEEECCEEEEEEEECCccCC--------------HHHHHHHHhcCCCCCEEEEEEEEE
Confidence            469999999998876535577899999999999985432100              000000123588999999999987


Q ss_pred             ee-CCceEEEEEEEEEcC
Q 043474          117 SY-RGDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f-~~~~qi~~~~i~~v~  133 (160)
                      .- .|...|.+.++..+.
T Consensus       122 ~t~~ge~ei~~~~i~~l~  139 (521)
T 3bju_A          122 KTKKGELSIIPYEITLLS  139 (521)
T ss_dssp             ECTTCCEEEEEEEEEEEE
T ss_pred             ecCCCCEEEEEeEEEEee
Confidence            54 367889998887664

>4gs3_A Single-stranded DNA-binding protein; primosome, oligonucleotide/oligosaccharide binding domain, D binding protein; 1.09A {Thermoanaerobacter tengcongensis}

Probab=96.95  E-value=0.011  Score=40.51  Aligned_cols=75  Identities=16%  Similarity=0.401  Sum_probs=49.7

Q ss_pred             eEEEEEEEEEEee-----ccCCceEEEEEe-----CCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccC
Q 043474           37 SRAEIVGTITSRD-----HKPSKFIKFTVD-----DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIG  106 (160)
Q Consensus        37 ~~v~ivG~V~~~~-----~~~~~~~~~~Id-----DgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G  106 (160)
                      .+|.++|.+..--     .....+..|+|.     |.+--|+|++|....+.                      .....|
T Consensus        12 N~V~LiGrl~~dpelr~t~~G~~v~~f~lAV~R~~~~~Dfi~ivvw~klAe~----------------------~~~~kG   69 (107)
T 4gs3_A           12 NTVTLVGKVFTPLEFSHELYGEKFFNFILEVPRLSETKDYLPITISNRLFEG----------------------MNLEVG   69 (107)
T ss_dssp             SCEEEEEEECSCCEEEEEETTEEEEEEEEEEECTTSCEEEEEEEEEGGGSTT----------------------CCCCTT
T ss_pred             CEEEEEEEECCCceEEEecCCcEEEEEEEEeCCCCCCCcEEEEEEEhHHhhH----------------------HhhcCC
Confidence            6788888887521     122356666665     55667999999877641                      124589


Q ss_pred             cEEEEEEEeceeC------Cc----eEEEEEEEEEcC
Q 043474          107 LVARVRGRIASYR------GD----VQITVSDVVIEK  133 (160)
Q Consensus       107 ~~V~V~G~v~~f~------~~----~qi~~~~i~~v~  133 (160)
                      +.|.|.|++++|+      |+    ..+.+..|.-++
T Consensus        70 ~~v~v~G~lrsy~~~~~~dG~~R~v~eV~a~~i~fld  106 (107)
T 4gs3_A           70 TRVKIEGQLRSYNRKSPEEGKNKLILTVFARDISVVP  106 (107)
T ss_dssp             CEEEEEEEEEEEECC--------EEEEEEEEEEEEEC
T ss_pred             CEEEEEEEEEecceEECCCCCEEEEEEEEEEEEEEcc
Confidence            9999999998864      22    356677666554

>3kdf_A Replication protein A 14 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 1quq_B 1l1o_A

Probab=96.50  E-value=0.057  Score=37.58  Aligned_cols=80  Identities=19%  Similarity=0.247  Sum_probs=53.0

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      +.|++||+|.++.... +  .++|+++-| .+.+.+-.+.+                        .  .++.+|.|.|++
T Consensus        23 k~VrivGkV~~~~~~g-~--~~~l~s~Dg~~Vtv~l~~p~~------------------------~--~l~~~vEViG~V   73 (121)
T 3kdf_A           23 KPVCFVGRLEKIHPTG-K--MFILSDGEGKNGTIELMEPLD------------------------E--EISGIVEVVGRV   73 (121)
T ss_dssp             CEEEEEEEEEEECTTS-S--EEEEECTTSCEEEEECSSCCS------------------------S--CCCSEEEEEEEE
T ss_pred             CeEEEEEEEEEEcCCC-C--EEEEEeCCCCEEEEEeCCCCC------------------------c--ccCcEEEEEEEE
Confidence            8899999999986544 3  678888776 58887522111                        1  235699999999


Q ss_pred             ceeCCceEEEEEEEEEcCCh--hHHHHHHHHHHHH
Q 043474          116 ASYRGDVQITVSDVVIEKDP--NMEVLHWLDCLRL  148 (160)
Q Consensus       116 ~~f~~~~qi~~~~i~~v~d~--n~~~~h~le~~~~  148 (160)
                      ..   ...|.+.......+.  +.++.-+-+++++
T Consensus        74 ~~---~~tI~~~~~~~fg~~~~~fD~~~yn~lv~l  105 (121)
T 3kdf_A           74 TA---KATILCTSYVQFKEDSHPFDLGLYNEAVKI  105 (121)
T ss_dssp             CT---TSCEEEEEEEECCCSSSCCCHHHHHHHHHH
T ss_pred             CC---CCeEEEEEEEecCCCCcccCHHHHHHHHHH
Confidence            84   457888887777643  1333444445544

>2pi2_E Replication protein A 14 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_B 2z6k_C

Probab=96.37  E-value=0.15  Score=36.44  Aligned_cols=80  Identities=19%  Similarity=0.264  Sum_probs=53.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      +.|+|||+|.+..... +  .++|..+.| .|.|.+-  ...                        .-..+.+|.|.|+|
T Consensus        44 k~VriVGkV~~~~~~G-~--~~~l~s~Dg~~VtV~l~--~pL------------------------~~~~~~~VEViG~V   94 (142)
T 2pi2_E           44 KPVCFVGRLEKIHPTG-K--MFILSDGEGKNGTIELM--EPL------------------------DEEISGIVEVVGRV   94 (142)
T ss_dssp             CEEEEEEEEEEECTTS-S--EEEEECTTSCEEEEECS--SCC------------------------SSCCCSEEEEEEEE
T ss_pred             CEEEEEEEEeEEcCCC-C--EEEEEeCCCcEEEEEeC--CCC------------------------CccCCCEEEEEEEE
Confidence            8999999999985544 3  678888766 5888752  110                        01247899999999


Q ss_pred             ceeCCceEEEEEEEEEcCCh--hHHHHHHHHHHHH
Q 043474          116 ASYRGDVQITVSDVVIEKDP--NMEVLHWLDCLRL  148 (160)
Q Consensus       116 ~~f~~~~qi~~~~i~~v~d~--n~~~~h~le~~~~  148 (160)
                      ..   ...|.+.......+.  +.++.=+-+++.+
T Consensus        95 ~~---~~tI~~~~~~~fGd~~~~fD~~~yn~lv~l  126 (142)
T 2pi2_E           95 TA---KATILCTSYVQFKEDSHPFDLGLYNEAVKI  126 (142)
T ss_dssp             CT---TSCEEEEEEEECCCSSSCCCHHHHHHHHHH
T ss_pred             CC---CCcEEEEEEEecCCCccccCHHHHHHHHHH
Confidence            66   456778887777754  2444444455554

>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=96.19  E-value=0.0039  Score=42.90  Aligned_cols=42  Identities=19%  Similarity=0.243  Sum_probs=33.7

Q ss_pred             CceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEE
Q 043474           53 SKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGR  114 (160)
Q Consensus        53 ~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~  114 (160)
                      ++.+.+.|-|.||.|.|.+|.+...                    ...+.++.|+.+.|.|-
T Consensus        39 g~~~~~~L~De~G~I~at~~~~~~~--------------------~f~~~l~eG~vy~Is~~   80 (114)
T 1ynx_A           39 GKLFNVNFLDTSGEIRATAFNDFAT--------------------KFNEILQEGKVYYVSKA   80 (114)
T ss_dssp             EEEEEEEEEETTEEEEEEECHHHHH--------------------HHHHHSCSSSEEEEESC
T ss_pred             ceEEEEEEECCCCeEEEEECHHHHH--------------------HHHhhcccCcEEEECCc
Confidence            4678999999999999999986532                    23467899999988864

>1txy_A Primosomal replication protein N; OB fold, dimer, DNA binding protein; 2.00A {Escherichia coli} SCOP: b.40.4.3 PDB: 1woc_A 2pnh_A 4apv_A

Probab=96.05  E-value=0.081  Score=35.55  Aligned_cols=77  Identities=16%  Similarity=0.310  Sum_probs=49.4

Q ss_pred             eEEEEEEEEEEeec-----cCCceEEEEEe-----CCCce-------EEEEEeecCccCCCCCCCCCCcccccccccccc
Q 043474           37 SRAEIVGTITSRDH-----KPSKFIKFTVD-----DGTGC-------VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF   99 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-----~~~~~~~~~Id-----DgTG~-------I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (160)
                      .+|.++|.+..--+     ...+...|+|.     +.|+-       |+|+.|.+..+.                    .
T Consensus         3 N~v~L~G~l~~dpelR~t~~G~~v~~f~lA~~~~~~~~~~~r~~~~~~~vv~~g~~Ae~--------------------~   62 (104)
T 1txy_A            3 NRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQA--------------------I   62 (104)
T ss_dssp             EEEEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESSTTHH--------------------H
T ss_pred             EEEEEEEEECCCceEEECCCCCEEEEEEEEEeCccccCCceeceeEEEEEEEEhHHHHH--------------------H
Confidence            56778888776321     11255666663     34567       999999775431                    2


Q ss_pred             ccccccCcEEEEEEEeceeC---C--ceEEEEEEEEEcC
Q 043474          100 AAKIKIGLVARVRGRIASYR---G--DVQITVSDVVIEK  133 (160)
Q Consensus       100 ~~~~~~G~~V~V~G~v~~f~---~--~~qi~~~~i~~v~  133 (160)
                      ...++.|+.|.|.|+++.-.   |  ...|.+..|..++
T Consensus        63 ~~~l~KG~~V~V~G~L~~~~~~~G~~r~~v~~~~i~~l~  101 (104)
T 1txy_A           63 THSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELID  101 (104)
T ss_dssp             HTTCCTTCEEEEEEEEEC--------CCEEEEEEEEEC-
T ss_pred             HhhCCCCCEEEEEEEEEeccCCCCCEEEEEEEEEEEECc
Confidence            35689999999999998642   1  1347777777654

>3koj_A Uncharacterized protein YCF41; single-strand binding protein family, PF00436, SNR59A, NESG, structural genomics, PSI-2; 1.90A {Synechococcus elongatus pcc 6301}

Probab=95.75  E-value=0.076  Score=36.20  Aligned_cols=76  Identities=13%  Similarity=0.212  Sum_probs=47.8

Q ss_pred             eeEEEEEEEEEEee-----ccC-CceEEEEEe-------CCCceEEEEEeecCccCCCCCCCCCCccccccccccccccc
Q 043474           36 LSRAEIVGTITSRD-----HKP-SKFIKFTVD-------DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAK  102 (160)
Q Consensus        36 i~~v~ivG~V~~~~-----~~~-~~~~~~~Id-------DgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (160)
                      ...|.++|.+..--     ..+ .....|+|.       |.|--++|++|.+..+.                    ....
T Consensus        11 ~~~v~LiGrL~~DPelR~t~~g~~~va~f~lAv~~~~~~~~t~fi~vv~wgk~AE~--------------------~~~y   70 (108)
T 3koj_A           11 MNSCILQATVVEAPQLRYAQDNQTPVAEMVVQFPGLSSKDAPARLKVVGWGAVAQE--------------------LQDR   70 (108)
T ss_dssp             CEEEEEEEEEEEEEEEEECTTSSSEEEEEEEEECC-----CCEEEEEEEETHHHHH--------------------HHHH
T ss_pred             cceEEEEEEECCCCEEEEeCCCCEEEEEEEEEECCcccCCCcEEEEEEEEhHHHHH--------------------HHHh
Confidence            46778888877522     112 245566553       45566999999875531                    2356


Q ss_pred             cccCcEEEEEEEece--eCCc-------eEEEEEEEEE
Q 043474          103 IKIGLVARVRGRIAS--YRGD-------VQITVSDVVI  131 (160)
Q Consensus       103 ~~~G~~V~V~G~v~~--f~~~-------~qi~~~~i~~  131 (160)
                      ++.|+.|.|.|+++.  |.++       -+|.+.+|.|
T Consensus        71 l~KG~~V~VeGrL~~r~y~~kdG~kr~~tEVva~~i~P  108 (108)
T 3koj_A           71 CRLNDEVVLEGRLRINSLLKPDGNREKQTELTVTRVHH  108 (108)
T ss_dssp             CCTTCEEEEEEEEEEEC--------CCEEEEEEEEEEC
T ss_pred             CCCCCEEEEEEEEEeeeEECCCCCEEEEEEEEEEEEEC
Confidence            899999999999975  4331       3567776654

>1qzg_A Protection of telomeres protein 1; protrein-DNA complex, single-stranded telomeric DNA, DNA binding protein/DNA complex; HET: TMP; 1.90A {Schizosaccharomyces pombe} SCOP: b.40.4.3 PDB: 1qzh_A

Probab=95.73  E-value=0.25  Score=36.93  Aligned_cols=71  Identities=15%  Similarity=0.172  Sum_probs=52.9

Q ss_pred             eEEEEEEEEEEeec-----cCC-ce-EEEEEeCCC----c-eEEEEEeecCccCCCCCCCCCCcccccccccccccccc-
Q 043474           37 SRAEIVGTITSRDH-----KPS-KF-IKFTVDDGT----G-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKI-  103 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-----~~~-~~-~~~~IdDgT----G-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  103 (160)
                      ..|.++|.|+....     +++ .| ++|+|-|.|    + .|.|.++.+..+.                     .+.+ 
T Consensus        43 ~~VNviGVVvd~~~P~~S~rGtkD~~~TltI~D~S~~~~~~gL~v~iF~~~~e~---------------------LP~V~  101 (187)
T 1qzg_A           43 TIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGND---------------------LPVIK  101 (187)
T ss_dssp             EEEEEEEEEEEEEEEEECSSTTCCEEEEEEEECTTSCTTSCCEEEEEEESSSSC---------------------SCCCC
T ss_pred             CEEEEEEEEEEccCceecCCCCccEEEEEEEEeCCCCCCCCceEEEEECCChhh---------------------CCCCC
Confidence            67888999988662     333 34 799999987    3 3999999876541                     2344 


Q ss_pred             ccCcEEEEEEE-eceeCCceEEEEEE
Q 043474          104 KIGLVARVRGR-IASYRGDVQITVSD  128 (160)
Q Consensus       104 ~~G~~V~V~G~-v~~f~~~~qi~~~~  128 (160)
                      ..||+|++..- ++.|+|+.|....+
T Consensus       102 ~~GDIIlL~rvkiq~~~g~~~~v~~~  127 (187)
T 1qzg_A          102 QVGQPLLLHQITLRSYRDRTQGLSKD  127 (187)
T ss_dssp             STTCEEEEEEEEEEEETTEEEEEEEE
T ss_pred             CCCCEEEEEEEEEEEECCeEEEEEcC
Confidence            78999999864 78899999986555

>4gop_A Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=95.65  E-value=0.079  Score=36.45  Aligned_cols=67  Identities=13%  Similarity=0.110  Sum_probs=45.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      +.|+|+|+|.+...   +  .++|+.++| .|.|++-  .+                        ..+..+.+|.|.|++
T Consensus        19 ~~VrivGkV~~~~g---~--~~~l~s~d~~~Vtv~l~--~~------------------------~~~~~~~~vEViG~V   67 (114)
T 4gop_A           19 QTVRIVGKVHKVTG---N--TLLMQTSDLGNVEIAMT--PD------------------------SDVSSSTFVEVTGKV   67 (114)
T ss_dssp             SEEEEEEEEEEEET---T--EEEEECTTSCEEEEECC--SS------------------------CCGGGCSEEEEEEEE
T ss_pred             CeEEEEEEEeeeCC---C--EEEEEeCCCCEEEEEeC--CC------------------------CCcccCcEEEEEEEE
Confidence            78999999999875   2  678887765 5777652  11                        234578999999999


Q ss_pred             ceeCCc---eEEEEEEEEEcCC
Q 043474          116 ASYRGD---VQITVSDVVIEKD  134 (160)
Q Consensus       116 ~~f~~~---~qi~~~~i~~v~d  134 (160)
                      ..-.+.   ..|.+.......+
T Consensus        68 ~~~~~~~~~~~I~~~~~~~~g~   89 (114)
T 4gop_A           68 SDAGSSFQANQIREFTTVDCGH   89 (114)
T ss_dssp             CTTSSEEEEEEEEECSCCC---
T ss_pred             cCCCCcccCCeEEEEEEEeCCC
Confidence            864332   5677766555543

>1xjv_A Protection of telomeres 1; protein-DNA complex, single-stranded DNA, transcription/DNA complex; 1.73A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 3kjo_A 3kjp_A

Probab=95.52  E-value=0.23  Score=39.26  Aligned_cols=71  Identities=21%  Similarity=0.274  Sum_probs=51.5

Q ss_pred             eEEEEEEEEEEeec----cCC-ceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCcccccccccccccccc-ccCcEE
Q 043474           37 SRAEIVGTITSRDH----KPS-KFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKI-KIGLVA  109 (160)
Q Consensus        37 ~~v~ivG~V~~~~~----~~~-~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~G~~V  109 (160)
                      ..+.++|+|+....    +++ -.++|+|-|.|- .|.|.+|.+..+                     ....+ +.||+|
T Consensus        16 ~~vnvigVV~~~~~p~~s~G~d~~~tl~I~D~S~~gl~v~iF~~~~~---------------------~LP~v~~~GDII   74 (294)
T 1xjv_A           16 TIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYE---------------------ALPIIYKNGDIV   74 (294)
T ss_dssp             EEEEEEEEEEEEEEEEECSSSSEEEEEEEECTTCCEEEEEEEESSGG---------------------GSCCCCSTTCEE
T ss_pred             CeeEEEEEEEEcCCCccCCCCeEEEEEEEEcCCCCCEEEEEECCChH---------------------HCCCCCCCCCEE
Confidence            56788899988763    333 447999999663 299999987543                     12344 899999


Q ss_pred             EEEE-EeceeCCceEEEEEE
Q 043474          110 RVRG-RIASYRGDVQITVSD  128 (160)
Q Consensus       110 ~V~G-~v~~f~~~~qi~~~~  128 (160)
                      ++.. +++.|+++.|+....
T Consensus        75 ~l~~vki~~~~g~~~~v~~~   94 (294)
T 1xjv_A           75 RFHRLKIQVYKKETQGITSS   94 (294)
T ss_dssp             EEEEEEEEEETTEEEEEEEE
T ss_pred             EEEEEEEEEECCeEEEEccC
Confidence            9995 478999998875543

>4ah6_A Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo sapiens}

Probab=95.50  E-value=0.026  Score=49.46  Aligned_cols=77  Identities=17%  Similarity=0.270  Sum_probs=53.8

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|+|.|+|..+..  ..  .+.|.|+||.|+|++-.+...                .+..+....+..|+.|.|.|.|.
T Consensus        25 ~~V~l~GwV~~~R~--~~--Fi~LrD~~g~iQvv~~~~~~~----------------~~~~~~~~~l~~e~~V~V~G~v~   84 (617)
T 4ah6_A           25 QEVTLCGWIQYRRQ--NT--FLVLRDFDGLVQVIIPQDESA----------------ASVKKILCEAPVESVVQVSGTVI   84 (617)
T ss_dssp             CEEEEEEEECCCCT--TT--EEEEECSSCEEEEECCCSSSS----------------HHHHHHHHHCCSSCEEEEEEEEE
T ss_pred             CEEEEEEEeeeecC--eE--EEEEEeCCcCEEEEEeCCcCc----------------HHHHHHHhcCCCCCEEEEEEEEE
Confidence            47999999998653  24  577899999999987322110                00011235688999999999997


Q ss_pred             ee----------CCceEEEEEEEEEcC
Q 043474          117 SY----------RGDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f----------~~~~qi~~~~i~~v~  133 (160)
                      .-          .|...|.+..+..+.
T Consensus        85 ~~~~~~~n~~~~tgeiEl~~~~i~vL~  111 (617)
T 4ah6_A           85 SRPAGQENPKMPTGEIEIKVKTAELLN  111 (617)
T ss_dssp             ECSTTCCCTTSTTTTEEEEEEEEEEEE
T ss_pred             eCCccccCccCCCCcEEEEEeEEEEee
Confidence            52          256889998888653

>3fhw_A Primosomal replication protein N; PRIB BPR162 X-RAY NESG, structural genomics, PSI-2, protein initiative; 1.90A {Bordetella parapertussis} PDB: 3dm4_A 3klw_A

Probab=95.48  E-value=0.13  Score=35.37  Aligned_cols=47  Identities=17%  Similarity=0.205  Sum_probs=35.9

Q ss_pred             EEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEeceeC--C-ceEEEEEEEEEcCC
Q 043474           67 VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYR--G-DVQITVSDVVIEKD  134 (160)
Q Consensus        67 I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~--~-~~qi~~~~i~~v~d  134 (160)
                      |+|++|.+..+                     ....++.|..|.|.|+++.-.  + +..|.+..|..++.
T Consensus        49 i~vv~~Gk~AE---------------------~~~~l~kGs~V~VeGrL~trs~~G~kl~l~a~~Ie~l~~   98 (115)
T 3fhw_A           49 ISAVALGDLAL---------------------LLADTPLGTEMQVQGFLAPARKDSVKVKLHLQQARRIAG   98 (115)
T ss_dssp             EEEEEETHHHH---------------------HHTTCCTTCEEEEEEEEEESSTTCSSEEEEEEEEEECCC
T ss_pred             EEEEEEhHHHH---------------------hhhccCCCCEEEEEEEEEECCCCCCEEEEEEEEEEEcCC
Confidence            88999976543                     125689999999999998632  2 45799999998754

>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding replication protein A(RPA), single stranded DNA-binding protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A

Probab=95.09  E-value=0.023  Score=43.57  Aligned_cols=77  Identities=16%  Similarity=0.297  Sum_probs=50.5

Q ss_pred             EEEEEEEEEEeec--------cCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEE
Q 043474           38 RAEIVGTITSRDH--------KPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVA  109 (160)
Q Consensus        38 ~v~ivG~V~~~~~--------~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V  109 (160)
                      +..|.|+|.+...        .+++.+.+.|-|.||.|.|.+|.+...                    ...+.++.|+.+
T Consensus        20 ~w~I~~rV~~k~~~r~~~~~~~~g~~~~~~L~De~G~I~at~~~~~~~--------------------~~~~~l~~G~vy   79 (246)
T 1jmc_A           20 KWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNEQVD--------------------KFFPLIEVNKVY   79 (246)
T ss_dssp             CCEEEEEEEEECCCEEEECSSCEEEEEEEEEECSSCEEEEEEEHHHHH--------------------HHGGGCCTTCEE
T ss_pred             ceEEEEEEEEecccceeeCCCCCceEEEEEEECCCCeEEEEEChHHHH--------------------HhhhhcccCCEE
Confidence            4567777776432        124668999999999999999975432                    234678999999


Q ss_pred             EEEEE-ece----e---CCceEEEEE---EEEEcCC
Q 043474          110 RVRGR-IAS----Y---RGDVQITVS---DVVIEKD  134 (160)
Q Consensus       110 ~V~G~-v~~----f---~~~~qi~~~---~i~~v~d  134 (160)
                      .+.+- |+.    |   .+..+|.+.   .|.++.+
T Consensus        80 ~i~~~~v~~~~~~y~~~~~~~ei~~~~~T~I~~~~~  115 (246)
T 1jmc_A           80 YFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCED  115 (246)
T ss_dssp             EEECCEEEECCGGGCCCCCSEEEECCTTCEEEECCS
T ss_pred             EECCCEEEEcccCcccCCCCEEEEEcCCcEEEEccC
Confidence            88873 332    2   234455544   3565544

>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding replication protein A(RPA), single stranded DNA-binding protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A

Probab=94.82  E-value=0.055  Score=41.45  Aligned_cols=68  Identities=18%  Similarity=0.275  Sum_probs=47.0

Q ss_pred             eEEEEEEEEEEeec------c--C--CceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCcccccccccccccccccc
Q 043474           37 SRAEIVGTITSRDH------K--P--SKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKI  105 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~--~--~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (160)
                      ..+-++|.|.++..      +  +  .....++|.|.|| +|.|.+|.+....                      -....
T Consensus       139 ~~vDViG~V~~v~~~~~~~~k~~g~~~~~r~~~l~D~sg~~i~~tLWg~~a~~----------------------~~~~~  196 (246)
T 1jmc_A          139 SLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADK----------------------FDGSR  196 (246)
T ss_dssp             CEEEEEEEEEEECCCEEEEETTTTEEEEEEEEEEECTTCCEEEEEEEHHHHHH----------------------CCCTT
T ss_pred             CceeEEEEEEEecCeEEEEEecCCCccEEEEEEEECCCCCEEEEEEEchhhhh----------------------cccCC
Confidence            35778888887653      2  1  2456899999999 5999999876431                      11357


Q ss_pred             CcEEEEEEE-eceeCCceEEEEE
Q 043474          106 GLVARVRGR-IASYRGDVQITVS  127 (160)
Q Consensus       106 G~~V~V~G~-v~~f~~~~qi~~~  127 (160)
                      |.+|.+.|- ++.|+ .++|.+.
T Consensus       197 ~~vv~i~~~~v~~f~-g~~ls~~  218 (246)
T 1jmc_A          197 QPVLAIKGARVSDFG-GRSLSVL  218 (246)
T ss_dssp             CCEEEEEEEEEECTT-SSEEECC
T ss_pred             CCEEEEEEEEEEecC-CeEEEec
Confidence            778777764 77885 4676643

>3en2_A Probable primosomal replication protein N; PRIB RSR213C NESG X-RAY Q8XZT7 Q8XZT7_ralso, structural genomics, PSI-2; 2.30A {Ralstonia solanacearum}

Probab=94.53  E-value=0.14  Score=34.47  Aligned_cols=43  Identities=14%  Similarity=0.098  Sum_probs=27.0

Q ss_pred             EEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece--eCCce-EEEEEEEE
Q 043474           67 VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS--YRGDV-QITVSDVV  130 (160)
Q Consensus        67 I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~--f~~~~-qi~~~~i~  130 (160)
                      |+|++|.+..+                     ....+..|..|.|.|+++.  |+++. -+.+..+.
T Consensus        50 i~vv~wGk~AE---------------------~~~~~~kGs~V~VeGrL~trs~~s~~lvlhi~~~~   95 (101)
T 3en2_A           50 IEALGAGKMAS---------------------VLDRIAPGTVLECVGFLARKHRSSKALVFHISGLE   95 (101)
T ss_dssp             EEEEEETHHHH---------------------HHTTSCTTCEEEEEEEEEECC----CEEEEEEEEE
T ss_pred             EEEEEEhHHHH---------------------HHhhcCCCCEEEEEEEEEeCcCCCCeeEEEEeccc
Confidence            88899986543                     2245789999999999984  44432 24444443

>1v1q_A Primosomal replication protein N; primosome, DNA replication, DNA binding; 2.1A {Escherichia coli} SCOP: b.40.4.3 PDB: 2ccz_A

Probab=94.33  E-value=0.91  Score=31.99  Aligned_cols=78  Identities=14%  Similarity=0.265  Sum_probs=50.1

Q ss_pred             eEEEEEEEEEEeec-----cCCceEEEEEeC-----CCc-------eEEEEEeecCccCCCCCCCCCCcccccccccccc
Q 043474           37 SRAEIVGTITSRDH-----KPSKFIKFTVDD-----GTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF   99 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-----~~~~~~~~~IdD-----gTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (160)
                      .+|.++|.+..--+     .......|+|.-     .+|       -|+|++|.+..+.                    .
T Consensus        20 NkViLiGrL~~DPElRyTpsG~~Va~ftLA~~~~~~~~G~~~~~~~~i~vv~wGk~AE~--------------------~   79 (134)
T 1v1q_A           20 NRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQA--------------------I   79 (134)
T ss_dssp             EEEEEEEEEEEEEEEEECTTCCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESTGGGG--------------------G
T ss_pred             eEEEEEEEECcCCceEECCCCCEEEEEEEEEeCcCcCCCCEecceEEEEEEEEhHHHHH--------------------H
Confidence            77888888876321     122555555532     123       2899999775541                    2


Q ss_pred             ccccccCcEEEEEEEeceeCC-----ceEEEEEEEEEcCC
Q 043474          100 AAKIKIGLVARVRGRIASYRG-----DVQITVSDVVIEKD  134 (160)
Q Consensus       100 ~~~~~~G~~V~V~G~v~~f~~-----~~qi~~~~i~~v~d  134 (160)
                      ...++.|..|.|.|+++...+     +.-+.+..|..++.
T Consensus        80 ~~yl~KGs~V~VeGrL~tr~~k~G~kr~~~~a~~i~~l~~  119 (134)
T 1v1q_A           80 THSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDS  119 (134)
T ss_dssp             GTTCCTTCEEEEEEEEEEECTTTTSCEEEEEEEEEEETTS
T ss_pred             HHhcCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEEECcC
Confidence            246899999999999997632     22356777777654

>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold, DNA binding protein; 2.70A {Neisseria gonorrhoeae fa 1090}

Probab=94.28  E-value=0.62  Score=31.26  Aligned_cols=74  Identities=14%  Similarity=0.146  Sum_probs=46.3

Q ss_pred             eEEEEEEEEEEeec-----cCCceEEEEEe-------CC----Cce-EEEEEeecCccCCCCCCCCCCcccccccccccc
Q 043474           37 SRAEIVGTITSRDH-----KPSKFIKFTVD-------DG----TGC-VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF   99 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-----~~~~~~~~~Id-------Dg----TG~-I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (160)
                      .+|.++|.+..--+     ...+...|+|.       +|    +-. |+|+.|.+..+                      
T Consensus         8 Nkv~LiG~L~~dPelRytp~G~~v~~f~lA~~~~~~~~g~~~~~~~~i~vv~~gk~Ae----------------------   65 (103)
T 3k8a_A            8 NLVSLAALIEKAFPIRYTPAGIPVLDIILKHESWQEENGQQCLVQLEIPARILGRQAE----------------------   65 (103)
T ss_dssp             EEEEEEEEEEEECCCEECTTSCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEHHHHH----------------------
T ss_pred             cEEEEEEEECCCCceEECCCCCEEEEEEEEEcccCccCCCEEEeeEEEEEEEEhHHhh----------------------
Confidence            66777787776321     11244455544       22    123 78888876431                      


Q ss_pred             ccccccCcEEEEEEEec--eeCCc-eEEEEEEEEEc
Q 043474          100 AAKIKIGLVARVRGRIA--SYRGD-VQITVSDVVIE  132 (160)
Q Consensus       100 ~~~~~~G~~V~V~G~v~--~f~~~-~qi~~~~i~~v  132 (160)
                      ...++.|+.|.|.|+++  .|++. .-+.+..|..+
T Consensus        66 ~~~l~KG~~v~veGrL~~rs~~~~~lvlhi~~i~~i  101 (103)
T 3k8a_A           66 EWQYRQGDCATVEGFLAQKSRRSLMPMLRIQNIKEY  101 (103)
T ss_dssp             HSTTCTTCEEEEEEEEEESSSSCCCEEEEEEEEEEC
T ss_pred             hhccCCCCEEEEEEEEEECccCCccEEEEEEEEEEc
Confidence            24599999999999997  46554 34677777755

>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii}

Probab=94.01  E-value=0.32  Score=35.16  Aligned_cols=81  Identities=11%  Similarity=0.220  Sum_probs=52.2

Q ss_pred             EeeEEEEEEEEEEe---ec--cCCceEEEEEe------CC-Cc-------eEEEEEeecCccCCCCCCCCCCcccccccc
Q 043474           35 LLSRAEIVGTITSR---DH--KPSKFIKFTVD------DG-TG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        35 ~i~~v~ivG~V~~~---~~--~~~~~~~~~Id------Dg-TG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~   95 (160)
                      .+.+|.|+|.|..-   ..  ....++.|+|.      |. +|       -+.|++|.+..+                  
T Consensus         7 ~mN~V~LiGrL~~dPelr~t~~G~~v~~f~lA~~~~~~d~~~Ge~~e~t~~i~vv~wg~~Ae------------------   68 (158)
T 3tqy_A            7 GVNKVILIGNLGQDPEVRYTPNGNAVANVTLATSTTWRDKQTGELQERTEWHRIAFFNRLAE------------------   68 (158)
T ss_dssp             CEEEEEEEEEESSSCEEEECTTCCEEEEEEEEEEEEEECTTTCCEEEEEEEEEEEEETHHHH------------------
T ss_pred             ccCEEEEEEEECCCCEEEECCCCCEEEEEEEEEcCceeccCCCCEeeeeEEEEEEEEhHHHH------------------
Confidence            46788888888762   11  11255666652      22 33       378999976432                  


Q ss_pred             ccccccccccCcEEEEEEEece--eC---Cc----eEEEEEEEEEcCCh
Q 043474           96 ATDFAAKIKIGLVARVRGRIAS--YR---GD----VQITVSDVVIEKDP  135 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~~--f~---~~----~qi~~~~i~~v~d~  135 (160)
                        .....++.|+.|.|.|+|+.  |.   |+    ..|.+..|..+...
T Consensus        69 --~~~~~l~KG~~V~VeG~L~~~~~~dkdG~~r~~~eV~a~~i~~L~~k  115 (158)
T 3tqy_A           69 --IVGEYLRKGSKIYIEGSLRTRKWQDKNGVDRYTTEIIANEMHMLDNR  115 (158)
T ss_dssp             --HHHHHCCTTCEEEEEEEEEEEEEECSSSCEEEEEEEEEEEEEECC--
T ss_pred             --HHHhhcCCCCEEEEEEEEEeeeEECCCCCEEEEEEEEEeEEEEccCC
Confidence              12245899999999999975  53   22    47888999887654

>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis}

Probab=93.97  E-value=0.21  Score=34.03  Aligned_cols=82  Identities=20%  Similarity=0.350  Sum_probs=50.9

Q ss_pred             EeeEEEEEEEEEEe---e--ccCCceEEEEEe------C-----CCceEEEEEeecCccCCCCCCCCCCccccccccccc
Q 043474           35 LLSRAEIVGTITSR---D--HKPSKFIKFTVD------D-----GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATD   98 (160)
Q Consensus        35 ~i~~v~ivG~V~~~---~--~~~~~~~~~~Id------D-----gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (160)
                      .+.+|.++|.|..-   .  ....++..|+|.      |     .|--++|++|....+.                    
T Consensus         4 mmN~v~l~G~l~~dpe~r~t~~G~~v~~f~la~~~~~~~~~g~~~t~~~~v~~wg~~Ae~--------------------   63 (116)
T 3vdy_A            4 MFNQVMLVGRLTKDPDLRYTSAGAAVAHVTLAVNRSFKNASGEIEADYVNCTLWRKTAEN--------------------   63 (116)
T ss_dssp             CCCCEEEEEEESSCCEEEECTTSCEEEEEEEEEECSSCCSSSCCCEEEEEEEEEHHHHHH--------------------
T ss_pred             eEeEEEEEEEEccCcEEEECCCCCEEEEEEEEEeccccCCCCccccEEEEEEEECHHHHH--------------------
Confidence            45677788887751   1  111255566652      1     1223999999765431                    


Q ss_pred             cccccccCcEEEEEEEece--eCC---c----eEEEEEEEEEcCChh
Q 043474           99 FAAKIKIGLVARVRGRIAS--YRG---D----VQITVSDVVIEKDPN  136 (160)
Q Consensus        99 ~~~~~~~G~~V~V~G~v~~--f~~---~----~qi~~~~i~~v~d~n  136 (160)
                      ....++.|+.|.|.|+++.  |.+   +    ..|.+..|..++..+
T Consensus        64 ~~~~l~KG~~V~V~G~l~~~~~~d~dG~~~~~~ev~a~~i~~l~~~~  110 (116)
T 3vdy_A           64 TALYCQKGSLVGVSGRIQTRSYENEEGVNVYVTEVLADTVRFMDPKP  110 (116)
T ss_dssp             HHHHCCTTCEEEEEEEEEEEEEC----CCEEEEEEEEEEEEECC---
T ss_pred             HHHhCCCCCEEEEEEEEEeeEEECCCCCEEEEEEEEEEEEEEccCCC
Confidence            2245899999999999974  543   1    478999998876543

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=93.68  E-value=0.08  Score=47.60  Aligned_cols=70  Identities=20%  Similarity=0.299  Sum_probs=50.2

Q ss_pred             eEEEEEEEEEEeec---cCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCcccccccccccccccccc--CcEEEE
Q 043474           37 SRAEIVGTITSRDH---KPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKI--GLVARV  111 (160)
Q Consensus        37 ~~v~ivG~V~~~~~---~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--G~~V~V  111 (160)
                      ..+.+.|.|.+...   +....+.+++.|+||.+.++.|....                      ....+++  |..+.+
T Consensus       166 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~f~~~~----------------------~~~~~~~~~g~~~~~  223 (780)
T 1gm5_A          166 EKVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQDY----------------------LQTYLKQLTGKEVFV  223 (780)
T ss_dssp             CCCEEEECCCCCEEEECSSCEEEEEEECCSSCCEEEEECSCCT----------------------THHHHHTTCSSCEEE
T ss_pred             CEEEEEEEEEEEEeecCCCCeEEEEEEEECCceEEEEEECcHH----------------------HHhhCccCCCCEEEE
Confidence            47788888887542   22356789999999999998665222                      2256788  999999


Q ss_pred             EEEecee--CCceEEEEEE
Q 043474          112 RGRIASY--RGDVQITVSD  128 (160)
Q Consensus       112 ~G~v~~f--~~~~qi~~~~  128 (160)
                      .|+++.|  .+..|+.--.
T Consensus       224 ~G~~~~~~~~~~~~~~~p~  242 (780)
T 1gm5_A          224 TGTVKSNAYTGQYEIHNAE  242 (780)
T ss_dssp             EEEECSCCTTSSCCEEEEE
T ss_pred             EEEEEEccCCCcEEEEcCE
Confidence            9999986  5665654433

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=93.63  E-value=0.077  Score=44.38  Aligned_cols=70  Identities=17%  Similarity=0.332  Sum_probs=47.0

Q ss_pred             EEEEEEEEEEeec------c--C--CceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccC
Q 043474           38 RAEIVGTITSRDH------K--P--SKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIG  106 (160)
Q Consensus        38 ~v~ivG~V~~~~~------~--~--~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G  106 (160)
                      .|-|+|.|.++..      +  +  +....++|-|.|| .|+|.+|.+....                 . ........|
T Consensus       135 ~vDViG~V~~v~~~~~i~~k~~g~~~~kr~i~L~D~sg~~i~~tLWg~~A~~-----------------f-~~~~~~~~~  196 (444)
T 4gop_C          135 QCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTLWGKTAET-----------------F-PTNAGVDEK  196 (444)
T ss_dssp             CCBEEEEEEEECCCEEECCTTTCSCEEEEEEEEECTTCBEEEEEEEHHHHHT-----------------S-TTSTTSSSC
T ss_pred             ceEEEEEEEEcCCcEEEEEccCCceeeEEEEEEEeCCCCEEEEEEEhhhhhh-----------------h-hhhhccCCC
Confidence            4566777777643      2  1  2557999999999 7999999876541                 0 001225678


Q ss_pred             cEEEEEE-EeceeCCceEEEE
Q 043474          107 LVARVRG-RIASYRGDVQITV  126 (160)
Q Consensus       107 ~~V~V~G-~v~~f~~~~qi~~  126 (160)
                      .+|.++| +|+.|+|+ .|.+
T Consensus       197 ~VV~i~~~kV~~f~G~-~ls~  216 (444)
T 4gop_C          197 PVLAFKGVKVGDFGGR-SLSM  216 (444)
T ss_dssp             CEEEEESCEEECTTSS-EEEC
T ss_pred             CEEEEEeEEEeecCCe-EEec
Confidence            8888876 57889885 6644

>1z9f_A Single-strand binding protein; TM0604, single stranded DNA-binding protein, structural GENO joint center for structural genomics, JCSG; 2.30A {Thermotoga maritima}

Probab=93.45  E-value=0.21  Score=36.06  Aligned_cols=81  Identities=11%  Similarity=0.177  Sum_probs=49.2

Q ss_pred             EeeEEEEEEEEEEe---e--ccCCceEEEEEe--C-----C------CceEEEEEeecCccCCCCCCCCCCccccccccc
Q 043474           35 LLSRAEIVGTITSR---D--HKPSKFIKFTVD--D-----G------TGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA   96 (160)
Q Consensus        35 ~i~~v~ivG~V~~~---~--~~~~~~~~~~Id--D-----g------TG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~   96 (160)
                      .+.+|.|+|.+..-   .  ..+..+..|+|.  .     .      |--+.|++|....+.                  
T Consensus        15 ~~N~V~LiGrL~~DPelr~t~~G~~va~f~lAv~~r~~~~~~Ge~~~t~~~~v~~wg~~Ae~------------------   76 (153)
T 1z9f_A           15 FFNKIILIGRLVRDPEERYTLSGTPVTTFTIAVDRVPRKNAPDDAQTTDFFRIVTFGRLAEF------------------   76 (153)
T ss_dssp             CCCCEEEEEEESSCCEEEECC--CEEEEEEEEEEC-----------CEEEEEEEEEHHHHHH------------------
T ss_pred             ceeEEEEEEEECCCCEEEECCCCCEEEEEEEEEcCCccccCCCCEeeeEEEEEEEECHHHHH------------------
Confidence            35677777777651   1  111255566653  2     1      234899999765431                  


Q ss_pred             cccccccccCcEEEEEEEece--eCC---c----eEEEEEEEEEcCCh
Q 043474           97 TDFAAKIKIGLVARVRGRIAS--YRG---D----VQITVSDVVIEKDP  135 (160)
Q Consensus        97 ~~~~~~~~~G~~V~V~G~v~~--f~~---~----~qi~~~~i~~v~d~  135 (160)
                        ....++.|+.|.|.|+++.  |.+   +    ..|.+..|..+...
T Consensus        77 --~~~~l~KG~~V~VeGrL~~~~~~dkdG~~r~~~eV~a~~i~~l~~~  122 (153)
T 1z9f_A           77 --ARTYLTKGRLVLVEGEMRMRRWETPTGEKRVSPEVVANVVRFMDRK  122 (153)
T ss_dssp             --HHHHCCTTCEEEEEEEEEEEC-------CCCEEEEEEEEEEECC--
T ss_pred             --HHhhCCCCCEEEEEEEEEeceEECCCCCEEEEEEEEEEEEEEccCC
Confidence              2346899999999999986  542   2    46899999888654

>2vw9_A Single-stranded DNA binding protein; DNA replication, single-stranded DNA, single-stranded DNA binding protein, oligonucleotide/oligosaccharide binding fold, OB-fold; 2.30A {Helicobacter pylori}

Probab=93.45  E-value=0.22  Score=34.98  Aligned_cols=50  Identities=12%  Similarity=0.152  Sum_probs=36.7

Q ss_pred             eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece--eCCc-------eEEEEEEEEEcCCh
Q 043474           66 CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS--YRGD-------VQITVSDVVIEKDP  135 (160)
Q Consensus        66 ~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~--f~~~-------~qi~~~~i~~v~d~  135 (160)
                      -++|++|....+.                    ....++.|+.|.|.|+++.  |.++       ..|.+..|..+...
T Consensus        50 ~~~v~~wg~~Ae~--------------------~~~~l~KG~~V~V~G~L~~~~~~dkdG~~r~~~ev~a~~i~~l~~~  108 (134)
T 2vw9_A           50 FIDARLFGRTAEI--------------------ANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMDKK  108 (134)
T ss_dssp             EEEEEEEHHHHHH--------------------HHHHCCTTCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEEECCCC
T ss_pred             EEEEEEEcHHHHH--------------------HHHhCCCCCEEEEEEEEEeeeEECCCCCEEEEEEEEEEEEEEccCC
Confidence            4999999765431                    2245899999999999975  5432       35899999988654

>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB, ssDNA binding protein, OB-fold; 2.80A {Homo sapiens} SCOP: b.40.4.3

Probab=93.11  E-value=0.27  Score=36.28  Aligned_cols=84  Identities=14%  Similarity=0.126  Sum_probs=51.1

Q ss_pred             EEEEEeCCCceEEEEEeecCccCCCCCCCCCCcccccccc-------c-cccccccc--cC--cEEEEEEEeceeCCc--
Q 043474           56 IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGV-------A-TDFAAKIK--IG--LVARVRGRIASYRGD--  121 (160)
Q Consensus        56 ~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~-------~-~~~~~~~~--~G--~~V~V~G~v~~f~~~--  121 (160)
                      +.+.|.|.||.+.|.++.+..+..         +-.++++       + ......+.  .+  -.++++.+...|++.  
T Consensus        81 l~~~i~D~Tg~~~~t~F~~~ae~i---------lG~sA~el~~l~e~~~~~~~~~~~~~~~~~~~f~l~vk~e~yn~e~r  151 (181)
T 1l1o_C           81 LSVNIADFQENQWVTCFQESAEAI---------LGQNAAYLGELKDKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESR  151 (181)
T ss_dssp             EEEEEECSSCEEEEEEEHHHHHHH---------HSSCHHHHHHHTTSCHHHHHHHHHHTTTCEEEEEEEEECCCC-----
T ss_pred             EEEEEEeCCCCEEEEEEhHHHHHH---------hCCCHHHHHHHHhhChHHHHHHHHHhcCceEEEEEEEEEeecCCEEE
Confidence            689999999999999998765321         0001110       0 00001111  13  366777777789876  


Q ss_pred             eEEEEEEEEEcCChhHHHHHHHHHHHHH
Q 043474          122 VQITVSDVVIEKDPNMEVLHWLDCLRLA  149 (160)
Q Consensus       122 ~qi~~~~i~~v~d~n~~~~h~le~~~~~  149 (160)
                      ....+.++.|++ ..++..+.++.+..+
T Consensus       152 ~~~~v~~~~~vd-~~~e~~~L~~~i~~~  178 (181)
T 1l1o_C          152 IKATVMDVKPVD-YREYGRRLVMSIRRS  178 (181)
T ss_dssp             CEEEEEEEEECC-HHHHHHHHHHHHHHH
T ss_pred             EEEEEEEeeeCC-HHHHHHHHHHHHHHh
Confidence            457888888865 788899999988643

>3rn5_A Interferon-inducible protein AIM2; OB fold, DNA binding, cytosolic, immune system-DNA complex; HET: DNA; 2.50A {Homo sapiens} PDB: 3rn2_A*

Probab=93.07  E-value=0.82  Score=34.35  Aligned_cols=49  Identities=29%  Similarity=0.233  Sum_probs=33.5

Q ss_pred             ceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEE-EeceeCCceEEE
Q 043474           54 KFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRG-RIASYRGDVQIT  125 (160)
Q Consensus        54 ~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G-~v~~f~~~~qi~  125 (160)
                      +++.|.|.|.||.|+++....-..                       -.+++||-+|..- .++...+++||.
T Consensus       139 ~~~~YeI~DnTG~MeVvv~G~~~~-----------------------i~CEeGDKLrL~cFeL~~~~~~~qL~  188 (208)
T 3rn5_A          139 KNILFDLSDNTGKMEVLGVRNEDT-----------------------MKCKEGDKVRLTFFTLSKNGEKLQLT  188 (208)
T ss_dssp             SEEEEEEEETTEEEEEEEECSTGG-----------------------GSCCTTCEEEEEEEEEEECSSSEEEE
T ss_pred             ceEEEEEecCCCcEEEEEeccCcc-----------------------cccCCCCeeEEEEEEEeccCCeeeEE
Confidence            679999999999999998755432                       3577888665443 244444555553

>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor}

Probab=92.34  E-value=0.6  Score=35.12  Aligned_cols=47  Identities=21%  Similarity=0.461  Sum_probs=32.1

Q ss_pred             ceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEece--eCC-------ceEEEEEEEEE
Q 043474           65 GCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIAS--YRG-------DVQITVSDVVI  131 (160)
Q Consensus        65 G~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~--f~~-------~~qi~~~~i~~  131 (160)
                      --|+|++|.+..+                    .....++.|+.|.|.|+|+.  |.+       ..+|.+.+|.+
T Consensus        53 ~wi~VvawgklAE--------------------~v~~~L~KG~~V~VeGrL~~rswedkdG~kr~~~eVvA~~Ig~  108 (199)
T 3eiv_A           53 LFLTCSVWRQAAE--------------------NVAESLQRGMRVIVQGRLKQRSYEDREGVKRTVYELDVDEVGA  108 (199)
T ss_dssp             EEEEEEEETHHHH--------------------HHHHHCCTTCEEEEEEEEEEEC--------CCEEEEEEEEEEE
T ss_pred             EEEEEEEEhHHHH--------------------HHHHhcCCCCEEEEEEEEEeeEEECCCCCEEEEEEEEEEEEec
Confidence            3489999976543                    12346899999999999975  543       24677777765

>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3

Probab=92.27  E-value=0.57  Score=37.35  Aligned_cols=79  Identities=13%  Similarity=0.337  Sum_probs=53.7

Q ss_pred             eeEEEEEEEEEEe---ec--cCCceEEEEEe------CCCc-------eEEEEEeecCccCCCCCCCCCCcccccccccc
Q 043474           36 LSRAEIVGTITSR---DH--KPSKFIKFTVD------DGTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        36 i~~v~ivG~V~~~---~~--~~~~~~~~~Id------DgTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      +..|.|+|.|..-   ..  ....++.|+|.      |..|       -|.|++|....+                    
T Consensus       129 mN~V~L~GrL~~dPelr~t~~G~~v~~f~lAv~~~~~d~~Ge~~~~t~~i~vvawg~~Ae--------------------  188 (301)
T 1se8_A          129 MNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLAE--------------------  188 (301)
T ss_dssp             EEEEEEEEEECSCCEEEECTTCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHH--------------------
T ss_pred             eeEEEEEEEECcCCEEEECCCCCEEEEEEEEEcCceEcCCCCcccccEEEEEEECCHHHH--------------------
Confidence            6789999999872   11  12366777764      2223       499999976543                    


Q ss_pred             ccccccccCcEEEEEEEece--eCCc-------eEEEEEEEEEcCCh
Q 043474           98 DFAAKIKIGLVARVRGRIAS--YRGD-------VQITVSDVVIEKDP  135 (160)
Q Consensus        98 ~~~~~~~~G~~V~V~G~v~~--f~~~-------~qi~~~~i~~v~d~  135 (160)
                      .... ++.|+.|.|.|+++.  |.++       ..|.+.+|..+...
T Consensus       189 ~~~~-l~KG~~V~V~GrL~~~~y~dkdG~~r~~~ev~a~~i~~l~~k  234 (301)
T 1se8_A          189 NMKE-LRKGDPVMIMGRLVNEGWTDKDGNKRNSTRVEATRVEALARG  234 (301)
T ss_dssp             HHTT-CCTTCEEEEEEEEEEEECC------CEEEEEEEEEEEECCC-
T ss_pred             HHHh-cCCCCEEEEEEEEeeeeEECCCCcEEEEEEEEEEEEEEeccC
Confidence            1234 999999999999975  5432       46899999988643

>1sr3_A APO-CCME; OB fold, beta barrel, flexible C-terminal domain, chaperone; NMR {Escherichia coli} SCOP: b.40.9.1

Probab=92.20  E-value=0.82  Score=32.37  Aligned_cols=57  Identities=19%  Similarity=0.231  Sum_probs=42.6

Q ss_pred             eEEEEEEEEEE--eecc-CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEE
Q 043474           37 SRAEIVGTITS--RDHK-PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRG  113 (160)
Q Consensus        37 ~~v~ivG~V~~--~~~~-~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G  113 (160)
                      ++++|.|.|..  +... ++..++|.|.|+.++|.+.+-..                        ..+.|+.|.=|-+.|
T Consensus        29 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------------------------lPDlFrEGqgVVa~G   84 (136)
T 1sr3_A           29 QRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVSYEGI------------------------LPDLFREGQGVVVQG   84 (136)
T ss_dssp             SEEEEEEEECTTTCEECSSSSEEEEEEECSSCEEEEEEESC------------------------CCTTCCTTSEEEEEE
T ss_pred             CEEEEeeEEeCCcEEEcCCCCEEEEEEEeCCcEEEEEECCC------------------------CCccccCCCeEEEEE
Confidence            68999999983  4432 23458999999988888876332                        235789999999999


Q ss_pred             Eece
Q 043474          114 RIAS  117 (160)
Q Consensus       114 ~v~~  117 (160)
                      ++..
T Consensus        85 ~l~~   88 (136)
T 1sr3_A           85 ELEK   88 (136)
T ss_dssp             EECS
T ss_pred             EECC
Confidence            9853

>2fxq_A Single-strand binding protein; strand beta-sheet extended loops, DNA binding protein; 1.85A {Thermus aquaticus} PDB: 2ihe_A 2cwa_A 2ihf_A

Probab=91.96  E-value=0.64  Score=36.16  Aligned_cols=80  Identities=11%  Similarity=0.216  Sum_probs=54.3

Q ss_pred             EeeEEEEEEEEEEee-----ccCCceEEEEEe----------CCCceEEEEEeecCccCCCCCCCCCCcccccccccccc
Q 043474           35 LLSRAEIVGTITSRD-----HKPSKFIKFTVD----------DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDF   99 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~-----~~~~~~~~~~Id----------DgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (160)
                      .+..|.++|.|..--     .....+..|+|.          |.|--|.|++|....+                    ..
T Consensus       127 ~~N~v~l~G~l~~dpe~r~t~~G~~v~~f~lAv~~~~~g~~~~~t~~~~v~~wg~~Ae--------------------~~  186 (264)
T 2fxq_A          127 ALNQVILMGNLTRDPDLRYTPQGTAVVRLGLAVNERRRGQEEERTHFLEVQAWRELAE--------------------WA  186 (264)
T ss_dssp             CCEEEEEEEEESSCCCCEECTTCCEEEEEEEEEECCC-------EEEEEEEEEHHHHH--------------------HH
T ss_pred             ceEEEEEEEEECCCCEEEECCCCCEEEEEEEEEcCCcCCCCccccEEEEEEEEChHHH--------------------Hh
Confidence            368899999998721     112366777763          2344599999976443                    13


Q ss_pred             ccccccCcEEEEEEEece--eCC---c----eEEEEEEEEEcCCh
Q 043474          100 AAKIKIGLVARVRGRIAS--YRG---D----VQITVSDVVIEKDP  135 (160)
Q Consensus       100 ~~~~~~G~~V~V~G~v~~--f~~---~----~qi~~~~i~~v~d~  135 (160)
                      . .++.|+.|.|.|+++.  |.+   +    ..|.+.+|..+...
T Consensus       187 ~-~l~KG~~V~V~G~l~~~~~~~~dG~~~~~~ev~a~~i~~l~~~  230 (264)
T 2fxq_A          187 S-ELRKGDGLLVIGRLVNDSWTSSSGERRFQTRVEALRLERPTRG  230 (264)
T ss_dssp             T-TCCTTCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEECCCC-
T ss_pred             h-hcCCCCEEEEEEEEEeeEEECCCCCEEEEEEEEEEEEEECccc
Confidence            3 7899999999999975  543   2    46889999877654

>1qvc_A Single stranded DNA binding protein monomer; beta-barrel; 2.20A {Escherichia coli} SCOP: b.40.4.3 PDB: 1kaw_A 1eyg_A 1sru_A

Probab=91.52  E-value=0.4  Score=34.07  Aligned_cols=65  Identities=14%  Similarity=0.209  Sum_probs=43.8

Q ss_pred             EeeEEEEEEEEEEe---ec--cCCceEEEEEe------C--------CCceEEEEEeecCccCCCCCCCCCCcccccccc
Q 043474           35 LLSRAEIVGTITSR---DH--KPSKFIKFTVD------D--------GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        35 ~i~~v~ivG~V~~~---~~--~~~~~~~~~Id------D--------gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~   95 (160)
                      .+..|.|+|.|..-   ..  ....++.|+|.      |        .|--|+|++|.+..+.                 
T Consensus         4 ~mN~v~L~GrL~~dPelr~t~~G~~v~~f~lA~~~~~~~~~~Ge~~~~t~~~~v~~wg~~Ae~-----------------   66 (145)
T 1qvc_A            4 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEV-----------------   66 (145)
T ss_dssp             CEEEEEEEEEESSCCEEECCSSSCCEEEEEEEECCCCSCCSSSSCCCCCEEEEEEEETHHHHH-----------------
T ss_pred             ceEEEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCCcccccCCcEecccEEEEEEEehHHHHH-----------------
Confidence            36788899998762   11  12366777773      1        1334999999764431                 


Q ss_pred             ccccccccccCcEEEEEEEece--eC
Q 043474           96 ATDFAAKIKIGLVARVRGRIAS--YR  119 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~~--f~  119 (160)
                         ....++.|+.|.|.|+++.  |.
T Consensus        67 ---~~~~l~KG~~V~V~G~L~~~~~~   89 (145)
T 1qvc_A           67 ---ASEYLRKGSQVYIEGQLRTRKWT   89 (145)
T ss_dssp             ---HHHHCCTTCEEEEEEEEEEEEEC
T ss_pred             ---HHHhcCCCCEEEEEEEEEeeEEE
Confidence               2245899999999999975  64

>4dka_C RNA-editing complex protein MP81; krepa1, VHH, single domain antibody, protein binding, RNA BI protein-immune system complex; 1.97A {Trypanosoma brucei} PDB: 4dk3_C 4dk6_C

Probab=91.48  E-value=1.7  Score=29.29  Aligned_cols=65  Identities=18%  Similarity=0.338  Sum_probs=38.2

Q ss_pred             eEEEEEEEEEEeec---cCCceEEEEEe-CCCc-----eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCc
Q 043474           37 SRAEIVGTITSRDH---KPSKFIKFTVD-DGTG-----CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGL  107 (160)
Q Consensus        37 ~~v~ivG~V~~~~~---~~~~~~~~~Id-DgTG-----~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  107 (160)
                      +++.++|.|.+++.   .+.+-..|+|. |+.+     .+..+++.+....                  ....+.++.|.
T Consensus         4 sn~vlvG~V~DVQ~Gfl~~~~V~Qftl~~d~e~~~eke~~tVRC~Gd~~~~------------------~~lk~~lk~g~   65 (105)
T 4dka_C            4 SNALMIGRIADVQHGFLGAMTVTQYVLEVDGGASGEKEFIVIRCMGDNFPA------------------SLLKDQVKLGS   65 (105)
T ss_dssp             CEEEEEEEEEEEEEEEETTEEEEEEEEEECC----CCEEEEEEEECC---------------------------CCCTTC
T ss_pred             cceEEEEEEEEeeecccccceEEEEEEEEeCCCCCcccEEEEEEcCccchH------------------HHHHHHHhCCC
Confidence            67899999999997   23244444442 4443     2444555443321                  12457899999


Q ss_pred             EEEEEEEeceeC
Q 043474          108 VARVRGRIASYR  119 (160)
Q Consensus       108 ~V~V~G~v~~f~  119 (160)
                      .|.|.|+++...
T Consensus        66 ~v~V~GrLRm~p   77 (105)
T 4dka_C           66 RVLVQGTLRMNR   77 (105)
T ss_dssp             EEEEEEEEECCC
T ss_pred             EEEEEeEEEeee
Confidence            999999998744

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=91.46  E-value=0.53  Score=39.26  Aligned_cols=90  Identities=12%  Similarity=0.117  Sum_probs=54.0

Q ss_pred             EEEEEeCCCceEEEEEeecCccCCCCCCCCCC-cccccccccc-----ccccccccCcEEEEEEEeceeCCce--EEEEE
Q 043474           56 IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPS-TVRLIAGVAT-----DFAAKIKIGLVARVRGRIASYRGDV--QITVS  127 (160)
Q Consensus        56 ~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~-~~~~~~~~~~-----~~~~~~~~G~~V~V~G~v~~f~~~~--qi~~~  127 (160)
                      +.+.|+|+||.+.|.+|.+..+..-   |.+. ++.-..+.+.     ......-.--.++++.+...|++..  ...+.
T Consensus       346 l~~~v~D~Tg~~~~~~F~~~a~~ll---G~sa~el~~~~~~d~~~~~~~~~~~~~k~~~f~~~~k~~~y~~~~r~~~~v~  422 (444)
T 4gop_C          346 LSTNVADATGQMWLSGFNEDATQLI---GMSAGELHKLREESESEFSAALHRAANRMYMFNCRAKMDTFNDTARVRYTIS  422 (444)
T ss_dssp             EEEEEEETTEEEEEEECHHHHHHHT---TSCHHHHHHHHTTCHHHHHHHHHTTSSCEEEEEEEEEEEEETTEEEEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEehHHHHHHc---CCCHHHHHHHHhcChHHHHHHHHHhhCcEEEEEEEEEeeeeCCeeEEEEEEE
Confidence            6889999999999999977654210   0000 0000000000     0011222334677777788999874  46777


Q ss_pred             EEEEcCChhHHHHHHHHHHHHH
Q 043474          128 DVVIEKDPNMEVLHWLDCLRLA  149 (160)
Q Consensus       128 ~i~~v~d~n~~~~h~le~~~~~  149 (160)
                      ++.|++ +.++..++++.+..|
T Consensus       423 ~~~~~d-~~~~~~~l~~~i~~~  443 (444)
T 4gop_C          423 RAAPVD-FAKAGMELVDAIRAY  443 (444)
T ss_dssp             EEEECC-HHHHHHHHHHHHHHH
T ss_pred             EeeeCC-HHHHHHHHHHHHHhh
Confidence            777764 888899999888654

>3ull_A DNA binding protein; DNA replication, mitochondrion, transit peptide; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 PDB: 1s3o_A* 2dud_A

Probab=91.34  E-value=0.7  Score=32.17  Aligned_cols=36  Identities=19%  Similarity=0.317  Sum_probs=25.4

Q ss_pred             cccccCcEEEEEEEece--eCC---c----eEEEEEEEEEcCChh
Q 043474          101 AKIKIGLVARVRGRIAS--YRG---D----VQITVSDVVIEKDPN  136 (160)
Q Consensus       101 ~~~~~G~~V~V~G~v~~--f~~---~----~qi~~~~i~~v~d~n  136 (160)
                      ..++.|+.|.|.|+++.  |.+   +    ..|.+..|..+...+
T Consensus        84 ~~l~KG~~V~V~G~L~~~~~~d~dG~~r~~~ev~a~~i~~l~~~~  128 (132)
T 3ull_A           84 QYVKKGSRIYLEGKIDYGEYMDKNNVRRQATTIIADNIIFLSDQT  128 (132)
T ss_dssp             HHCCTTCEEEEEEEEECCCEESSSSEECCCEEEEEEEEECC----
T ss_pred             hhCCCCCEEEEEEEEEeeEEECCCCCEEEEEEEEEEEEEEccCCC
Confidence            46899999999999974  632   2    468899888776553

>3ulp_A Single-strand binding protein; OB-fold, DNA binding, single-stranded DNA, apicoplast, DNA B protein-DNA complex; HET: DNA; 2.10A {Plasmodium falciparum}

Probab=91.23  E-value=0.3  Score=33.66  Aligned_cols=67  Identities=18%  Similarity=0.292  Sum_probs=43.8

Q ss_pred             eEeeEEEEEEEEEEe---e--ccCCceEEEEEe------CC-Cc-------eEEEEEee-cCccCCCCCCCCCCcccccc
Q 043474           34 KLLSRAEIVGTITSR---D--HKPSKFIKFTVD------DG-TG-------CVPCVLWL-NHLTSLYLPRRDPSTVRLIA   93 (160)
Q Consensus        34 ~~i~~v~ivG~V~~~---~--~~~~~~~~~~Id------Dg-TG-------~I~~~~w~-~~~~~~~~~~~~~~~~~~~~   93 (160)
                      ..+.+|.|+|.+..-   .  ....++..|+|.      |. +|       -+.|++|. ...+                
T Consensus         4 ~~~N~v~l~Grl~~dpelr~t~~G~~v~~f~lA~~~~~~~~~~G~~~~~t~~~~v~~wg~~~Ae----------------   67 (124)
T 3ulp_A            4 KSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVD----------------   67 (124)
T ss_dssp             CCEEEEEEEEEECSCCEEEECTTSCEEEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCHHHHH----------------
T ss_pred             ccceEEEEEEEECCCcEEEECCCCCEEEEEEEEEccceecccCCcEecccEEEEEEEEEchHHH----------------
Confidence            457888899988762   1  112256667663      21 23       39999998 4432                


Q ss_pred             ccccccccccccCcEEEEEEEec--eeCC
Q 043474           94 GVATDFAAKIKIGLVARVRGRIA--SYRG  120 (160)
Q Consensus        94 ~~~~~~~~~~~~G~~V~V~G~v~--~f~~  120 (160)
                          .....++.|+.|.|.|+++  .|.+
T Consensus        68 ----~~~~~l~KG~~V~V~G~L~~~~~~d   92 (124)
T 3ulp_A           68 ----LIDKYLRKGRRVYVQGSLHTRKWHT   92 (124)
T ss_dssp             ----HHHHHCCTTCEEEEEEEEEEEEECC
T ss_pred             ----HHHhhcCCCCEEEEEEEEEeEEEeC
Confidence                1224689999999999997  5754

>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions, DNA HYDR sodium ION, quadruplex DNA, DNA-binding protein-DNA complex; 1.86A {Sterkiella nova} SCOP: b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1kix_A 1otc_A* 2i0q_A 1ph6_A 1ph1_A 1phj_A* 1ph3_A 1pa6_A 1ph4_A 1ph7_A 1ph8_A 1ph9_A 1ph5_A* 1ph2_A* 1k8g_A

Probab=91.20  E-value=1.7  Score=37.08  Aligned_cols=71  Identities=15%  Similarity=0.222  Sum_probs=50.0

Q ss_pred             eeEEEEEEEEEEeec----cCCc-eEEEEEeCCC-c-------eE-----EEEEeecCccCCCCCCCCCCcccccccccc
Q 043474           36 LSRAEIVGTITSRDH----KPSK-FIKFTVDDGT-G-------CV-----PCVLWLNHLTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        36 i~~v~ivG~V~~~~~----~~~~-~~~~~IdDgT-G-------~I-----~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      -..|.++|+|+....    +++. .++|+|-|.| +       -|     .|.++.+..+                    
T Consensus        49 ~~~VnviGVVvd~~~P~~T~G~D~~~t~tI~D~S~~~~~~~~~Gl~~~~~~v~iF~~~~e--------------------  108 (495)
T 1jb7_A           49 AQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFE--------------------  108 (495)
T ss_dssp             CSCEEEEEEEEEECCCEECSSSCEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSGG--------------------
T ss_pred             CCeEEEEEEEeecCCceecCCCeEEEEEEEEeCCCCcccccccccccCceEEEEECCChH--------------------
Confidence            356788999998652    2233 3689999955 2       16     8888877543                    


Q ss_pred             cccccc-ccCcEEEEE-EEeceeCCceEEEEE
Q 043474           98 DFAAKI-KIGLVARVR-GRIASYRGDVQITVS  127 (160)
Q Consensus        98 ~~~~~~-~~G~~V~V~-G~v~~f~~~~qi~~~  127 (160)
                       ....+ ..||+|++. -+|+.|+|..|....
T Consensus       109 -~LP~V~~~GDII~LhrvkIq~~ng~~~~v~~  139 (495)
T 1jb7_A          109 -DLPIIHRAGDIIRVHRATLRLYNGQRQFNAN  139 (495)
T ss_dssp             -GSCCCCEETCEEEEEEEEEEEETTEEEEEEE
T ss_pred             -HCCCCCCCCCEEEEEEEEEEEECCcEEEEec
Confidence             22445 699999995 468999999987654

>1j6q_A Cytochrome C maturation protein E; all-beta protein, heme delivery,cytochrome C maturation, OB- (oligonucleotide binding)fold; NMR {Shewanella putrefaciens} SCOP: b.40.9.1 PDB: 1lm0_A

Probab=91.08  E-value=1.1  Score=31.74  Aligned_cols=76  Identities=20%  Similarity=0.227  Sum_probs=48.7

Q ss_pred             eEEEEEEEEE--Eeecc-CCceEEEEEeC-CCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTIT--SRDHK-PSKFIKFTVDD-GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~--~~~~~-~~~~~~~~IdD-gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      ++++|.|.|.  ++... ++..++|.|.| +..+|.+.+-..                        ..+.|+.|.-|-+.
T Consensus        33 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~~v~V~Y~Gi------------------------lPDlFrEGqgVVa~   88 (136)
T 1j6q_A           33 QRIRVGGMVTVGSMVRDPNSLHVQFAVHDSLGGEILVTYDDL------------------------LPDLFREGQGIVAQ   88 (136)
T ss_dssp             CEEEEEEEECTTCCEECTTSSCEEEEEECTTCCCEEEEECSC------------------------CTTSCCSSSEEEEE
T ss_pred             CEEEEeEEEeCCcEEecCCCCEEEEEEEcCCCCEEEEEECCC------------------------CCccccCCCeEEEE
Confidence            6899999996  34432 23458999999 777888875322                        23578999999999


Q ss_pred             EEeceeCCceEEEEEEEEEcCChhHHH
Q 043474          113 GRIASYRGDVQITVSDVVIEKDPNMEV  139 (160)
Q Consensus       113 G~v~~f~~~~qi~~~~i~~v~d~n~~~  139 (160)
                      |++..   .--+.+..|-.--|.++..
T Consensus        89 G~l~~---~g~F~A~eVLaKhdekY~p  112 (136)
T 1j6q_A           89 GVLGE---DGKLAATEVLAKHDENYMP  112 (136)
T ss_dssp             EEECS---TTSEEEEEEECCC------
T ss_pred             EEECC---CCeEEEEEEEecCCCCCCC
Confidence            99853   1246677766444444443

>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3

Probab=90.93  E-value=1.3  Score=35.18  Aligned_cols=79  Identities=13%  Similarity=0.145  Sum_probs=49.6

Q ss_pred             eeEEEEEEEEEEe---e--ccCCceEEEEEe------CCCc-------eEEEEEeecCccCCCCCCCCCCcccccccccc
Q 043474           36 LSRAEIVGTITSR---D--HKPSKFIKFTVD------DGTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        36 i~~v~ivG~V~~~---~--~~~~~~~~~~Id------DgTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      +.+|.|+|.|..-   .  .....++.|+|.      |.+|       -+.|++|....+                    
T Consensus         5 mN~V~LiGrL~~dPelr~t~~G~~v~~f~LAv~r~~~~~~G~~~~~t~~i~vv~~g~~Ae--------------------   64 (301)
T 1se8_A            5 MNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAE--------------------   64 (301)
T ss_dssp             EEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEEEC-------CEEEEEEEEEEESHHHH--------------------
T ss_pred             eeEEEEEEEECCCceEEECCCCCEEEEEEEEEcCceECCCCCEecceEEEEEEEEcHHHH--------------------
Confidence            5778888888652   1  122356666663      1223       388999976432                    


Q ss_pred             ccccc-cccCcEEEEEEEec--eeCCc-------eEEEEEEEEEcCC
Q 043474           98 DFAAK-IKIGLVARVRGRIA--SYRGD-------VQITVSDVVIEKD  134 (160)
Q Consensus        98 ~~~~~-~~~G~~V~V~G~v~--~f~~~-------~qi~~~~i~~v~d  134 (160)
                      ..... ++.|+.|.|.|+++  .|.++       ..|.+..|..+..
T Consensus        65 ~~~~~~l~KG~~V~VeG~L~~r~~~dkdG~~r~~~ev~a~~i~~l~~  111 (301)
T 1se8_A           65 WQAERNLKGGDAVVVEGTLEYRQWEAPEGGKRSAVNVKALRMEQLGT  111 (301)
T ss_dssp             HHHHTCCCTTCEEEEEEEEEEEEEC-----CEEEEEEEEEEEEECSS
T ss_pred             HHHhhCCCCCCEEEEEEEEEeeeEECCCCCEEEEEEEEEeEEEEeec
Confidence            12245 79999999999998  47542       3588888887754

>3rlo_A Gamma-interferon-inducible protein 16; HIN200/OB fold/DNA binding, DNA binding/cytosolic DNA sensor cytosol, DNA binding protein; 1.80A {Homo sapiens} PDB: 3rnu_A* 3b6y_A 3rln_A

Probab=90.28  E-value=0.85  Score=34.16  Aligned_cols=22  Identities=23%  Similarity=0.386  Sum_probs=19.0

Q ss_pred             ceEEEEEeCCCceEEEEEeecC
Q 043474           54 KFIKFTVDDGTGCVPCVLWLNH   75 (160)
Q Consensus        54 ~~~~~~IdDgTG~I~~~~w~~~   75 (160)
                      +++.|.|.|.||.|+++....-
T Consensus       135 ~~~~YeI~DnTG~MeVvv~G~~  156 (204)
T 3rlo_A          135 EFTYYEIQDNTGKMEVVVHGRL  156 (204)
T ss_dssp             TEEEEEEEETTEEEEEEECGGG
T ss_pred             ceEEEEEecCCCcEEEEEeccC
Confidence            6799999999999999986553

>3lgj_A Single-stranded DNA-binding protein; niaid, CAT scratch fever, rochalimaea, LYME disease, ALS collaborative crystallography, DNA replication; 2.50A {Bartonella henselae}

Probab=89.54  E-value=0.74  Score=33.65  Aligned_cols=81  Identities=10%  Similarity=0.264  Sum_probs=49.2

Q ss_pred             EeeEEEEEEEEEEe---ec--cCCceEEEEEe------C--------CCceEEEEEeec-CccCCCCCCCCCCccccccc
Q 043474           35 LLSRAEIVGTITSR---DH--KPSKFIKFTVD------D--------GTGCVPCVLWLN-HLTSLYLPRRDPSTVRLIAG   94 (160)
Q Consensus        35 ~i~~v~ivG~V~~~---~~--~~~~~~~~~Id------D--------gTG~I~~~~w~~-~~~~~~~~~~~~~~~~~~~~   94 (160)
                      .+.+|.|+|.|..-   ..  ....++.|+|.      |        .|--+.|++|.+ ..+                 
T Consensus        22 ~mNkV~LiGrL~~DPelr~t~~G~~v~~FslAv~~~~~~~~~Ge~~~~t~~i~vv~wg~~lAe-----------------   84 (169)
T 3lgj_A           22 MLNKVMLIGYLGDDPESKTMTSGAEVVNFRMATFESYMNKNTHQKVEKTEWHSVVVFNPHFAK-----------------   84 (169)
T ss_dssp             CEEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEC------------CEEEEEEEECCHHHHH-----------------
T ss_pred             ceeEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecccCCccccccEEEEEEEeCHHHHH-----------------
Confidence            57899999998762   11  12255666653      1        233489999976 332                 


Q ss_pred             cccccccccccCcEEEEEEEece--eCC---c----eEEEE----EEEEEcCCh
Q 043474           95 VATDFAAKIKIGLVARVRGRIAS--YRG---D----VQITV----SDVVIEKDP  135 (160)
Q Consensus        95 ~~~~~~~~~~~G~~V~V~G~v~~--f~~---~----~qi~~----~~i~~v~d~  135 (160)
                         .....++.|+.|.|.|+++.  |.+   +    ..|.+    ..|..++..
T Consensus        85 ---~~~~~l~KG~~V~VeGrL~~r~~~dkdG~~r~~~eIva~~~~~~i~~L~~k  135 (169)
T 3lgj_A           85 ---IALQYLHKGSKVYIEGKLQTRKWQDKNGHDRYTTEIVLPQYKGELHLLDAK  135 (169)
T ss_dssp             ---HHHHHCCTTCEEEEEEEEEEECC--------CEEEEEECTTCCEEEEECC-
T ss_pred             ---HHHHhCCCCCEEEEEEEEEEEEEECCCCCEEEEEEEEEEeccCcEEEccCC
Confidence               12346899999999999975  542   2    23554    356666544

>3afp_A Single-stranded DNA-binding protein; OB-fold, quaternary structure and stability, changes on oligomerisation, water-bridges, DNA damage; 2.05A {Mycobacterium leprae} PDB: 3afq_A 1ue1_A 1ue5_A 1ue6_A 1ue7_A 1x3e_A 1x3f_A 1x3g_A 3a5u_A*

Probab=89.39  E-value=0.64  Score=33.88  Aligned_cols=62  Identities=24%  Similarity=0.423  Sum_probs=39.7

Q ss_pred             eeEEEEEEEEEEee-----ccCCceEEEEEe------C---------CCceEEEEEeecCccCCCCCCCCCCcccccccc
Q 043474           36 LSRAEIVGTITSRD-----HKPSKFIKFTVD------D---------GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        36 i~~v~ivG~V~~~~-----~~~~~~~~~~Id------D---------gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~   95 (160)
                      +..|.|+|.|..--     .....++.|+|.      |         .|--|+|++|.+..+                  
T Consensus         4 ~N~V~LiG~L~~dPelr~t~~G~~va~f~lAv~~~~~~~~~Ge~~d~~t~~~~v~~wg~~Ae------------------   65 (168)
T 3afp_A            4 DTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIWREAAE------------------   65 (168)
T ss_dssp             CCEEEEEEEESSSCCCEECTTSCEEEEEEEEECC--------CCCCCCCEEEEEEEEHHHHH------------------
T ss_pred             cCEEEEEEEECCCCEEEECCCCCEEEEEEEEEccccccccCCcEecCCcEEEEEEEehHHHH------------------
Confidence            45677777776521     111245566664      1         133499999976543                  


Q ss_pred             ccccccccccCcEEEEEEEece
Q 043474           96 ATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                        .....++.|+.|.|.|+|+.
T Consensus        66 --~~~~~l~KG~~V~VeGrL~~   85 (168)
T 3afp_A           66 --NVAESLTRGARVIVTGRLKQ   85 (168)
T ss_dssp             --HHHHHCCTTCEEEEEEEEEE
T ss_pred             --HHHHhCCCCCEEEEEEEEEe
Confidence              12356899999999999975

>3k7u_C MP18 RNA editing complex protein; OB-fold, RNA-editing proteins, kinetoplastids, system, RNA binding protein; 2.10A {Trypanosoma brucei} PDB: 3k80_D 3stb_D

Probab=89.16  E-value=0.74  Score=32.96  Aligned_cols=62  Identities=18%  Similarity=0.214  Sum_probs=40.1

Q ss_pred             eeEEEEEEEEEEeecc--C-CceEEEEEe--------------CCCceEEEEEeecC-ccCCCCCCCCCCcccccccccc
Q 043474           36 LSRAEIVGTITSRDHK--P-SKFIKFTVD--------------DGTGCVPCVLWLNH-LTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~--~-~~~~~~~Id--------------DgTG~I~~~~w~~~-~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      +.+|.|+|.+..--++  + ..+..|+|.              +.|--+.|++|.+. .+                    
T Consensus         6 ~NkV~LiGrLg~DPer~t~G~~va~FslAv~~~~~~~~Ge~~~~~t~w~~vv~wgk~lAe--------------------   65 (148)
T 3k7u_C            6 VNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGELFSA--------------------   65 (148)
T ss_dssp             CCCEEEEEEEEEEEEEESSSSEEEEEEEEEECC-----------CEEEEEEEEESHHHHH--------------------
T ss_pred             CcEEEEEEEeccCCEeeeCCcEEEEEEEEECCceecCCCCEEccccEEEEEEEECcHHHH--------------------
Confidence            5677788877664322  1 245555552              23345999999864 32                    


Q ss_pred             ccccccccCcEEEEEEEece
Q 043474           98 DFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        98 ~~~~~~~~G~~V~V~G~v~~  117 (160)
                      .....++.|+.|.|.|+++.
T Consensus        66 ~~~~yl~KG~~V~VeGrL~~   85 (148)
T 3k7u_C           66 EVKQKVKEGNVVCVNGRLRL   85 (148)
T ss_dssp             HHHHHCCTTCEEEEEEEEEE
T ss_pred             HHHhhCCCCCEEEEEEEEEe
Confidence            12356999999999999975

>4dam_A Single-stranded DNA-binding protein 1; OB-fold; 1.70A {Streptomyces coelicolor}

Probab=88.32  E-value=0.51  Score=32.89  Aligned_cols=78  Identities=15%  Similarity=0.138  Sum_probs=49.1

Q ss_pred             eEeeEEEEEEEEEEee----ccCCceEEEEEe------C---C------CceEEEEEeecCccCCCCCCCCCCccccccc
Q 043474           34 KLLSRAEIVGTITSRD----HKPSKFIKFTVD------D---G------TGCVPCVLWLNHLTSLYLPRRDPSTVRLIAG   94 (160)
Q Consensus        34 ~~i~~v~ivG~V~~~~----~~~~~~~~~~Id------D---g------TG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~   94 (160)
                      -.+..|.|+|.+..--    ..++.+..|+|.      |   |      |--++|++|.+..+.                
T Consensus        13 ~~~N~V~LiGrL~~dPelr~t~~G~v~~fslAv~~~~~d~~~Ge~~d~~t~w~~v~~wg~~Ae~----------------   76 (128)
T 4dam_A           13 MNEIMICAVGNVATTPVFRDLANGPSVRFRLAVTARYWDREKNAWTDGHTNFFTVWANRQLATN----------------   76 (128)
T ss_dssp             BCCCEEEEEEEECSCCEEEEETTEEEEEEEEEEEEEEEETTTTEEEEEEEEEEEEEEEHHHHHH----------------
T ss_pred             cceeEEEEEEEECCCCEEEEcCCCCEEEEEEEEcCceecccCCceecCCcEEEEEEEEcHHHHH----------------
Confidence            4678888889887621    111256667663      1   2      223889999765431                


Q ss_pred             cccccccccccCcEEEEEEEece--eC--Cc----eEEEEEEEEE
Q 043474           95 VATDFAAKIKIGLVARVRGRIAS--YR--GD----VQITVSDVVI  131 (160)
Q Consensus        95 ~~~~~~~~~~~G~~V~V~G~v~~--f~--~~----~qi~~~~i~~  131 (160)
                          ....++.|+.|.|.|+++.  |.  |+    ..|.+..|-+
T Consensus        77 ----~~~~l~KG~~V~VeGrL~~~~~dkdG~~r~~~ev~a~~vg~  117 (128)
T 4dam_A           77 ----ASGSLAVGDPVVVQGRLKVRTDVREGQSRTSADIDAVAIGH  117 (128)
T ss_dssp             ----HHHHCCTTCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEE
T ss_pred             ----HHHhcCCCCEEEEEEEEEEeEEcCCCCEEEEEEEEEEEEEe
Confidence                2356899999999999964  62  22    3466666654

>2fxq_A Single-strand binding protein; strand beta-sheet extended loops, DNA binding protein; 1.85A {Thermus aquaticus} PDB: 2ihe_A 2cwa_A 2ihf_A

Probab=88.32  E-value=3  Score=32.29  Aligned_cols=81  Identities=19%  Similarity=0.295  Sum_probs=49.8

Q ss_pred             eeEEEEEEEEEEee-----ccCCceEEEEEe------CCCc-------eEEEEEeecCccCCCCCCCCCCcccccccccc
Q 043474           36 LSRAEIVGTITSRD-----HKPSKFIKFTVD------DGTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        36 i~~v~ivG~V~~~~-----~~~~~~~~~~Id------DgTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      +.+|.|+|.|..--     .....+..|+|.      |..|       -+.|++|....+                    
T Consensus         5 ~N~v~L~G~l~~dpelr~t~~G~~v~~f~lA~~~~~~~~~G~~~~~t~~~~v~~~g~~Ae--------------------   64 (264)
T 2fxq_A            5 LNQVFLIGTLTARPDMRYTPGGLAILDLNLAGQDAFTDESGQEREVPWYHRVRLLGRQAE--------------------   64 (264)
T ss_dssp             EEEEEEEEEESSCCCCEECTTCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHH--------------------
T ss_pred             eeEEEEEEEeccCCeEEECCCCCEEEEEEEEECCcEECCCCCEecccEEEEEEEEchHHH--------------------
Confidence            56788888876521     111255666653      2223       388999976432                    


Q ss_pred             ccccccccCcEEEEEEEec--eeC--Cc----eEEEEEEEEEcCChh
Q 043474           98 DFAAKIKIGLVARVRGRIA--SYR--GD----VQITVSDVVIEKDPN  136 (160)
Q Consensus        98 ~~~~~~~~G~~V~V~G~v~--~f~--~~----~qi~~~~i~~v~d~n  136 (160)
                      .....++.|+.|.|.|+++  .|.  |+    ..|.+..|..+...+
T Consensus        65 ~~~~~l~KG~~V~V~G~L~~~~~~~dG~~r~~~ev~a~~i~~l~~~~  111 (264)
T 2fxq_A           65 MWGDLLEKGQLIFVEGRLEYRQWEKDGEKKSEVQVRAEFIDPLEGRG  111 (264)
T ss_dssp             HHTTTCCTTCEEEEEEEEEEC---------CCEEEEEEEEEECCCC-
T ss_pred             HHHHhCCCCCEEEEEEEEEeeeEEeCCEEEEEEEEEEEEEEECcCCc
Confidence            1224689999999999995  464  22    368999999887554

>2oq0_A Gamma-interferon-inducible protein IFI-16; OB folds, beta-barrels, structural genomics, PSI-2, protein initiative; 2.00A {Homo sapiens} SCOP: b.40.16.1 b.40.16.1

Probab=87.98  E-value=5  Score=30.10  Aligned_cols=22  Identities=18%  Similarity=0.110  Sum_probs=18.9

Q ss_pred             ceEEEEEeCCCceEEEEEeecC
Q 043474           54 KFIKFTVDDGTGCVPCVLWLNH   75 (160)
Q Consensus        54 ~~~~~~IdDgTG~I~~~~w~~~   75 (160)
                      +++.|.|.|.||.++++....-
T Consensus       143 ~~~~yeI~D~tG~MeVvv~G~~  164 (206)
T 2oq0_A          143 KTTIYEIQDDRGKMDVVGTGQC  164 (206)
T ss_dssp             SEEEEEEEETTEEEEEEEEGGG
T ss_pred             ceEEEEEccCCCcEEEEEeCcc
Confidence            6799999999999999876544

>3pgz_A Single-stranded DNA-binding protein; ssgcid, single-strand binding protein, structural genomics center for infectious disease; 2.10A {Bartonella henselae}

Probab=87.47  E-value=0.97  Score=33.82  Aligned_cols=65  Identities=12%  Similarity=0.269  Sum_probs=42.7

Q ss_pred             EeeEEEEEEEEEEe---ec--cCCceEEEEEe------CC-Cc-------eEEEEEeec-CccCCCCCCCCCCccccccc
Q 043474           35 LLSRAEIVGTITSR---DH--KPSKFIKFTVD------DG-TG-------CVPCVLWLN-HLTSLYLPRRDPSTVRLIAG   94 (160)
Q Consensus        35 ~i~~v~ivG~V~~~---~~--~~~~~~~~~Id------Dg-TG-------~I~~~~w~~-~~~~~~~~~~~~~~~~~~~~   94 (160)
                      .+.+|.|+|.|..-   ..  ...+++.|+|.      |. +|       -++|++|.+ ..+                 
T Consensus        25 ~mNkV~LiGrLg~DPElR~t~~G~~Va~FsLAvnr~~kd~~~Ge~~e~Tdwi~Vvawgk~lAe-----------------   87 (193)
T 3pgz_A           25 SLNKVILIGNLGADPEIRRLNSGDQVANLRIATSESWRDRNTNERKERTEWHNIVIFNENLVK-----------------   87 (193)
T ss_dssp             CEEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEEEECCC-----EEEEEEEEEEECCHHHHH-----------------
T ss_pred             hcCEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceeccCCCceeeeeEEEEEEEECHHHHH-----------------
Confidence            57899999999872   21  12356667664      21 33       388999975 322                 


Q ss_pred             cccccccccccCcEEEEEEEec--eeC
Q 043474           95 VATDFAAKIKIGLVARVRGRIA--SYR  119 (160)
Q Consensus        95 ~~~~~~~~~~~G~~V~V~G~v~--~f~  119 (160)
                         .....++.|+.|.|.|+|+  .|.
T Consensus        88 ---~~~~yL~KGs~V~VeGrL~trswe  111 (193)
T 3pgz_A           88 ---VVEQYLKKGSKIYIEGQLQTRKWQ  111 (193)
T ss_dssp             ---HHHHHCCTTCEEEEEEEEEEEEEE
T ss_pred             ---HHHhhcCCCCEEEEEEEEEEEEeE
Confidence               0124689999999999997  564

>3stb_C RNA-editing complex protein MP42; editosome, nanobody, single domain antibody, VH krepa3, krepa6, RNA binding protein-immune system complex; 2.50A {Trypanosoma brucei}

Probab=86.31  E-value=1.3  Score=31.83  Aligned_cols=73  Identities=14%  Similarity=0.178  Sum_probs=44.7

Q ss_pred             CCceEECCeEeeEEEEEEEEEEeeccC---CceEEEE--EeCCC---c-----eEEEEEeecCccCCCCCCCCCCccccc
Q 043474           26 PATFSRSGKLLSRAEIVGTITSRDHKP---SKFIKFT--VDDGT---G-----CVPCVLWLNHLTSLYLPRRDPSTVRLI   92 (160)
Q Consensus        26 ~~~~~~~~~~i~~v~ivG~V~~~~~~~---~~~~~~~--IdDgT---G-----~I~~~~w~~~~~~~~~~~~~~~~~~~~   92 (160)
                      ++.....-+.+++|.++|+|.+.+.+-   .....|+  ++...   |     -+.|++|. ...               
T Consensus        34 ~~~~~~h~r~vN~VvLmGRvtdpq~ry~~~~~Va~FtLAV~~~~~r~ge~~tdf~~V~vfG-g~l---------------   97 (148)
T 3stb_C           34 EGEVAAHWRCVNHCVMLGVVQNIQEGFVFEDKVLQFTLITDFEGPSPGDPDKDFHTVRVFD-SDY---------------   97 (148)
T ss_dssp             ----CCCCSCSEEEEEEEEEEEEEEEEETTEEEEEEEEEEECSSCCTTSCSEEEEEEEECS-HHH---------------
T ss_pred             chhhhhhheecceEEEEEEecCccccccCCCcEEEEEEEEecCCCCCCCCccceEEEEEEC-ChH---------------
Confidence            344555667899999999999776541   1233333  43321   2     26777775 111               


Q ss_pred             cccccccccccccCcEEEEEEEece
Q 043474           93 AGVATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        93 ~~~~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                         +......++.|+.|.|.|+|+.
T Consensus        98 ---AE~i~~ylkkG~rVlVeGRLrm  119 (148)
T 3stb_C           98 ---SSRVKEQLRDGEWFLVTGRLRM  119 (148)
T ss_dssp             ---HHHHHHHCCTTCEEEEEEEEEE
T ss_pred             ---HHHHHHHhcCCCEEEEEEEEEc
Confidence               0113468999999999999985

>1eqq_A Single stranded DNA binding protein; beta barrel, protein-DNA complex, replication/RNA complex; HET: 5MU; 3.20A {Escherichia coli} SCOP: b.40.4.3

Probab=85.74  E-value=0.34  Score=35.79  Aligned_cols=66  Identities=15%  Similarity=0.262  Sum_probs=41.4

Q ss_pred             EeeEEEEEEEEEEeec-----cCCceEEEEEe------C-CCc-------eEEEEEeecCccCCCCCCCCCCcccccccc
Q 043474           35 LLSRAEIVGTITSRDH-----KPSKFIKFTVD------D-GTG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~-----~~~~~~~~~Id------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~   95 (160)
                      .+..|.|+|.|..--+     ....++.|+|.      | .||       -|.|++|.+..+.                 
T Consensus         5 ~~N~V~LiGrL~~dPelr~t~~G~~v~~f~LAv~~~~~d~~~Ge~~~~t~~i~vv~wg~~Ae~-----------------   67 (178)
T 1eqq_A            5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEV-----------------   67 (178)
T ss_dssp             CEEEEEEEEEESSSCCCCEETTTEECCCCEEEEEECCCCSSSSSCCCEEEEEEEEECHHHHHH-----------------
T ss_pred             CeeEEEEEEEECCCCEEEECCCCCEEEEEEEEEcCCeecCCCCceecccEEEEEEEccHHHHH-----------------
Confidence            3577888888876211     11234455552      2 123       4899999765431                 


Q ss_pred             ccccccccccCcEEEEEEEece--eCC
Q 043474           96 ATDFAAKIKIGLVARVRGRIAS--YRG  120 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~~--f~~  120 (160)
                         ....++.|+.|.|.|+|+.  |.+
T Consensus        68 ---~~~~l~KG~~V~VeGrL~~r~~~d   91 (178)
T 1eqq_A           68 ---ASEYLRKGSQVYIEGQLRTRKWTD   91 (178)
T ss_dssp             ---HHHHCCTTCEEEECCEEEEEEEEC
T ss_pred             ---HHHhcCCCCEEEEEEEEEeeeEEC
Confidence               2246899999999999975  643

>2kct_A Cytochrome C-type biogenesis protein CCME; solution structure, heme chaperone, cytochrome C biogenesis, OB-fold domain, NESG, PSI-2; NMR {Desulfovibrio vulgaris str}

Probab=84.61  E-value=6.6  Score=25.83  Aligned_cols=71  Identities=13%  Similarity=0.172  Sum_probs=48.3

Q ss_pred             eEEEEEEEEEE--eecc-CCceEEEEEeCC---CceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEE
Q 043474           37 SRAEIVGTITS--RDHK-PSKFIKFTVDDG---TGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVAR  110 (160)
Q Consensus        37 ~~v~ivG~V~~--~~~~-~~~~~~~~IdDg---TG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~  110 (160)
                      +++++-|.|..  +... .+..++|.|.|+   ..+|.+.+-..                        ..+.|+.|.-|-
T Consensus         9 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~~~~v~V~Y~Gi------------------------lPDlFrEGqgVV   64 (94)
T 2kct_A            9 HTVRLFGTVAADGLTMLDGAPGVRFRLEDKDNTSKTVWVLYKGA------------------------VPDTFKPGVEVI   64 (94)
T ss_dssp             CCEEEEEEECSTTCEECTTSSEEEEEEECSSCTTCEEEEEEESC------------------------CCTTCCTTCEEE
T ss_pred             CeEEEeeEEeCCeEEecCCCCEEEEEEEcCCCCCcEEEEEECCC------------------------CCccccCCCeEE
Confidence            67889999864  3332 235589999998   67788876332                        235789999999


Q ss_pred             EEEEeceeCCceEEEEEEEEEcC
Q 043474          111 VRGRIASYRGDVQITVSDVVIEK  133 (160)
Q Consensus       111 V~G~v~~f~~~~qi~~~~i~~v~  133 (160)
                      ++|++..=  ..-+.+..|-.--
T Consensus        65 ~~G~l~~~--~g~F~A~evLaKh   85 (94)
T 2kct_A           65 IEGGLAPG--EDTFKARTLMTKC   85 (94)
T ss_dssp             EEEEECTT--CSEEEEEEEEESS
T ss_pred             EEEEEeCC--CCEEEEeEEEEeC
Confidence            99997521  2246677765333

>4dni_A Fusion protein of RNA-editing complex proteins MP MP18; krepa3, krepa6, editosome, protein/RNA binding, protein BIND binding protein; 2.55A {Trypanosoma brucei}

Probab=83.18  E-value=2.4  Score=33.03  Aligned_cols=62  Identities=18%  Similarity=0.216  Sum_probs=42.5

Q ss_pred             EeeEEEEEEEEEEeecc---CCceEEEEEe------CC--------CceEEEEEeecC--ccCCCCCCCCCCcccccccc
Q 043474           35 LLSRAEIVGTITSRDHK---PSKFIKFTVD------DG--------TGCVPCVLWLNH--LTSLYLPRRDPSTVRLIAGV   95 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~~---~~~~~~~~Id------Dg--------TG~I~~~~w~~~--~~~~~~~~~~~~~~~~~~~~   95 (160)
                      .+.+|.++|.+..-+-+   ...+..|+|.      |+        |--++|++|.+.  .+                  
T Consensus       145 ~lNkV~LiGrL~DPElR~t~G~~Va~FslAv~~~~~~~~~~e~~~~Tdw~~Vv~wgk~~~AE------------------  206 (257)
T 4dni_A          145 SVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGELFSAE------------------  206 (257)
T ss_dssp             CEEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEECCCTTCSCEEEEEEEEEEEESHHHHHH------------------
T ss_pred             ccCEEEEEEEcCCCEEEEeCCcEEEEEEEEECCCccCCCCceEccceEEEEEEEECCccHHH------------------
Confidence            37999999999433321   2356677772      22        223899999765  32                  


Q ss_pred             ccccccccccCcEEEEEEEece
Q 043474           96 ATDFAAKIKIGLVARVRGRIAS  117 (160)
Q Consensus        96 ~~~~~~~~~~G~~V~V~G~v~~  117 (160)
                         ....++.|+.|.|.|+++.
T Consensus       207 ---i~~~L~KG~~V~VeGrL~t  225 (257)
T 4dni_A          207 ---VKQKVKEGNVVCVNGRLRL  225 (257)
T ss_dssp             ---HHHHCCTTCEEEEEEEEEE
T ss_pred             ---HHhhCCCCCEEEEEEEEEe
Confidence               2345999999999999975

>1xjv_A Protection of telomeres 1; protein-DNA complex, single-stranded DNA, transcription/DNA complex; 1.73A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 3kjo_A 3kjp_A

Probab=80.48  E-value=8.3  Score=30.17  Aligned_cols=30  Identities=13%  Similarity=0.120  Sum_probs=22.2

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCce
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGC   66 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~   66 (160)
                      ..+-+++.|+.+.........+.+-|||+.
T Consensus       155 ~f~DLv~qVv~v~~~~~~~~~LyVwDgT~~  184 (294)
T 1xjv_A          155 QYFDLTCQLLGKAEVDGASFLLKVWDGTRT  184 (294)
T ss_dssp             CEEEEEEEEEEEEECSSSEEEEEEECSSCC
T ss_pred             CeeeEEEEEEEEEecCCCeEEEEEECCCCC
Confidence            567888888877644445578899999974

---

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	160
d2pi2a1	128	b.40.4.3 (A:44-171) Replication protein A 32 KDa s	4e-15

>d2pi2a1 b.40.4.3 (A:44-171) Replication protein A 32 KDa subunit (RPA32) fragment {Human (Homo sapiens) [TaxId: 9606]} Length = 128

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 32 KDa subunit (RPA32) fragment
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.6 bits (160), Expect = 4e-15
 Identities = 20/126 (15%), Positives = 41/126 (32%), Gaps = 20/126 (15%)

Query: 23  TPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYL 81
           T     F      +S+  IVG I   +  P+  I + +DD T   +    W++       
Sbjct: 15  TLVDEVFRIGNVEISQVTIVGIIRHAEKAPT-NIVYKIDDMTAAPMDVRQWVD------- 66

Query: 82  PRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLH 141
                          +     +      +V G + S++    +    ++  +D N    H
Sbjct: 67  -----------TDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTH 115

Query: 142 WLDCLR 147
            L+ + 
Sbjct: 116 ILEVIN 121

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	160
d2pi2a1	128	Replication protein A 32 KDa subunit (RPA32) fragm	99.97
d1n9wa1	93	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	98.33
d1o7ia_	115	Archaeal ssDNA-binding protein {Archaeon Sulfolobu	98.27
d1eova1	134	Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S	98.07
d1b8aa1	103	Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ	98.07
d1c0aa1	106	Aspartyl-tRNA synthetase (AspRS) {Escherichia coli	98.02
d1l0wa1	104	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	97.93
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	97.91
d1wjja_	145	Hypothetical protein At4g28440 (F20O9.120) {Thale	97.82
d1nnxa_	106	Hypothetical protein YgiW {Escherichia coli [TaxId	97.71
d1jmca1	116	Replication protein A 70 KDa subunit (RPA70) {Huma	96.93
d1gm5a2	180	RecG "wedge" domain {Thermotoga maritima [TaxId: 2	96.83
d1v1qa_	111	Primosomal replication protein N, PriB {Escherichi	96.66
d1xjva1	140	Protection of telomeres protein 1, Pot1 {Human (Ho	96.58
d2oq0a1	88	Gamma-interferon-inducible protein Ifi-16 {Human (	95.88
d1jmca2	122	Replication protein A 70 KDa subunit (RPA70) {Huma	95.83
d1qzga_	170	Protection of telomeres protein 1, Pot1 {Fission y	95.67
d2pi2e1	115	Replication protein A 14 KDa (RPA14) subunit {Huma	95.42
d1jb7a1	169	Telomere end binding protein alpha subunit {Oxytri	95.02
d1l1oc_	178	Replication protein A 70 KDa subunit (RPA70) {Huma	93.61
d1se8a_	231	ssDNA-binding protein {Deinococcus radiodurans [Ta	93.42
d1qvca_	145	ssDNA-binding protein {Escherichia coli [TaxId: 56	93.0
d1ue1a_	118	ssDNA-binding protein {Mycobacterium tuberculosis	92.97
d3ulla_	115	ssDNA-binding protein {Human (Homo sapiens), mitoc	92.33
d1se8a_	231	ssDNA-binding protein {Deinococcus radiodurans [Ta	91.67
d1sr3a_	114	Heme chaperone CcmE {Escherichia coli [TaxId: 562]	90.01
d1j6qa_	100	Heme chaperone CcmE {Shewanella putrefaciens [TaxI	82.38

>d2pi2a1 b.40.4.3 (A:44-171) Replication protein A 32 KDa subunit (RPA32) fragment {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 32 KDa subunit (RPA32) fragment
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.3e-31  Score=189.87  Aligned_cols=122  Identities=20%  Similarity=0.237  Sum_probs=105.6

Q ss_pred             ccceehhhhhccCCCCCCCceEECCeEeeEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCC
Q 043474            9 HVKLLAFDLLSLTPTPDPATFSRSGKLLSRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPS   87 (160)
Q Consensus         9 ~~~l~i~~i~~l~~~~~~~~~~~~~~~i~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~   87 (160)
                      .+|+.|+||++++.  .++.|.++|+++++|++||.|++++.++ +++.|+|||||| +|+|+.|.+.+..         
T Consensus         3 i~PvtI~ql~~a~~--~~~~f~i~g~~v~~V~iVG~V~~i~~~~-t~~~y~idDgTG~~i~v~~w~~~~~~---------   70 (128)
T d2pi2a1           3 IVPCTISQLLSATL--VDEVFRIGNVEISQVTIVGIIRHAEKAP-TNIVYKIDDMTAAPMDVRQWVDTDDT---------   70 (128)
T ss_dssp             CEECCHHHHHHCEE--ETTEEEETTEEESEEEEEEEEEEEEECS-SEEEEEEECSSSSCEEEEEECC-------------
T ss_pred             eeeEEHHHHhcCcC--CCCCEEECCEEEEEEEEEEEEEEEEecC-CEEEEEEECCCCCcEEEEEECCCCCC---------
Confidence            47999999999754  3568999999999999999999999988 679999999999 6999999865431         


Q ss_pred             ccccccccccccccccccCcEEEEEEEeceeCCceEEEEEEEEEcCChhHHHHHHHHHHHHHHh
Q 043474           88 TVRLIAGVATDFAAKIKIGLVARVRGRIASYRGDVQITVSDVVIEKDPNMEVLHWLDCLRLARK  151 (160)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~G~~V~V~G~v~~f~~~~qi~~~~i~~v~d~n~~~~h~le~~~~~~~  151 (160)
                               ......++.|+||||.|+++.|+++++|.+++|+|++|+||.++|||||+++|..
T Consensus        71 ---------~~~~~~i~~g~yVrV~G~lk~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~hL~  125 (128)
T d2pi2a1          71 ---------SSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMV  125 (128)
T ss_dssp             ------------CCCCCTTCEEEEEEEEEEETTEEEEEEEEEEECSCTHHHHHHHHHHHHHHHH
T ss_pred             ---------ccccccccCCCEEEEEEEEEeeCCeEEEEEEEEEEeCCcCHHHHHHHHHHHHHHh
Confidence                     1133578999999999999999999999999999999999999999999998654

>d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-2 [TaxId: 274]

Probab=98.33  E-value=6.4e-06  Score=53.62  Aligned_cols=71  Identities=18%  Similarity=0.228  Sum_probs=57.3

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+.|+|.++.... +...+.|-|+||.++|++= ..                         ..+..|+.|.|.|.+.
T Consensus        14 ~~V~v~GwV~~~R~~g-k~~Fi~LrD~sg~iQ~v~~-~~-------------------------~~~~~e~~v~v~G~v~   66 (93)
T d1n9wa1          14 QEVELLGFLHWRRDLG-RIQFLLLRDRSGVVQVVTG-GL-------------------------KLPLPESALRVRGLVV   66 (93)
T ss_dssp             SEEEEEEEEEEEEECS-SEEEEEEEETTEEEEEEEE-SC-------------------------CCCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEeEEeCC-CcEEEEEEcCCccceEEec-cc-------------------------cccccceEEEEEEEEE
Confidence            5789999999998776 7789999999999999862 11                         2345789999999997


Q ss_pred             eeC---CceEEEEEEEEEcCC
Q 043474          117 SYR---GDVQITVSDVVIEKD  134 (160)
Q Consensus       117 ~f~---~~~qi~~~~i~~v~d  134 (160)
                      .-.   +...|.+.++..+..
T Consensus        67 ~~~~~~~~~Ei~v~~i~il~~   87 (93)
T d1n9wa1          67 ENAKAPGGLEVQAKEVEVLSP   87 (93)
T ss_dssp             ECTTSTTSEEEEEEEEEEEEC
T ss_pred             ECCCCCCCEEEEEeEEEEEec
Confidence            654   568999999987754

>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Archaeal ssDNA-binding protein
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=98.27  E-value=3.8e-06  Score=56.80  Aligned_cols=75  Identities=21%  Similarity=0.378  Sum_probs=58.1

Q ss_pred             eEEEEEEEEEEeec------c--CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcE
Q 043474           37 SRAEIVGTITSRDH------K--PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLV  108 (160)
Q Consensus        37 ~~v~ivG~V~~~~~------~--~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~  108 (160)
                      ..+.+.|+|.++..      +  ++....+.|.|.||+|.+.+|.+..                        ..+++|++
T Consensus        13 ~~v~i~~~V~~~~~~r~~~~~~g~~~v~~~~i~DeTG~i~~~~W~~~~------------------------~~l~~Gdv   68 (115)
T d1o7ia_          13 ESVNVTVRVLEASEARQIQTKNGVRTISEAIVGDETGRVKLTLWGKHA------------------------GSIKEGQV   68 (115)
T ss_dssp             SSEEEEEEEEEECCCEEECCTTCCEEEEEEEEEETTEEEEEEEEGGGT------------------------TCCCTTCE
T ss_pred             CCEEEEEEEEECCCCceeecCCCCEEEEEEEEEcCCCeEEEEEecccc------------------------ccCCCCCE
Confidence            45778888888642      1  1355688999999999999996432                        35789999


Q ss_pred             EEEE-EEeceeCCceEEEEEE---EEEcCCh
Q 043474          109 ARVR-GRIASYRGDVQITVSD---VVIEKDP  135 (160)
Q Consensus       109 V~V~-G~v~~f~~~~qi~~~~---i~~v~d~  135 (160)
                      |++. |+++.|+|..+|.+.+   |..+.+.
T Consensus        69 v~i~na~v~~~~g~~el~~~~~s~i~~~~d~   99 (115)
T d1o7ia_          69 VKIENAWTTAFKGQVQLNAGSKTKIAEASED   99 (115)
T ss_dssp             EEEEEEEEEEETTEEEEEECTTCEEEECCCT
T ss_pred             EEEeeEEEEEECCeEEEEECCCeEEEECCCc
Confidence            9996 7899999999998876   6666653

>d1eova1 b.40.4.1 (A:71-204) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.07  E-value=1.9e-05  Score=54.68  Aligned_cols=86  Identities=8%  Similarity=0.176  Sum_probs=62.9

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.|.|+|..+.....+...++|.|+||.++|.+-........             ....+....+..|++|.|.|.|.
T Consensus        37 ~~V~v~GwV~~~R~~G~kl~F~~LrD~sg~iQ~~v~~~~~~~~~-------------~~~~~~~~~l~~es~V~V~G~v~  103 (134)
T d1eova1          37 KEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTIS-------------KNMVKWAGSLNLESIVLVRGIVK  103 (134)
T ss_dssp             CEEEEEEEEEEEEECSSSEEEEEEEETTEEEEEEEECCSSSSSC-------------HHHHHHHTTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEEEeCCCcEEEEEEEcCCCcEEEEEEeccccchh-------------HHHHHHHhcCCCCCEEEEEEEEE
Confidence            67889999999987653556899999999999998765443110             00011235789999999999997


Q ss_pred             eeC--------CceEEEEEEEEEcCCh
Q 043474          117 SYR--------GDVQITVSDVVIEKDP  135 (160)
Q Consensus       117 ~f~--------~~~qi~~~~i~~v~d~  135 (160)
                      .-.        +...|.+.++..+...
T Consensus       104 ~~~~~~~~~~~~~~Ei~v~~i~vls~a  130 (134)
T d1eova1         104 KVDEPIKSATVQNLEIHITKIYTISET  130 (134)
T ss_dssp             ECSSCCTTSSEEEEEEEEEEEEEEECC
T ss_pred             eCCccCCCCCCCcEEEEEEEEEEEeCC
Confidence            642        3468999999877644

>d1b8aa1 b.40.4.1 (A:1-103) Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococcus kodakaraensis [TaxId: 311400]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Archaeon Pyrococcus kodakaraensis [TaxId: 311400]

Probab=98.07  E-value=2.4e-05  Score=51.72  Aligned_cols=80  Identities=13%  Similarity=0.085  Sum_probs=58.3

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+.|+|.++.... +...+.|.|+||.|+|++-.+...                .+..+....+..|+.|.|.|.+.
T Consensus        17 ~~V~v~Gwv~~~R~~g-~i~Fi~LrD~sg~iQ~v~~~~~~~----------------~~~~~~~~~l~~es~v~V~G~v~   79 (103)
T d1b8aa1          17 QKVKVAGWVWEVKDLG-GIKFLWIRDRDGIVQITAPKKKVD----------------PELFKLIPKLRSEDVVAVEGVVN   79 (103)
T ss_dssp             CEEEEEEEEEEEEEET-TEEEEEEEETTEEEEEEEETTTSC----------------HHHHHHGGGCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEehhccCC-CcEEEEEEcCCEeeeEEEeccccc----------------hhhhhHHhhCCcceEEEEEEEEE
Confidence            5689999999998765 778899999999999997432211                01112345788999999999997


Q ss_pred             eeC---CceEEEEEEEEEcC
Q 043474          117 SYR---GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~---~~~qi~~~~i~~v~  133 (160)
                      .-.   +...|.+..+..+.
T Consensus        80 ~~~~~~~~iEi~v~~i~ils   99 (103)
T d1b8aa1          80 FTPKAKLGFEILPEKIVVLN   99 (103)
T ss_dssp             ECTTSTTSEEEEEEEEEEEE
T ss_pred             ECCCCCccEEEEeeEEEEEE
Confidence            532   23568888887654

>d1c0aa1 b.40.4.1 (A:1-106) Aspartyl-tRNA synthetase (AspRS) {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Escherichia coli [TaxId: 562]

Probab=98.02  E-value=2.1e-05  Score=52.33  Aligned_cols=78  Identities=17%  Similarity=0.311  Sum_probs=58.7

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+.|+|..+.... +...+.|-|+||.++|++-.+...                  ..+....+..+..|.|.|+|.
T Consensus        16 ~~V~v~GWv~~~R~~g-~i~Fi~LRD~~G~~Q~v~~~~~~~------------------~~~~~~~l~~Es~v~V~G~V~   76 (106)
T d1c0aa1          16 QQVTLCGWVNRRRDLG-SLIFIDMRDREGIVQVFFDPDRAD------------------ALKLASELRNEFCIQVTGTVR   76 (106)
T ss_dssp             CEEEEEEEEEEEEECS-SCEEEEEEETTEEEEEEECGGGHH------------------HHHHHTTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEEeeeCC-CcEEEEEEcCCeEEeEEecccchh------------------HHHHHHhhCccceEEEEeEEe
Confidence            7889999999987765 667889999999999987433211                  112335688899999999997


Q ss_pred             eeC----------CceEEEEEEEEEcC
Q 043474          117 SYR----------GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~----------~~~qi~~~~i~~v~  133 (160)
                      .-.          |..+|.+..+..+.
T Consensus        77 ~r~~~~~n~~~~tg~iEi~v~~i~vl~  103 (106)
T d1c0aa1          77 ARDEKNINRDMATGEIEVLASSLTIIN  103 (106)
T ss_dssp             ECCTTTCCTTSTTTTEEEEEEEEEEEE
T ss_pred             ccCccccCCCCCCCcEEEEEeEEEEEe
Confidence            532          24789999988765

>d1l0wa1 b.40.4.1 (A:1-104) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-1 [TaxId: 274]

Probab=97.93  E-value=6.5e-05  Score=49.76  Aligned_cols=77  Identities=18%  Similarity=0.232  Sum_probs=57.8

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+.|+|.++.... +...+.|-|+||.++|++-.+.+.                   ......+..+.+|.|.|.|.
T Consensus        17 ~~V~l~GWV~~~R~~g-~i~Fi~LRD~~G~iQ~v~~~~~~~-------------------~~~~~~l~~Es~I~V~G~V~   76 (104)
T d1l0wa1          17 EEVVLEGWVNRRRDLG-GLIFLDLRDREGLVQLVAHPASPA-------------------YATAERVRPEWVVRAKGLVR   76 (104)
T ss_dssp             CEEEEEEEEEEEEECS-SCEEEEEEETTEEEEEEECTTSTT-------------------HHHHTTCCTTCEEEEEEEEE
T ss_pred             CEEEEEEEEEehhcCC-CeEEEEEECCCCceEEecccchhH-------------------HHHHhhcCcccEEEEEEEEe
Confidence            6899999999987666 767899999999999997322211                   12335688999999999996


Q ss_pred             eeC--------CceEEEEEEEEEcC
Q 043474          117 SYR--------GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~--------~~~qi~~~~i~~v~  133 (160)
                      .-.        |...|.+..+..+.
T Consensus        77 ~r~~~n~~~~tG~iEi~v~~i~iL~  101 (104)
T d1l0wa1          77 LRPEPNPRLATGRVEVELSALEVLA  101 (104)
T ss_dssp             ECSSCCTTSTTTTEEEEEEEEEEEE
T ss_pred             eCCccCCCCCCCCEEEEEeEEEEEE
Confidence            422        23689999988654

>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Lysyl-tRNA synthetase (LysRS)
species: Escherichia coli, gene lysU [TaxId: 562]

Probab=97.91  E-value=7.1e-05  Score=52.29  Aligned_cols=81  Identities=20%  Similarity=0.274  Sum_probs=61.0

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+.|+|..+...+ +-..+.|.|.||.|++.+=.+.-..               .........+.+||+|.|.|.+.
T Consensus        55 ~~V~vaGRI~~~R~~G-k~~F~~i~D~~g~iQi~~~~~~~~~---------------~~~~~~~k~ld~GDiIgv~G~~~  118 (143)
T d1e1oa1          55 IEVSVAGRMMTRRIMG-KASFVTLQDVGGRIQLYVARDSLPE---------------GVYNDQFKKWDLGDIIGARGTLF  118 (143)
T ss_dssp             CEEEEEEEEEEEEEET-TEEEEEEEETTEEEEEEEETTTSST---------------THHHHTGGGCCTTCEEEEEEEEE
T ss_pred             ceEEEEEEEEEEcccC-CeeEEEEEeCCceEEEEEccccchh---------------hhHHHHHhcCCcccEEEeecccE
Confidence            3689999999998776 6689999999999999874332210               01112336788999999999997


Q ss_pred             eeC-CceEEEEEEEEEcC
Q 043474          117 SYR-GDVQITVSDVVIEK  133 (160)
Q Consensus       117 ~f~-~~~qi~~~~i~~v~  133 (160)
                      .-+ |.+.|.+..+..++
T Consensus       119 ~TktGElsi~~~~~~lLs  136 (143)
T d1e1oa1         119 KTQTGELSIHCTELRLLT  136 (143)
T ss_dssp             ECTTCCEEEEEEEEEEEE
T ss_pred             ECCCCcEEEEeeEEEEec
Confidence            544 88999999987654

>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Hypothetical protein At4g28440 (F20O9.120)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.82  E-value=4.4e-05  Score=53.52  Aligned_cols=76  Identities=16%  Similarity=0.338  Sum_probs=58.4

Q ss_pred             eeEEEEEEEEEEeecc------------------CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCcccccccccc
Q 043474           36 LSRAEIVGTITSRDHK------------------PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        36 i~~v~ivG~V~~~~~~------------------~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      .+.+.+.++|+++...                  +.......|.|.||+|...+|.+..                     
T Consensus        26 ~~~vnl~vkVl~~~~~~~~~r~~~~~~~~~~~g~~~~v~~~~v~DeTG~i~~tlW~~~~---------------------   84 (145)
T d1wjja_          26 TTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFTARNDQV---------------------   84 (145)
T ss_dssp             CCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEEECTTHH---------------------
T ss_pred             CCCceEEEEEEEcccceeecccccccccccccCCCcEEEEEEEEccCCeEEEEEEeccc---------------------
Confidence            4778889999987521                  1135688999999999999997532                     


Q ss_pred             ccccccccCcEEEEEEE-eceeCCceEEEEEE---EEEcCCh
Q 043474           98 DFAAKIKIGLVARVRGR-IASYRGDVQITVSD---VVIEKDP  135 (160)
Q Consensus        98 ~~~~~~~~G~~V~V~G~-v~~f~~~~qi~~~~---i~~v~d~  135 (160)
                         ..+++|++|++.+- ++.|+|.++|.+.+   |.++.+.
T Consensus        85 ---~~l~~Gd~v~i~na~v~~~~G~~~L~vg~~g~I~~~~e~  123 (145)
T d1wjja_          85 ---DLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAA  123 (145)
T ss_dssp             ---HHTCTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCSCC
T ss_pred             ---cccCcCCEEEEeeEEEEEECCEEEEEECCCEEEEECCCC
Confidence               35789999998875 77899999999985   6555443

>d1nnxa_ b.40.10.1 (A:) Hypothetical protein YgiW {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Hypothetical protein YgiW
family: Hypothetical protein YgiW
domain: Hypothetical protein YgiW
species: Escherichia coli [TaxId: 562]

Probab=97.71  E-value=0.00026  Score=46.92  Aligned_cols=70  Identities=13%  Similarity=0.209  Sum_probs=53.1

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEec
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRIA  116 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v~  116 (160)
                      ..|.+-|.|+..-..+    .|.+.|+||+|.+-+=.+.-.                      -..+.+++.|+|.|.+.
T Consensus        37 t~V~L~G~Iv~~l~~d----~Y~F~D~TG~I~VeId~~~w~----------------------g~~v~p~~kV~i~GevD   90 (106)
T d1nnxa_          37 TWVTLRGNIVERISDD----LYVFKDASGTINVDIDHKRWN----------------------GVTVTPKDTVEIQGEVD   90 (106)
T ss_dssp             EEEEEEEEEEEEEETT----EEEEEETTEEEEEECCGGGST----------------------TCCCCTTSCEEEEEEEE
T ss_pred             CeEEEEEEEEEEeCCc----eEEEECCCCcEEEEEChhhcC----------------------CcccCCCCEEEEEEEEc
Confidence            5688889888876664    577899999999876222111                      13577899999999999


Q ss_pred             eeCCceEEEEEEEEEc
Q 043474          117 SYRGDVQITVSDVVIE  132 (160)
Q Consensus       117 ~f~~~~qi~~~~i~~v  132 (160)
                      .-.+...|.+.+|+.+
T Consensus        91 k~~~~~eIdV~~I~~l  106 (106)
T d1nnxa_          91 KDWNSVEIDVKQIRKV  106 (106)
T ss_dssp             EETTEEEEEEEEEEEC
T ss_pred             CCCCceEEEEEEEEEC
Confidence            6567789999998754

>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.93  E-value=0.00046  Score=46.05  Aligned_cols=79  Identities=16%  Similarity=0.288  Sum_probs=52.3

Q ss_pred             eEEEEEEEEEEee------cc--CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcE
Q 043474           37 SRAEIVGTITSRD------HK--PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLV  108 (160)
Q Consensus        37 ~~v~ivG~V~~~~------~~--~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~  108 (160)
                      .+.+|.|+|++..      ..  +++.+.+.|.|.||.|.|.+|.+...                    .....++.|++
T Consensus        13 ~~~~I~~RV~~k~~~r~f~~~~~~g~v~~~~l~De~G~I~~t~~~~~~~--------------------~f~~~l~~G~v   72 (116)
T d1jmca1          13 SKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNEQVD--------------------KFFPLIEVNKV   72 (116)
T ss_dssp             CCCEEEEEEEEECCCEEEECSSCEEEEEEEEEECSSCEEEEEEEHHHHH--------------------HHGGGCCTTCE
T ss_pred             CCEEEEEEEEEeccceEEECCCCCceEEEEEEEcCCCCEEEEEchhhhh--------------------hhHhhcccCCE
Confidence            4566778887642      11  13668999999999999999966542                    24467999999


Q ss_pred             EEEEEE-ece----eC---CceEEEEE---EEEEcCCh
Q 043474          109 ARVRGR-IAS----YR---GDVQITVS---DVVIEKDP  135 (160)
Q Consensus       109 V~V~G~-v~~----f~---~~~qi~~~---~i~~v~d~  135 (160)
                      ..+.|- |+.    |+   +..+|...   .|.++.|+
T Consensus        73 y~i~~~~V~~~~~~y~~~~~~yei~f~~~T~I~~~~d~  110 (116)
T d1jmca1          73 YYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDD  110 (116)
T ss_dssp             EEEECCEEEECCGGGCCCCCSEEEECCTTCEEEECCSC
T ss_pred             EEEcceEEEEccCcEeccCCcEEEEECCCcEEEECCCC
Confidence            888763 443    22   23355554   46666554

>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RecG "wedge" domain
domain: RecG "wedge" domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.83  E-value=0.00074  Score=48.11  Aligned_cols=74  Identities=22%  Similarity=0.286  Sum_probs=49.8

Q ss_pred             eEEEEEEEEEEeec---cCCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEE
Q 043474           37 SRAEIVGTITSRDH---KPSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRG  113 (160)
Q Consensus        37 ~~v~ivG~V~~~~~---~~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G  113 (160)
                      ..+.+.|.|.....   +....+.+++.|+||.|+++.+.....                    .......+|+.+.|.|
T Consensus        61 ~~vti~g~V~~~~~~~~~~~~~~~~~v~D~~g~i~l~fFn~~~~--------------------~~~~k~~~G~~v~v~G  120 (180)
T d1gm5a2          61 EKVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQDYL--------------------QTYLKQLTGKEVFVTG  120 (180)
T ss_dssp             CCCEEEECCCCCEEEECSSCEEEEEEECCSSCCEEEEECSCCTT--------------------HHHHHTTCSSCEEEEE
T ss_pred             eeeeeeeEEEeeccccccccceeEEEEEeccceEEEEEeCcHHH--------------------HHHHhhhcCceEEEEE
Confidence            45677888876543   223557899999999999987654321                    0111223699999999


Q ss_pred             Eece--eCCceEEEEEEEE
Q 043474          114 RIAS--YRGDVQITVSDVV  130 (160)
Q Consensus       114 ~v~~--f~~~~qi~~~~i~  130 (160)
                      +++.  |+++.|+.-..+.
T Consensus       121 kvk~~~~~~~~q~~~p~~~  139 (180)
T d1gm5a2         121 TVKSNAYTGQYEIHNAEVT  139 (180)
T ss_dssp             EECSCCTTSSCCEEEEEEE
T ss_pred             EEeeccccceeeccCceec
Confidence            9954  8888776544443

>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Primosomal replication protein N, PriB
species: Escherichia coli [TaxId: 562]

Probab=96.66  E-value=0.015  Score=38.15  Aligned_cols=82  Identities=13%  Similarity=0.259  Sum_probs=55.0

Q ss_pred             EeeEEEEEEEEEEeec-----cCCceEEEEEeCC-----Cc-------eEEEEEeecCccCCCCCCCCCCcccccccccc
Q 043474           35 LLSRAEIVGTITSRDH-----KPSKFIKFTVDDG-----TG-------CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVAT   97 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~~-----~~~~~~~~~IdDg-----TG-------~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~   97 (160)
                      ...+|.++|.|..-.+     ...++..|+|.=.     .|       .++|+.|.+..+.                   
T Consensus         5 m~N~v~L~G~l~~dpelr~T~~G~~v~~f~la~~~~~~e~~~~r~~~~~i~vv~~g~~Ae~-------------------   65 (111)
T d1v1qa_           5 MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQA-------------------   65 (111)
T ss_dssp             CCEEEEEEEEEEEEEEEEECTTCCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESTGGGG-------------------
T ss_pred             ceEEEEEEEEecCCcceEECCCCCEEEEEEEEeccEEecccceEEEEEEEEEEEeCHHHHH-------------------
Confidence            4567888888886431     2236677777511     12       2788889766541                   


Q ss_pred             ccccccccCcEEEEEEEece--eCC---ceEEEEEEEEEcCChh
Q 043474           98 DFAAKIKIGLVARVRGRIAS--YRG---DVQITVSDVVIEKDPN  136 (160)
Q Consensus        98 ~~~~~~~~G~~V~V~G~v~~--f~~---~~qi~~~~i~~v~d~n  136 (160)
                       ....++.|+.|.|.|++..  |++   +..+.++.|.-++..+
T Consensus        66 -~~~~l~kG~~v~v~G~L~~~~~~~~~~r~v~~a~~ie~l~s~~  108 (111)
T d1v1qa_          66 -ITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSVD  108 (111)
T ss_dssp             -GGTTCCTTCEEEEEEEEEEECTTTTSCEEEEEEEEEEETTSCS
T ss_pred             -HHHHhcCCCEEEEEEEEEEecccCCCCEEEEEEEEEEEecCCC
Confidence             2357899999999999986  454   4467788888776443

>d1xjva1 b.40.4.3 (A:6-145) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Protection of telomeres protein 1, Pot1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.58  E-value=0.027  Score=38.47  Aligned_cols=72  Identities=19%  Similarity=0.305  Sum_probs=52.4

Q ss_pred             eEEEEEEEEEEeec----cCCce-EEEEEeCCCce-EEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEE
Q 043474           37 SRAEIVGTITSRDH----KPSKF-IKFTVDDGTGC-VPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVAR  110 (160)
Q Consensus        37 ~~v~ivG~V~~~~~----~~~~~-~~~~IdDgTG~-I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~  110 (160)
                      ..|-+.|.|.....    +++.| ++++|-|-|-. +.|.++.+..+.                    .....+.||+|+
T Consensus        16 ~~vnv~gVV~~~~~p~~s~g~D~~~tl~I~D~S~~gl~v~iF~~~~~~--------------------LP~v~~~GDII~   75 (140)
T d1xjva1          16 TIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYEA--------------------LPIIYKNGDIVR   75 (140)
T ss_dssp             EEEEEEEEEEEEEEEEECSSSSEEEEEEEECTTCCEEEEEEEESSGGG--------------------SCCCCSTTCEEE
T ss_pred             CEEEEEEEEeecCCCEEcCCCeEEEEEEEEeCCCCCeEEEEECCChHH--------------------CCCCCCCCCEEE
Confidence            46788899988762    33445 46899998854 999999876541                    222346899999


Q ss_pred             EEEE-eceeCCceEEEEEE
Q 043474          111 VRGR-IASYRGDVQITVSD  128 (160)
Q Consensus       111 V~G~-v~~f~~~~qi~~~~  128 (160)
                      +..- ++.|+++.|.....
T Consensus        76 l~r~~v~~~~~~~~~~~~~   94 (140)
T d1xjva1          76 FHRLKIQVYKKETQGITSS   94 (140)
T ss_dssp             EEEEEEEEETTEEEEEEEE
T ss_pred             EEEEEEEEECCeEEEEecC
Confidence            9975 78999998876554

>d2oq0a1 b.40.16.1 (A:115-202) Gamma-interferon-inducible protein Ifi-16 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: HIN-2000 domain-like
family: HIN-200/IF120x domain
domain: Gamma-interferon-inducible protein Ifi-16
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.88  E-value=0.02  Score=35.92  Aligned_cols=25  Identities=16%  Similarity=0.078  Sum_probs=20.4

Q ss_pred             ccCCceEEEEEeCCCceEEEEEeecC
Q 043474           50 HKPSKFIKFTVDDGTGCVPCVLWLNH   75 (160)
Q Consensus        50 ~~~~~~~~~~IdDgTG~I~~~~w~~~   75 (160)
                      .+. +++.|.|.|.||.|+++....-
T Consensus        26 ~~~-~~~~YeI~D~TG~MeVvv~G~~   50 (88)
T d2oq0a1          26 VNQ-KTTIYEIQDDRGKMDVVGTGQC   50 (88)
T ss_dssp             ECS-SEEEEEEEETTEEEEEEEEGGG
T ss_pred             EcC-CeEEEEEecCCCcEEEEEeccE
Confidence            344 7899999999999999976544

>d1jmca2 b.40.4.3 (A:299-420) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.83  E-value=0.018  Score=38.32  Aligned_cols=67  Identities=19%  Similarity=0.355  Sum_probs=44.8

Q ss_pred             EEEEEEEEEEeec------c-C---CceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccC
Q 043474           38 RAEIVGTITSRDH------K-P---SKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIG  106 (160)
Q Consensus        38 ~v~ivG~V~~~~~------~-~---~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G  106 (160)
                      .|-|+|.|.++..      + .   .....++|-|.|| +|+|.+|.+....                    .  ....+
T Consensus        18 ~vDViGvv~~v~~~~~i~~k~~g~~~~kR~i~i~D~t~~~i~vtLWg~~a~~--------------------~--~~~~~   75 (122)
T d1jmca2          18 LVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADK--------------------F--DGSRQ   75 (122)
T ss_dssp             EEEEEEEEEEECCCEEEEETTTTEEEEEEEEEEECTTCCEEEEEEEHHHHHH--------------------C--CCTTC
T ss_pred             eEEEEEEEEEccCcEEEEEcCCCCceeEEEEEEEcCCCCEEEEEEEchHhhh--------------------h--CCCCC
Confidence            4777788877642      2 1   2346899999999 5999999876431                    1  12356


Q ss_pred             cEEEEEEE-eceeCCceEEEEE
Q 043474          107 LVARVRGR-IASYRGDVQITVS  127 (160)
Q Consensus       107 ~~V~V~G~-v~~f~~~~qi~~~  127 (160)
                      .+|-+.|- ++.|+++ .|...
T Consensus        76 ~Vi~~k~~~v~~~~g~-sL~~~   96 (122)
T d1jmca2          76 PVLAIKGARVSDFGGR-SLSVL   96 (122)
T ss_dssp             CEEEEEEEEEECTTSS-EEECC
T ss_pred             CEEEEeeeEEeeccCc-eEecc
Confidence            67777775 6789975 55443

>d1qzga_ b.40.4.3 (A:) Protection of telomeres protein 1, Pot1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Protection of telomeres protein 1, Pot1
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=95.67  E-value=0.13  Score=36.11  Aligned_cols=71  Identities=13%  Similarity=0.135  Sum_probs=51.2

Q ss_pred             eEEEEEEEEEEeec-----cCC-ce-EEEEEeCCC----c-eEEEEEeecCccCCCCCCCCCCccccccccccccccccc
Q 043474           37 SRAEIVGTITSRDH-----KPS-KF-IKFTVDDGT----G-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIK  104 (160)
Q Consensus        37 ~~v~ivG~V~~~~~-----~~~-~~-~~~~IdDgT----G-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (160)
                      ..|-+.|+|.....     +++ .| ++|+|-|.|    + .|.|.++.+..+.                    .....+
T Consensus        37 ~~VnviGVV~~~~~P~rs~~G~~Dy~~tl~I~D~S~~~~~~gl~v~iF~~~~e~--------------------LP~V~~   96 (170)
T d1qzga_          37 TIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGND--------------------LPVIKQ   96 (170)
T ss_dssp             EEEEEEEEEEEEEEEEECSSTTCCEEEEEEEECTTSCTTSCCEEEEEEESSSSC--------------------SCCCCS
T ss_pred             CEEEEEEEEeeccCceecCCCCCcEEEEEEEEcCCCCCCCCceEEEEECCChHH--------------------CCCcCC
Confidence            67888888888762     222 34 569999977    3 3999999887542                    222346


Q ss_pred             cCcEEEEEEE-eceeCCceEEEEE
Q 043474          105 IGLVARVRGR-IASYRGDVQITVS  127 (160)
Q Consensus       105 ~G~~V~V~G~-v~~f~~~~qi~~~  127 (160)
                      .||+|++..- ++.|+|+.|....
T Consensus        97 vGDII~l~rvkvq~~~g~~q~v~~  120 (170)
T d1qzga_          97 VGQPLLLHQITLRSYRDRTQGLSK  120 (170)
T ss_dssp             TTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             CCCEEEEEEEEEEEECCceEEEec
Confidence            8999999975 7899999995554

>d2pi2e1 b.40.4.3 (E:3-117) Replication protein A 14 KDa (RPA14) subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 14 KDa (RPA14) subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.42  E-value=0.11  Score=34.02  Aligned_cols=65  Identities=23%  Similarity=0.245  Sum_probs=46.6

Q ss_pred             eEEEEEEEEEEeeccCCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEEEe
Q 043474           37 SRAEIVGTITSRDHKPSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRGRI  115 (160)
Q Consensus        37 ~~v~ivG~V~~~~~~~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G~v  115 (160)
                      +.|++||+|.++.... .  ++++.++-| .+.|.+-.+.                          ....+.+|.|.|++
T Consensus        21 k~V~ivGkV~~v~~~g-~--~~~~~s~D~~~V~v~l~~~~--------------------------~~~~~~~vEViG~V   71 (115)
T d2pi2e1          21 KPVCFVGRLEKIHPTG-K--MFILSDGEGKNGTIELMEPL--------------------------DEEISGIVEVVGRV   71 (115)
T ss_dssp             CEEEEEEEEEEECTTS-S--EEEEECTTSCEEEEECSSCC--------------------------SSCCCSEEEEEEEE
T ss_pred             CeEEEEEEEEEEcCCC-C--EEEEEcCCCCEEEEEeCCCC--------------------------CCccCCeEEEEEEE
Confidence            6899999999987554 3  677888776 5777653221                          12478899999999


Q ss_pred             ceeCCceEEEEEEEEEcC
Q 043474          116 ASYRGDVQITVSDVVIEK  133 (160)
Q Consensus       116 ~~f~~~~qi~~~~i~~v~  133 (160)
                      .   ++..|.+..+....
T Consensus        72 ~---~~~sI~~~~~~~fg   86 (115)
T d2pi2e1          72 T---AKATILCTSYVQFK   86 (115)
T ss_dssp             C---TTSCEEEEEEEECC
T ss_pred             C---CCCcEEEEEEEEcC
Confidence            5   45568888777664

>d1jb7a1 b.40.4.3 (A:36-204) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Telomere end binding protein alpha subunit
species: Oxytricha nova [TaxId: 200597]

Probab=95.02  E-value=0.18  Score=35.23  Aligned_cols=72  Identities=14%  Similarity=0.268  Sum_probs=50.7

Q ss_pred             eEEEEEEEEEEeec----cCCce-EEEEEeCCC------------c-eEEEEEeecCccCCCCCCCCCCccccccccccc
Q 043474           37 SRAEIVGTITSRDH----KPSKF-IKFTVDDGT------------G-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATD   98 (160)
Q Consensus        37 ~~v~ivG~V~~~~~----~~~~~-~~~~IdDgT------------G-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (160)
                      ..+.+.|.|+....    +.+.| ++|+|-|-|            + .|.|.++.+..+.                    
T Consensus        15 ~~vNv~GVV~~~~~p~~s~g~D~~~tl~I~D~S~~~~~~~~~~~~~~~l~v~~F~~~~~~--------------------   74 (169)
T d1jb7a1          15 QPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFED--------------------   74 (169)
T ss_dssp             SCEEEEEEEEEECCCEECSSSCEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSGGG--------------------
T ss_pred             CeEEEEEEEeecCCceecCCCcEEEEEEEEeCCCCccccccccccCCceEEEEECCCHHH--------------------
Confidence            34678899988652    22333 689998876            2 3889998776541                    


Q ss_pred             cccccccCcEEEEEEE-eceeCCceEEEEEE
Q 043474           99 FAAKIKIGLVARVRGR-IASYRGDVQITVSD  128 (160)
Q Consensus        99 ~~~~~~~G~~V~V~G~-v~~f~~~~qi~~~~  128 (160)
                      +....+.||+|++..- ++.|+++.|.....
T Consensus        75 LP~V~~~GDII~l~rv~i~~~~g~~~~v~~~  105 (169)
T d1jb7a1          75 LPIIHRAGDIIRVHRATLRLYNGQRQFNANV  105 (169)
T ss_dssp             SCCCCEETCEEEEEEEEEEEETTEEEEEEET
T ss_pred             CCCCCCCCCEEEEEEEEEEEECCceeEEEcc
Confidence            2223468999999874 78999999987653

>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.61  E-value=0.077  Score=37.46  Aligned_cols=82  Identities=15%  Similarity=0.086  Sum_probs=50.2

Q ss_pred             EEEEEeCCCceEEEEEeecCccCCCCCCCCCCcccccccc-------c-cccccc--cccCc--EEEEEEEeceeCCc--
Q 043474           56 IKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGV-------A-TDFAAK--IKIGL--VARVRGRIASYRGD--  121 (160)
Q Consensus        56 ~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~-------~-~~~~~~--~~~G~--~V~V~G~v~~f~~~--  121 (160)
                      +.++|+|+||.+.+.+|.+.....-         -.++++       + ......  --.|.  .++++++...|++.  
T Consensus        78 l~~~i~D~Tg~~~~~~F~~~a~~l~---------G~sA~EL~~~~~~d~~~~~~~~~~l~~k~~~f~~~~k~~~yn~e~r  148 (178)
T d1l1oc_          78 LSVNIADFQENQWVTCFQESAEAIL---------GQNAAYLGELKDKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESR  148 (178)
T ss_dssp             EEEEEECSSCEEEEEEEHHHHHHHH---------SSCHHHHHHHTTSCHHHHHHHHHHTTTCEEEEEEEEECCCC-----
T ss_pred             EEEEEecCCCCEEEEEehhhHHHHh---------CCCHHHHHHHhhcCHHHHHHHHHHhcCcEEEEEEEEEecccCCeeE
Confidence            6889999999999999977643210         001110       0 000011  11344  55666667789874  


Q ss_pred             eEEEEEEEEEcCChhHHHHHHHHHHH
Q 043474          122 VQITVSDVVIEKDPNMEVLHWLDCLR  147 (160)
Q Consensus       122 ~qi~~~~i~~v~d~n~~~~h~le~~~  147 (160)
                      ....+.++.|++ ..++..++++-+.
T Consensus       149 ~k~~v~~i~pvd-~~~e~~~L~~~I~  173 (178)
T d1l1oc_         149 IKATVMDVKPVD-YREYGRRLVMSIR  173 (178)
T ss_dssp             CEEEEEEEEECC-HHHHHHHHHHHHH
T ss_pred             EEEEEEEeEeCC-HHHHHHHHHHHHH
Confidence            457888899876 8888999988876

>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Deinococcus radiodurans [TaxId: 1299]

Probab=93.42  E-value=0.18  Score=36.64  Aligned_cols=77  Identities=12%  Similarity=0.289  Sum_probs=50.1

Q ss_pred             EeeEEEEEEEEEEee-----ccCCceEEEEEe------CC-------CceEEEEEeecCccCCCCCCCCCCccccccccc
Q 043474           35 LLSRAEIVGTITSRD-----HKPSKFIKFTVD------DG-------TGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA   96 (160)
Q Consensus        35 ~i~~v~ivG~V~~~~-----~~~~~~~~~~Id------Dg-------TG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~   96 (160)
                      .+.+|.|+|.+..--     .....++.|.|.      |.       |--++|++|....+                   
T Consensus       126 ~~N~v~l~G~l~~dpe~r~t~~G~~~~~f~va~~~~~~~~~g~~~~~t~~~~v~~~g~~Ae-------------------  186 (231)
T d1se8a_         126 AMNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLAE-------------------  186 (231)
T ss_dssp             CEEEEEEEEEECSCCEEEECTTCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHH-------------------
T ss_pred             cceeEEEEEEeCCCcEEEECCCCCEEEEEEEEECCCeECCCCceeeeeEEEEeEecCcHHH-------------------
Confidence            368999999998731     122367777773      22       33489999965432                   


Q ss_pred             cccccccccCcEEEEEEEec--eeCCc-------eEEEEEEEEEc
Q 043474           97 TDFAAKIKIGLVARVRGRIA--SYRGD-------VQITVSDVVIE  132 (160)
Q Consensus        97 ~~~~~~~~~G~~V~V~G~v~--~f~~~-------~qi~~~~i~~v  132 (160)
                        ....++.|+.|.|.|+++  .|.++       ..|.+..|..+
T Consensus       187 --~~~~l~KG~~V~V~G~l~~~~~~~kdG~~r~~~~i~a~~v~~L  229 (231)
T d1se8a_         187 --NMKELRKGDPVMIMGRLVNEGWTDKDGNKRNSTRVEATRVEAL  229 (231)
T ss_dssp             --HHTTCCTTCEEEEEEEEEEEECC------CEEEEEEEEEEEEC
T ss_pred             --HhhhCCCCCEEEEEEEeEeceEECCCCCEEEEEEEEEEEEEEc
Confidence              124589999999999996  46532       35666666654

>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Escherichia coli [TaxId: 562]

Probab=93.00  E-value=0.099  Score=35.40  Aligned_cols=67  Identities=12%  Similarity=0.194  Sum_probs=45.4

Q ss_pred             eEeeEEEEEEEEEEe---ec-cC-CceEEEEEe--------------CCCceEEEEEeecCccCCCCCCCCCCccccccc
Q 043474           34 KLLSRAEIVGTITSR---DH-KP-SKFIKFTVD--------------DGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAG   94 (160)
Q Consensus        34 ~~i~~v~ivG~V~~~---~~-~~-~~~~~~~Id--------------DgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~   94 (160)
                      +.+..|.|+|.|..-   .. .+ ..++.|.|.              +.|-=++|++|....+                 
T Consensus         3 ~~mN~v~LiG~l~~dpe~r~~~~G~~v~~f~va~~~~~~~~~~~~~~~~t~w~~v~~~g~~Ae-----------------   65 (145)
T d1qvca_           3 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAE-----------------   65 (145)
T ss_dssp             CCEEEEEEEEEESSCCEEECCSSSCCEEEEEEEECCCCSCCSSSSCCCCCEEEEEEEETHHHH-----------------
T ss_pred             CcceEEEEEEECCCCCEEEECCCCCEEEEEEEEecccccccccccccccceEEeeEEecchhh-----------------
Confidence            457889999999862   11 11 356777773              2333489999976433                 


Q ss_pred             cccccccccccCcEEEEEEEece--eCC
Q 043474           95 VATDFAAKIKIGLVARVRGRIAS--YRG  120 (160)
Q Consensus        95 ~~~~~~~~~~~G~~V~V~G~v~~--f~~  120 (160)
                         .....++.|+.|.|.|+++.  |.+
T Consensus        66 ---~~~~~l~KG~~V~V~G~l~~~~~~~   90 (145)
T d1qvca_          66 ---VASEYLRKGSQVYIEGQLRTRKWTD   90 (145)
T ss_dssp             ---HHHHHCCTTCEEEEEEEEEEEEECS
T ss_pred             ---hHhhhcccCCEEEEEEEEEEeeeEC
Confidence               13357899999999999864  653

>d1ue1a_ b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=92.97  E-value=0.4  Score=30.93  Aligned_cols=75  Identities=20%  Similarity=0.386  Sum_probs=48.2

Q ss_pred             eEEEEEEEEEE---ee--ccCCceEEEEEe--C-------------CCceEEEEEeecCccCCCCCCCCCCccccccccc
Q 043474           37 SRAEIVGTITS---RD--HKPSKFIKFTVD--D-------------GTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA   96 (160)
Q Consensus        37 ~~v~ivG~V~~---~~--~~~~~~~~~~Id--D-------------gTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~   96 (160)
                      ..|.|+|.+..   +.  ....+++.|+|.  +             .|=-++|++|....+                   
T Consensus         3 N~V~L~G~l~~dpe~r~~~~G~~v~~f~lA~~~~~~~~~~~~~~~~~t~~~~v~~~g~~Ae-------------------   63 (118)
T d1ue1a_           3 TTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQTGEWKDGEALFLRCNIWREAAE-------------------   63 (118)
T ss_dssp             CEEEEEEEESSCCEEEECTTSCEEEEEEEEECCCCCC-----CCCCCCEEEEEEEEHHHHH-------------------
T ss_pred             CEEEEEEEcCcCCEEEECCCCCEEEEEEEEecccccccCCCcccccceeeEEEEeChHHHH-------------------
Confidence            46788888875   11  122367778873  1             122399999976543                   


Q ss_pred             cccccccccCcEEEEEEEece--eCCc-------eEEEEEEEEE
Q 043474           97 TDFAAKIKIGLVARVRGRIAS--YRGD-------VQITVSDVVI  131 (160)
Q Consensus        97 ~~~~~~~~~G~~V~V~G~v~~--f~~~-------~qi~~~~i~~  131 (160)
                       .....++.|+.|.|.|+++.  |.++       ..|.+..|-+
T Consensus        64 -~~~~~l~KG~~V~V~G~L~~~~~~~~dG~~r~~~~v~a~~vg~  106 (118)
T d1ue1a_          64 -NVAESLTRGARVIVSGRLKQRSFETREGEKRTVIEVEVDEIGP  106 (118)
T ss_dssp             -HHHHHCCTTCEEEEEEEEEEEEECSSSSSCEEEEEEEEEEEEE
T ss_pred             -HHHHhccCCCEEEEEeEeeeceEECCCCCEEEEEEEEEEEecc
Confidence             12356899999999999974  5432       3566666654

>d3ulla_ b.40.4.3 (A:) ssDNA-binding protein {Human (Homo sapiens), mitochondria [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Human (Homo sapiens), mitochondria [TaxId: 9606]

Probab=92.33  E-value=0.27  Score=31.64  Aligned_cols=77  Identities=17%  Similarity=0.300  Sum_probs=45.3

Q ss_pred             eEeeEEEEEEEEEE---eec--cCCceEEEEEe------C------CCc-------eEEEEEeecCccCCCCCCCCCCcc
Q 043474           34 KLLSRAEIVGTITS---RDH--KPSKFIKFTVD------D------GTG-------CVPCVLWLNHLTSLYLPRRDPSTV   89 (160)
Q Consensus        34 ~~i~~v~ivG~V~~---~~~--~~~~~~~~~Id------D------gTG-------~I~~~~w~~~~~~~~~~~~~~~~~   89 (160)
                      +.+.+|.|+|.+.+   +..  ....+..|.|.      |      ..|       -+.|++|.+...            
T Consensus         3 ~~mN~V~L~G~l~~dpe~r~t~~G~~v~~f~vAv~~~~~~~~~~~~~~g~~~~~t~w~~v~~~g~~~a------------   70 (115)
T d3ulla_           3 RSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLGDVSQKTTWHRISVFRPGLR------------   70 (115)
T ss_dssp             CCEEEEEEEEEECSCCEEECCTTSCCEEEEEEEEEEEECC---------CCEEEEEEEEEEECSTTHH------------
T ss_pred             CceeEEEEEEECCCCCEEEEeCCCCEEEEEEEEcccccccccccccccccceeeeeeeeeeeeecccc------------
Confidence            45788999999975   221  12356777773      1      122       245555543211            


Q ss_pred             cccccccccc-ccccccCcEEEEEEEece--eCCc-------eEEEEEEEE
Q 043474           90 RLIAGVATDF-AAKIKIGLVARVRGRIAS--YRGD-------VQITVSDVV  130 (160)
Q Consensus        90 ~~~~~~~~~~-~~~~~~G~~V~V~G~v~~--f~~~-------~qi~~~~i~  130 (160)
                              +. ...++.|+.|.|.|+++.  |.++       .+|.+.+|.
T Consensus        71 --------~~~~~~l~KG~~V~V~Grl~~~~~~dkdG~~r~~~~v~a~~i~  113 (115)
T d3ulla_          71 --------DVAYQYVKKGSRIYLEGKIDYGEYMDKNNVRRQATTIIADNII  113 (115)
T ss_dssp             --------HHHHHHCCTTCEEEEEEEEECCCEESSSSEECCCEEEEEEEEE
T ss_pred             --------hhhhhhccCCCEEEEEEEEeeeeEECCCCCEEEEEEEEEEEEE
Confidence                    11 135789999999999975  5432       456666654

>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Deinococcus radiodurans [TaxId: 1299]

Probab=91.67  E-value=0.58  Score=33.72  Aligned_cols=80  Identities=11%  Similarity=0.070  Sum_probs=52.3

Q ss_pred             EeeEEEEEEEEEE---ee--ccCCceEEEEEe------CCC-------ceEEEEEeecCccCCCCCCCCCCccccccccc
Q 043474           35 LLSRAEIVGTITS---RD--HKPSKFIKFTVD------DGT-------GCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVA   96 (160)
Q Consensus        35 ~i~~v~ivG~V~~---~~--~~~~~~~~~~Id------DgT-------G~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~   96 (160)
                      .+..|.|+|.+.+   +.  ...+.++.|+|.      |..       --++|.+|....+.                  
T Consensus         2 ~mN~v~l~G~l~~dpe~r~t~~G~~~~~f~lA~~~~~~~~~g~~~~~t~~~~v~~~g~~Ae~------------------   63 (231)
T d1se8a_           2 GMNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAEW------------------   63 (231)
T ss_dssp             CEEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEEEC-------CEEEEEEEEEEESHHHHH------------------
T ss_pred             CccEEEEEEEECcCCEEEECCCCCEEEEEEEEECCcEECCCCCEEeeeeeeeEEEeCchhhh------------------
Confidence            3578899999875   22  122367788883      322       23889999765421                  


Q ss_pred             cccc-cccccCcEEEEEEEec--eeCCc-------eEEEEEEEEEcCC
Q 043474           97 TDFA-AKIKIGLVARVRGRIA--SYRGD-------VQITVSDVVIEKD  134 (160)
Q Consensus        97 ~~~~-~~~~~G~~V~V~G~v~--~f~~~-------~qi~~~~i~~v~d  134 (160)
                        .. ..++.|+.|.|.|+++  .|.++       ..|.+.++..+..
T Consensus        64 --~~~~~l~KG~~V~V~G~l~~~~~~~~dG~~r~~~~i~a~~v~~l~~  109 (231)
T d1se8a_          64 --QAERNLKGGDAVVVEGTLEYRQWEAPEGGKRSAVNVKALRMEQLGT  109 (231)
T ss_dssp             --HHHTCCCTTCEEEEEEEEEEEEEC-----CEEEEEEEEEEEEECSS
T ss_pred             --hhhhccCCCCEEEEEEEEEeeeeECCCCCEEEEEEEEEEEEEEccC
Confidence              12 3589999999999986  46432       4788888887764

>d1sr3a_ b.40.9.1 (A:) Heme chaperone CcmE {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Heme chaperone CcmE
family: Heme chaperone CcmE
domain: Heme chaperone CcmE
species: Escherichia coli [TaxId: 562]

Probab=90.01  E-value=1.2  Score=28.74  Aligned_cols=56  Identities=20%  Similarity=0.235  Sum_probs=40.9

Q ss_pred             eEEEEEEEEEE--eecc-CCceEEEEEeCCCceEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEEE
Q 043474           37 SRAEIVGTITS--RDHK-PSKFIKFTVDDGTGCVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVRG  113 (160)
Q Consensus        37 ~~v~ivG~V~~--~~~~-~~~~~~~~IdDgTG~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~G  113 (160)
                      ++++|=|.|..  +... ++..+.|.|.|+.+.|.+.+-.-                        ..+.|+.|.-|-|.|
T Consensus        29 ~~iRvgG~V~~gSi~~~~~~~~~~F~itD~~~~i~V~Y~Gi------------------------lPdlF~eg~~VVveG   84 (114)
T d1sr3a_          29 QRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVSYEGI------------------------LPDLFREGQGVVVQG   84 (114)
T ss_dssp             SEEEEEEEECTTTCEECSSSSEEEEEEECSSCEEEEEEESC------------------------CCTTCCTTSEEEEEE
T ss_pred             cEEEEeeEEEEeEEEeecCcceEEEEEccCCcEEEEEecCC------------------------CChhhcCCCeEEEEE
Confidence            57888999953  3322 22357999999999998876321                        235688999999999


Q ss_pred             Eec
Q 043474          114 RIA  116 (160)
Q Consensus       114 ~v~  116 (160)
                      ++.
T Consensus        85 ~~~   87 (114)
T d1sr3a_          85 ELE   87 (114)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            974

>d1j6qa_ b.40.9.1 (A:) Heme chaperone CcmE {Shewanella putrefaciens [TaxId: 24]}

class: All beta proteins
fold: OB-fold
superfamily: Heme chaperone CcmE
family: Heme chaperone CcmE
domain: Heme chaperone CcmE
species: Shewanella putrefaciens [TaxId: 24]

Probab=82.38  E-value=3.7  Score=25.69  Aligned_cols=56  Identities=18%  Similarity=0.191  Sum_probs=40.5

Q ss_pred             eEEEEEEEEEE--eecc-CCceEEEEEeCCCc-eEEEEEeecCccCCCCCCCCCCccccccccccccccccccCcEEEEE
Q 043474           37 SRAEIVGTITS--RDHK-PSKFIKFTVDDGTG-CVPCVLWLNHLTSLYLPRRDPSTVRLIAGVATDFAAKIKIGLVARVR  112 (160)
Q Consensus        37 ~~v~ivG~V~~--~~~~-~~~~~~~~IdDgTG-~I~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~V~V~  112 (160)
                      +++++-|.|..  +... ++..+.|.|.|+.+ .|.+.+-.-                        ..+.++.|.-|-+.
T Consensus        27 ~~iRvGG~V~~gSi~~~~~~~~~~F~itD~~~~~i~V~Y~G~------------------------lPdlF~eg~gVVve   82 (100)
T d1j6qa_          27 QRIRVGGMVTVGSMVRDPNSLHVQFAVHDSLGGEILVTYDDL------------------------LPDLFREGQGIVAQ   82 (100)
T ss_dssp             CEEEEEEEECTTCCEECTTSSCEEEEEECTTCCCEEEEECSC------------------------CTTSCCSSSEEEEE
T ss_pred             CEEEEeeEEeeeEEEecCCccEEEEEEcCCceeEEEEEeCCC------------------------CCchhcCCCeEEEE
Confidence            78899999984  3332 23347999999986 588875221                        22568999999999


Q ss_pred             EEec
Q 043474          113 GRIA  116 (160)
Q Consensus       113 G~v~  116 (160)
                      |++.
T Consensus        83 G~~~   86 (100)
T d1j6qa_          83 GVLG   86 (100)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9974