Citrus Sinensis ID: 044496

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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--
Protein Sequence
MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDFV
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHccccccccccccccEEEEEEEEEEEEEEEcccccEEEEEcccEEEEEEEccccccEEcccccccccccEEEEEEEEEEEEcccccEEEEEEEEcccccccccccHHHHHHHHHHHHHHHcHHHcc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHccccccccccccccEEEEHEHEEcEEEEccccccEEEEccccEEEEEEEccHHccccccccccccccccEEEEEEEEEEccccccEEEEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
MDYSLAALKLLCVQLKdarespsqnavTLGGILFQRVWLqgvlvsppdddgrlllddgtGVVQIYLSGDfrirrwntgvfFFDFWMYVMVVGGFvirtddipvikvhkivdlsafpdreAMWYLEVMEAYKLFYQPLIEDFV
Flexible Loop (DISEMBL)
MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIylsgdfrirRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDFV
Low Complexity Region (SEG)
MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPdddgrlllddgtgVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDFV
Disordered region (IsUnstruct)
****LAALKLLCVQLKD*******NAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIE***
Disordered Region (DISOPRED)
***SLAALKLLCVQ*****************ILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDF*
Disordered Region (DISEMBL)
MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDFV
Disordered Region (DISPRO)
MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDFV
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDFV
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	142	2.2.26 [Sep-21-2011]
Q96E14	147	RecQ-mediated genome inst	yes	no	0.795	0.768	0.338	5e-05
A5PJU7	157	RecQ-mediated genome inst	yes	no	0.816	0.738	0.297	9e-05
Q5ZM20	137	RecQ-mediated genome inst	yes	no	0.845	0.875	0.300	0.0001
Q3UPE3	149	RecQ-mediated genome inst	yes	no	0.838	0.798	0.300	0.0007

>sp|Q96E14|RMI2_HUMAN RecQ-mediated genome instability protein 2 OS=Homo sapiens GN=RMI2 PE=1 SV=2

 Score = 46.6 bits (109), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 45/133 (33%), Positives = 60/133 (45%), Gaps = 20/133 (15%)

Query: 8   LKLLCVQLK-DARESP-----SQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGV 61
           LK+L  QL+ DA   P     S+ A   G +    VW+QG +V    D G   L D    
Sbjct: 23  LKVLAEQLRRDAEGGPGAWRLSRAAAGRGPLDLAAVWMQGRVVM--ADRGEARLRD---- 76

Query: 62  VQIYLSGDFRIR---RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDR 118
                SGDF +R   R   G        YVMV+G  V      P ++  K+ DLS  P  
Sbjct: 77  ----PSGDFSVRGLERVPRGRPCLVPGKYVMVMG-VVQACSPEPCLQAVKMTDLSDNPIH 131

Query: 119 EAMWYLEVMEAYK 131
           E+MW LEV + ++
Sbjct: 132 ESMWELEVEDLHR 144

Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. The complex is therefore essential for the stability, localization, and function of complexes containing BLM. In the RMI complex, it is required to target BLM to chromatin and stress-induced nuclear foci and mitotic phosphorylation of BLM.
Homo sapiens (taxid: 9606)

>sp|A5PJU7|RMI2_BOVIN RecQ-mediated genome instability protein 2 OS=Bos taurus GN=RMI2 PE=2 SV=1

 Score = 45.4 bits (106), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 41/138 (29%), Positives = 63/138 (45%), Gaps = 22/138 (15%)

Query: 8   LKLLCVQLK-DARESP-----SQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGV 61
           +K+L  QL+ DA   P     S+ AV    +  + VW+QG +V           + G GV
Sbjct: 24  IKVLAEQLRRDAEGGPGSWRLSRAAVGREPLELRAVWMQGTVV-----------EAGGGV 72

Query: 62  VQIY-LSGDFRIR---RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPD 117
            ++   SG F +R   R   G        YVMV+G  +      P ++  K+ DLS  P 
Sbjct: 73  ARLRDPSGSFSVRGLERVPRGRPCLVPGKYVMVMG-VIQACSPEPCLQAVKMTDLSDNPL 131

Query: 118 REAMWYLEVMEAYKLFYQ 135
            E++W LEV + ++  Y 
Sbjct: 132 HESLWELEVEDLHRHIYS 149

Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. The complex is therefore essential for the stability, localization, and function of complexes containing BLM. In the RMI complex, it is required to target BLM to chromatin and stress-induced nuclear foci and mitotic phosphorylation of BLM.

Bos taurus (taxid: 9913)

>sp|Q5ZM20|RMI2_CHICK RecQ-mediated genome instability protein 2 OS=Gallus gallus GN=RMI2 PE=2 SV=1

 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 55/133 (41%), Gaps = 13/133 (9%)

Query: 8   LKLLCVQLKDARESP------SQNAVTLGGILFQRVWLQG-VLVSPPDDDGRLLLDDGTG 60
           LK+L  QL+ A          S+       +  + VW+QG VL       G   L DG+G
Sbjct: 10  LKVLAAQLRAAGRGAGGTWRLSRTETGRAPLCLRAVWMQGTVLQVERGGGGSARLRDGSG 69

Query: 61  VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREA 120
              +    D        G        YVMV+G  V      PV++  K+ DLS  P  E 
Sbjct: 70  HFTVLGVEDV-----PRGRPCLSAGKYVMVMG-MVRACSPEPVLRAIKMTDLSENPVHEE 123

Query: 121 MWYLEVMEAYKLF 133
           MW LEV E +++ 
Sbjct: 124 MWGLEVEELHRVI 136

Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. The complex is therefore essential for the stability, localization, and function of complexes containing BLM. In the RMI complex, it is required to target BLM to chromatin and stress-induced nuclear foci and mitotic phosphorylation of BLM.

Gallus gallus (taxid: 9031)

>sp|Q3UPE3|RMI2_MOUSE RecQ-mediated genome instability protein 2 OS=Mus musculus GN=Rmi2 PE=2 SV=1

 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 62/133 (46%), Gaps = 14/133 (10%)

Query: 5   LAALKLLCVQLK-DARESP-----SQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDG 58
           L  LK+L  QL+  A   P     S+ AV    +    VW+QG +++   + G+  L D 
Sbjct: 22  LPPLKVLAGQLRRHAEGGPGAWRLSRAAVGRAPLELVAVWMQGTVLA--AEGGQARLRDS 79

Query: 59  TGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDR 118
           +G   +   G  R+ R    +       YVMV+G  V      P ++  K+ DLS  P  
Sbjct: 80  SGAFSVR--GLERVPRGRPCLLPGK---YVMVMG-VVQACSPEPCLQAVKMTDLSDNPVH 133

Query: 119 EAMWYLEVMEAYK 131
           E+MW LEV + ++
Sbjct: 134 ESMWELEVEDLHR 146

Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. The complex is therefore essential for the stability, localization, and function of complexes containing BLM. In the RMI complex, it is required to target BLM to chromatin and stress-induced nuclear foci and mitotic phosphorylation of BLM.

Mus musculus (taxid: 10090)

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	142
224131682	134	predicted protein [Populus trichocarpa]	0.943	1.0	0.753	2e-54
225436377	134	PREDICTED: recQ-mediated genome instabil	0.936	0.992	0.659	3e-46
449443382	135	PREDICTED: recQ-mediated genome instabil	0.950	1.0	0.640	7e-46
449443380	164	PREDICTED: recQ-mediated genome instabil	1.0	0.865	0.579	1e-45
297843618	136	hypothetical protein ARALYDRAFT_470900 [	0.943	0.985	0.633	6e-45
15223204	137	uncharacterized protein [Arabidopsis tha	0.943	0.978	0.615	8e-44
117166018	143	hypothetical protein [Ipomoea trifida]	0.943	0.937	0.625	3e-41
224065533	205	predicted protein [Populus trichocarpa]	0.802	0.556	0.640	2e-40
356539406	142	PREDICTED: recQ-mediated genome instabil	0.943	0.943	0.626	3e-40
45935131	155	hypothetical protein [Ipomoea trifida]	0.943	0.864	0.578	1e-38

>gi|224131682|ref|XP_002328082.1| predicted protein [Populus trichocarpa] gi|118483555|gb|ABK93675.1| unknown [Populus trichocarpa] gi|222837597|gb|EEE75962.1| predicted protein [Populus trichocarpa]

 Score =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 107/142 (75%), Positives = 123/142 (86%), Gaps = 8/142 (5%)

Query: 1   MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTG 60
           MDYSLAALKLLCVQLKDA E+PSQNA+TLGGILFQR WLQG+LVS  D DGRLLLDDGTG
Sbjct: 1   MDYSLAALKLLCVQLKDASETPSQNALTLGGILFQRAWLQGILVSN-DGDGRLLLDDGTG 59

Query: 61  VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREA 120
           V+++ LS DFR+R W++G       MYVMVVGG+ +R  + P+IKVHK+VDLSAFPDREA
Sbjct: 60  VIELCLSPDFRLRHWDSG-------MYVMVVGGYFVRHGETPMIKVHKMVDLSAFPDREA 112

Query: 121 MWYLEVMEAYKLFYQPLIEDFV 142
           MWYLEVMEAYKLFYQPLIE+F+
Sbjct: 113 MWYLEVMEAYKLFYQPLIEEFM 134

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436377|ref|XP_002271178.1| PREDICTED: recQ-mediated genome instability protein 2 [Vitis vinifera] gi|297734866|emb|CBI17100.3| unnamed protein product [Vitis vinifera]

 Score =  189 bits (480), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 93/141 (65%), Positives = 112/141 (79%), Gaps = 8/141 (5%)

Query: 1   MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDD-DGRLLLDDGT 59
           MDYSLAALK++C QL+ A+E+ SQNA TLGG+LFQR WLQGVLVS  DD  GR +LDDGT
Sbjct: 1   MDYSLAALKVMCGQLRKAKETTSQNAFTLGGVLFQRAWLQGVLVSVSDDAQGRFVLDDGT 60

Query: 60  GVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDRE 119
           GV+ + LSGDF  R W  G       MYVMVVGG+ +R+ + P+IKVHKIVDLS FPDRE
Sbjct: 61  GVIHLSLSGDFLHRNWKIG-------MYVMVVGGYFVRSGEPPMIKVHKIVDLSPFPDRE 113

Query: 120 AMWYLEVMEAYKLFYQPLIED 140
           +MWYLEV+EA++LFYQPL E+
Sbjct: 114 SMWYLEVIEAFRLFYQPLYEE 134

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443382|ref|XP_004139456.1| PREDICTED: recQ-mediated genome instability protein 2-like isoform 2 [Cucumis sativus] gi|449501627|ref|XP_004161421.1| PREDICTED: recQ-mediated genome instability protein 2-like [Cucumis sativus]

 Score =  188 bits (477), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 91/142 (64%), Positives = 110/142 (77%), Gaps = 7/142 (4%)

Query: 1   MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTG 60
           MDYSL ALKLLC QLKDAR +PS     LGGILFQR WLQG+LVS   ++G+L+LDD TG
Sbjct: 1   MDYSLGALKLLCRQLKDARGTPSHPTANLGGILFQRAWLQGILVSVDKENGKLILDDATG 60

Query: 61  VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREA 120
            V++ LS DF +R W+ G       MYVMVVG F+ RT+++P I VHKI+DLS  P+REA
Sbjct: 61  TVELSLSRDFLLRPWSLG-------MYVMVVGAFLFRTNELPFIVVHKIIDLSKSPNREA 113

Query: 121 MWYLEVMEAYKLFYQPLIEDFV 142
           MWYLEVMEAYKLFY+PL+EDF+
Sbjct: 114 MWYLEVMEAYKLFYEPLVEDFL 135

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443380|ref|XP_004139455.1| PREDICTED: recQ-mediated genome instability protein 2-like isoform 1 [Cucumis sativus]

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 95/164 (57%), Positives = 115/164 (70%), Gaps = 22/164 (13%)

Query: 1   MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTG 60
           MDYSL ALKLLC QLKDAR +PS     LGGILFQR WLQG+LVS   ++G+L+LDD TG
Sbjct: 1   MDYSLGALKLLCRQLKDARGTPSHPTANLGGILFQRAWLQGILVSVDKENGKLILDDATG 60

Query: 61  VVQIYLSGDFRIRRWNTGV--------------------FFFDFW--MYVMVVGGFVIRT 98
            V++ LS DF +R W+ G+                    FFF F   MYVMVVG F+ RT
Sbjct: 61  TVELSLSRDFLLRPWSLGIFPTTSPFSFLLLHFELDSLAFFFCFCSGMYVMVVGAFLFRT 120

Query: 99  DDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDFV 142
           +++P I VHKI+DLS  P+REAMWYLEVMEAYKLFY+PL+EDF+
Sbjct: 121 NELPFIVVHKIIDLSKSPNREAMWYLEVMEAYKLFYEPLVEDFL 164

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843618|ref|XP_002889690.1| hypothetical protein ARALYDRAFT_470900 [Arabidopsis lyrata subsp. lyrata] gi|297335532|gb|EFH65949.1| hypothetical protein ARALYDRAFT_470900 [Arabidopsis lyrata subsp. lyrata]

 Score =  185 bits (469), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 90/142 (63%), Positives = 113/142 (79%), Gaps = 8/142 (5%)

Query: 1   MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVS-PPDDDGRLLLDDGT 59
           MDYSLAA+K+LC QL+DA+ +PSQNA  LGG+LFQR WLQGVLV      D  ++LDDGT
Sbjct: 1   MDYSLAAVKMLCSQLRDAKPTPSQNATALGGVLFQRAWLQGVLVPISGGGDNHMVLDDGT 60

Query: 60  GVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDRE 119
           G+V++ LS DF +R+W +G       MYVMVVG + IRT DIP++KVHK+VDLS  PDRE
Sbjct: 61  GLVELGLSSDFALRQWKSG-------MYVMVVGVYHIRTGDIPLLKVHKMVDLSVSPDRE 113

Query: 120 AMWYLEVMEAYKLFYQPLIEDF 141
           AMWYLEVM+AY+LFY+PLI++F
Sbjct: 114 AMWYLEVMDAYRLFYEPLIQEF 135

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15223204|ref|NP_172315.1| uncharacterized protein [Arabidopsis thaliana] gi|20258784|gb|AAM13914.1| unknown protein [Arabidopsis thaliana] gi|332190163|gb|AEE28284.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  181 bits (459), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 88/143 (61%), Positives = 114/143 (79%), Gaps = 9/143 (6%)

Query: 1   MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLV--SPPDDDGRLLLDDG 58
           MDYSLAA+K+LC QL+DA+ +PSQNA +LGG+LFQR WLQGVLV  S    D  L+LDDG
Sbjct: 1   MDYSLAAVKMLCSQLRDAKPTPSQNAASLGGVLFQRAWLQGVLVPFSGGGGDNCLVLDDG 60

Query: 59  TGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDR 118
           TG++++ L+ DF +R+W +G       MYVMVVG + +RT  IP++KVHK+VDLS  PDR
Sbjct: 61  TGLLELGLTNDFALRQWKSG-------MYVMVVGVYQVRTGQIPLLKVHKMVDLSVSPDR 113

Query: 119 EAMWYLEVMEAYKLFYQPLIEDF 141
           EAMWYLEVM+AY+LFY+PLI++F
Sbjct: 114 EAMWYLEVMDAYRLFYEPLIQEF 136

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|117166018|dbj|BAF36320.1| hypothetical protein [Ipomoea trifida]

 Score =  172 bits (437), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 92/147 (62%), Positives = 108/147 (73%), Gaps = 13/147 (8%)

Query: 1   MDYSLAALKLLCVQLKDARE--SPSQNAVTLGGILFQRVWLQGVLVS---PPDDDGRLLL 55
           MDYSL ALK+LC  L  A E  S SQ A +LGGILFQRVWLQGVLVS   P +D GR LL
Sbjct: 1   MDYSLGALKILCSHLTTATEATSHSQPAFSLGGILFQRVWLQGVLVSKPSPSNDAGRFLL 60

Query: 56  DDGTGVVQIYLSGDF-RIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSA 114
           DDGTGV+++ LSGD+ +   W  G       MYVMVVGG+ +R +    IKVHKIVDLS 
Sbjct: 61  DDGTGVIELKLSGDYLQNDAWELG-------MYVMVVGGYAVRKNGTSFIKVHKIVDLSP 113

Query: 115 FPDREAMWYLEVMEAYKLFYQPLIEDF 141
            PDREAMWYLEV+EA++LFYQPLIE++
Sbjct: 114 VPDREAMWYLEVVEAFRLFYQPLIEEY 140

Source: Ipomoea trifida

Species: Ipomoea trifida

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224065533|ref|XP_002301844.1| predicted protein [Populus trichocarpa] gi|222843570|gb|EEE81117.1| predicted protein [Populus trichocarpa]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 91/142 (64%), Positives = 103/142 (72%), Gaps = 28/142 (19%)

Query: 1   MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTG 60
           MDYSLAALKLL VQLKD  E+PSQNA+TLGGILFQR WLQG+LVS  D DGRLLLDDGTG
Sbjct: 20  MDYSLAALKLLRVQLKDTSETPSQNALTLGGILFQRAWLQGILVS-NDGDGRLLLDDGTG 78

Query: 61  VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREA 120
           V+++ LSGDFR+R W+ G       MYVMVVGG+ +R                     EA
Sbjct: 79  VIELCLSGDFRLRHWDLG-------MYVMVVGGYFVRP--------------------EA 111

Query: 121 MWYLEVMEAYKLFYQPLIEDFV 142
           MWYLEVMEAYKLFYQPLIE+F+
Sbjct: 112 MWYLEVMEAYKLFYQPLIEEFI 133

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539406|ref|XP_003538189.1| PREDICTED: recQ-mediated genome instability protein 2-like [Glycine max]

 Score =  169 bits (429), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 94/150 (62%), Positives = 109/150 (72%), Gaps = 16/150 (10%)

Query: 1   MDYSLAALKLLCVQLKDARE--------SPSQNAVTLGGILFQRVWLQGVLVSPPDDDGR 52
           MDY LAALKL C QLK ARE        S SQ++ TLGG+LFQR WLQGVLVS   D G 
Sbjct: 1   MDYDLAALKLFCSQLKQAREVAMPCQTQSQSQSSFTLGGLLFQRPWLQGVLVSA-SDAGS 59

Query: 53  LLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDL 112
           LLLDDGT +V++ L+ +FR R W  G       MYVMVVGG+  R   +P+IKVHKIVDL
Sbjct: 60  LLLDDGTDLVELSLNSEFRHRPWKLG-------MYVMVVGGYAARPGKLPMIKVHKIVDL 112

Query: 113 SAFPDREAMWYLEVMEAYKLFYQPLIEDFV 142
           S+ P+REAMWYLEVMEAYKLFYQPL+E+F 
Sbjct: 113 SSSPNREAMWYLEVMEAYKLFYQPLVEEFT 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|45935131|gb|AAS79589.1| hypothetical protein [Ipomoea trifida]

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 92/159 (57%), Positives = 108/159 (67%), Gaps = 25/159 (15%)

Query: 1   MDYSLAALKLLCVQLKDARE--SPSQNAVTLGGILFQRVWLQGVLVS---PPDDDGRLLL 55
           MDYSL ALK+LC  L  A E  S SQ A +LGGILFQRVWLQGVLVS   P +D GR LL
Sbjct: 1   MDYSLGALKILCSHLTTATEATSHSQPAFSLGGILFQRVWLQGVLVSKPSPSNDAGRFLL 60

Query: 56  DDGTGVVQIYLSGDF-RIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK--------- 105
           DDGTGV+++ LSGD+ +   W  G       MYVMVVGG+ +R +    IK         
Sbjct: 61  DDGTGVIELKLSGDYLQNDAWELG-------MYVMVVGGYAVRKNGTSFIKMRDQEECIS 113

Query: 106 ---VHKIVDLSAFPDREAMWYLEVMEAYKLFYQPLIEDF 141
              VHKIVDLS  PDREAMWYLEV+EA++LFYQPLIE++
Sbjct: 114 FSKVHKIVDLSPVPDREAMWYLEVVEAFRLFYQPLIEEY 152

Source: Ipomoea trifida

Species: Ipomoea trifida

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

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	142
TAIR|locus:2201846	137	AT1G08390 [Arabidopsis thalian	0.943	0.978	0.559	8.9e-38
UNIPROTKB|Q5ZM20	137	RMI2 "RecQ-mediated genome ins	0.316	0.328	0.434	0.00073

TAIR|locus:2201846 AT1G08390 [Arabidopsis thaliana (taxid:3702)]

 Score = 405 (147.6 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 80/143 (55%), Positives = 105/143 (73%)

Query:     1 MDYSLAALKLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLV--SPPXXXXXXXXXXX 58
             MDYSLAA+K+LC QL+DA+ +PSQNA +LGG+LFQR WLQGVLV  S             
Sbjct:     1 MDYSLAAVKMLCSQLRDAKPTPSQNAASLGGVLFQRAWLQGVLVPFSGGGGDNCLVLDDG 60

Query:    59 XXVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDR 118
               ++++ L+ DF +R+W +G       MYVMVVG + +RT  IP++KVHK+VDLS  PDR
Sbjct:    61 TGLLELGLTNDFALRQWKSG-------MYVMVVGVYQVRTGQIPLLKVHKMVDLSVSPDR 113

Query:   119 EAMWYLEVMEAYKLFYQPLIEDF 141
             EAMWYLEVM+AY+LFY+PLI++F
Sbjct:   114 EAMWYLEVMDAYRLFYEPLIQEF 136

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q5ZM20 RMI2 "RecQ-mediated genome instability protein 2" [Gallus gallus (taxid:9031)]

 Score = 82 (33.9 bits), Expect = 0.00073, Sum P(2) = 0.00073
 Identities = 20/46 (43%), Positives = 27/46 (58%)

Query:    87 YVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKL 132
             YVMV+G  V      PV++  K+ DLS  P  E MW LEV E +++
Sbjct:    91 YVMVMG-MVRACSPEPVLRAIKMTDLSENPVHEEMWGLEVEELHRV 135

GO:0003677 "DNA binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5ZM20	RMI2_CHICK	No assigned EC number	0.3007	0.8450	0.8759	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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	142
COG0340	238	COG0340, BirA, Biotin-(acetyl-CoA carboxylase) lig	0.004

>gnl|CDD|223417 COG0340, BirA, Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 13/28 (46%), Positives = 17/28 (60%)

Query: 48  DDDGRLLLDDGTGVVQIYLSGDFRIRRW 75
           D+DG LLL+   G VQ   SG+  +RR 
Sbjct: 211 DEDGALLLETDDGEVQTIYSGEVSLRRA 238

Length = 238

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	142
cd04478	95	RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor	98.48
KOG3108	265	consensus Single-stranded DNA-binding replication	98.37
cd04483	92	hOBFC1_like hOBFC1_like: A subfamily of OB folds s	98.31
COG3390	196	Uncharacterized protein conserved in archaea [Func	98.3
PF01336	75	tRNA_anti-codon: OB-fold nucleic acid binding doma	98.2
COG5235	258	RFA2 Single-stranded DNA-binding replication prote	97.61
PF04076	103	BOF: Bacterial OB fold (BOF) protein; InterPro: IP	97.56
TIGR00156	126	conserved hypothetical protein TIGR00156. As of th	97.4
PRK10053	130	hypothetical protein; Provisional	97.31
cd04489	78	ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol	96.93
cd03524	75	RPA2_OBF_family RPA2_OBF_family: A family of oligo	96.9
PF08661	109	Rep_fac-A_3: Replication factor A protein 3; Inter	96.86
cd04492	83	YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol	96.82
PF10451	256	Stn1: Telomere regulation protein Stn1; InterPro:	96.72
COG3111	128	Periplasmic protein with OB-fold [Function unknown	96.57
cd04479	101	RPA3 RPA3: A subfamily of OB folds similar to huma	96.29
cd04100	85	Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant	96.12
PRK05159	437	aspC aspartyl-tRNA synthetase; Provisional	95.82
cd04316	108	ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a	95.77
cd04323	84	AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, a	95.71
cd04317	135	EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod	95.64
cd04322	108	LysRS_N LysRS_N: N-terminal, anticodon recognition	95.63
cd04485	84	DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp	95.34
cd04320	102	AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r	95.29
cd04482	91	RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara	94.96
COG4085	204	Predicted RNA-binding protein, contains TRAM domai	94.9
cd04318	82	EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticod	94.84
cd04488	75	RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f	94.69
TIGR00499	496	lysS_bact lysyl-tRNA synthetase, eukaryotic and no	94.54
PF13742	99	tRNA_anti_2: OB-fold nucleic acid binding domain	94.35
TIGR00458	428	aspS_arch aspartyl-tRNA synthetase, archaeal type.	94.21
cd04321	86	ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, a	94.17
cd04319	103	PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticod	93.44
TIGR00457	453	asnS asparaginyl-tRNA synthetase. In a multiple se	93.32
PLN02850	530	aspartate-tRNA ligase	93.3
cd04487	73	RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f	93.29
PLN02502	553	lysyl-tRNA synthetase	92.92
cd04491	82	SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil	92.86
PRK12445	505	lysyl-tRNA synthetase; Reviewed	92.8
PRK00484	491	lysS lysyl-tRNA synthetase; Reviewed	92.37
PRK03932	450	asnC asparaginyl-tRNA synthetase; Validated	91.92
cd04490	79	PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds	91.83
PRK02983	1094	lysS lysyl-tRNA synthetase; Provisional	91.7
COG1570	440	XseA Exonuclease VII, large subunit [DNA replicati	91.48
PF01455	68	HupF_HypC: HupF/HypC family; InterPro: IPR001109 T	91.27
PTZ00401	550	aspartyl-tRNA synthetase; Provisional	90.67
PRK07373	449	DNA polymerase III subunit alpha; Reviewed	90.66
TIGR00459	583	aspS_bact aspartyl-tRNA synthetase, bacterial type	90.52
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	90.3
PRK00476	588	aspS aspartyl-tRNA synthetase; Validated	89.96
PLN02221	572	asparaginyl-tRNA synthetase	89.7
PF07076	61	DUF1344: Protein of unknown function (DUF1344); In	89.7
COG0017	435	AsnS Aspartyl/asparaginyl-tRNA synthetases [Transl	88.65
PRK06386	358	replication factor A; Reviewed	88.23
PF15490	118	Ten1_2: Telomere-capping, CST complex subunit	87.33
PRK04036	504	DNA polymerase II small subunit; Validated	87.03
PTZ00385	659	lysyl-tRNA synthetase; Provisional	86.92
PRK07218	423	replication factor A; Provisional	86.89
PLN02903	652	aminoacyl-tRNA ligase	85.91
PRK12820	706	bifunctional aspartyl-tRNA synthetase/aspartyl/glu	85.82
PF03100	131	CcmE: CcmE; InterPro: IPR004329 CcmE is the produc	85.22
PRK13150	159	cytochrome c-type biogenesis protein CcmE; Reviewe	84.8
PRK13165	160	cytochrome c-type biogenesis protein CcmE; Reviewe	84.67
PLN02603	565	asparaginyl-tRNA synthetase	83.65
PRK10413	82	hydrogenase 2 accessory protein HypG; Provisional	83.31
TIGR00237	432	xseA exodeoxyribonuclease VII, large subunit. This	82.84
PRK13480	314	3'-5' exoribonuclease YhaM; Provisional	82.31
TIGR00074	76	hypC_hupF hydrogenase assembly chaperone HypC/HupF	81.71
PRK07218	423	replication factor A; Provisional	81.49
PRK00286	438	xseA exodeoxyribonuclease VII large subunit; Revie	81.33
PRK05672	1046	dnaE2 error-prone DNA polymerase; Validated	80.68
PRK07217	311	replication factor A; Reviewed	80.6
PRK08402	355	replication factor A; Reviewed	80.34
PRK13254	148	cytochrome c-type biogenesis protein CcmE; Reviewe	80.27

>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=98.48  E-value=2.2e-06  Score=59.63  Aligned_cols=85  Identities=24%  Similarity=0.279  Sum_probs=66.2

Q ss_pred             EEEEEEEEeeeCC--CCcEEEEcCCeeEEEEe-cccc-----ccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496           37 VWLQGVLVSPPDD--DGRLLLDDGTGVVQIYL-SGDF-----RIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK  108 (142)
Q Consensus        37 VWlQG~vv~~~~~--~~~~~LdDgTG~~~v~~-~~~~-----~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K  108 (142)
                      |-+.|.|.++...  .-++.|+|+||.+++.. ....     ....++.|       +||.|.|.+.. .+..+-|++.+
T Consensus         2 v~~vG~V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g-------~~v~v~G~v~~-~~g~~ql~i~~   73 (95)
T cd04478           2 VTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEG-------TYVRVFGNLKS-FQGKKSIMAFS   73 (95)
T ss_pred             EEEEEEEEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccC-------CEEEEEEEEcc-cCCeeEEEEEE
Confidence            5578999999654  34899999999999987 3222     22359999       99999999977 77888888887


Q ss_pred             EeeCCCCcCccchhHHHHHHHH
Q 044496          109 IVDLSAFPDREAMWYLEVMEAY  130 (142)
Q Consensus       109 ~~DLS~~p~re~mW~lEV~e~~  130 (142)
                      +.-+. +|+.-.+=.|||..+|
T Consensus        74 i~~v~-d~ne~~~h~l~~~~~~   94 (95)
T cd04478          74 IRPVT-DFNEVTYHLLEVIYVH   94 (95)
T ss_pred             EEEeC-CccHHHHhHhhhhhhh
Confidence            77554 5777777788888776

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

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

Probab=98.37  E-value=2.9e-06  Score=71.86  Aligned_cols=112  Identities=21%  Similarity=0.299  Sum_probs=82.5

Q ss_pred             HHHHHhhccCCCCCCceeecCeEEeEEEEEEEEEeeeCC--CCcEEEEcCCeeEEEEe-cc---ccccc-cccCCccccc
Q 044496           11 LCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDD--DGRLLLDDGTGVVQIYL-SG---DFRIR-RWNTGVFFFD   83 (142)
Q Consensus        11 f~~QL~~a~~~~s~~~~~l~gl~~~~VWlQG~vv~~~~~--~~~~~LdDgTG~~~v~~-~~---~~~~~-~~~~G~~~~~   83 (142)
                      =++||-++...... .|.++|+++++|-+.|.|......  +-.+.|+||||++++.. ..   ..... ++.+|     
T Consensus        46 ti~qi~s~~~~~~~-~~~i~~~~v~~v~~VGivr~~e~~~t~i~y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~-----  119 (265)
T KOG3108|consen   46 TIKQILSSTQDDDS-VFKIGGVEVSAVSIVGIVRNIEKSATNITYEIEDGTGQIDVRQWFHDNAESEEMPALETG-----  119 (265)
T ss_pred             ceeeeccccccccc-cEEEccEEEEEEEEEEEEEeceecCcceEEEEecCcccEEEEEeccccchhhhCcccccC-----
Confidence            34566666655433 888999999999999999998644  55899999999999987 22   22233 59999     


Q ss_pred             ceeEEEEEeeEeeccCCCceEEEEEEe---eCCCCcCccchhHHHHHHHHHHHhh
Q 044496           84 FWMYVMVVGGFVIRTDDIPVIKVHKIV---DLSAFPDREAMWYLEVMEAYKLFYQ  135 (142)
Q Consensus        84 ~~~YVmViG~~~~~~~~~p~i~a~K~~---DLS~~p~re~mW~lEV~e~~~~~y~  135 (142)
                        +||.|.|.++. -+..-.|.+.|+.   |.++.-.|    .||++++|..+=+
T Consensus       120 --~yVkv~G~Lk~-f~Gk~sl~~fkI~pv~D~Nevt~h----~LE~i~~hl~~s~  167 (265)
T KOG3108|consen  120 --TYVKVYGHLKP-FQGKKSLQVFKIRPVEDFNEVTTH----FLEVINAHLSLSK  167 (265)
T ss_pred             --cEEEeeecccC-CCCceeEEEEeeeeeecCCceeEE----eehhhHHHHHhhh
Confidence              99999999976 4445566666654   44444444    5899999876543

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

Probab=98.31  E-value=6.4e-06  Score=59.04  Aligned_cols=64  Identities=22%  Similarity=0.183  Sum_probs=49.9

Q ss_pred             EEEEEEeeeCC--CCcEEEEcCCeeEEEEe-cccc---------------------ccc-cccCCcccccceeEEEEEee
Q 044496           39 LQGVLVSPPDD--DGRLLLDDGTGVVQIYL-SGDF---------------------RIR-RWNTGVFFFDFWMYVMVVGG   93 (142)
Q Consensus        39 lQG~vv~~~~~--~~~~~LdDgTG~~~v~~-~~~~---------------------~~~-~~~~G~~~~~~~~YVmViG~   93 (142)
                      +.|+|+++.+.  .-.|.||||||.+++.. ....                     +.. .+++|       +||.|.|.
T Consensus         2 ivG~V~sv~~~~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G-------~vvrV~G~   74 (92)
T cd04483           2 ILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIG-------DLLRVRGS   74 (92)
T ss_pred             eEEEEEEEEecCCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCC-------CEEEEEEE
Confidence            57999999655  44899999999999987 2111                     222 48999       99999999


Q ss_pred             EeeccCCCceEEEEEEe
Q 044496           94 FVIRTDDIPVIKVHKIV  110 (142)
Q Consensus        94 ~~~~~~~~p~i~a~K~~  110 (142)
                      +.. ....+-+++.+|.
T Consensus        75 i~~-frg~~ql~i~~~~   90 (92)
T cd04483          75 IRT-YRGEREINASVVY   90 (92)
T ss_pred             Eec-cCCeeEEEEEEEE
Confidence            977 7778888887764

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.

>COG3390 Uncharacterized protein conserved in archaea [Function unknown]

Probab=98.30  E-value=4.6e-06  Score=68.13  Aligned_cols=85  Identities=20%  Similarity=0.277  Sum_probs=64.2

Q ss_pred             chHHHHHHHHHhhccCCCCC-------C-ceeecCeEEeEEEEEEEEEeeeCCC--C---cEEEEcCCeeEEEEe-cccc
Q 044496            5 LAALKLLCVQLKDARESPSQ-------N-AVTLGGILFQRVWLQGVLVSPPDDD--G---RLLLDDGTGVVQIYL-SGDF   70 (142)
Q Consensus         5 ~pa~Kvf~~QL~~a~~~~s~-------~-~~~l~gl~~~~VWlQG~vv~~~~~~--~---~~~LdDgTG~~~v~~-~~~~   70 (142)
                      .+|-.+|++-|+++.-+-++       + ..+.-|+.++|+.+.|+|+++...+  +   ++.++|+||.|-+.- -..|
T Consensus         8 eva~rVFa~El~e~~~s~~e~~e~~sp~yliTPlG~k~nRifivGtltek~~i~ed~~~~R~rVvDpTGsF~Vyag~yqP   87 (196)
T COG3390           8 EVAYRVFAKELRESKFSKKEEDEERSPNYLITPLGLKVNRIFIVGTLTEKEGIGEDREYWRIRVVDPTGSFYVYAGQYQP   87 (196)
T ss_pred             hHHHHHHHHHHhhcceeccccccccCCcEEechhhhheeEEEEEEEEEeccCcCCcccEEEEEEecCCceEEEEcCCCCh
Confidence            57889999999998654321       1 3445599999999999999995443  3   899999999999953 2222


Q ss_pred             cc----ccccCCcccccceeEEEEEeeEee
Q 044496           71 RI----RRWNTGVFFFDFWMYVMVVGGFVI   96 (142)
Q Consensus        71 ~~----~~~~~G~~~~~~~~YVmViG~~~~   96 (142)
                      ..    .....+       .+|||+|++..
T Consensus        88 Ea~a~l~~ve~~-------~~VaViGKi~~  110 (196)
T COG3390          88 EAKAFLEDVEVP-------DLVAVIGKIRT  110 (196)
T ss_pred             HHHHHHHhccCC-------ceEEEecccce
Confidence            22    147889       99999999977

>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=98.20  E-value=1.2e-05  Score=52.35  Aligned_cols=69  Identities=28%  Similarity=0.260  Sum_probs=53.0

Q ss_pred             EEEEEEEEeee-CCCC--cEEEEcCCeeEEEEecc--ccccc-cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEe
Q 044496           37 VWLQGVLVSPP-DDDG--RLLLDDGTGVVQIYLSG--DFRIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIV  110 (142)
Q Consensus        37 VWlQG~vv~~~-~~~~--~~~LdDgTG~~~v~~~~--~~~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~  110 (142)
                      |++.|+|.+++ ....  .+.|+|+||.+++..-.  ..+.. .+++|       +.|.|.|.+....+.++.|.+.++.
T Consensus         1 V~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g-------~~v~v~G~v~~~~~~~~~l~~~~i~   73 (75)
T PF01336_consen    1 VTVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEG-------DIVRVRGKVKRYNGGELELIVPKIE   73 (75)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TT-------SEEEEEEEEEEETTSSEEEEEEEEE
T ss_pred             CEEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCC-------eEEEEEEEEEEECCccEEEEECEEE
Confidence            68999999994 2222  88999999999999833  33333 59999       9999999998844445999999987


Q ss_pred             eC
Q 044496          111 DL  112 (142)
Q Consensus       111 DL  112 (142)
                      +|
T Consensus        74 ~l   75 (75)
T PF01336_consen   74 IL   75 (75)
T ss_dssp             EE
T ss_pred             EC
Confidence            65

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 ....

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

Probab=97.61  E-value=0.0013  Score=55.30  Aligned_cols=114  Identities=15%  Similarity=0.278  Sum_probs=79.8

Q ss_pred             HHHHhhccCCCCCCceeecCeEEeEEEEEEEEEeeeCC--CCcEEEEcCCeeEEEEe-cccc---c-cccccCCcccccc
Q 044496           12 CVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDD--DGRLLLDDGTGVVQIYL-SGDF---R-IRRWNTGVFFFDF   84 (142)
Q Consensus        12 ~~QL~~a~~~~s~~~~~l~gl~~~~VWlQG~vv~~~~~--~~~~~LdDgTG~~~v~~-~~~~---~-~~~~~~G~~~~~~   84 (142)
                      ++|+-.|.+-.....|..++.|+.+|-..|+|.+....  +--+.|-||||.++|+. +.+.   . .+....|      
T Consensus        44 IKQIl~~~qd~~d~~f~vd~~Ev~~V~fVGvvrni~~~ttn~~~~iEDGTG~Ievr~W~~~~~~~e~~~d~~~~------  117 (258)
T COG5235          44 IKQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQ------  117 (258)
T ss_pred             HHHhhcccccccCCceeecceEEeeEEEEEEEEeeeecccceEEEEecCCceEEEEecCCCchHHHhccccccc------
Confidence            67888888766555899999999999999999998543  66899999999999997 3332   2 3348889      


Q ss_pred             eeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHHh
Q 044496           85 WMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFY  134 (142)
Q Consensus        85 ~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~y  134 (142)
                       .||.|.|.++. -+...-|.+-.|.-+-+ .+-=.--.||++-.|..+=
T Consensus       118 -~yvkV~G~lk~-F~GK~~I~~~~i~~I~d-~NeV~~HfLe~I~~Hl~~t  164 (258)
T COG5235         118 -NYVKVNGSLKT-FNGKRSISASHISAIED-SNEVTYHFLECIYQHLFYT  164 (258)
T ss_pred             -cEEEEecceee-eCCeeEEehhheeeccc-cchhHHHHHHHHHHHHHHH
Confidence             99999999976 44444444333322222 1111234688887775543

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

Probab=97.56  E-value=0.00083  Score=49.67  Aligned_cols=71  Identities=21%  Similarity=0.197  Sum_probs=53.5

Q ss_pred             CeEEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496           31 GILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI  109 (142)
Q Consensus        31 gl~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~  109 (142)
                      .-.=+.|-|.|.|++. -+++.+++.|+||.+.|.. +....++++.++       .=|.+.|.+-+ ....+.|.+.+|
T Consensus        31 ~~Dd~~V~L~G~Iv~~-l~~d~Y~F~D~TG~I~VeId~~~w~g~~vt~~-------~~Vri~GeVDk-~~~~~~IdV~~I  101 (103)
T PF04076_consen   31 AKDDTPVTLEGNIVKQ-LGDDKYLFRDATGEIEVEIDDDVWRGQTVTPD-------DKVRISGEVDK-DWNKTEIDVDRI  101 (103)
T ss_dssp             S-SSEEEEEEEEEEEE-EETTEEEEEETTEEEEEE--GGGSTT----TT-------SEEEEEEEEEE-ETTEEEEEEEEE
T ss_pred             CcCCCeEEEEEEEEEE-ecCCEEEEECCCCcEEEEEChhhcCCcccCCC-------CEEEEEEEEeC-CCCceEEEEEEE
Confidence            3444678899999995 4789999999999999999 555778889999       99999999987 445688887776


Q ss_pred             e
Q 044496          110 V  110 (142)
Q Consensus       110 ~  110 (142)
                      .
T Consensus       102 ~  102 (103)
T PF04076_consen  102 E  102 (103)
T ss_dssp             E
T ss_pred             E
Confidence            3

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.

>TIGR00156 conserved hypothetical protein TIGR00156

Probab=97.40  E-value=0.0014  Score=50.41  Aligned_cols=68  Identities=19%  Similarity=0.243  Sum_probs=55.5

Q ss_pred             EEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496           33 LFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI  109 (142)
Q Consensus        33 ~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~  109 (142)
                      +=+.|-|+|.|++. -+++.++..|+||.+.|.. +...++.++.++       .=|.+.|.+-+. -..+.|-+.+|
T Consensus        56 Ddt~V~L~G~Iv~~-l~~d~Y~F~D~TG~I~VeId~~~w~G~~v~p~-------d~V~I~GeVDk~-~~~~~IdV~~I  124 (126)
T TIGR00156        56 DGASVTLRGNIISH-IGDDRYVFRDKSGEINVVIPAAVWNGREVQPK-------DMVNISGSLDKK-SAPAEVDVTHI  124 (126)
T ss_pred             CCCEEEEEEEEEEE-eCCceEEEECCCCCEEEEECHHHcCCCcCCCC-------CEEEEEEEECCC-CCCeEEEEEEE
Confidence            34678899999995 5788999999999999999 556688899999       999999999873 33466666665

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

>PRK10053 hypothetical protein; Provisional

Probab=97.31  E-value=0.0019  Score=49.77  Aligned_cols=68  Identities=21%  Similarity=0.353  Sum_probs=55.9

Q ss_pred             EEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496           33 LFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI  109 (142)
Q Consensus        33 ~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~  109 (142)
                      .=+.|-|+|.|++ +-+++..+..|+||.+.|.. ....++.++.+.       .-|.+.|.+-+. -..+.|.+.+|
T Consensus        60 Dd~~V~L~G~Iv~-~lg~d~Y~F~D~tG~I~VeID~~~w~G~~v~p~-------~kV~I~GevDk~-~~~~~IdV~~i  128 (130)
T PRK10053         60 DGATVSLRGNLID-HKGDDRYVFRDKSGEINVIIPAAVFDGREVQPD-------QMININGSLDKK-SAPPVVRVTHL  128 (130)
T ss_pred             CCCeEEEEEEEEE-EeCCceEEEECCCCcEEEEeCHHHcCCCcCCCC-------CEEEEEEEECCC-CCCeEEEEEEE
Confidence            3456889999999 46788999999999999999 556788899999       999999999873 33457766665

>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=96.93  E-value=0.017  Score=38.33  Aligned_cols=67  Identities=21%  Similarity=0.343  Sum_probs=51.1

Q ss_pred             EEEEEEEEeeeC-CCC--cEEEEcCCeeEEEEe-ccccc-cc-cccCCcccccceeEEEEEeeEeecc-CCCceEEEEEE
Q 044496           37 VWLQGVLVSPPD-DDG--RLLLDDGTGVVQIYL-SGDFR-IR-RWNTGVFFFDFWMYVMVVGGFVIRT-DDIPVIKVHKI  109 (142)
Q Consensus        37 VWlQG~vv~~~~-~~~--~~~LdDgTG~~~v~~-~~~~~-~~-~~~~G~~~~~~~~YVmViG~~~~~~-~~~p~i~a~K~  109 (142)
                      +|+.|.|.+... ..|  .+.|.|+||.+++.. +...+ .+ .+++|       +-|.+.|.+.... +..+.+.+.++
T Consensus         2 ~~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g-------~~v~v~g~v~~~~~~~~~~l~v~~i   74 (78)
T cd04489           2 VWVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNARRLGFPLEEG-------MEVLVRGKVSFYEPRGGYQLIVEEI   74 (78)
T ss_pred             EEEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchhhhCCCCCCCC-------CEEEEEEEEEEECCCCEEEEEEEEE
Confidence            699999999864 333  788999999999986 44333 23 38999       9999999998632 45678888877


Q ss_pred             e
Q 044496          110 V  110 (142)
Q Consensus       110 ~  110 (142)
                      .
T Consensus        75 ~   75 (78)
T cd04489          75 E   75 (78)
T ss_pred             E
Confidence            4

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.

>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=96.90  E-value=0.0075  Score=37.37  Aligned_cols=61  Identities=20%  Similarity=0.207  Sum_probs=45.9

Q ss_pred             EEEEEEeeeCCC-----CcEEEEcCC-eeEEEEe-cccccc--ccccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496           39 LQGVLVSPPDDD-----GRLLLDDGT-GVVQIYL-SGDFRI--RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH  107 (142)
Q Consensus        39 lQG~vv~~~~~~-----~~~~LdDgT-G~~~v~~-~~~~~~--~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~  107 (142)
                      ++|+|+++....     ..+.|+|+| |.+.+.. +.....  ..++.|       +++.+.|.+.. .+..+.+.+.
T Consensus         2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g-------~~v~v~g~v~~-~~~~~~l~~~   71 (75)
T cd03524           2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEG-------QVVYIKGKVKK-FRGRLQLIVE   71 (75)
T ss_pred             eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCC-------CEEEEEEEEEe-cCCeEEEEee
Confidence            689999986544     589999999 9999987 333322  248999       99999999976 4555666655

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

>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=96.86  E-value=0.0097  Score=43.25  Aligned_cols=75  Identities=21%  Similarity=0.225  Sum_probs=47.0

Q ss_pred             eEEEEEEEEEeeeCCCCcEEEEcCC-eeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCC
Q 044496           35 QRVWLQGVLVSPPDDDGRLLLDDGT-GVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLS  113 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~~~LdDgT-G~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS  113 (142)
                      ++|.+-|+|.+.+.+++++++.-+. |.++|.++...   .+..+       .||-|+|.+.. .+....|++...++++
T Consensus        19 k~VrivGkv~~~~~~g~~~~l~~~d~~~V~v~l~~~~---~~~~~-------~~vEviG~V~~-~~~~~~i~~~~~~~~g   87 (109)
T PF08661_consen   19 KTVRIVGKVESVDPDGGSATLSTSDGGQVTVSLNPPS---DEELS-------KYVEVIGKVND-DGTVLSIRYFSFTDFG   87 (109)
T ss_dssp             SEEEEEEEEEEE-TTSSEEEEE-TTS-EEEEEESS-----SS----------SEEEEEEEE-T-TS-EEEEEEEE---SS
T ss_pred             CeEEEEEEEeeEcCCCCEEEEEcCCCCEEEEEeCCCC---CCCCC-------CEEEEEEEEcC-CCCceEEEEEEeccCC
Confidence            3688999999998779999999654 45888876532   34567       99999999965 3333499999999999


Q ss_pred             CCcCccc
Q 044496          114 AFPDREA  120 (142)
Q Consensus       114 ~~p~re~  120 (142)
                      ++-+-+.
T Consensus        88 ~~~D~~~   94 (109)
T PF08661_consen   88 DDFDMDL   94 (109)
T ss_dssp             S---HHH
T ss_pred             CCcCHHH
Confidence            9766543

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

>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=96.82  E-value=0.0089  Score=39.34  Aligned_cols=55  Identities=22%  Similarity=0.240  Sum_probs=44.8

Q ss_pred             cEEEEcCCeeEEEEe-ccccccc-cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCC
Q 044496           52 RLLLDDGTGVVQIYL-SGDFRIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSA  114 (142)
Q Consensus        52 ~~~LdDgTG~~~v~~-~~~~~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~  114 (142)
                      .+.|.|+||.+++.. +..+... .++.|       .+|.+.|.+.. .+..+.+.+.++..|.+
T Consensus        22 ~~~l~D~tg~i~~~~f~~~~~~~~~l~~g-------~~v~v~G~v~~-~~~~~~l~~~~i~~l~~   78 (83)
T cd04492          22 ALTLQDKTGEIEAKLWDASEEDEEKFKPG-------DIVHVKGRVEE-YRGRLQLKIQRIRLVTE   78 (83)
T ss_pred             EEEEEcCCCeEEEEEcCCChhhHhhCCCC-------CEEEEEEEEEE-eCCceeEEEEEEEECCc
Confidence            789999999999987 5444333 59999       99999999976 56678888999988875

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.

>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=96.72  E-value=0.03  Score=47.21  Aligned_cols=114  Identities=21%  Similarity=0.170  Sum_probs=71.5

Q ss_pred             HHHHHHHhhccC-C----------CCCCceeecCeEEeEEEEEEEEEeeeC------CCCcEEEEcCCe--eEEEEecc-
Q 044496            9 KLLCVQLKDARE-S----------PSQNAVTLGGILFQRVWLQGVLVSPPD------DDGRLLLDDGTG--VVQIYLSG-   68 (142)
Q Consensus         9 Kvf~~QL~~a~~-~----------~s~~~~~l~gl~~~~VWlQG~vv~~~~------~~~~~~LdDgTG--~~~v~~~~-   68 (142)
                      .+|++-|..+-+ +          ..++.+..++-.++.|-+.|+|++...      +.-.+.|||+||  .+.+..+. 
T Consensus        30 PlfI~DI~~~~~~Sr~~~~~y~~~~~~~~~f~~NhPI~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~~~~~  109 (256)
T PF10451_consen   30 PLFISDIHKRLKQSRKVCENYYAPQQQNIYFYNNHPIRWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECKCSKS  109 (256)
T ss_dssp             E--HHHHCT----C--THHHHGGGG-TT-EEETTEEE-EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEEEEHH
T ss_pred             cEEHHHhhhhcccccchhhhhhhhccCCEEEECCcccEEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEEEEcc
Confidence            677777776322 1          234567788999999999999999963      334789999999  77776522 


Q ss_pred             -cccc---ccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHH
Q 044496           69 -DFRI---RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLF  133 (142)
Q Consensus        69 -~~~~---~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~  133 (142)
                       ....   -.-..|       +-|-|-|.+.   .+...+.+.+|.-+. +.+.|--.=-|..+.-+.+
T Consensus       110 ~~~~~~l~~~~~~G-------~~V~VkG~vs---r~~~ql~ve~i~~~~-~l~~Ei~fW~~~~~~R~~L  167 (256)
T PF10451_consen  110 SYLSMGLPINDLIG-------KVVEVKGTVS---RNERQLDVERIELVR-DLNAEIEFWKERMRFRKEL  167 (256)
T ss_dssp             HHHCCCHHCTT-TT--------EEEEEEEEE---SSSEEEEEEEEEEET-SCCHHHHHHHHHHHHHHHC
T ss_pred             cccccCCCccCCCC-------cEEEEEEEEc---cCcEEEEEEEEEccC-ChHHHHHHHHHHHHHHHHc
Confidence             1111   122389       9999999996   567778888887554 4666655555666654443

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.

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

Probab=96.57  E-value=0.016  Score=44.90  Aligned_cols=66  Identities=20%  Similarity=0.202  Sum_probs=54.3

Q ss_pred             eEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496           35 QRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI  109 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~  109 (142)
                      ..|-|+|.+++ .-+++++...|+||.+.|.. +....++.++|-       .-|.+-|.+-+ .-..|.|.+-.+
T Consensus        58 a~V~l~GnIv~-qi~~D~y~FrD~sGeI~VeIdd~~w~g~tv~P~-------dkV~I~GevDk-~~~~~eIdV~~I  124 (128)
T COG3111          58 AWVSLEGNIVR-QIGDDRYVFRDASGEINVDIDDKVWNGQTVTPK-------DKVRIQGEVDK-DWNSVEIDVKHI  124 (128)
T ss_pred             CeEEEEeeEEE-eeCCceEEEEcCCccEEEEecccccCCcccCcc-------cEEEEEeEEcC-CCccceeEhhhe
Confidence            46779999999 57899999999999999998 667788889999       99999999977 344566655444

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

Probab=96.29  E-value=0.076  Score=38.43  Aligned_cols=67  Identities=22%  Similarity=0.220  Sum_probs=52.7

Q ss_pred             eEEEEEEEEEeeeCCCCcEEEEcCCe-eEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCC
Q 044496           35 QRVWLQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLS  113 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS  113 (142)
                      ++|.+-|+|.+.+  ++.+.+.++-| .++|.++...   ....|       .||-|+|.+..    .-.|++.-.+|+.
T Consensus        16 k~V~ivGkV~~~~--~~~~~~~~~Dg~~v~v~l~~~~---~~~~~-------~~vEViG~V~~----~~~I~~~~~~~~g   79 (101)
T cd04479          16 KTVRIVGKVEKVD--GDSLTLISSDGVNVTVELNRPL---DLPIS-------GYVEVIGKVSP----DLTIRVLSYIDFG   79 (101)
T ss_pred             CEEEEEEEEEEec--CCeEEEEcCCCCEEEEEeCCCC---CcccC-------CEEEEEEEECC----CCeEEEEEEEECC
Confidence            5799999999984  34788888777 7888876533   46778       99999998854    4789999999999


Q ss_pred             CCcC
Q 044496          114 AFPD  117 (142)
Q Consensus       114 ~~p~  117 (142)
                      ++=+
T Consensus        80 ~~~D   83 (101)
T cd04479          80 DDFD   83 (101)
T ss_pred             CccC
Confidence            8633

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.

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

Probab=96.12  E-value=0.11  Score=35.51  Aligned_cols=68  Identities=26%  Similarity=0.312  Sum_probs=47.6

Q ss_pred             EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccc-----c-cccccCCcccccceeEEEEEeeEeecc-----CCCce
Q 044496           37 VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDF-----R-IRRWNTGVFFFDFWMYVMVVGGFVIRT-----DDIPV  103 (142)
Q Consensus        37 VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~-----~-~~~~~~G~~~~~~~~YVmViG~~~~~~-----~~~p~  103 (142)
                      |+++|.|.++..-+.  =+.|.|+||.+++..+...     + ...++.|       ++|.|-|.+..+.     .....
T Consensus         2 V~i~Gwv~~~R~~g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~-------s~V~v~G~~~~~~~~~~~~~~~E   74 (85)
T cd04100           2 VTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTE-------SVVGVTGTVVKRPEGNLATGEIE   74 (85)
T ss_pred             EEEEEEEehhccCCCEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCC-------CEEEEEeEEEECCCCCCCCCCEE
Confidence            789999999854333  3678999999999873321     1 2358999       9999999998732     33456


Q ss_pred             EEEEEEee
Q 044496          104 IKVHKIVD  111 (142)
Q Consensus       104 i~a~K~~D  111 (142)
                      |.+.++.=
T Consensus        75 l~~~~i~i   82 (85)
T cd04100          75 LQAEELEV   82 (85)
T ss_pred             EEEeEEEE
Confidence            66665543

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

>PRK05159 aspC aspartyl-tRNA synthetase; Provisional

Probab=95.82  E-value=0.077  Score=47.08  Aligned_cols=74  Identities=23%  Similarity=0.281  Sum_probs=55.0

Q ss_pred             eEEEEEEEEEeeeCCCCc--EEEEcCCeeEEEEeccc-----c-ccccccCCcccccceeEEEEEeeEeeccC--CCceE
Q 044496           35 QRVWLQGVLVSPPDDDGR--LLLDDGTGVVQIYLSGD-----F-RIRRWNTGVFFFDFWMYVMVVGGFVIRTD--DIPVI  104 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~--~~LdDgTG~~~v~~~~~-----~-~~~~~~~G~~~~~~~~YVmViG~~~~~~~--~~p~i  104 (142)
                      +.|++.|+|.++..-++.  +.|.|++|.+++..+..     . ....++.|       ..|.|.|.+..+..  .+..|
T Consensus        17 ~~V~i~GrV~~~R~~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~g-------s~V~v~G~v~~~~~~~~~~el   89 (437)
T PRK05159         17 EEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRE-------SVVSVTGTVKANPKAPGGVEV   89 (437)
T ss_pred             CEEEEEEEeEeeecCCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCC-------cEEEEEEEEEcCCCCCCCEEE
Confidence            458899999999654432  67999999999987432     1 12358999       99999999987322  45678


Q ss_pred             EEEEEeeCCCC
Q 044496          105 KVHKIVDLSAF  115 (142)
Q Consensus       105 ~a~K~~DLS~~  115 (142)
                      ++.++.=||.+
T Consensus        90 ~~~~i~vls~a  100 (437)
T PRK05159         90 IPEEIEVLNKA  100 (437)
T ss_pred             EEeEEEEEeCC
Confidence            88888777764

>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=95.77  E-value=0.18  Score=36.17  Aligned_cols=74  Identities=22%  Similarity=0.210  Sum_probs=52.5

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--c-----ccccccCCcccccceeEEEEEeeEeeccC--CCce
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--F-----RIRRWNTGVFFFDFWMYVMVVGGFVIRTD--DIPV  103 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~-----~~~~~~~G~~~~~~~~YVmViG~~~~~~~--~~p~  103 (142)
                      +.|++.|.|.++..-++  =+.|+|+||.+++..+..  .     ..+.+..|       ..|-|.|.+..+..  ....
T Consensus        13 ~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~~E   85 (108)
T cd04316          13 EEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRE-------SVISVTGTVKAEPKAPNGVE   85 (108)
T ss_pred             CEEEEEEEEEeeeccCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCc-------CEEEEEEEEEeCCCCCCCEE
Confidence            45899999999864433  467899999999887432  1     11358899       99999999877322  1356


Q ss_pred             EEEEEEeeCCCC
Q 044496          104 IKVHKIVDLSAF  115 (142)
Q Consensus       104 i~a~K~~DLS~~  115 (142)
                      |.+.++.=||..
T Consensus        86 i~~~~i~il~~~   97 (108)
T cd04316          86 IIPEEIEVLSEA   97 (108)
T ss_pred             EEEeEEEEEeCC
Confidence            777777777764

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.

>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=95.71  E-value=0.3  Score=33.39  Aligned_cols=71  Identities=23%  Similarity=0.195  Sum_probs=47.9

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccc-----ccccccCCcccccceeEEEEEeeEeecc-----CCCce
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDF-----RIRRWNTGVFFFDFWMYVMVVGGFVIRT-----DDIPV  103 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~-----~~~~~~~G~~~~~~~~YVmViG~~~~~~-----~~~p~  103 (142)
                      .|++.|.|-++..-++  =+.|.|+||.+++..+...     ....+..|       ..|.|-|.+..+.     .....
T Consensus         1 ~V~v~Gwv~~~R~~g~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~~~~~E   73 (84)
T cd04323           1 RVKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQE-------SSVEVTGEVKEDPRAKQAPGGYE   73 (84)
T ss_pred             CEEEEEEEEEEecCCCcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCc-------CEEEEEEEEEECCcccCCCCCEE
Confidence            3789999999864432  4568999999998774321     12358889       9999999997721     11235


Q ss_pred             EEEEEEeeCC
Q 044496          104 IKVHKIVDLS  113 (142)
Q Consensus       104 i~a~K~~DLS  113 (142)
                      |.+.++.=||
T Consensus        74 i~~~~i~vl~   83 (84)
T cd04323          74 LQVDYLEIIG   83 (84)
T ss_pred             EEEEEEEEEc
Confidence            6666655443

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

>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=95.64  E-value=0.16  Score=37.69  Aligned_cols=73  Identities=21%  Similarity=0.235  Sum_probs=53.5

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc----c-ccccccCCcccccceeEEEEEeeEeecc---------C
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD----F-RIRRWNTGVFFFDFWMYVMVVGGFVIRT---------D   99 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~----~-~~~~~~~G~~~~~~~~YVmViG~~~~~~---------~   99 (142)
                      .|.+.|.|.++..-++  =+.|.||||.+++..+..    . ..+.+..|       .+|.|-|.+..+.         .
T Consensus        16 ~V~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~g-------s~V~V~G~~~~~~~~~~~~~~~~   88 (135)
T cd04317          16 EVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNE-------SVIQVTGKVRARPEGTVNPKLPT   88 (135)
T ss_pred             EEEEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCc-------cEEEEEEEEECCCccccCCCCCC
Confidence            4889999999854333  456899999999887432    1 12358899       9999999988632         2


Q ss_pred             CCceEEEEEEeeCCCC
Q 044496          100 DIPVIKVHKIVDLSAF  115 (142)
Q Consensus       100 ~~p~i~a~K~~DLS~~  115 (142)
                      .+..|.+.++.-||.+
T Consensus        89 ~~~El~~~~i~vl~~~  104 (135)
T cd04317          89 GEIEVVASELEVLNKA  104 (135)
T ss_pred             CcEEEEEeEEEEEECC
Confidence            2468888888888865

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

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

Probab=95.63  E-value=0.18  Score=36.11  Aligned_cols=72  Identities=22%  Similarity=0.230  Sum_probs=52.4

Q ss_pred             EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc---cc----ccc-ccCCcccccceeEEEEEeeEeeccCCCceEEE
Q 044496           37 VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD---FR----IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKV  106 (142)
Q Consensus        37 VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~---~~----~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a  106 (142)
                      |++.|.|-++..-++  =+.|.||||.+++..+..   +.    -.. ++.|       +.|.|.|.+..+...+-.|.+
T Consensus         2 v~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g-------~~V~v~G~v~~~~~g~~El~~   74 (108)
T cd04322           2 VSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLG-------DIIGVTGTPFKTKTGELSIFV   74 (108)
T ss_pred             EEEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCC-------CEEEEEEEEEecCCCCEEEEe
Confidence            789999999864433  356899999999876321   11    124 8899       999999999875555667777


Q ss_pred             EEEeeCCCC
Q 044496          107 HKIVDLSAF  115 (142)
Q Consensus       107 ~K~~DLS~~  115 (142)
                      .++.=||.+
T Consensus        75 ~~~~ils~~   83 (108)
T cd04322          75 KEFTLLSKS   83 (108)
T ss_pred             CEeEEeecc
Confidence            777666663

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

>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=95.34  E-value=0.038  Score=35.68  Aligned_cols=55  Identities=20%  Similarity=0.294  Sum_probs=41.7

Q ss_pred             CcEEEEcCCeeEEEEe-cccc-ccc-cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCC
Q 044496           51 GRLLLDDGTGVVQIYL-SGDF-RIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLS  113 (142)
Q Consensus        51 ~~~~LdDgTG~~~v~~-~~~~-~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS  113 (142)
                      -.+.|.|+||.+.+.. +... +.+ .+++|       .+|.+.|.+.. .+..+.+.+.++.+|.
T Consensus        21 ~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g-------~~v~v~G~v~~-~~~~~~l~~~~i~~~~   78 (84)
T cd04485          21 AFVTLEDLTGSIEVVVFPETYEKYRDLLKED-------ALLLVEGKVER-RDGGLRLIAERIEDLE   78 (84)
T ss_pred             EEEEEEeCCCeEEEEECHHHHHHHHHHhcCC-------CEEEEEEEEEe-cCCceEEEeeccccHH
Confidence            4789999999999987 4332 233 48999       99999999976 5566788877776553

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.

>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=95.29  E-value=0.34  Score=34.22  Aligned_cols=72  Identities=15%  Similarity=0.086  Sum_probs=51.1

Q ss_pred             EEEEEEEEeeeCCC-C--cEEEEcCCeeEEEEeccc----ccc-----ccccCCcccccceeEEEEEeeEeeccC-----
Q 044496           37 VWLQGVLVSPPDDD-G--RLLLDDGTGVVQIYLSGD----FRI-----RRWNTGVFFFDFWMYVMVVGGFVIRTD-----   99 (142)
Q Consensus        37 VWlQG~vv~~~~~~-~--~~~LdDgTG~~~v~~~~~----~~~-----~~~~~G~~~~~~~~YVmViG~~~~~~~-----   99 (142)
                      |.+.|.|.++..-+ +  =+.|.|+||.+++..+..    ...     +.+..|       ..|.|.|.+..+..     
T Consensus         2 V~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~~   74 (102)
T cd04320           2 VLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKE-------SIVDVEGTVKKPEEPIKSC   74 (102)
T ss_pred             EEEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCc-------cEEEEEEEEECCCCcccCC
Confidence            77999999986433 2  567999999999988422    111     247899       99999999976311     


Q ss_pred             --CCceEEEEEEeeCCCC
Q 044496          100 --DIPVIKVHKIVDLSAF  115 (142)
Q Consensus       100 --~~p~i~a~K~~DLS~~  115 (142)
                        .+-.|.+.++.=||.+
T Consensus        75 ~~~~~El~~~~i~il~~~   92 (102)
T cd04320          75 TQQDVELHIEKIYVVSEA   92 (102)
T ss_pred             CcCcEEEEEEEEEEEecC
Confidence              3457777777666654

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.

>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=94.96  E-value=0.41  Score=34.00  Aligned_cols=65  Identities=22%  Similarity=0.301  Sum_probs=45.5

Q ss_pred             EEEEEEEEeeeC--CC--CcEEEEcCCeeEEEEe-ccc--c-cc-ccccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496           37 VWLQGVLVSPPD--DD--GRLLLDDGTGVVQIYL-SGD--F-RI-RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH  107 (142)
Q Consensus        37 VWlQG~vv~~~~--~~--~~~~LdDgTG~~~v~~-~~~--~-~~-~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~  107 (142)
                      .|+.|.|.+...  ..  -.|.|.|+++.+.+.. ...  . +. ..+++|       +-|.|.|.+.. ..   .|.+-
T Consensus         1 ~~v~GeVs~~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~G-------d~V~v~G~v~~-y~---ql~ve   69 (91)
T cd04482           1 YRVTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPG-------DEVTVYGSVRP-GT---TLNLE   69 (91)
T ss_pred             CEEEEEEeCCeecCCCCCEEEEEECCCcEEEEEEECcccccccccCCCCCC-------CEEEEEEEEec-CC---EEEEE
Confidence            489999998743  33  4788999999988864 322  2 22 249999       99999999977 33   45555


Q ss_pred             EEeeC
Q 044496          108 KIVDL  112 (142)
Q Consensus       108 K~~DL  112 (142)
                      +|.-+
T Consensus        70 ~l~~~   74 (91)
T cd04482          70 KLRVI   74 (91)
T ss_pred             EEEEC
Confidence            54433

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

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

Probab=94.90  E-value=0.17  Score=41.96  Aligned_cols=80  Identities=25%  Similarity=0.311  Sum_probs=59.5

Q ss_pred             CeEEeEEEEEEEEEeeeCC--CC--cEEEEcCCeeEEEEecccc-------cccc-ccCCcccccceeEEEEEeeEeecc
Q 044496           31 GILFQRVWLQGVLVSPPDD--DG--RLLLDDGTGVVQIYLSGDF-------RIRR-WNTGVFFFDFWMYVMVVGGFVIRT   98 (142)
Q Consensus        31 gl~~~~VWlQG~vv~~~~~--~~--~~~LdDgTG~~~v~~~~~~-------~~~~-~~~G~~~~~~~~YVmViG~~~~~~   98 (142)
                      |....-|-+.|.|++....  .|  ++.|+||||++++..+.-+       +.++ ..+|       +||-|.|.+.- .
T Consensus        48 G~l~e~v~vkg~V~~~~n~~~~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~~eG-------e~veVtGrv~~-y  119 (204)
T COG4085          48 GRLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRSTEETLELNEGMPVTVEG-------EIVEVTGRVEE-Y  119 (204)
T ss_pred             ceeeccceeeeEEEeeecccccceEEEEEECCCCcEEEEEecChhHhHhhcCCCCccccC-------cEEEEEEEEEE-e
Confidence            6666668889999998633  22  8999999999997763222       2234 7899       99999998866 7


Q ss_pred             CCCceEEEEEEeeCCCCcCc
Q 044496           99 DDIPVIKVHKIVDLSAFPDR  118 (142)
Q Consensus        99 ~~~p~i~a~K~~DLS~~p~r  118 (142)
                      ...+-++.-...|+-..|.+
T Consensus       120 rG~~eVkvnq~~d~~~l~k~  139 (204)
T COG4085         120 RGSSEVKVNQPNDSRPLPKH  139 (204)
T ss_pred             CCCceeeccCcccccccccc
Confidence            77777777777777766655

>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=94.84  E-value=0.77  Score=31.08  Aligned_cols=69  Identities=25%  Similarity=0.315  Sum_probs=47.5

Q ss_pred             EEEEEEEEeeeCCCC-c-EEEEcCCee--EEEEeccccc----cccccCCcccccceeEEEEEeeEeeccC--CCceEEE
Q 044496           37 VWLQGVLVSPPDDDG-R-LLLDDGTGV--VQIYLSGDFR----IRRWNTGVFFFDFWMYVMVVGGFVIRTD--DIPVIKV  106 (142)
Q Consensus        37 VWlQG~vv~~~~~~~-~-~~LdDgTG~--~~v~~~~~~~----~~~~~~G~~~~~~~~YVmViG~~~~~~~--~~p~i~a  106 (142)
                      |++.|.|.++...++ . +.|.||||.  +++..+....    ...++.|       ..|.|-|.+..+..  ....|.+
T Consensus         2 v~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~g-------s~V~v~G~v~~~~~~~~~~El~~   74 (82)
T cd04318           2 VTVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTG-------SSIRVEGVLVKSPGAKQPFELQA   74 (82)
T ss_pred             EEEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCc-------eEEEEEEEEEeCCCCCCCEEEEE
Confidence            689999999865433 3 456699995  8887743221    2358899       99999999987433  3456766


Q ss_pred             EEEeeC
Q 044496          107 HKIVDL  112 (142)
Q Consensus       107 ~K~~DL  112 (142)
                      .++.=|
T Consensus        75 ~~i~il   80 (82)
T cd04318          75 EKIEVL   80 (82)
T ss_pred             EEEEEe
Confidence            666443

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

>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=94.69  E-value=0.29  Score=30.99  Aligned_cols=51  Identities=24%  Similarity=0.261  Sum_probs=37.7

Q ss_pred             EEEEEEeeeCC------CCcEEEEcCCeeEEEEe-ccccc-cccccCCcccccceeEEEEEeeEee
Q 044496           39 LQGVLVSPPDD------DGRLLLDDGTGVVQIYL-SGDFR-IRRWNTGVFFFDFWMYVMVVGGFVI   96 (142)
Q Consensus        39 lQG~vv~~~~~------~~~~~LdDgTG~~~v~~-~~~~~-~~~~~~G~~~~~~~~YVmViG~~~~   96 (142)
                      ++|+|.++...      --++.+.|+||.+++.. +..+. .+.+++|       +.+.+.|.+..
T Consensus         2 i~~~V~~~~~~~~~~~~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G-------~~~~v~Gkv~~   60 (75)
T cd04488           2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPG-------TRVRVSGKVKR   60 (75)
T ss_pred             EEEEEEEEEeccCCCccEEEEEEEcCCCEEEEEEECCCHHHHhcCCCC-------CEEEEEEEEee
Confidence            57888776322      12789999999999986 53332 3359999       99999999976

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

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

Probab=94.54  E-value=0.32  Score=44.23  Aligned_cols=73  Identities=18%  Similarity=0.189  Sum_probs=56.0

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--cc-----ccc-ccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--FR-----IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~~-----~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      .|.+.|+|.++...++  =+.|.|+||.+++..+..  ..     ... +..|       +.|.|.|.+......+..|.
T Consensus        55 ~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~g-------d~V~v~G~~~~t~~gelel~  127 (496)
T TIGR00499        55 EVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLG-------DIIGVTGYPFKTKTGELSVH  127 (496)
T ss_pred             EEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCC-------CEEEEEEEEEECCCCcEEEE
Confidence            4889999999974433  457899999999987321  11     122 6889       99999999988556678999


Q ss_pred             EEEEeeCCCC
Q 044496          106 VHKIVDLSAF  115 (142)
Q Consensus       106 a~K~~DLS~~  115 (142)
                      |.++.=||.+
T Consensus       128 ~~~i~ilsk~  137 (496)
T TIGR00499       128 VTELQILTKA  137 (496)
T ss_pred             eeEEEEEecC
Confidence            9999888885

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.

>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain

Probab=94.35  E-value=0.31  Score=34.95  Aligned_cols=61  Identities=21%  Similarity=0.322  Sum_probs=47.0

Q ss_pred             eEEeEEEEEEEEEeeeC-CCC--cEEEEcCCeeEEEEe--cccccc--ccccCCcccccceeEEEEEeeEeeccCC
Q 044496           32 ILFQRVWLQGVLVSPPD-DDG--RLLLDDGTGVVQIYL--SGDFRI--RRWNTGVFFFDFWMYVMVVGGFVIRTDD  100 (142)
Q Consensus        32 l~~~~VWlQG~vv~~~~-~~~--~~~LdDgTG~~~v~~--~~~~~~--~~~~~G~~~~~~~~YVmViG~~~~~~~~  100 (142)
                      ..+.++|++|-|.+... ..|  -|.|-|+...+.+..  +...+.  ..++.|       |=|.|.|.+.- ..+
T Consensus        19 ~~~~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G-------~~V~v~g~~~~-y~~   86 (99)
T PF13742_consen   19 PPLPNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDG-------DKVLVRGRVSF-YEP   86 (99)
T ss_pred             CCcCCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCC-------CEEEEEEEEEE-ECC
Confidence            45789999999999976 344  789999988888876  333333  369999       99999999876 444

>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type

Probab=94.21  E-value=0.46  Score=42.24  Aligned_cols=74  Identities=26%  Similarity=0.206  Sum_probs=54.1

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--cc-----cccccCCcccccceeEEEEEeeEeecc--CCCce
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPV  103 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~  103 (142)
                      +.|.+.|.|.++..-++  =+.|.|+||.+++..+..  .+     ...++.|       ..|.|.|.+..+.  ..+..
T Consensus        13 ~~v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~-------s~v~v~G~v~~~~~~~~~~e   85 (428)
T TIGR00458        13 QEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLE-------SVVAVRGIVKIKEKAPGGFE   85 (428)
T ss_pred             CEEEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCC-------cEEEEEEEEEecCCCCCcEE
Confidence            45889999999965444  367899999999887321  11     1248899       9999999998632  25678


Q ss_pred             EEEEEEeeCCCC
Q 044496          104 IKVHKIVDLSAF  115 (142)
Q Consensus       104 i~a~K~~DLS~~  115 (142)
                      |.+.++.=||.+
T Consensus        86 l~~~~i~vl~~~   97 (428)
T TIGR00458        86 IIPTKIEVINEA   97 (428)
T ss_pred             EEEeEEEEEecC
Confidence            888777766664

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).

>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=94.17  E-value=1.1  Score=30.93  Aligned_cols=69  Identities=22%  Similarity=0.223  Sum_probs=46.6

Q ss_pred             EEEEEEEEeeeC-CCC--cEEEEcCCe-eEEEEecccc---c-cccccCCcccccceeEEEEEeeEeeccC------CCc
Q 044496           37 VWLQGVLVSPPD-DDG--RLLLDDGTG-VVQIYLSGDF---R-IRRWNTGVFFFDFWMYVMVVGGFVIRTD------DIP  102 (142)
Q Consensus        37 VWlQG~vv~~~~-~~~--~~~LdDgTG-~~~v~~~~~~---~-~~~~~~G~~~~~~~~YVmViG~~~~~~~------~~p  102 (142)
                      |.+.|.|.++.. ..+  =+.|.|||| .+++..+...   . ...+..|       .-|.|-|.+..+..      ...
T Consensus         2 V~v~Gwv~~~R~~~~~~~Fi~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~-------s~V~V~G~v~~~~~~~~~~~~~~   74 (86)
T cd04321           2 VTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLVSTAKKDAFSLLKSITAE-------SPVQVRGKLQLKEAKSSEKNDEW   74 (86)
T ss_pred             EEEEEeEeeEeCCCCceEEEEEECCCCCEEEEEECCCHHHHHHHhcCCCC-------cEEEEEEEEEeCCCcCCCCCCCE
Confidence            678999999865 222  367899999 6888764321   1 1247889       99999999987321      345


Q ss_pred             eEEEEEEeeC
Q 044496          103 VIKVHKIVDL  112 (142)
Q Consensus       103 ~i~a~K~~DL  112 (142)
                      .|.+.++.=|
T Consensus        75 Ei~~~~i~il   84 (86)
T cd04321          75 ELVVDDIQTL   84 (86)
T ss_pred             EEEEEEEEEe
Confidence            6666665433

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

>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=93.44  E-value=1.6  Score=30.90  Aligned_cols=71  Identities=23%  Similarity=0.228  Sum_probs=48.2

Q ss_pred             EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc-c----c-cccccCCcccccceeEEEEEeeEeecc--CCCceEEE
Q 044496           37 VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD-F----R-IRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPVIKV  106 (142)
Q Consensus        37 VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~-~----~-~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~i~a  106 (142)
                      |.+.|.|.++..-++  =+.|.||||.+++..+.. .    . ...+..|       ..|.|-|.+..+.  ...-.|.+
T Consensus         2 V~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~-------s~v~V~G~v~~~~~~~~~~Ei~~   74 (103)
T cd04319           2 VTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIE-------SSVIVEGAVKADPRAPGGAEVHG   74 (103)
T ss_pred             EEEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCC-------CEEEEEEEEEECCCCCCCEEEEE
Confidence            789999999864332  467899999999887432 1    1 1247889       9999999987621  11235666


Q ss_pred             EEEeeCCC
Q 044496          107 HKIVDLSA  114 (142)
Q Consensus       107 ~K~~DLS~  114 (142)
                      .++.=||.
T Consensus        75 ~~i~vl~~   82 (103)
T cd04319          75 EKLEIIQN   82 (103)
T ss_pred             EEEEEEec
Confidence            66655554

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.

>TIGR00457 asnS asparaginyl-tRNA synthetase

Probab=93.32  E-value=0.66  Score=41.67  Aligned_cols=74  Identities=24%  Similarity=0.311  Sum_probs=53.0

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCC--eeEEEEeccc-c-----ccccccCCcccccceeEEEEEeeEeec--cCCCc
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGT--GVVQIYLSGD-F-----RIRRWNTGVFFFDFWMYVMVVGGFVIR--TDDIP  102 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgT--G~~~v~~~~~-~-----~~~~~~~G~~~~~~~~YVmViG~~~~~--~~~~p  102 (142)
                      +.|.+.|.|.++...++  =+.|.|||  |.+++..+.. .     ....++.|       +.|.|.|.+..+  ....-
T Consensus        17 ~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~g-------s~V~v~G~v~~~~~~~~~~   89 (453)
T TIGR00457        17 DEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTG-------SSVSVTGKVVESPGKGQPV   89 (453)
T ss_pred             CEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCC-------cEEEEEEEEEcCCCCCCCE
Confidence            45889999999974333  36789999  9999987432 1     11248999       999999999863  23456


Q ss_pred             eEEEEEEeeCCCC
Q 044496          103 VIKVHKIVDLSAF  115 (142)
Q Consensus       103 ~i~a~K~~DLS~~  115 (142)
                      .|.+.++.=||.+
T Consensus        90 El~~~~i~vl~~~  102 (453)
T TIGR00457        90 ELQVKKIEVVGEA  102 (453)
T ss_pred             EEEEeEEEEEecC
Confidence            6777777666654

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.

>PLN02850 aspartate-tRNA ligase

Probab=93.30  E-value=0.73  Score=42.43  Aligned_cols=74  Identities=20%  Similarity=0.100  Sum_probs=54.6

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecc----cccc-----ccccCCcccccceeEEEEEeeEee------c
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSG----DFRI-----RRWNTGVFFFDFWMYVMVVGGFVI------R   97 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~----~~~~-----~~~~~G~~~~~~~~YVmViG~~~~------~   97 (142)
                      +.||+.|+|.++..-+.  =+.|.|++|.+++..+.    ..+.     ..++.|       ..|-|.|.++.      .
T Consensus        82 ~~V~v~Grv~~~R~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~  154 (530)
T PLN02850         82 SEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRE-------SVVDVEGVVSVPKKPVKG  154 (530)
T ss_pred             CEEEEEEEEEEEccCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCC-------CEEEEEEEEEccCcCCCC
Confidence            67999999999864443  36789999999988732    1222     248999       99999999984      2


Q ss_pred             cCCCceEEEEEEeeCCCC
Q 044496           98 TDDIPVIKVHKIVDLSAF  115 (142)
Q Consensus        98 ~~~~p~i~a~K~~DLS~~  115 (142)
                      +..+-.|.+.++.=||.+
T Consensus       155 ~t~~~El~~~~i~vls~a  172 (530)
T PLN02850        155 TTQQVEIQVRKIYCVSKA  172 (530)
T ss_pred             CCccEEEEEeEEEEEeCC
Confidence            344567888888777664

>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=93.29  E-value=1.4  Score=30.25  Aligned_cols=53  Identities=26%  Similarity=0.280  Sum_probs=39.5

Q ss_pred             EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEe-cc-cccc-ccccCCcccccceeEEEEEeeEee
Q 044496           37 VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYL-SG-DFRI-RRWNTGVFFFDFWMYVMVVGGFVI   96 (142)
Q Consensus        37 VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~-~~-~~~~-~~~~~G~~~~~~~~YVmViG~~~~   96 (142)
                      ||+.|.|.+.....|  -|.|.|+++.+++.. .+ ..+. ..+++|       |=|.+.|.+..
T Consensus         1 v~v~GeVs~~~~~~GHvyfsLkD~~a~i~cv~f~~~~~~~~~~l~~G-------d~V~v~G~v~~   58 (73)
T cd04487           1 VHIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAGVRAYPEVEVG-------DIVRVTGEVEP   58 (73)
T ss_pred             CEEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhccCCcCCCCCC-------CEEEEEEEEec
Confidence            699999997643443  788999999988864 22 2222 248999       99999999864

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.

>PLN02502 lysyl-tRNA synthetase

Probab=92.92  E-value=1  Score=41.89  Aligned_cols=74  Identities=19%  Similarity=0.121  Sum_probs=56.9

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--------cc-c-ccccCCcccccceeEEEEEeeEeeccCCCc
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--------FR-I-RRWNTGVFFFDFWMYVMVVGGFVIRTDDIP  102 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--------~~-~-~~~~~G~~~~~~~~YVmViG~~~~~~~~~p  102 (142)
                      +.|.+.|+|.++..-++  =+.|.|+||.+++..+..        +. . ..+..|       +.|.|.|.+..+...+-
T Consensus       109 ~~V~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~g-------diV~V~G~~~~t~~gel  181 (553)
T PLN02502        109 VSVSVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRG-------DIVGVTGTPGKTKKGEL  181 (553)
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCC-------cEEEEEEEEEecCCCCE
Confidence            45889999999965443  457899999999876321        11 1 137889       99999999988666688


Q ss_pred             eEEEEEEeeCCCC
Q 044496          103 VIKVHKIVDLSAF  115 (142)
Q Consensus       103 ~i~a~K~~DLS~~  115 (142)
                      .|.|.++.=||.+
T Consensus       182 el~~~~i~vLs~~  194 (553)
T PLN02502        182 SIFPTSFEVLTKC  194 (553)
T ss_pred             EEEEeEEEEEecc
Confidence            9999999888885

>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=92.86  E-value=0.84  Score=30.86  Aligned_cols=48  Identities=19%  Similarity=0.210  Sum_probs=34.6

Q ss_pred             cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496           52 RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH  107 (142)
Q Consensus        52 ~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~  107 (142)
                      ++.|-|.||.+++.+ +... ...+++|       +.|.+.|.........+.|...
T Consensus        26 ~~~l~D~TG~i~~~~W~~~~-~~~~~~G-------~vv~i~~~~v~~~~g~~ql~i~   74 (82)
T cd04491          26 SGLVGDETGTIRFTLWDEKA-ADDLEPG-------DVVRIENAYVREFNGRLELSVG   74 (82)
T ss_pred             EEEEECCCCEEEEEEECchh-cccCCCC-------CEEEEEeEEEEecCCcEEEEeC
Confidence            789999999999998 3322 4459999       9999994444436666666543

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

>PRK12445 lysyl-tRNA synthetase; Reviewed

Probab=92.80  E-value=1.1  Score=41.09  Aligned_cols=73  Identities=16%  Similarity=0.205  Sum_probs=55.4

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecc--cc----c-c-ccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSG--DF----R-I-RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~--~~----~-~-~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      .|.+.|+|.++..-++  =+.|.|+||.+++..+.  ..    . . ..+..|       +.|.|.|.+......+..|.
T Consensus        67 ~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~G-------d~V~v~G~~~~t~~gelel~  139 (505)
T PRK12445         67 EVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLG-------DIIGARGTLFKTQTGELSIH  139 (505)
T ss_pred             EEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCC-------CEEEEEEEEEecCCCcEEEE
Confidence            4889999999964433  45689999999988732  11    1 1 248899       99999999987556688898


Q ss_pred             EEEEeeCCCC
Q 044496          106 VHKIVDLSAF  115 (142)
Q Consensus       106 a~K~~DLS~~  115 (142)
                      |.++.=||.+
T Consensus       140 ~~~~~llsk~  149 (505)
T PRK12445        140 CTELRLLTKA  149 (505)
T ss_pred             EeEEEEEecC
Confidence            8888877774

>PRK00484 lysS lysyl-tRNA synthetase; Reviewed

Probab=92.37  E-value=1.3  Score=40.35  Aligned_cols=74  Identities=20%  Similarity=0.236  Sum_probs=55.4

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--cc-----cccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      ..|.+.|+|.++..-++  =+.|.|+||.+++..+..  ..     -+.++.|       +.|-|.|.+..+...+..|.
T Consensus        55 ~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g-------~~v~v~G~v~~t~~ge~el~  127 (491)
T PRK00484         55 IEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLG-------DIIGVEGTLFKTKTGELSVK  127 (491)
T ss_pred             cEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCC-------CEEEEEEEEEEcCCCcEEEE
Confidence            56899999999964433  367899999999987432  11     1238899       99999999988655678888


Q ss_pred             EEEEeeCCCC
Q 044496          106 VHKIVDLSAF  115 (142)
Q Consensus       106 a~K~~DLS~~  115 (142)
                      |.++.=||.+
T Consensus       128 ~~~~~vls~~  137 (491)
T PRK00484        128 ATELTLLTKS  137 (491)
T ss_pred             EeEEEEEecc
Confidence            8887777664

>PRK03932 asnC asparaginyl-tRNA synthetase; Validated

Probab=91.92  E-value=1.6  Score=39.06  Aligned_cols=73  Identities=26%  Similarity=0.331  Sum_probs=54.0

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEe--ccc---cc-cccccCCcccccceeEEEEEeeEeecc--CCCceE
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYL--SGD---FR-IRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPVI  104 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~--~~~---~~-~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~i  104 (142)
                      +.|.+.|.|.++..-++  =+.|.|+||.+++..  +..   .+ .+.++.|       ..|.|-|.+..+.  ..+..|
T Consensus        17 ~~V~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~-------s~v~v~G~v~~~~~~~~~~el   89 (450)
T PRK03932         17 QEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTG-------SSVIVTGTVVESPRAGQGYEL   89 (450)
T ss_pred             CEEEEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCC-------cEEEEEEEEEcCCCCCCCEEE
Confidence            56889999999964432  367899999988876  221   11 1248999       9999999998732  246789


Q ss_pred             EEEEEeeCCC
Q 044496          105 KVHKIVDLSA  114 (142)
Q Consensus       105 ~a~K~~DLS~  114 (142)
                      .|.++.=||.
T Consensus        90 ~~~~i~vl~~   99 (450)
T PRK03932         90 QATKIEVIGE   99 (450)
T ss_pred             EEEEEEEccC
Confidence            9999988886

>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=91.83  E-value=2.7  Score=29.04  Aligned_cols=63  Identities=17%  Similarity=0.170  Sum_probs=43.3

Q ss_pred             EEEEEEEeee-CCCC--cEEEEcCCeeEEEEe-ccccc---ccc-ccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496           38 WLQGVLVSPP-DDDG--RLLLDDGTGVVQIYL-SGDFR---IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI  109 (142)
Q Consensus        38 WlQG~vv~~~-~~~~--~~~LdDgTG~~~v~~-~~~~~---~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~  109 (142)
                      -+-|+|.++. ...|  .+.|.|.||++++.. +....   .+. +..|       .-|+|.|.+.. .+ . .+.+-++
T Consensus         3 ~i~GiI~~v~~TK~g~~~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d-------~~v~v~g~v~~-~~-~-~l~~~~I   72 (79)
T cd04490           3 SIIGMVNDVRSTKNGHRIVELEDTTGRITVLLTKDKEELFEEAEDILPD-------EVIGVSGTVSK-DG-G-LIFADEI   72 (79)
T ss_pred             EEEEEEeEEEEcCCCCEEEEEECCCCEEEEEEeCchhhhhhhhhhccCC-------CEEEEEEEEec-CC-C-EEEEEEe
Confidence            3556666663 1122  999999999999997 44433   233 8999       99999999955 22 3 6666666


Q ss_pred             e
Q 044496          110 V  110 (142)
Q Consensus       110 ~  110 (142)
                      .
T Consensus        73 ~   73 (79)
T cd04490          73 F   73 (79)
T ss_pred             E
Confidence            5

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.

>PRK02983 lysS lysyl-tRNA synthetase; Provisional

Probab=91.70  E-value=1.5  Score=43.73  Aligned_cols=73  Identities=19%  Similarity=0.111  Sum_probs=55.5

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccccc--------cccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFR--------IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~--------~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      .|.+.|+|.++..-++  =+.|.|+||.+++..+....        .+.+..|       +.|.|.|.+..+...+..|.
T Consensus       653 ~V~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~g-------d~V~v~G~v~~t~~ge~ei~  725 (1094)
T PRK02983        653 EVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLG-------DLVEVTGTMGTSRNGTLSLL  725 (1094)
T ss_pred             EEEEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCC-------CEEEEEEEEEEcCCCCEEEE
Confidence            5889999999965443  45689999999998733211        1237889       99999999988666788888


Q ss_pred             EEEEeeCCCC
Q 044496          106 VHKIVDLSAF  115 (142)
Q Consensus       106 a~K~~DLS~~  115 (142)
                      +.++.=||.+
T Consensus       726 ~~~i~ll~k~  735 (1094)
T PRK02983        726 VTSWRLAGKC  735 (1094)
T ss_pred             EeEEEEEecc
Confidence            8887767653

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

Probab=91.48  E-value=1.1  Score=41.03  Aligned_cols=64  Identities=19%  Similarity=0.330  Sum_probs=49.9

Q ss_pred             EeEEEEEEEEEeeeCC-C--CcEEEEcCCeeEEEEe--ccccccc-cccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           34 FQRVWLQGVLVSPPDD-D--GRLLLDDGTGVVQIYL--SGDFRIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        34 ~~~VWlQG~vv~~~~~-~--~~~~LdDgTG~~~v~~--~~~~~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      |..||+.|-|...... .  -.|.|-|++..+++..  ....+.+ +++.|       |.|.|.|.+.. +.|.-..+
T Consensus        23 ~~~V~v~GEISn~t~~~sgH~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG-------~~V~v~G~is~-Y~~rG~YQ   92 (440)
T COG1570          23 LGQVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNNRRLKFRPEEG-------MQVLVRGKISL-YEPRGDYQ   92 (440)
T ss_pred             CCeEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCcccccCCCccCC-------CEEEEEEEEEE-EcCCCceE
Confidence            8899999999998633 3  4799999999999986  3334433 59999       99999999977 65554443

>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site

Probab=91.27  E-value=0.93  Score=31.11  Aligned_cols=47  Identities=28%  Similarity=0.365  Sum_probs=35.3

Q ss_pred             EEEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496           39 LQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV   95 (142)
Q Consensus        39 lQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~   95 (142)
                      +=|+|+++.++++..+.+-+-.+-++...-.+.   .++|       +||+|+.++-
T Consensus         5 iP~~Vv~v~~~~~~A~v~~~G~~~~V~~~lv~~---v~~G-------d~VLVHaG~A   51 (68)
T PF01455_consen    5 IPGRVVEVDEDGGMAVVDFGGVRREVSLALVPD---VKVG-------DYVLVHAGFA   51 (68)
T ss_dssp             EEEEEEEEETTTTEEEEEETTEEEEEEGTTCTS---B-TT--------EEEEETTEE
T ss_pred             ccEEEEEEeCCCCEEEEEcCCcEEEEEEEEeCC---CCCC-------CEEEEecChh
Confidence            458899997778888888886667777666553   8999       9999999874

This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.

>PTZ00401 aspartyl-tRNA synthetase; Provisional

Probab=90.67  E-value=1.9  Score=40.04  Aligned_cols=74  Identities=18%  Similarity=0.122  Sum_probs=53.0

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEec---ccccc-----ccccCCcccccceeEEEEEeeEeecc------
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLS---GDFRI-----RRWNTGVFFFDFWMYVMVVGGFVIRT------   98 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~---~~~~~-----~~~~~G~~~~~~~~YVmViG~~~~~~------   98 (142)
                      +.||+.|+|.++..-++  =+.|.|+||.+++..+   ...+.     ..++.|       ..|.|.|.+..+.      
T Consensus        79 ~~V~v~Grv~~~R~~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~e-------siV~V~G~v~~~~~~~~~~  151 (550)
T PTZ00401         79 KTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTE-------SIVDVEATVCKVEQPITST  151 (550)
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCC-------CEEEEEEEEEecCccCCCC
Confidence            56999999999865443  4678999999998863   12232     248999       9999999988632      


Q ss_pred             -CCCceEEEEEEeeCCCC
Q 044496           99 -DDIPVIKVHKIVDLSAF  115 (142)
Q Consensus        99 -~~~p~i~a~K~~DLS~~  115 (142)
                       ...-.|.+.++.=||.+
T Consensus       152 ~~~~~El~v~~i~vls~a  169 (550)
T PTZ00401        152 SHSDIELKVKKIHTVTES  169 (550)
T ss_pred             CCccEEEEeeEEEEEeCC
Confidence             22347777777666664

>PRK07373 DNA polymerase III subunit alpha; Reviewed

Probab=90.66  E-value=0.98  Score=40.85  Aligned_cols=72  Identities=14%  Similarity=0.109  Sum_probs=55.7

Q ss_pred             eEEEEEEEEEeeeCC----C---CcEEEEcCCeeEEEEe-cccccc-cc-ccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496           35 QRVWLQGVLVSPPDD----D---GRLLLDDGTGVVQIYL-SGDFRI-RR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVI  104 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~----~---~~~~LdDgTG~~~v~~-~~~~~~-~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i  104 (142)
                      ++|.+-|+|.++...    +   .-+.|.|.||.+++.. +...+. +. ++.|       .-|.|-|.+.. ....+.+
T Consensus       281 ~~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~~y~~~~~~l~~~-------~~v~v~G~v~~-~~~~~~l  352 (449)
T PRK07373        281 TKVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYERISELLQVD-------ARLIIWGKVDR-RDDQVQL  352 (449)
T ss_pred             CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEe-cCCeEEE
Confidence            467889999997422    2   2678999999999997 555543 33 8999       99999999976 3456788


Q ss_pred             EEEEEeeCCC
Q 044496          105 KVHKIVDLSA  114 (142)
Q Consensus       105 ~a~K~~DLS~  114 (142)
                      .+.++.+|.+
T Consensus       353 iv~~i~~l~~  362 (449)
T PRK07373        353 IVEDAEPIEE  362 (449)
T ss_pred             EEeEeecHhh
Confidence            8999998865

>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type

Probab=90.52  E-value=2.3  Score=39.82  Aligned_cols=73  Identities=25%  Similarity=0.185  Sum_probs=54.1

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccccc----cccccCCcccccceeEEEEEeeEeec---------cCC
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFR----IRRWNTGVFFFDFWMYVMVVGGFVIR---------TDD  100 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~----~~~~~~G~~~~~~~~YVmViG~~~~~---------~~~  100 (142)
                      .|.+.|.|.++..-++  =+.|.|+||.+++..+....    ...++.|       ..|.|.|.+..+         ...
T Consensus        17 ~V~l~GwV~~~R~~Gkl~Fi~LrD~sg~iQvv~~~~~~~~~~~~~L~~e-------svV~V~G~v~~r~~~~~n~~~~tg   89 (583)
T TIGR00459        17 TVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNE-------DVVQVKGKVSARPEGNINRNLDTG   89 (583)
T ss_pred             EEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCHHHHHHHhcCCCC-------CEEEEEEEEEeCCccccCccCCCC
Confidence            5889999999864443  35689999999998743311    1258899       999999999752         234


Q ss_pred             CceEEEEEEeeCCCC
Q 044496          101 IPVIKVHKIVDLSAF  115 (142)
Q Consensus       101 ~p~i~a~K~~DLS~~  115 (142)
                      +..|.|.++.-||.+
T Consensus        90 ~iEl~~~~i~iL~~a  104 (583)
T TIGR00459        90 EIEILAESITLLNKS  104 (583)
T ss_pred             cEEEEEeEEEEeecC
Confidence            678888888888764

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.

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

Probab=90.30  E-value=0.7  Score=44.11  Aligned_cols=71  Identities=21%  Similarity=0.261  Sum_probs=50.4

Q ss_pred             eEEEEEEEEEeee--CCCCcEEEEcCCeeEEEEe---cccccccc-ccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496           35 QRVWLQGVLVSPP--DDDGRLLLDDGTGVVQIYL---SGDFRIRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK  108 (142)
Q Consensus        35 ~~VWlQG~vv~~~--~~~~~~~LdDgTG~~~v~~---~~~~~~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K  108 (142)
                      ..|.+.|-|+++.  .+-..|+|.|+||.+...-   .+. |-.| ++.|       ++|.|+|.+..+.+ .--|....
T Consensus       214 ~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGv-RAyP~IevG-------diV~ViG~V~~r~g-~lQiE~~~  284 (715)
T COG1107         214 KTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGV-RAYPEIEVG-------DIVEVIGEVTRRDG-RLQIEIEA  284 (715)
T ss_pred             ceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCc-ccCCCCCCC-------ceEEEEEEEeecCC-cEEEeehh
Confidence            4688999999984  4456999999999988864   332 2234 9999       99999999976433 33444555


Q ss_pred             EeeCCC
Q 044496          109 IVDLSA  114 (142)
Q Consensus       109 ~~DLS~  114 (142)
                      |..|+-
T Consensus       285 me~L~G  290 (715)
T COG1107         285 MEKLTG  290 (715)
T ss_pred             hHHhhC
Confidence            555543

>PRK00476 aspS aspartyl-tRNA synthetase; Validated

Probab=89.96  E-value=2.4  Score=39.62  Aligned_cols=73  Identities=22%  Similarity=0.252  Sum_probs=52.4

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc---cc-cccccCCcccccceeEEEEEeeEeecc---------CC
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD---FR-IRRWNTGVFFFDFWMYVMVVGGFVIRT---------DD  100 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~---~~-~~~~~~G~~~~~~~~YVmViG~~~~~~---------~~  100 (142)
                      .|.+.|.|.++..-++  =+.|.|+||.+++..+..   ++ ...++.|       ..|.|.|.+..+.         ..
T Consensus        19 ~V~l~GwV~~~R~~g~l~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~n~~~~~g   91 (588)
T PRK00476         19 TVTLCGWVHRRRDHGGLIFIDLRDREGIVQVVFDPDAEAFEVAESLRSE-------YVIQVTGTVRARPEGTVNPNLPTG   91 (588)
T ss_pred             EEEEEEEEEEEEeCCCeEEEEEEeCCceEEEEEeCCHHHHHHHhCCCCC-------CEEEEEEEEEecCCcccCccCCCC
Confidence            4889999999864433  456899999999987542   11 1358899       9999999998732         22


Q ss_pred             CceEEEEEEeeCCCC
Q 044496          101 IPVIKVHKIVDLSAF  115 (142)
Q Consensus       101 ~p~i~a~K~~DLS~~  115 (142)
                      +..|.|.++.=||.+
T Consensus        92 ~~El~~~~i~il~~a  106 (588)
T PRK00476         92 EIEVLASELEVLNKS  106 (588)
T ss_pred             cEEEEEeEEEEEecC
Confidence            457777777766664

>PLN02221 asparaginyl-tRNA synthetase

Probab=89.70  E-value=2.1  Score=40.03  Aligned_cols=73  Identities=21%  Similarity=0.329  Sum_probs=51.3

Q ss_pred             eEEEEEEEEEeeeCCCC----cEEEEcCC--eeEEEEeccc-cc-cccccCCcccccceeEEEEEeeEeecc-----CCC
Q 044496           35 QRVWLQGVLVSPPDDDG----RLLLDDGT--GVVQIYLSGD-FR-IRRWNTGVFFFDFWMYVMVVGGFVIRT-----DDI  101 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~----~~~LdDgT--G~~~v~~~~~-~~-~~~~~~G~~~~~~~~YVmViG~~~~~~-----~~~  101 (142)
                      +.|++.|-|-++..-++    =+.|.|||  |.+++..+.. .. ...++.|       .-|.|.|.++.+.     ...
T Consensus        51 ~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~~~~~~L~~E-------S~V~V~G~V~~~~~~~~~~~~  123 (572)
T PLN02221         51 QKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLYDLSTLVATG-------TCVTVDGVLKVPPEGKGTKQK  123 (572)
T ss_pred             CEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchhhHHhcCCCc-------eEEEEEEEEEeCCccCCCCcc
Confidence            57999999999965543    36789999  8999987432 21 1147889       9999999997632     123


Q ss_pred             ceEEEEEEeeCCC
Q 044496          102 PVIKVHKIVDLSA  114 (142)
Q Consensus       102 p~i~a~K~~DLS~  114 (142)
                      -.|.+-++.=||.
T Consensus       124 iEl~v~~i~vl~~  136 (572)
T PLN02221        124 IELSVEKVIDVGT  136 (572)
T ss_pred             EEEEEeEEEEEec
Confidence            4666666666664

>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length

Probab=89.70  E-value=1  Score=30.93  Aligned_cols=44  Identities=27%  Similarity=0.409  Sum_probs=35.1

Q ss_pred             EEEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEe
Q 044496           39 LQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVG   92 (142)
Q Consensus        39 lQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG   92 (142)
                      .+|+|.+++...-++.||||.-   -.++..+.-..+++|       |=|+|.=
T Consensus         5 veG~I~~id~~~~titLdDGks---y~lp~ef~~~~L~~G-------~kV~V~y   48 (61)
T PF07076_consen    5 VEGTIKSIDPETMTITLDDGKS---YKLPEEFDFDGLKPG-------MKVVVFY   48 (61)
T ss_pred             ceEEEEEEcCCceEEEecCCCE---EECCCcccccccCCC-------CEEEEEE
Confidence            6899999988888999999974   345666766679999       8877753

Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.

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

Probab=88.65  E-value=4.7  Score=36.86  Aligned_cols=73  Identities=23%  Similarity=0.261  Sum_probs=50.9

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecc--cc----ccccccCCcccccceeEEEEEeeEeecc--CCCceE
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSG--DF----RIRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPVI  104 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~--~~----~~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~i  104 (142)
                      +.|-++|-|-++.+-++  =+.|.||||.+++..+.  ..    +-+.++.+       ..|.|-|.+.++.  ...-.|
T Consensus        17 ~~V~v~GWV~~~R~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~e-------s~v~V~G~v~~~~~a~~g~El   89 (435)
T COG0017          17 QEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLE-------SSVVVTGIVKASPKAPQGFEL   89 (435)
T ss_pred             cEEEEEEEeeeecccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCc-------cEEEEEEEEEcCCCCCCCEEE
Confidence            88999999999865555  35789999999998732  21    22358999       9999999998732  223355


Q ss_pred             EEEEEeeCCC
Q 044496          105 KVHKIVDLSA  114 (142)
Q Consensus       105 ~a~K~~DLS~  114 (142)
                      ++.++-=||.
T Consensus        90 ~v~~i~Vl~~   99 (435)
T COG0017          90 QVEKIEVLGE   99 (435)
T ss_pred             EEEEEEEeec
Confidence            5555444443

>PRK06386 replication factor A; Reviewed

Probab=88.23  E-value=2.7  Score=37.34  Aligned_cols=68  Identities=15%  Similarity=0.118  Sum_probs=52.9

Q ss_pred             EEEEEEEEeeeC----C-CC-----cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           37 VWLQGVLVSPPD----D-DG-----RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        37 VWlQG~vv~~~~----~-~~-----~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      |=+.|+|++..+    . ++     +.+|-|.||++++.+ ..     .++.|       +.+.+.+.+....+..|.|.
T Consensus       120 v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGrIr~TlW~~-----~l~eG-------d~v~i~na~v~e~~G~~el~  187 (358)
T PRK06386        120 VSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTARVRISSFGK-----PLEDN-------RFVRIENARVSQYNGYIEIS  187 (358)
T ss_pred             eEEEEEEEEccCceEecCCCccEEEEEEEEcCCCeEEEEEccc-----cccCC-------CEEEEeeeEEEccCCeEEEE
Confidence            446888887744    2 33     799999999999998 33     48899       99999999988777888888


Q ss_pred             EEEEeeCCCCc
Q 044496          106 VHKIVDLSAFP  116 (142)
Q Consensus       106 a~K~~DLS~~p  116 (142)
                      +-+.+-+...|
T Consensus       188 v~~~t~I~~~~  198 (358)
T PRK06386        188 VGNKSVIKEVE  198 (358)
T ss_pred             eCCeEEEEECC
Confidence            87777666543

>PF15490 Ten1_2: Telomere-capping, CST complex subunit

Probab=87.33  E-value=11  Score=28.59  Aligned_cols=71  Identities=15%  Similarity=0.060  Sum_probs=55.2

Q ss_pred             EEEEEEEEEeeeCCCCcEEE----EcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeec-cCCCceEEEEEEe
Q 044496           36 RVWLQGVLVSPPDDDGRLLL----DDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIR-TDDIPVIKVHKIV  110 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~~~~L----dDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~-~~~~p~i~a~K~~  110 (142)
                      .|..-|++.+-+.....++|    .|+.-.+.|..... +.-+.+.|       ++++++|-+... .+..++|+|--..
T Consensus        23 svR~~GrL~~yD~~~~~a~l~~~~~~~~~~l~V~t~~l-~~~~~~~g-------slyq~iGEl~~~~~~~~~~L~ARV~r   94 (118)
T PF15490_consen   23 SVRTFGRLQSYDVATSRATLTAQHESDQHSLKVDTKLL-EPFQARVG-------SLYQFIGELEHQPQDGGIVLKARVLR   94 (118)
T ss_pred             eEEEEEEEEEEeccCCEEEEEeeccCCCcEEEEEeeEc-cccccCCC-------CEEEEEEEEEEEcCCCcEEEEEEEEE
Confidence            46788999999888999999    88877777776442 11246899       999999999986 5678899988777


Q ss_pred             eCCC
Q 044496          111 DLSA  114 (142)
Q Consensus       111 DLS~  114 (142)
                      ....
T Consensus        95 ~VdG   98 (118)
T PF15490_consen   95 CVDG   98 (118)
T ss_pred             ecCC
Confidence            6655

>PRK04036 DNA polymerase II small subunit; Validated

Probab=87.03  E-value=6.2  Score=35.92  Aligned_cols=54  Identities=19%  Similarity=0.222  Sum_probs=38.6

Q ss_pred             eEEEEEEEEEeeeCC-CC--cEEEEcCCeeEEEEecccc---cc--ccccCCcccccceeEEEEEeeEe
Q 044496           35 QRVWLQGVLVSPPDD-DG--RLLLDDGTGVVQIYLSGDF---RI--RRWNTGVFFFDFWMYVMVVGGFV   95 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~-~~--~~~LdDgTG~~~v~~~~~~---~~--~~~~~G~~~~~~~~YVmViG~~~   95 (142)
                      ..+|+-|+|.++.+. +|  .+.|-|.||++.+.++...   ..  ..+-+|       .-|.|.|.+.
T Consensus       154 ~~~~viG~v~~~~~~~~g~~~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg-------~vv~v~G~~~  215 (504)
T PRK04036        154 EEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKDREDLAELADELLLD-------EVIGVEGTLS  215 (504)
T ss_pred             ceEEEEEEEEEeecccCCceEEEEECCCCeEEEEeecchhhhhhhhhcccCc-------eEEEEEEEEc
Confidence            568999999988522 33  5899999999999874321   11  246777       7778888754

>PTZ00385 lysyl-tRNA synthetase; Provisional

Probab=86.92  E-value=5.9  Score=37.89  Aligned_cols=72  Identities=14%  Similarity=0.027  Sum_probs=54.1

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc---cc------cccccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD---FR------IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVI  104 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~---~~------~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i  104 (142)
                      .|++.|+|.++..-++  =+.|.|+||.+++..+..   .+      ...+..|       +.|-|-|.+......+..|
T Consensus       109 ~V~vaGrV~~~R~~Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~g-------diV~V~G~v~~t~~GeleI  181 (659)
T PTZ00385        109 TVRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVG-------DIIGADGVPCRMQRGELSV  181 (659)
T ss_pred             EEEEEEEEEeeeccCCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCC-------CEEEEEEEEEecCCceEEE
Confidence            4999999999864444  356789999999987321   11      1247888       9999999988744567888


Q ss_pred             EEEEEeeCCC
Q 044496          105 KVHKIVDLSA  114 (142)
Q Consensus       105 ~a~K~~DLS~  114 (142)
                      .|.++.=||.
T Consensus       182 ~~~~i~lLsk  191 (659)
T PTZ00385        182 AASRMLILSP  191 (659)
T ss_pred             EeeEEEEech
Confidence            8888887776

>PRK07218 replication factor A; Provisional

Probab=86.89  E-value=3.1  Score=37.59  Aligned_cols=68  Identities=16%  Similarity=0.224  Sum_probs=50.9

Q ss_pred             eEEEEEEEEEeeeC-----CCC-----cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCce
Q 044496           35 QRVWLQGVLVSPPD-----DDG-----RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPV  103 (142)
Q Consensus        35 ~~VWlQG~vv~~~~-----~~~-----~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~  103 (142)
                      ..|-+-|+|+++.+     +++     +.+|-|+||++++.+ ...+   .+++|       +.|.+.+.+....+..|.
T Consensus       173 ~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG~Ir~tlW~~~~---~l~~G-------d~v~I~na~v~e~~G~~e  242 (423)
T PRK07218        173 RGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPLP---EIEIG-------ASIRIEDAYVREFRGVPS  242 (423)
T ss_pred             CceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCceEEEEEecccc---cCCCC-------CEEEEeeeEEeccCCeEE
Confidence            34667888888733     122     678999999999998 4322   48999       999999999887788898


Q ss_pred             EEEEEEeeC
Q 044496          104 IKVHKIVDL  112 (142)
Q Consensus       104 i~a~K~~DL  112 (142)
                      |.+.+-+.+
T Consensus       243 lnv~~~t~I  251 (423)
T PRK07218        243 VNVSEFTTV  251 (423)
T ss_pred             EEECCceEE
Confidence            888744433

>PLN02903 aminoacyl-tRNA ligase

Probab=85.91  E-value=7.4  Score=37.16  Aligned_cols=74  Identities=27%  Similarity=0.238  Sum_probs=51.4

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc-cc-----cccccCCcccccceeEEEEEeeEeecc--------
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD-FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRT--------   98 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~-~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~--------   98 (142)
                      +.|.+.|.|-++..-++  =+.|.|+||.++|..+.. ..     ...++.|       ..|.|.|.+..+.        
T Consensus        73 k~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~e-------svV~V~G~V~~r~~~~~n~~~  145 (652)
T PLN02903         73 SRVTLCGWVDLHRDMGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNE-------YVVAVEGTVRSRPQESPNKKM  145 (652)
T ss_pred             CEEEEEEEEEEEecCCCcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCC-------CEEEEEEEEEeCCCcCcCCCC
Confidence            35889999999865443  456899999999887422 11     1248899       9999999998631        


Q ss_pred             -CCCceEEEEEEeeCCCC
Q 044496           99 -DDIPVIKVHKIVDLSAF  115 (142)
Q Consensus        99 -~~~p~i~a~K~~DLS~~  115 (142)
                       ..+-.|.|.++.=||.+
T Consensus       146 ~tGeiEl~~~~i~VL~~a  163 (652)
T PLN02903        146 KTGSVEVVAESVDILNVV  163 (652)
T ss_pred             CCCCEEEEEeEEEEEecC
Confidence             12346666666655553

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

Probab=85.82  E-value=6  Score=38.05  Aligned_cols=74  Identities=20%  Similarity=0.174  Sum_probs=52.3

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--cc-----cccccCCcccccceeEEEEEeeEeecc----C--
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRT----D--   99 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~----~--   99 (142)
                      +.|.+.|.|.++..-++  =+.|.|+||.+++..+..  ..     ...++.|       ..|.|.|.++.+.    +  
T Consensus        19 ~~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~E-------svV~V~G~v~~r~~~~~n~~   91 (706)
T PRK12820         19 REVCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAE-------FCVALQGEVQKRLEETENPH   91 (706)
T ss_pred             CEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCC-------CEEEEEeEEeccCccccCCC
Confidence            45889999999865444  456899999999987321  11     1248999       9999999998731    1  


Q ss_pred             ---CCceEEEEEEeeCCCC
Q 044496          100 ---DIPVIKVHKIVDLSAF  115 (142)
Q Consensus       100 ---~~p~i~a~K~~DLS~~  115 (142)
                         .+-.|.|.++.=||.+
T Consensus        92 ~~tg~iEl~~~~i~iL~~a  110 (706)
T PRK12820         92 IETGDIEVFVRELSILAAS  110 (706)
T ss_pred             CCCCcEEEEeeEEEEEecC
Confidence               2346777777766664

>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=85.22  E-value=11  Score=28.40  Aligned_cols=63  Identities=21%  Similarity=0.302  Sum_probs=40.0

Q ss_pred             eEEEEEEEEE--eeeC--C--CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496           35 QRVWLQGVLV--SPPD--D--DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK  108 (142)
Q Consensus        35 ~~VWlQG~vv--~~~~--~--~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K  108 (142)
                      +++.+-|.|+  ++.-  +  .-+|.|.|+...+.|.+.+... ..++.|       .-|.|.|.+..    .-.+.|-+
T Consensus        51 ~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~~P-d~F~eg-------~~VVv~G~~~~----~g~F~A~~  118 (131)
T PF03100_consen   51 RKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGPLP-DLFREG-------QGVVVEGRLGE----DGVFEATE  118 (131)
T ss_dssp             SEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--C-TT--TT-------SEEEEEEEECC----TSEEEEEE
T ss_pred             ceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCCCC-ccccCC-------CeEEEEEEECC----CCEEEEEE
Confidence            4566788887  3322  2  3399999999999999866432 248899       99999998833    34677766


Q ss_pred             E
Q 044496          109 I  109 (142)
Q Consensus       109 ~  109 (142)
                      +
T Consensus       119 l  119 (131)
T PF03100_consen  119 L  119 (131)
T ss_dssp             E
T ss_pred             E
Confidence            5

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.

>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=84.80  E-value=10  Score=30.31  Aligned_cols=64  Identities=22%  Similarity=0.291  Sum_probs=44.5

Q ss_pred             eEEEEEEEEE--eeeC-C---CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496           35 QRVWLQGVLV--SPPD-D---DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK  108 (142)
Q Consensus        35 ~~VWlQG~vv--~~~~-~---~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K  108 (142)
                      +++.+-|.|+  |+.- +   .-+|.+.|+.+.+.|.+.+... --++.|       .=|.+.|.+..    .-++.|.+
T Consensus        58 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilP-DlFrEG-------~gVVveG~~~~----~g~F~A~e  125 (159)
T PRK13150         58 QRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGILP-DLFREG-------QGVVVQGTLEK----GNHVLAHE  125 (159)
T ss_pred             CEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEeccCC-ccccCC-------CeEEEEEEECC----CCEEEEeE
Confidence            5566777776  4422 2   2399999999999999866431 027788       88999998854    34677777


Q ss_pred             Ee
Q 044496          109 IV  110 (142)
Q Consensus       109 ~~  110 (142)
                      +.
T Consensus       126 vL  127 (159)
T PRK13150        126 VL  127 (159)
T ss_pred             EE
Confidence            64

>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=84.67  E-value=11  Score=30.13  Aligned_cols=64  Identities=20%  Similarity=0.287  Sum_probs=44.2

Q ss_pred             eEEEEEEEEE--eee-CCC---CcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496           35 QRVWLQGVLV--SPP-DDD---GRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK  108 (142)
Q Consensus        35 ~~VWlQG~vv--~~~-~~~---~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K  108 (142)
                      +++.+-|.|+  |+. +++   -+|.+-|+...+.|.+.+... -.++.|       .=|.+.|.+..    .-++.|.+
T Consensus        58 ~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~GilP-DlFrEG-------~gVVveG~~~~----~g~F~A~~  125 (160)
T PRK13165         58 QRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGILP-DLFREG-------QGIVAQGVLEE----GNHIEAKE  125 (160)
T ss_pred             CEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEcccCC-ccccCC-------CeEEEEEEECC----CCeEEEEE
Confidence            5666777777  443 223   389999999999999865431 027778       88999998854    34677766


Q ss_pred             Ee
Q 044496          109 IV  110 (142)
Q Consensus       109 ~~  110 (142)
                      +.
T Consensus       126 vL  127 (160)
T PRK13165        126 VL  127 (160)
T ss_pred             EE
Confidence            63

>PLN02603 asparaginyl-tRNA synthetase

Probab=83.65  E-value=10  Score=35.56  Aligned_cols=74  Identities=22%  Similarity=0.229  Sum_probs=51.7

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCee--EEEEeccccc------cccccCCcccccceeEEEEEeeEeeccCC--Cc
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGV--VQIYLSGDFR------IRRWNTGVFFFDFWMYVMVVGGFVIRTDD--IP  102 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~--~~v~~~~~~~------~~~~~~G~~~~~~~~YVmViG~~~~~~~~--~p  102 (142)
                      +.|.+.|.|-++...++  =+.|.||||.  +++..+....      ...+..|       ..|.|-|.+..+.+.  .-
T Consensus       108 ~~V~v~GwV~~iR~~g~~~Fi~l~Dgs~~~~lQ~v~~~~~~~~~~l~~~~l~~g-------s~V~V~G~v~~~~~~~~~~  180 (565)
T PLN02603        108 KTLNVMGWVRTLRAQSSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVESGLITTG-------ASVLVQGTVVSSQGGKQKV  180 (565)
T ss_pred             CEEEEEEEEEEEEeCCCeEEEEEECCCCCEeEEEEEECcHHHHHHHhhcCCCCC-------CEEEEEEEEEecCCCCccE
Confidence            57889999999864433  3568999985  7777633211      1137889       999999999873222  35


Q ss_pred             eEEEEEEeeCCCC
Q 044496          103 VIKVHKIVDLSAF  115 (142)
Q Consensus       103 ~i~a~K~~DLS~~  115 (142)
                      .|++.++.=|+.+
T Consensus       181 EL~v~~i~vlg~a  193 (565)
T PLN02603        181 ELKVSKIVVVGKS  193 (565)
T ss_pred             EEEEeEEEEEECC
Confidence            7888888777764

>PRK10413 hydrogenase 2 accessory protein HypG; Provisional

Probab=83.31  E-value=4.8  Score=28.78  Aligned_cols=50  Identities=14%  Similarity=0.050  Sum_probs=34.7

Q ss_pred             EEEEEEeeeCCC-CcEEEEcCCeeEEEEeccccccc-cccCCcccccceeEEEEEeeEe
Q 044496           39 LQGVLVSPPDDD-GRLLLDDGTGVVQIYLSGDFRIR-RWNTGVFFFDFWMYVMVVGGFV   95 (142)
Q Consensus        39 lQG~vv~~~~~~-~~~~LdDgTG~~~v~~~~~~~~~-~~~~G~~~~~~~~YVmViG~~~   95 (142)
                      +=|.|+++.++. ...+.+.+-.+-+|++.-.+... ..++|       +||+|+-++-
T Consensus         5 iP~kVi~i~~~~~~~A~vd~~Gv~r~V~l~Lv~~~~~~~~vG-------DyVLVHaGfA   56 (82)
T PRK10413          5 VPGQVLAVGEDIHQLAQVEVCGIKRDVNIALICEGNPADLLG-------QWVLVHVGFA   56 (82)
T ss_pred             cceEEEEECCCCCcEEEEEcCCeEEEEEeeeeccCCcccccC-------CEEEEecchh
Confidence            347899985442 56778877666666655444333 48999       9999998873

>TIGR00237 xseA exodeoxyribonuclease VII, large subunit

Probab=82.84  E-value=6.3  Score=35.14  Aligned_cols=64  Identities=25%  Similarity=0.412  Sum_probs=48.2

Q ss_pred             EeEEEEEEEEEeeeC-CC--CcEEEEcCCeeEEEEe-cccc-ccc-cccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           34 FQRVWLQGVLVSPPD-DD--GRLLLDDGTGVVQIYL-SGDF-RIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        34 ~~~VWlQG~vv~~~~-~~--~~~~LdDgTG~~~v~~-~~~~-~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      |.+||++|-|.+... ..  -.|.|-|....+.+.. .+.. +.. .++.|       |=|.|.|.+.. ..+.-.++
T Consensus        17 ~~~v~V~GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G-------~~V~v~g~v~~-y~~~G~~q   86 (432)
T TIGR00237        17 FLQVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNNRLKFRPQNG-------QQVLVRGGISV-YEPRGDYQ   86 (432)
T ss_pred             CCcEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhhCCCCCCCCC-------CEEEEEEEEEE-ECCCCcEE
Confidence            679999999999853 23  3899999999998875 3333 222 48999       99999999977 66654443

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.

>PRK13480 3'-5' exoribonuclease YhaM; Provisional

Probab=82.31  E-value=18  Score=31.38  Aligned_cols=51  Identities=22%  Similarity=0.238  Sum_probs=39.0

Q ss_pred             cEEEEcCCeeEEEEe-ccccccc-cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEe
Q 044496           52 RLLLDDGTGVVQIYL-SGDFRIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIV  110 (142)
Q Consensus        52 ~~~LdDgTG~~~v~~-~~~~~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~  110 (142)
                      +++|-|.||.++... +...... .+++|       ++|.|-|.+.. .+..+-++...+.
T Consensus        36 ~l~l~D~tG~I~ak~W~~~~~~~~~~~~g-------~vv~v~G~v~~-y~g~~Ql~i~~i~   88 (314)
T PRK13480         36 TLILQDKSGDIEAKLWDVSPEDEATYVPE-------TIVHVKGDIIN-YRGRKQLKVNQIR   88 (314)
T ss_pred             EEEEEcCCcEEEEEeCCCChhhHhhcCCC-------CEEEEEEEEEE-ECCcceEEEEEeE
Confidence            789999999999988 4433433 59999       99999999987 6666656555443

>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF

Probab=81.71  E-value=5.5  Score=28.04  Aligned_cols=44  Identities=25%  Similarity=0.204  Sum_probs=32.7

Q ss_pred             EEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496           40 QGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV   95 (142)
Q Consensus        40 QG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~   95 (142)
                      =|+|+++  +++..+.+.+-.+-++++.-.+   +.++|       +||+|+-++-
T Consensus         6 P~~V~~i--~~~~A~v~~~G~~~~v~l~lv~---~~~vG-------D~VLVH~G~A   49 (76)
T TIGR00074         6 PGQVVEI--DENIALVEFCGIKRDVSLDLVG---EVKVG-------DYVLVHVGFA   49 (76)
T ss_pred             ceEEEEE--cCCEEEEEcCCeEEEEEEEeeC---CCCCC-------CEEEEecChh
Confidence            4788887  3467888888666666665543   58899       9999998873

An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.

>PRK07218 replication factor A; Provisional

Probab=81.49  E-value=7  Score=35.36  Aligned_cols=67  Identities=21%  Similarity=0.288  Sum_probs=48.9

Q ss_pred             eEEEEEEEEEeeeCC----CC------cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCce
Q 044496           35 QRVWLQGVLVSPPDD----DG------RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPV  103 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~----~~------~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~  103 (142)
                      .+|-+-|+|+++.+.    ++      ..+|-|.||++++.+ . +.   ++++|       +.+.+.+.+.......|.
T Consensus        69 ~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~-~~---~l~~G-------dvv~I~na~vre~~g~~e  137 (423)
T PRK07218         69 KNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWK-DF---GLSPG-------DTVTIGNAGVREWDGRPE  137 (423)
T ss_pred             ceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEEC-CC---CCCCC-------CEEEEeccEeeccCCceE
Confidence            677889999998532    12      789999999999998 5 22   49999       999999877665555666


Q ss_pred             EEEEEEeeC
Q 044496          104 IKVHKIVDL  112 (142)
Q Consensus       104 i~a~K~~DL  112 (142)
                      +.+.+-+-+
T Consensus       138 l~ig~~t~I  146 (423)
T PRK07218        138 LNIGESTTV  146 (423)
T ss_pred             EeccCcceE
Confidence            665444333

>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed

Probab=81.33  E-value=9.2  Score=33.62  Aligned_cols=68  Identities=22%  Similarity=0.427  Sum_probs=50.0

Q ss_pred             EeEEEEEEEEEeeeCC-CC--cEEEEcCCeeEEEEe-cccc-ccc-cccCCcccccceeEEEEEeeEeeccCCCc--eEE
Q 044496           34 FQRVWLQGVLVSPPDD-DG--RLLLDDGTGVVQIYL-SGDF-RIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIP--VIK  105 (142)
Q Consensus        34 ~~~VWlQG~vv~~~~~-~~--~~~LdDgTG~~~v~~-~~~~-~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p--~i~  105 (142)
                      +.+||++|-|...... .|  .|.|-|.+..+.+.. .+.. +.. .++.|       |=|.|.|.+.. ..+.-  -+.
T Consensus        23 ~~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G-------~~v~v~g~~~~-y~~~g~~ql~   94 (438)
T PRK00286         23 LGQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSARRLKFKPEEG-------MKVLVRGKVSL-YEPRGDYQLI   94 (438)
T ss_pred             CCcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhhcCCCCCCCC-------CEEEEEEEEEE-ECCCCCEEEE
Confidence            7899999999998533 33  889999999999886 3333 322 48999       99999999986 55544  444


Q ss_pred             EEEE
Q 044496          106 VHKI  109 (142)
Q Consensus       106 a~K~  109 (142)
                      +.+|
T Consensus        95 v~~i   98 (438)
T PRK00286         95 VEEI   98 (438)
T ss_pred             EEEe
Confidence            4444

>PRK05672 dnaE2 error-prone DNA polymerase; Validated

Probab=80.68  E-value=5.6  Score=39.69  Aligned_cols=71  Identities=25%  Similarity=0.368  Sum_probs=54.4

Q ss_pred             EEEEEEEEEeeeCC---C--CcEEEEcCCeeEEEEe-cccccc-cc-ccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496           36 RVWLQGVLVSPPDD---D--GRLLLDDGTGVVQIYL-SGDFRI-RR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH  107 (142)
Q Consensus        36 ~VWlQG~vv~~~~~---~--~~~~LdDgTG~~~v~~-~~~~~~-~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~  107 (142)
                      .|++-|+|.++...   .  .-+.|.|.||.+++.. +...+. +. ++.|       ..+.|-|.+.. .++...+.|.
T Consensus       955 ~v~v~g~i~~~~~~~TkkGmaf~~leD~~g~~e~~ifp~~~~~~~~~l~~~-------~~~~v~g~v~~-~~~~~~~~~~ 1026 (1046)
T PRK05672        955 RVRVAGVVTHRQRPGTASGVTFLTLEDETGMVNVVVWPGLWERQRREALGA-------RLLLVRGRVQN-AEGVRHLVAD 1026 (1046)
T ss_pred             EEEEEEEEEEEEEecCCCceEEEEEecCCCCEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEe-cCCeEEEEEe
Confidence            48889999887432   2  3588999999999997 555433 33 8999       99999999986 4556788899


Q ss_pred             EEeeCCC
Q 044496          108 KIVDLSA  114 (142)
Q Consensus       108 K~~DLS~  114 (142)
                      ++.+|..
T Consensus      1027 ~i~~~~~ 1033 (1046)
T PRK05672       1027 RLEDLSP 1033 (1046)
T ss_pred             eeechHH
Confidence            9988854

>PRK07217 replication factor A; Reviewed

Probab=80.60  E-value=11  Score=33.11  Aligned_cols=80  Identities=15%  Similarity=0.109  Sum_probs=55.4

Q ss_pred             eeecCeE--EeEEEEEEEEEeeeCCCC-----cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeecc
Q 044496           27 VTLGGIL--FQRVWLQGVLVSPPDDDG-----RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRT   98 (142)
Q Consensus        27 ~~l~gl~--~~~VWlQG~vv~~~~~~~-----~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~   98 (142)
                      ..+..+.  =++|-+-|+|++..++..     .-+|-|.||++++.. .. .....++.|       +-+.+-+.+....
T Consensus        73 ~kI~Di~~~~~~VsV~aKVl~l~e~~~~si~qvGllgDETG~IkfT~W~~-s~~~~leeG-------d~~rI~na~v~ey  144 (311)
T PRK07217         73 VNIADIDEPEQWVDVTAKVVQLWEPSSDSIAQVGLLGDETGTIKFTKWAK-SDLPELEEG-------KSYLLKNVVTDEY  144 (311)
T ss_pred             eeeeecCCCCCcEEEEEEEEEecCCCCCceEEEEEEEcCCceEEEEEccC-CCCCcccCC-------CEEEEEeEEEeeE
Confidence            3455443  456778999999854422     347999999999998 32 112248899       8888888887777


Q ss_pred             CCCceEEEEEEeeCCC
Q 044496           99 DDIPVIKVHKIVDLSA  114 (142)
Q Consensus        99 ~~~p~i~a~K~~DLS~  114 (142)
                      +..|.|...+-+-++.
T Consensus       145 ~G~~~lnlg~~t~I~~  160 (311)
T PRK07217        145 QGRFSVKLNRTTSIEE  160 (311)
T ss_pred             CCEEEEEeCCceEEEe
Confidence            7778777666555544

>PRK08402 replication factor A; Reviewed

Probab=80.34  E-value=8.4  Score=34.00  Aligned_cols=71  Identities=20%  Similarity=0.329  Sum_probs=46.0

Q ss_pred             eEEEEEEEEEeeeCC------CC------cEEEEcCCeeEEEEe-ccccc--cccccCCcccccceeEEEEEeeEeec-c
Q 044496           35 QRVWLQGVLVSPPDD------DG------RLLLDDGTGVVQIYL-SGDFR--IRRWNTGVFFFDFWMYVMVVGGFVIR-T   98 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~------~~------~~~LdDgTG~~~v~~-~~~~~--~~~~~~G~~~~~~~~YVmViG~~~~~-~   98 (142)
                      ..|-+.|+|+++.+.      +|      +++|-|.||.+++.+ +....  ...+++|       .-|.+.|..... .
T Consensus        73 ~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~ir~TlW~~~a~~~~~~l~~G-------dvi~I~~a~V~e~~  145 (355)
T PRK08402         73 RGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVAKYYNKINVG-------DVIKVIDAQVRESL  145 (355)
T ss_pred             ceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechhhhhhcccCCCC-------CEEEEECCEEeecC
Confidence            567789999998542      33      289999999999988 33221  1247888       777777666553 2


Q ss_pred             CCCceEEEEEEeeC
Q 044496           99 DDIPVIKVHKIVDL  112 (142)
Q Consensus        99 ~~~p~i~a~K~~DL  112 (142)
                      +..|.|..-.-+-+
T Consensus       146 ~G~~eLsvg~~s~i  159 (355)
T PRK08402        146 SGLPELHINFRARI  159 (355)
T ss_pred             CCcEEEEECCCceE
Confidence            55555554433333

>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=80.27  E-value=18  Score=28.29  Aligned_cols=64  Identities=20%  Similarity=0.316  Sum_probs=44.0

Q ss_pred             eEEEEEEEEEe--ee--CC-CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496           35 QRVWLQGVLVS--PP--DD-DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI  109 (142)
Q Consensus        35 ~~VWlQG~vv~--~~--~~-~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~  109 (142)
                      +++.+-|.|+.  +.  ++ .-+|.|.|+...+.|.+.+... -.++.|       .-|.+.|.+..    .-.+.|.++
T Consensus        52 ~~vrvgG~V~~gSi~~~~~~~~~F~ltD~~~~i~V~Y~G~lP-d~F~eg-------~~VVv~G~~~~----~g~F~A~~v  119 (148)
T PRK13254         52 RRFRLGGLVEKGSVQRGDGLTVRFVVTDGNATVPVVYTGILP-DLFREG-------QGVVAEGRLQD----GGVFVADEV  119 (148)
T ss_pred             CeEEEeEEEecCcEEeCCCCEEEEEEEeCCeEEEEEECCCCC-ccccCC-------CEEEEEEEECC----CCeEEEEEE
Confidence            45666677653  21  22 3499999999999999865421 137889       99999999954    236777776


Q ss_pred             e
Q 044496          110 V  110 (142)
Q Consensus       110 ~  110 (142)
                      .
T Consensus       120 L  120 (148)
T PRK13254        120 L  120 (148)
T ss_pred             E
Confidence            4

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	142
3mxn_B	150	Crystal Structure Of The Rmi Core Complex Length =		3e-04

>pdb|3MXN|B Chain B, Crystal Structure Of The Rmi Core Complex Length = 150

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 41/133 (30%), Positives = 56/133 (42%), Gaps = 20/133 (15%)
Query: 8   LKLLCVQLK-DARESP-----SQNAVTLGGILFQRVWLQGVLVSPPXXXXXXXXXXXXXV 61
           LK+L  QL+ DA   P     S+ A   G +    VW+QG +V                 
Sbjct: 26  LKVLAEQLRRDAEGGPGAWRLSRAAAGRGPLDLAAVWMQGRVV----------MADRGEA 75
Query: 62  VQIYLSGDFRIR---RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDR 118
                SGDF +R   R   G        YVMV+G  V      P ++  K+ DLS  P  
Sbjct: 76  RLRDPSGDFSVRGLERVPRGRPCLVPGKYVMVMG-VVQACSPEPCLQAVKMTDLSDNPIH 134
Query: 119 EAMWYLEVMEAYK 131
           E+MW LEV + ++
Sbjct: 135 ESMWELEVEDLHR 147

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	142
3mxn_B	150	RECQ-mediated genome instability protein 2; bloom	2e-24

>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 Length = 150

 Score = 90.7 bits (224), Expect = 2e-24
 Identities = 39/131 (29%), Positives = 56/131 (42%), Gaps = 14/131 (10%)

Query: 7   ALKLLCVQLKDARESP------SQNAVTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTG 60
            LK+L  QL+   E        S+ A   G +    VW+QG +V    D G   L D +G
Sbjct: 25  PLKVLAEQLRRDAEGGPGAWRLSRAAAGRGPLDLAAVWMQGRVVMA--DRGEARLRDPSG 82

Query: 61  VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREA 120
              +       + R   G        YVMV+G  V      P ++  K+ DLS  P  E+
Sbjct: 83  DFSV-----RGLERVPRGRPCLVPGKYVMVMG-VVQACSPEPCLQAVKMTDLSDNPIHES 136

Query: 121 MWYLEVMEAYK 131
           MW LEV + ++
Sbjct: 137 MWELEVEDLHR 147

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	142
3mxn_B	150	RECQ-mediated genome instability protein 2; bloom	100.0
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	99.46
4gop_B	136	Putative uncharacterized protein; OB fold, ssDNA b	99.46
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	99.18
3kf6_A	159	Protein STN1; OB fold, chromosomal protein, DNA-bi	98.74
1nnx_A	109	Protein YGIW; structural genomics, hypothetical pr	97.71
3kf8_A	220	Protein STN1; OB fold; 2.40A {Candida tropicalis m	96.63
3kdf_A	121	Replication protein A 14 kDa subunit; wheat GERM c	96.54
2pi2_E	142	Replication protein A 14 kDa subunit; FULL-length	96.5
2k50_A	115	Replication factor A related protein; uncharacteri	95.81
3dm3_A	105	Replication factor A; probably plays AN essential	95.45
1n9w_A	422	Aspartyl-tRNA synthetase 2; biosynthetic protein;	95.17
4gop_A	114	Putative uncharacterized protein; OB fold, ssDNA b	95.15
3e0e_A	97	Replication protein A; structural genomics, PSI-2,	94.95
2kbn_A	109	Conserved protein; nucleic acid binding protein, b	94.68
3m4p_A	456	Ehasnrs, asparaginyl-tRNA synthetase, putative; am	94.62
1e1o_A	504	Lysyl-tRNA synthetase, heat inducible; ligase, ami	94.59
3bju_A	521	Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase,	94.38
1wyd_A	429	Hypothetical aspartyl-tRNA synthetase; archaea, LI	94.36
1eov_A	487	ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy	94.33
3nem_A	438	Aspartyl-tRNA synthetase; rossmann fold, OB fold,	94.27
1l0w_A	580	Aspartyl-tRNA synthetase; space-grown crystal, dim	94.07
2xgt_A	435	Asparaginyl-tRNA synthetase, cytoplasmic; ligase,	93.92
4ex5_A	529	Lysine--tRNA ligase; structural genomics, niaid, n	93.88
3a74_A	493	Lysyl-tRNA synthetase; aminoacyl tRNA synthetase,	93.41
1c0a_A	585	Aspartyl tRNA synthetase; protein-RNA complex, lig	93.36
3i7f_A	548	Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-bi	93.03
2k75_A	106	Uncharacterized protein TA0387; closed beta barrel	92.79
1x54_A	434	Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthe	92.53
3au7_A	402	TIAS, putative uncharacterized protein; ATP hydrol	92.18
4ah6_A	617	Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo	87.14
3e0j_A	476	DNA polymerase subunit delta-2; DNA polymerase del	85.78
1o7i_A	119	SSB, SSO2364, single stranded DNA binding protein;	85.74
2hpi_A	1220	DNA polymerase III alpha subunit; POL-beta-like nu	85.18

>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=100.00  E-value=2.3e-45  Score=284.80  Aligned_cols=121  Identities=31%  Similarity=0.381  Sum_probs=109.5

Q ss_pred             ccchHHHHHHHHHhhccCCCCCCc------eeecCeEEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-cccccccc-
Q 044496            3 YSLAALKLLCVQLKDARESPSQNA------VTLGGILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRR-   74 (142)
Q Consensus         3 ~~~pa~Kvf~~QL~~a~~~~s~~~------~~l~gl~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~-   74 (142)
                      .+-||+|+|++||++|++.+...+      ....++++++|||||+||++  ++|+++||||||+|++.+ +++|++++ 
T Consensus        21 ~~~PpvK~l~~QLr~~~~~~~~~w~l~r~~~g~~~l~~s~VWmQG~VV~~--~~g~~~LdDgTG~~~v~g~~~vp~g~p~   98 (150)
T 3mxn_B           21 PRSPPLKVLAEQLRRDAEGGPGAWRLSRAAAGRGPLDLAAVWMQGRVVMA--DRGEARLRDPSGDFSVRGLERVPRGRPC   98 (150)
T ss_dssp             CSSCCEECCHHHHHHHEESCTTCCEECCTTTTCCCEECSEEEEEEEEEEE--ETTEEEEEETTEEEEEECGGGSCCCSCC
T ss_pred             CCCCcHHHHHHHHHHHhhCCCceEEEEecccCCccceeEEEEEEeEEEEe--CCCeEEEECCCceEEEeeccccCCCCcc
Confidence            478999999999999988653332      22347999999999999996  778999999999999986 89999998 


Q ss_pred             ccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHH
Q 044496           75 WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLF  133 (142)
Q Consensus        75 ~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~  133 (142)
                      |++|       |||||||.+++ |+++|+|+||||+|||++|+||+||+|||+|+||.+
T Consensus        99 l~~G-------~YVMV~G~v~~-~s~eP~i~AvKm~DLS~~p~~E~mW~lEV~el~r~i  149 (150)
T 3mxn_B           99 LVPG-------KYVMVMGVVQA-CSPEPCLQAVKMTDLSDNPIHESMWELEVEDLHRNI  149 (150)
T ss_dssp             CSTT-------CEEEEEEEEEE-CSSSCEEEEEEEEECCSCHHHHHHHHHHHHHHHTTC
T ss_pred             cCCC-------CEEEEEEEEEe-cCCCceEEEEEeeeCCCCcchHHHHHHHHHHHHhcC
Confidence            8999       99999999998 999999999999999999999999999999999875

>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=99.46  E-value=1.2e-12  Score=96.46  Aligned_cols=115  Identities=18%  Similarity=0.183  Sum_probs=94.4

Q ss_pred             HHHHHhhccCCCCCCceeecCeEEeEEEEEEEEEeeeCC--CCcEEEEcCCe-eEEEEe--ccc-c-c-cccccCCcccc
Q 044496           11 LCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDD--DGRLLLDDGTG-VVQIYL--SGD-F-R-IRRWNTGVFFF   82 (142)
Q Consensus        11 f~~QL~~a~~~~s~~~~~l~gl~~~~VWlQG~vv~~~~~--~~~~~LdDgTG-~~~v~~--~~~-~-~-~~~~~~G~~~~   82 (142)
                      -++||.+|.+.  .+.|.++|.++++|.+.|+|.++.+.  .-.+.|||||| .+++..  +.. . . ...+++|    
T Consensus        10 tIkqil~a~~~--~~~f~i~g~~i~~V~iVG~V~~~~~~~~~~~~~ldD~TG~~I~~~~W~~~~~~~~~~~~~~~g----   83 (132)
T 3kdf_D           10 TISQLLSATLV--DEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPE----   83 (132)
T ss_dssp             CHHHHHTCEES--SSCEEETTEECCEEEEEEEEEEEEECSSEEEEEEECSSSSCEEEEEEC---------CCCCTT----
T ss_pred             EHHHHhhCccC--CCcEEECCEEEEEEEEEEEEEEEEEcCCeEEEEEECCCCCEEEEEEEccCCCcccccccccCC----
Confidence            46999999875  35899999999999999999999655  34899999999 999987  222 1 1 2359999    


Q ss_pred             cceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHHhhh
Q 044496           83 DFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQP  136 (142)
Q Consensus        83 ~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~y~~  136 (142)
                         +||.|.|.++. .+..+-|.|.++.-+++ ++-...=.||++.+|..+=+|
T Consensus        84 ---~yVrV~G~l~~-f~g~~qi~~~~ir~v~d-~Nei~~H~Le~i~~hl~~~k~  132 (132)
T 3kdf_D           84 ---TYVKVAGHLRS-FQNKKSLVAFKIMPLED-MNEFTTHILEVINAHMVLSKA  132 (132)
T ss_dssp             ---CEEEEEEEEEE-ETTEEEEEEEEEEECSS-THHHHHHHHHHHHHHHHHHHC
T ss_pred             ---CEEEEEEEEEe-ECCEEEEEEEEEEEcCC-ccHHHHHHHHHHHHHHeecCC
Confidence               99999999987 88889999999998876 677778899999999887654

>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=99.46  E-value=9e-13  Score=97.63  Aligned_cols=114  Identities=15%  Similarity=0.186  Sum_probs=94.1

Q ss_pred             HHHHHhhccCCCCCCceeecCeEEeEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEe--cccc----ccccccCCcccc
Q 044496           11 LCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYL--SGDF----RIRRWNTGVFFF   82 (142)
Q Consensus        11 f~~QL~~a~~~~s~~~~~l~gl~~~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~--~~~~----~~~~~~~G~~~~   82 (142)
                      .++||.+|.+..+.+.|.++|.++++|.+.|+|+++.+...  .+.|+||||.+.+..  +...    ....+++|    
T Consensus        13 tIkqil~a~~~~~~~~f~i~g~~i~~V~iVG~V~~~~~~~~~~~~~ldD~TG~I~~~~W~~~~~~~~~~~~~~~~g----   88 (136)
T 4gop_B           13 TIRQILNAEQPHPDAEFILDGAELGQLTFVAVVRNISRNATNVAYSVEDGTGQIEVRQWLDSSSDDSSKASEIRNN----   88 (136)
T ss_dssp             CHHHHHHCBCCSSSCCCBSSSSBCCEEEEEEEEEEEEECSSEEEEEEECSSCEEEEEEECC--------CCSCCTT----
T ss_pred             EHHHHhhccccCCCCcEEECCEEEEEEEEEEEEEEEEecCCeEEEEEECCCCCEEEEEecccCCcccccccccCCC----
Confidence            46999999987545689999999999999999999965533  899999999999987  2221    12359999    


Q ss_pred             cceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHH
Q 044496           83 DFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLF  133 (142)
Q Consensus        83 ~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~  133 (142)
                         +||.|.|.++. ....+-|.|.++.-+.+ ++-...=.||++.+|..+
T Consensus        89 ---~yVrV~G~v~~-f~g~~qi~~~~ir~v~d-~Nei~~H~Le~i~~hl~~  134 (136)
T 4gop_B           89 ---VYVRVLGTLKS-FQNRRSISSGHMRPVID-YNEVMFHRLEAVHAHLQV  134 (136)
T ss_dssp             ---CEEEEEEEEEE-ETTEEEEEESEEEECSS-HHHHHHHHHHHHHHHHHH
T ss_pred             ---CEEEEEEEEEE-eCCEEEEEEEEEEECCC-ccHHHHHHHHHHHHHHhh
Confidence               99999999977 88889999999888866 777788899999998654

>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=99.18  E-value=1.9e-10  Score=93.83  Aligned_cols=116  Identities=18%  Similarity=0.170  Sum_probs=94.6

Q ss_pred             HHHHHHHhhccCCCCCCceeecCeEEeEEEEEEEEEeeeCC--CCcEEEEcCCe-eEEEEe--cccc---ccccccCCcc
Q 044496            9 KLLCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDD--DGRLLLDDGTG-VVQIYL--SGDF---RIRRWNTGVF   80 (142)
Q Consensus         9 Kvf~~QL~~a~~~~s~~~~~l~gl~~~~VWlQG~vv~~~~~--~~~~~LdDgTG-~~~v~~--~~~~---~~~~~~~G~~   80 (142)
                      -+.++||.+|.+.  .+.|.++|.++++|.+.|+|.++...  .-++.|+|+|| .+.+..  +...   ....+++|  
T Consensus        48 PvtIkqil~a~~~--d~~f~i~g~~i~~V~ivG~V~~i~~~~~~~~~~L~D~TG~~I~~k~W~~~~~~~~~~~~~~~G--  123 (270)
T 2pi2_A           48 PCTISQLLSATLV--DEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPE--  123 (270)
T ss_dssp             ECCHHHHHHCEEE--TTEEEETTEEESEEEEEEEEEEEEECSSEEEEEEECSSSSCEEEEEECC-------CCCCCTT--
T ss_pred             EEEHHHHhcCccC--CCcEEECCEEEEEEEEEEEEEEEEeccceEEEEEECCCCCEEEEEEEcCcCcccchhhcCCCC--
Confidence            3568999999753  34799999999999999999999655  34899999999 899987  2221   22359999  


Q ss_pred             cccceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHHhh
Q 044496           81 FFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQ  135 (142)
Q Consensus        81 ~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~y~  135 (142)
                           +||.|.|.+.. ....+-|++.+|.-+.+ ++....+.|||+.+|..+=+
T Consensus       124 -----~yVrV~G~v~~-f~g~~qi~i~~ir~v~d-~nEi~~H~Le~i~~hl~~~~  171 (270)
T 2pi2_A          124 -----TYVKVAGHLRS-FQNKKSLVAFKIMPLED-MNEFTTHILEVINAHMVLSK  171 (270)
T ss_dssp             -----CEEEEEEEEEE-ETTEEEEEEEEEEECSC-THHHHHHHHHHHHHHHHHHH
T ss_pred             -----CEEEEEEEEEe-cCCeeEEEEEEEEecCC-HhHHHHHHHHHHHHHHHHcc
Confidence                 99999999987 88899999999988876 66788999999999987644

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

Probab=98.74  E-value=1.2e-07  Score=73.23  Aligned_cols=118  Identities=14%  Similarity=0.108  Sum_probs=93.6

Q ss_pred             HHHHHHHHhhccCCCC---CCceeecCeEEeEEEEEEEEEeeeCCC--CcEEEEcCCee-EEEEe--cc-ccc---cccc
Q 044496            8 LKLLCVQLKDARESPS---QNAVTLGGILFQRVWLQGVLVSPPDDD--GRLLLDDGTGV-VQIYL--SG-DFR---IRRW   75 (142)
Q Consensus         8 ~Kvf~~QL~~a~~~~s---~~~~~l~gl~~~~VWlQG~vv~~~~~~--~~~~LdDgTG~-~~v~~--~~-~~~---~~~~   75 (142)
                      +|+|++=+-..++.+.   ++. -.++..++.|-+.|+|+++++.+  -.+.||||||. +.+..  +. .+.   ..++
T Consensus        19 v~L~i~DI~~l~~~~~~~~~~~-f~~n~PI~~V~IvGiVv~~~~~~~~~~ytIDD~TG~~I~cv~w~~~~~~~~~~~~~l   97 (159)
T 3kf6_A           19 NPMFISDVHKISFHPHLQRYIG-FWMGFPIRWIQIVGYIAAIDIYEGKHVLTVDDCSGMVLRVVFIIQDDFSMSKRAISM   97 (159)
T ss_dssp             CBCCHHHHTTCBCCCC---CCE-EETTEEECEEEEEEEEEEEEEETTEEEEEEECSSSCEEEEEEEGGGCHHHHHHHTTC
T ss_pred             ecchHHHHHhchhcCCCCCcce-eECCeEEEEEEEEEEEEEEEEeCCEEEEEEecCCCCeEEEEEEccCCCCcccccccC
Confidence            4778888888877663   233 47899999999999999996543  37899999995 88886  22 111   2258


Q ss_pred             cCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHHhhh
Q 044496           76 NTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFYQP  136 (142)
Q Consensus        76 ~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~y~~  136 (142)
                      ..|       .||.|.|.+.. ...+.-|.|-|+.-+.+ |+-|..+=.|..++-+.+ .|
T Consensus        98 ~~G-------~~VrV~G~v~~-fr~~rqI~~~~i~~v~d-~n~Ev~~W~~~~r~~~~l-~p  148 (159)
T 3kf6_A           98 SPG-------NVVCVFGKINS-FRSEVELIAQSFEELRD-PNDEWKAWQKRMRYKKNL-TK  148 (159)
T ss_dssp             CTT-------CEEEEEEEEEC-SSSSCEEEEEEEEEECS-THHHHHHHHHHHHHHHHH-HH
T ss_pred             CCC-------CEEEEEEEEEe-eCCEEEEEEEEEEECCC-cHHHHHHHHHHHHHHHhC-CC
Confidence            999       99999999977 78899999999999986 778888888998888873 44

>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=97.71  E-value=0.00025  Score=51.97  Aligned_cols=72  Identities=17%  Similarity=0.113  Sum_probs=58.3

Q ss_pred             eEEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEe
Q 044496           32 ILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIV  110 (142)
Q Consensus        32 l~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~  110 (142)
                      -.=+.|-|+|.|++. -+++.++..|+||.+.|.. +....++++.++       .-|.+.|.+-+ ....+.|.+.++.
T Consensus        35 ~Dd~~V~L~G~Iv~~-~~~d~Y~F~D~TG~I~VeId~~~w~g~~v~p~-------~~Vri~GevDk-d~~~~eIdV~~i~  105 (109)
T 1nnx_A           35 RDDTWVTLRGNIVER-ISDDLYVFKDASGTINVDIDHKRWNGVTVTPK-------DTVEIQGEVDK-DWNSVEIDVKQIR  105 (109)
T ss_dssp             CSSEEEEEEEEEEEE-EETTEEEEEETTEEEEEECCGGGSTTCCCCTT-------SCEEEEEEEEE-ETTEEEEEEEEEE
T ss_pred             cCCCeEEEEEEEEEE-eCCCeEEEECCCccEEEEEChhhcCCcccCCC-------CEEEEEEEECC-CCCceEEEEEEEE
Confidence            344678899999995 4688999999999999998 556788899999       99999999987 3446777776665


Q ss_pred             eC
Q 044496          111 DL  112 (142)
Q Consensus       111 DL  112 (142)
                      -|
T Consensus       106 ~~  107 (109)
T 1nnx_A          106 KV  107 (109)
T ss_dssp             EC
T ss_pred             Ec
Confidence            33

>3kf8_A Protein STN1; OB fold; 2.40A {Candida tropicalis mya-3404}

Probab=96.63  E-value=0.018  Score=46.78  Aligned_cols=103  Identities=21%  Similarity=0.204  Sum_probs=72.8

Q ss_pred             HHHHHHHHHhhccCCC---------CCCceeecCeEEeEEEEEEEEEeeeCCC----------CcEEEEcCCee---EEE
Q 044496            7 ALKLLCVQLKDARESP---------SQNAVTLGGILFQRVWLQGVLVSPPDDD----------GRLLLDDGTGV---VQI   64 (142)
Q Consensus         7 a~Kvf~~QL~~a~~~~---------s~~~~~l~gl~~~~VWlQG~vv~~~~~~----------~~~~LdDgTG~---~~v   64 (142)
                      .+++|++-|.+.++..         .++.+..++.-++.|-++|+||......          -.+.|||+||.   +.|
T Consensus        49 ~vpL~I~DI~~l~~~~~~yg~~~~~~~~i~f~~NhPI~~V~IvG~VVg~~~k~~r~~~~~~~~~~l~IDDsSG~~s~i~~  128 (220)
T 3kf8_A           49 TIPLFISDINNSPNLYGIYNYIADHLRHVVLVNNYPVNQINIFGKIVYEQYKEKEFNGVEESYVILVISDFIGIDSKIRV  128 (220)
T ss_dssp             EEECCHHHHHTCCCTHHHHGGGGGGCTTCEEETTEEECEEEEEEEEEEEEEECCBCSSCBCCEEEEEEECCCSSSCEEEE
T ss_pred             ccceEhHHhhhchhhhcccccccccCccEEEECCcccEEEEEEEEEEEEEEEeccccccccceEEEEEeCCCCCCceEEE
Confidence            3466666666554422         1346778999999999999999996443          36899999997   555


Q ss_pred             Eeccc---ccccc---ccCCcccccceeEEEEEeeEeeccCC--------CceEEEEEEeeCCCCcC
Q 044496           65 YLSGD---FRIRR---WNTGVFFFDFWMYVMVVGGFVIRTDD--------IPVIKVHKIVDLSAFPD  117 (142)
Q Consensus        65 ~~~~~---~~~~~---~~~G~~~~~~~~YVmViG~~~~~~~~--------~p~i~a~K~~DLS~~p~  117 (142)
                      ..+..   ..+.+   .+.|       +-|-|-|.+.. .-+        +..|.|.|++=|+..|+
T Consensus       129 k~~~~~~~~~gl~l~~~~~G-------~iV~VkG~i~~-~r~~~~~~~~~~rei~ve~i~vl~~~~~  187 (220)
T 3kf8_A          129 RLSQEQFKEVGLTLDKKNYG-------KIVELEGEIYN-WYDSINVSKKPDRELKVSKITVLSHRPD  187 (220)
T ss_dssp             EEEHHHHHTTTCCTTSCCTT-------CEEEEEEEEEE-CCCSTTTTSCCCEEEEEEEEEEEESSSC
T ss_pred             EecHHHhhccCccccccCCC-------eEEEEEEEEEe-eccccccccccceEEEEEEEEEeccCCC
Confidence            54321   12223   3478       99999999976 332        67999999999988733

>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=96.54  E-value=0.024  Score=41.69  Aligned_cols=67  Identities=22%  Similarity=0.178  Sum_probs=53.2

Q ss_pred             eEEEEEEEEEeeeCCCCcEEEEcCCe-eEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCC
Q 044496           35 QRVWLQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLS  113 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS  113 (142)
                      ++|.+.|+|.+...+++.++|+++-| .++|.++....   ...+       .||-|+|.+..    .-.|+|...+|++
T Consensus        23 k~VrivGkV~~~~~~g~~~~l~s~Dg~~Vtv~l~~p~~---~~l~-------~~vEViG~V~~----~~tI~~~~~~~fg   88 (121)
T 3kdf_A           23 KPVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLD---EEIS-------GIVEVVGRVTA----KATILCTSYVQFK   88 (121)
T ss_dssp             CEEEEEEEEEEECTTSSEEEEECTTSCEEEEECSSCCS---SCCC-------SEEEEEEEECT----TSCEEEEEEEECC
T ss_pred             CeEEEEEEEEEEcCCCCEEEEEeCCCCEEEEEeCCCCC---cccC-------cEEEEEEEECC----CCeEEEEEEEecC
Confidence            77999999999977788999998865 69999865211   1225       79999999854    4589999999999


Q ss_pred             CC
Q 044496          114 AF  115 (142)
Q Consensus       114 ~~  115 (142)
                      ++
T Consensus        89 ~~   90 (121)
T 3kdf_A           89 ED   90 (121)
T ss_dssp             CS
T ss_pred             CC
Confidence            86

>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=96.50  E-value=0.023  Score=43.07  Aligned_cols=67  Identities=22%  Similarity=0.178  Sum_probs=53.4

Q ss_pred             eEEEEEEEEEeeeCCCCcEEEEcCCe-eEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCC
Q 044496           35 QRVWLQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLS  113 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS  113 (142)
                      ++|.+.|+|.+...+++.++|..+.| .++|.++...   .-..+       .||-|+|.+..    .-.|++...++++
T Consensus        44 k~VriVGkV~~~~~~G~~~~l~s~Dg~~VtV~l~~pL---~~~~~-------~~VEViG~V~~----~~tI~~~~~~~fG  109 (142)
T 2pi2_E           44 KPVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPL---DEEIS-------GIVEVVGRVTA----KATILCTSYVQFK  109 (142)
T ss_dssp             CEEEEEEEEEEECTTSSEEEEECTTSCEEEEECSSCC---SSCCC-------SEEEEEEEECT----TSCEEEEEEEECC
T ss_pred             CEEEEEEEEeEEcCCCCEEEEEeCCCcEEEEEeCCCC---CccCC-------CEEEEEEEECC----CCcEEEEEEEecC
Confidence            67899999999987899999999865 5999886411   11347       89999999844    4579999999999


Q ss_pred             CC
Q 044496          114 AF  115 (142)
Q Consensus       114 ~~  115 (142)
                      ++
T Consensus       110 d~  111 (142)
T 2pi2_E          110 ED  111 (142)
T ss_dssp             CS
T ss_pred             CC
Confidence            86

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=95.81  E-value=0.035  Score=38.79  Aligned_cols=76  Identities=8%  Similarity=0.179  Sum_probs=51.3

Q ss_pred             EEEEEEEEEeeeC------CCC------cEEEEcCCeeEEEEe-ccccc-cccccCCcccccceeEEEEEeeEeec-cCC
Q 044496           36 RVWLQGVLVSPPD------DDG------RLLLDDGTGVVQIYL-SGDFR-IRRWNTGVFFFDFWMYVMVVGGFVIR-TDD  100 (142)
Q Consensus        36 ~VWlQG~vv~~~~------~~~------~~~LdDgTG~~~v~~-~~~~~-~~~~~~G~~~~~~~~YVmViG~~~~~-~~~  100 (142)
                      .+-+.|+|.++.+      .+|      .+.|-|+||.+++.+ +.... ...+++|       ++|++-|.+... .+.
T Consensus        18 ~v~i~~~V~~~~~~~~~~~k~G~~~~~~~~~l~D~TG~I~~t~w~~~~~~~~~l~~G-------~vv~i~g~~v~~~f~g   90 (115)
T 2k50_A           18 ETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVFWTENIKLLKKFREG-------DVIRIKDVNIRGGFGG   90 (115)
T ss_dssp             EEEEEEEEEEECCCEECCCTTSSCCEEEEEEEEETTEEEEEEEETTGGGGGGTCCTT-------SEEEEEEEEECCCSSS
T ss_pred             EeEEEEEEEECCCceEEEcCCCCEEEEEEEEEEeCCCeEEEEEeCchhhhhhcCCCC-------CEEEEEeeEEccccCC
Confidence            4567888888821      122      588999999999987 33222 2359999       999999998543 556


Q ss_pred             CceEEEEEEeeCCCCcCc
Q 044496          101 IPVIKVHKIVDLSAFPDR  118 (142)
Q Consensus       101 ~p~i~a~K~~DLS~~p~r  118 (142)
                      .+.|.+-+...+..+|+-
T Consensus        91 ~~qL~~~~~~~i~~~~~~  108 (115)
T 2k50_A           91 RKEAHLMPRSTVEVLDPL  108 (115)
T ss_dssp             SCEEEECTTCCEEEESSC
T ss_pred             eEEEEECCCceEEECCcc
Confidence            677776555544444443

>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii}

Probab=95.45  E-value=0.32  Score=34.33  Aligned_cols=72  Identities=21%  Similarity=0.193  Sum_probs=51.4

Q ss_pred             eEEEEEEEEEeeeC------CCC------cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCC
Q 044496           35 QRVWLQGVLVSPPD------DDG------RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDI  101 (142)
Q Consensus        35 ~~VWlQG~vv~~~~------~~~------~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~  101 (142)
                      .+|-+.|+|+++.+      .+|      ++.|.|.||.+++.+ ...... .+++|       +.|.+-|.++......
T Consensus        15 ~~v~v~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D~TG~IrvtlW~~~a~~-~l~~G-------dvv~i~g~vk~~~~g~   86 (105)
T 3dm3_A           15 MTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTDI-DVGRG-------DYVRVRGYIREGYYGG   86 (105)
T ss_dssp             EEEEEEEEEEEEEEEEEEECTTSCEEEEEEEEEEETTEEEEEEEEGGGGGS-CCCTT-------CEEEEEEEEEECTTSS
T ss_pred             CeEEEEEEEEECCCceEEEcCCCCeeEEEEEEEECCCCcEEEEEECccccc-ccCCC-------CEEEEEEEEEEccCCC
Confidence            67889999998842      133      699999999999997 333322 89999       8888877676633446


Q ss_pred             ceEEEEEEeeCCC
Q 044496          102 PVIKVHKIVDLSA  114 (142)
Q Consensus       102 p~i~a~K~~DLS~  114 (142)
                      ..|.+-+-.-+..
T Consensus        87 ~eL~~g~~~~i~~   99 (105)
T 3dm3_A           87 LECTANYVEILKK   99 (105)
T ss_dssp             EEEEEEEEEEEEC
T ss_pred             EEEEeCCceEEEe
Confidence            7777766555544

>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=95.17  E-value=0.13  Score=44.29  Aligned_cols=69  Identities=28%  Similarity=0.213  Sum_probs=53.9

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccccccccc-CCcccccceeEEEEEeeEeeccC--CCceEEEEEEe
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFRIRRWN-TGVFFFDFWMYVMVVGGFVIRTD--DIPVIKVHKIV  110 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~~~~~~-~G~~~~~~~~YVmViG~~~~~~~--~~p~i~a~K~~  110 (142)
                      .|.+.|.|.++..-++  =+.|.|+||.+++..+.    ..++ .|       ..|.|.|.+.++..  .+-.|+|.++.
T Consensus        15 ~V~v~Gwv~~~R~~g~~~F~~lrD~~g~iQ~v~~~----~~l~~~~-------~~v~v~G~v~~~~~~~~~~el~~~~~~   83 (422)
T 1n9w_A           15 EVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGG----LKLPLPE-------SALRVRGLVVENAKAPGGLEVQAKEVE   83 (422)
T ss_dssp             EEEEEEEEEEEEECSSEEEEEEEETTEEEEEEEES----CCCCCTT-------CEEEEEEEEEECTTSTTSEEEEEEEEE
T ss_pred             EEEEEEEEEEEecCCCeEEEEEEECCEEEEEEEEc----cccCCCC-------CEEEEEEEEEecCCCCccEEEEEeEEE
Confidence            5899999999965544  36688999999998754    4688 99       99999999988432  26788888777


Q ss_pred             eCCCC
Q 044496          111 DLSAF  115 (142)
Q Consensus       111 DLS~~  115 (142)
                      =||.+
T Consensus        84 vl~~~   88 (422)
T 1n9w_A           84 VLSPA   88 (422)
T ss_dssp             EEECC
T ss_pred             EeccC
Confidence            77754

>4gop_A Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=95.15  E-value=0.097  Score=37.90  Aligned_cols=70  Identities=23%  Similarity=0.258  Sum_probs=49.2

Q ss_pred             eEEEEEEEEEeeeCCCCcEEEEcCC-eeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCC---CceEEEEEEe
Q 044496           35 QRVWLQGVLVSPPDDDGRLLLDDGT-GVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDD---IPVIKVHKIV  110 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~~~LdDgT-G~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~---~p~i~a~K~~  110 (142)
                      ++|.+.|+|.+..  ++.++|..++ |.++|.++...   .+..|       .||-|+|.+.. .+.   --.|++...+
T Consensus        19 ~~VrivGkV~~~~--g~~~~l~s~d~~~Vtv~l~~~~---~~~~~-------~~vEViG~V~~-~~~~~~~~~I~~~~~~   85 (114)
T 4gop_A           19 QTVRIVGKVHKVT--GNTLLMQTSDLGNVEIAMTPDS---DVSSS-------TFVEVTGKVSD-AGSSFQANQIREFTTV   85 (114)
T ss_dssp             SEEEEEEEEEEEE--TTEEEEECTTSCEEEEECCSSC---CGGGC-------SEEEEEEEECT-TSSEEEEEEEEECSCC
T ss_pred             CeEEEEEEEeeeC--CCEEEEEeCCCCEEEEEeCCCC---CcccC-------cEEEEEEEEcC-CCCcccCCeEEEEEEE
Confidence            6799999999985  4899999874 45888886522   35578       99999998854 211   1788888888


Q ss_pred             eCCCCcC
Q 044496          111 DLSAFPD  117 (142)
Q Consensus       111 DLS~~p~  117 (142)
                      |+.++=+
T Consensus        86 ~~g~~~D   92 (114)
T 4gop_A           86 DCGHDVD   92 (114)
T ss_dssp             C----CC
T ss_pred             eCCCccC
Confidence            8876533

>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=94.95  E-value=0.44  Score=32.82  Aligned_cols=67  Identities=22%  Similarity=0.136  Sum_probs=45.9

Q ss_pred             eEEEEEEEEEeeeCC------CC------cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCC
Q 044496           35 QRVWLQGVLVSPPDD------DG------RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDI  101 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~------~~------~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~  101 (142)
                      .++-+.|+|+++.+-      +|      ++.|.|.||.+++.+ +..... .+++|       ++|.+-|.+.. ....
T Consensus        12 ~~v~i~~~V~~~~~~r~~~~~~G~~~~v~~~~l~DeTG~I~~tlW~~~~~~-~i~~G-------dvv~i~g~v~~-~~~~   82 (97)
T 3e0e_A           12 LSGTINAEVVTAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNELADF-EVKKG-------DIAEVSGYVKQ-GYSG   82 (97)
T ss_dssp             EEEEEEEEEEEECCCEEEC----CCEEEEEEEEEETTEEEEEEEEGGGGGC-CCCTT-------CEEEEEEEEEE-C--C
T ss_pred             CcEEEEEEEEECCCceEEEcCCCCeeEEEEEEEECCCCcEEEEEECCcccc-ccCCC-------CEEEEEEEEEE-cCCe
Confidence            567889999988421      23      589999999999997 332222 79999       99999887765 3445


Q ss_pred             ceEEEEEEe
Q 044496          102 PVIKVHKIV  110 (142)
Q Consensus       102 p~i~a~K~~  110 (142)
                      ..|.+-+-.
T Consensus        83 ~el~~g~~~   91 (97)
T 3e0e_A           83 LEISVDNIG   91 (97)
T ss_dssp             EEEEEEEEE
T ss_pred             EEEEECCCc
Confidence            566555443

>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_A

Probab=94.68  E-value=0.27  Score=34.70  Aligned_cols=70  Identities=17%  Similarity=0.182  Sum_probs=50.4

Q ss_pred             eEEEEEEEEEeeeCCCC-----cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496           35 QRVWLQGVLVSPPDDDG-----RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK  108 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~-----~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K  108 (142)
                      ..|-+.|+|+++.+..+     .++|-|.||++++.+ +.. ....+++|       +.|.+-+......+..+.|..-+
T Consensus        16 ~~v~v~~~V~~~~~~~~~~~~~~~~l~DeTG~I~~t~W~~~-~~~~~~~G-------~~V~i~n~~v~~~~G~~~L~v~~   87 (109)
T 2kbn_A           16 QWANLKAKVIQLWENTHESISQVGLLGDETGIIKFTIWKNA-ELPLLEQG-------ESYLLRSVVVGEYNDRFQVQVNK   87 (109)
T ss_dssp             CEEEEEEEEEEEEECCCSSEEEEEEEECTTCCEEEEEEGGG-CCCCCCTT-------CEEEEEEEEEEEETTEEEEEECS
T ss_pred             CcEEEEEEEEEeEcCCCCeEEEEEEEECCCCeEEEEEECcc-cccccCCC-------CEEEEEEEEEEEECCEEEEEECC
Confidence            44667888888854433     589999999999998 422 23369999       99999966655577778777655


Q ss_pred             EeeC
Q 044496          109 IVDL  112 (142)
Q Consensus       109 ~~DL  112 (142)
                      ...+
T Consensus        88 ~~~I   91 (109)
T 2kbn_A           88 NSSI   91 (109)
T ss_dssp             SSEE
T ss_pred             ceEE
Confidence            4433

>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=94.62  E-value=0.2  Score=43.68  Aligned_cols=75  Identities=15%  Similarity=0.156  Sum_probs=53.7

Q ss_pred             eEEEEEEEEEeeeCCCC--c-EEEEcCCeeEEEEecc-c-c---ccccccCCcccccceeEEEEEeeEeeccC-------
Q 044496           35 QRVWLQGVLVSPPDDDG--R-LLLDDGTGVVQIYLSG-D-F---RIRRWNTGVFFFDFWMYVMVVGGFVIRTD-------   99 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~-~~LdDgTG~~~v~~~~-~-~---~~~~~~~G~~~~~~~~YVmViG~~~~~~~-------   99 (142)
                      +.|++.|.|.++..-++  . +.|.|+||.+++..+. . .   ....+..|       ..|.|-|.+.++..       
T Consensus        31 ~~V~v~Gwv~~~R~~Gk~~~Fi~LrD~sg~iQvv~~~~~~~~~~~~~~l~~g-------~~V~V~G~v~~~~~~~~~~~~  103 (456)
T 3m4p_A           31 KLVTFKGWAYHIRKARKTLIFVELRDGSGYCQCVIFGKELCEPEKVKLLTRE-------CSLEITGRLNAYAGKNHPPEI  103 (456)
T ss_dssp             SEEEEEEEEEEEECCSSSEEEEEEECSSCEEEEEEESTTTTCHHHHTTCCTT-------CEEEEEEEEECCCSSSCCCSC
T ss_pred             CEEEEEEEEEEEecCCCceEEEEEEeCCccEEEEEecccchhhHHhhcCCCc-------cEEEEEeEEEecCCcccCccc
Confidence            56899999999875533  2 4699999999988743 1 1   11248889       99999999986321       


Q ss_pred             ---CCceEEEEEEeeCCCCc
Q 044496          100 ---DIPVIKVHKIVDLSAFP  116 (142)
Q Consensus       100 ---~~p~i~a~K~~DLS~~p  116 (142)
                         .+-.|+|.++.=||.++
T Consensus       104 ~t~g~~El~~~~i~vl~~a~  123 (456)
T 3m4p_A          104 ADILNLEMQVTEWKVIGESP  123 (456)
T ss_dssp             TTBCSSEEEEEEEEEEECCC
T ss_pred             CCCCcEEEEEeEEEEEecCC
Confidence               34588887776666643

>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=94.59  E-value=0.2  Score=44.26  Aligned_cols=74  Identities=18%  Similarity=0.246  Sum_probs=55.6

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--c----c--cccccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--F----R--IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVI  104 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~----~--~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i  104 (142)
                      +.|++.|.|.++..-++  =+.|.|+||.++|..+..  .    +  -..+..|       ..|.|.|.+..+...+-.|
T Consensus        65 ~~V~v~Gwv~~~R~~gk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~~l~~g-------~~V~V~G~v~~~~~ge~ei  137 (504)
T 1e1o_A           65 IEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLG-------DIIGARGTLFKTQTGELSI  137 (504)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSSTTHHHHTGGGCCTT-------CEEEEEEEEEECTTCCEEE
T ss_pred             CEEEEEEEEEEEecCCCcEEEEEEECCeeEEEEEECCcCCHHHHHHHHhcCCCC-------CEEEEEEEEEecCCceEEE
Confidence            36999999999864433  356789999999987322  1    1  1348899       9999999998865567788


Q ss_pred             EEEEEeeCCCC
Q 044496          105 KVHKIVDLSAF  115 (142)
Q Consensus       105 ~a~K~~DLS~~  115 (142)
                      +|.++.=||.+
T Consensus       138 ~~~~i~vl~~a  148 (504)
T 1e1o_A          138 HCTELRLLTKA  148 (504)
T ss_dssp             EEEEEEEEECC
T ss_pred             EEEEEEEeccc
Confidence            88888777753

>3bju_A Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP- binding, cytoplasm, ligase, nucleotide-binding, phosphoprotein, polymorphism; HET: LYS ATP; 2.31A {Homo sapiens}

Probab=94.38  E-value=0.17  Score=44.89  Aligned_cols=74  Identities=14%  Similarity=-0.019  Sum_probs=56.0

Q ss_pred             eEEEEEEEEEeeeCCC-C--cEEEEcCCeeEEEEecccc-------cc--ccccCCcccccceeEEEEEeeEeeccCCCc
Q 044496           35 QRVWLQGVLVSPPDDD-G--RLLLDDGTGVVQIYLSGDF-------RI--RRWNTGVFFFDFWMYVMVVGGFVIRTDDIP  102 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~-~--~~~LdDgTG~~~v~~~~~~-------~~--~~~~~G~~~~~~~~YVmViG~~~~~~~~~p  102 (142)
                      +.|++.|+|.++..-+ +  =+.|.|+||.+++..+...       ..  ..+..|       ..|.|.|.+..+...+-
T Consensus        56 ~~V~v~Grv~~~R~~gkk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~~~l~~g-------d~V~V~G~v~~t~~ge~  128 (521)
T 3bju_A           56 ITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRG-------DIIGVQGNPGKTKKGEL  128 (521)
T ss_dssp             CCEEEEEEEEEEEESSSSEEEEEEEETTEEEEEEEEGGGSSCHHHHHHHHHHCCTT-------CEEEEEEEEEECTTCCE
T ss_pred             cEEEEEEEEEEEecCCCCcEEEEEEECCEEEEEEEECCccCCHHHHHHHHhcCCCC-------CEEEEEEEEEecCCCCE
Confidence            4699999999996544 3  2678999999999873211       11  247899       99999999988555577


Q ss_pred             eEEEEEEeeCCCC
Q 044496          103 VIKVHKIVDLSAF  115 (142)
Q Consensus       103 ~i~a~K~~DLS~~  115 (142)
                      .|+|.++.=||.+
T Consensus       129 ei~~~~i~~l~~~  141 (521)
T 3bju_A          129 SIIPYEITLLSPC  141 (521)
T ss_dssp             EEEEEEEEEEECC
T ss_pred             EEEEeEEEEeecC
Confidence            8888888777753

>1wyd_A Hypothetical aspartyl-tRNA synthetase; archaea, LIGA; HET: EPE; 2.30A {Sulfolobus tokodaii}

Probab=94.36  E-value=0.26  Score=42.54  Aligned_cols=74  Identities=19%  Similarity=0.131  Sum_probs=54.2

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccc---c-cccccCCcccccceeEEEEEeeEeeccCC--CceEEE
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDF---R-IRRWNTGVFFFDFWMYVMVVGGFVIRTDD--IPVIKV  106 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~---~-~~~~~~G~~~~~~~~YVmViG~~~~~~~~--~p~i~a  106 (142)
                      +.|.+.|.|.++..-++  =+.|.|+||.+++..+...   + -..++.|       ..|.|.|.+..+...  +-.|.|
T Consensus        17 ~~V~v~Gwv~~~R~~g~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~l~~~-------~~v~v~G~v~~~~~~~~~~el~~   89 (429)
T 1wyd_A           17 KEVIWAGWVHLLRDLGGKKFIILRDKTGLGQVVVDKNSSAFGISQELTQE-------SVIQVRGIVKADKRAPRGIELHA   89 (429)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEECTTSTTHHHHTTCCTT-------CEEEEEEEEEECSSSGGGEEEEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEeCChHHHHHHHhCCCC-------CEEEEEEEEEecCCCCccEEEEE
Confidence            35889999999865444  2668899999999874321   1 1348999       999999999884332  567888


Q ss_pred             EEEeeCCCC
Q 044496          107 HKIVDLSAF  115 (142)
Q Consensus       107 ~K~~DLS~~  115 (142)
                      .++.=||.+
T Consensus        90 ~~~~vl~~~   98 (429)
T 1wyd_A           90 EEITLLSKA   98 (429)
T ss_dssp             EEEEEEECC
T ss_pred             eEEEEeccC
Confidence            877777654

>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=94.33  E-value=0.24  Score=43.42  Aligned_cols=74  Identities=16%  Similarity=0.161  Sum_probs=54.2

Q ss_pred             eEEEEEEEEEeeeCCCCc---EEEEcCCeeEEEEeccc-----ccc-----ccccCCcccccceeEEEEEeeEeeccC--
Q 044496           35 QRVWLQGVLVSPPDDDGR---LLLDDGTGVVQIYLSGD-----FRI-----RRWNTGVFFFDFWMYVMVVGGFVIRTD--   99 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~---~~LdDgTG~~~v~~~~~-----~~~-----~~~~~G~~~~~~~~YVmViG~~~~~~~--   99 (142)
                      +.|++.|.|.++..-++.   +.|.|+||.+++..+..     .+.     ..++.|       ..|.|.|.+.++..  
T Consensus        37 ~~V~v~GwV~~~R~~g~~l~Fi~LrD~~g~iQvv~~~~~~~~~~~~~~~~~~~l~~e-------~~V~V~G~v~~~~~~~  109 (487)
T 1eov_A           37 KEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLE-------SIVLVRGIVKKVDEPI  109 (487)
T ss_dssp             CEEEEEEEEEEEEECSSSEEEEEEEETTEEEEEEEECCSSSSSCHHHHHHHTTCCTT-------CEEEEEEEEEECSSCC
T ss_pred             CEEEEEEEEEEeeccCCccEEEEEEECCccEEEEEeccccccccHHHHHHHhcCCCC-------CEEEEEEEEEeCCCCC
Confidence            469999999999765554   57889999999987432     111     248899       99999999988432  


Q ss_pred             -----CCceEEEEEEeeCCCC
Q 044496          100 -----DIPVIKVHKIVDLSAF  115 (142)
Q Consensus       100 -----~~p~i~a~K~~DLS~~  115 (142)
                           .+-.|.|.++.=||.+
T Consensus       110 ~~~~~g~~El~~~~i~vl~~a  130 (487)
T 1eov_A          110 KSATVQNLEIHITKIYTISET  130 (487)
T ss_dssp             TTSSEEEEEEEEEEEEEEECC
T ss_pred             cCCCCCcEEEEEEEEEEeecc
Confidence                 2457778777777753

>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=94.27  E-value=0.24  Score=43.03  Aligned_cols=74  Identities=27%  Similarity=0.219  Sum_probs=54.0

Q ss_pred             eEEEEEEEEEeeeCCCC-c-EEEEcCCeeEEEEecccc------c-cccccCCcccccceeEEEEEeeEeeccC--CCce
Q 044496           35 QRVWLQGVLVSPPDDDG-R-LLLDDGTGVVQIYLSGDF------R-IRRWNTGVFFFDFWMYVMVVGGFVIRTD--DIPV  103 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~-~-~~LdDgTG~~~v~~~~~~------~-~~~~~~G~~~~~~~~YVmViG~~~~~~~--~~p~  103 (142)
                      +.|++.|.|.++..-++ . +.|.|+||.+++..+...      + ...++.|       ..|.|-|.+..+..  .+-.
T Consensus        17 ~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~~-------~~V~V~G~v~~~~~~~~~~e   89 (438)
T 3nem_A           17 QKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSE-------DVVAVEGVVNFTPKAKLGFE   89 (438)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSCHHHHHHGGGCCTT-------CEEEEEEEEEECTTSTTSEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEeCCcCCHHHHHHHhcCCCC-------CEEEEEEEEEeCCCCCCcEE
Confidence            46899999999864444 3 469999999998874321      1 2258999       99999999987432  4567


Q ss_pred             EEEEEEeeCCCC
Q 044496          104 IKVHKIVDLSAF  115 (142)
Q Consensus       104 i~a~K~~DLS~~  115 (142)
                      |+|.++.=||.+
T Consensus        90 l~~~~i~vl~~~  101 (438)
T 3nem_A           90 ILPEKIVVLNRA  101 (438)
T ss_dssp             EEEEEEEEEECB
T ss_pred             EEEEEEEEEecC
Confidence            888777766653

>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=94.07  E-value=0.29  Score=43.96  Aligned_cols=74  Identities=22%  Similarity=0.181  Sum_probs=53.9

Q ss_pred             eEEEEEEEEEeeeCCCCc--EEEEcCCeeEEEEecccc---c-cccccCCcccccceeEEEEEeeEeecc-------CCC
Q 044496           35 QRVWLQGVLVSPPDDDGR--LLLDDGTGVVQIYLSGDF---R-IRRWNTGVFFFDFWMYVMVVGGFVIRT-------DDI  101 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~--~~LdDgTG~~~v~~~~~~---~-~~~~~~G~~~~~~~~YVmViG~~~~~~-------~~~  101 (142)
                      +.|++.|.|.++..-++.  +.|.|+||.+++..+...   + -..++.|       ..|.|.|.+..+.       ..+
T Consensus        17 ~~V~l~GwV~~~R~~G~~~Fi~LrD~~g~iQvv~~~~~~~~~~~~~l~~e-------~~V~V~G~v~~~~~~~~~~~~ge   89 (580)
T 1l0w_A           17 EEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPE-------WVVRAKGLVRLRPEPNPRLATGR   89 (580)
T ss_dssp             CEEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECTTSTTHHHHTTCCTT-------CEEEEEEEEEECSSCCTTSTTTT
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEeCChhHHHHHhcCCCC-------cEEEEEEEEEcCCCcCccCCCcc
Confidence            358999999999655443  568899999999874321   1 1248899       9999999998842       235


Q ss_pred             ceEEEEEEeeCCCC
Q 044496          102 PVIKVHKIVDLSAF  115 (142)
Q Consensus       102 p~i~a~K~~DLS~~  115 (142)
                      -.|.|.++.=||.+
T Consensus        90 ~Ei~~~~i~vl~~a  103 (580)
T 1l0w_A           90 VEVELSALEVLAEA  103 (580)
T ss_dssp             EEEEEEEEEEEECC
T ss_pred             EEEEEeEEEEeccC
Confidence            67888777767654

>2xgt_A Asparaginyl-tRNA synthetase, cytoplasmic; ligase, ATP-binding, protein biosynthesis; HET: NSS; 1.90A {Brugia malayi} PDB: 2xti_A*

Probab=93.92  E-value=0.36  Score=41.61  Aligned_cols=72  Identities=19%  Similarity=0.196  Sum_probs=51.5

Q ss_pred             EEEEEEEEEeeeCCCC---cEEEEcCCeeEEEEecccc-c---cccccCCcccccceeEEEEEeeEeecc-----CCCce
Q 044496           36 RVWLQGVLVSPPDDDG---RLLLDDGTGVVQIYLSGDF-R---IRRWNTGVFFFDFWMYVMVVGGFVIRT-----DDIPV  103 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~---~~~LdDgTG~~~v~~~~~~-~---~~~~~~G~~~~~~~~YVmViG~~~~~~-----~~~p~  103 (142)
                      .|++.|.|.++..-++   =+.|.|+||.+++..+... .   ...+..|       ..|.|-|.+.++.     ..+-.
T Consensus        13 ~V~v~Gwv~~~R~~Gk~~~Fi~LrD~~g~iQvv~~~~~~~~~~~~~l~~~-------~~v~v~G~v~~~~~~~~~~g~~E   85 (435)
T 2xgt_A           13 RVCIKGWIHRMRRQGKSLMFFILRDGTGFLQVLLMDKLCQTYDALTVNTE-------CTVEIYGAIKEVPEGKEAPNGHE   85 (435)
T ss_dssp             EEEEEEEEEEEEECTTSEEEEEEECSSCEEEEEEEGGGGSSHHHHHCCTT-------CEEEEEEEEEECC------TTEE
T ss_pred             EEEEEEEEEEecccCCCcEEEEEEECCceEEEEECCcchhHHHHhcCCCC-------CEEEEEEEEEecCCCcCCCCcEE
Confidence            5899999999975543   3678999999999874221 1   1147889       9999999998732     23457


Q ss_pred             EEEEEEeeCCC
Q 044496          104 IKVHKIVDLSA  114 (142)
Q Consensus       104 i~a~K~~DLS~  114 (142)
                      |.|.++.=||.
T Consensus        86 l~~~~~~vl~~   96 (435)
T 2xgt_A           86 LIADFWKIIGN   96 (435)
T ss_dssp             EEEEEEEEEEC
T ss_pred             EEEEEEEEeec
Confidence            77777666663

>4ex5_A Lysine--tRNA ligase; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: LYS; 2.40A {Burkholderia thailandensis}

Probab=93.88  E-value=0.22  Score=44.60  Aligned_cols=74  Identities=16%  Similarity=0.249  Sum_probs=55.2

Q ss_pred             eEEEEEEEEEeeeCCCC-c-EEEEcCCeeEEEEeccc--cc-----cccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           35 QRVWLQGVLVSPPDDDG-R-LLLDDGTGVVQIYLSGD--FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~-~-~~LdDgTG~~~v~~~~~--~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      +.|++.|+|.++..-++ . +.|.|+||.+++..+..  ..     -+.+..|       +.|.|-|.+......+-.|.
T Consensus        87 ~~V~v~GwV~~~R~~Gk~~Fi~LrD~sg~iQvv~~~~~~~~~~~~~~~~l~~g-------d~V~V~G~v~~t~~gelel~  159 (529)
T 4ex5_A           87 LEVAIAGRMMLKRVMGKASFATVQDGSGQIQFFVTPADVGAETYDAFKKWDLG-------DIVAARGVLFRTNKGELSVK  159 (529)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEECSSCEEEEEECHHHHCHHHHHHHHTCCTT-------CEEEEEEEEEECTTSCEEEE
T ss_pred             cEEEEEEEEEeeecCCCeEEEEEEeCCeeEEEEEECCcCCHHHHHHHhcCCCC-------CEEEEEEEEEEcCCCcEEEE
Confidence            46899999999864443 3 46999999999987432  11     1248999       99999999988544577888


Q ss_pred             EEEEeeCCCC
Q 044496          106 VHKIVDLSAF  115 (142)
Q Consensus       106 a~K~~DLS~~  115 (142)
                      |.++.=||.+
T Consensus       160 ~~~i~vLs~a  169 (529)
T 4ex5_A          160 CTQLRLLAKA  169 (529)
T ss_dssp             EEEEEEEECC
T ss_pred             EEEEEEEecC
Confidence            8877767664

>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=93.41  E-value=0.24  Score=43.59  Aligned_cols=74  Identities=23%  Similarity=0.160  Sum_probs=55.8

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--c----c-cccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--F----R-IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~----~-~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      +.|++.|.|.++..-++  =+.|.|+||.+++..+..  .    + -..+..|       ..|.|-|.+.++...+-.|+
T Consensus        57 ~~V~v~Gwv~~~R~~gk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~l~~g-------~~v~V~G~v~~~~~ge~ei~  129 (493)
T 3a74_A           57 IEVAVAGRIMTKRGMGKAGFAHIQDVTGQIQIYVRQDDVGEQQYELFKISDLG-------DIVGVRGTMFKTKVGELSIK  129 (493)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEEHHHHHHHHHHHHHHCCTT-------CEEEEEEEEEECTTCCEEEE
T ss_pred             CEEEEEEEEEEEecCCCcEEEEEEECCEeEEEEEECCcCCHHHHHHHhcCCCC-------CEEEEEEEEEeCCCCcEEEE
Confidence            36999999999864433  356889999999987322  1    1 1248999       99999999988655677888


Q ss_pred             EEEEeeCCCC
Q 044496          106 VHKIVDLSAF  115 (142)
Q Consensus       106 a~K~~DLS~~  115 (142)
                      |.++.=||.+
T Consensus       130 ~~~i~vl~~~  139 (493)
T 3a74_A          130 VSSYEFLTKA  139 (493)
T ss_dssp             EEEEEEEECC
T ss_pred             EEEEEEcccc
Confidence            8888777754

>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=93.36  E-value=0.46  Score=42.64  Aligned_cols=73  Identities=16%  Similarity=0.199  Sum_probs=54.2

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccc----c-cccccCCcccccceeEEEEEeeEeecc---------C
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDF----R-IRRWNTGVFFFDFWMYVMVVGGFVIRT---------D   99 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~----~-~~~~~~G~~~~~~~~YVmViG~~~~~~---------~   99 (142)
                      .|++.|.|.++..-++  =+.|.|+||.++|..+...    + -..++.|       ..|.|-|.+..+.         .
T Consensus        17 ~V~l~GwV~~~R~~G~~~Fi~LrD~~g~iQvv~~~~~~~~~~~~~~l~~e-------~~V~V~G~v~~~~~~~~n~~~~~   89 (585)
T 1c0a_A           17 QVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNE-------FCIQVTGTVRARDEKNINRDMAT   89 (585)
T ss_dssp             EEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECGGGHHHHHHHTTCCTT-------CEEEEEEEEEECCTTTCCTTSTT
T ss_pred             EEEEEEEEEEEecCCCcEEEEEEECCeeEEEEEeCCchHHHHHHhcCCCC-------CEEEEEeEEEccCcccccccCCC
Confidence            5899999999965444  3668899999999874321    1 1248999       9999999998741         2


Q ss_pred             CCceEEEEEEeeCCCC
Q 044496          100 DIPVIKVHKIVDLSAF  115 (142)
Q Consensus       100 ~~p~i~a~K~~DLS~~  115 (142)
                      .+-.|.|.++.=||.+
T Consensus        90 geiEl~~~~i~vl~~a  105 (585)
T 1c0a_A           90 GEIEVLASSLTIINRA  105 (585)
T ss_dssp             TTEEEEEEEEEEEECC
T ss_pred             ccEEEEEeEEEEEecc
Confidence            3568888887777754

>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding, aminoacyl-tRNA synthetase, LI nucleotide-binding, protein biosynthesis; 2.80A {Entamoeba histolytica}

Probab=93.03  E-value=0.62  Score=41.90  Aligned_cols=74  Identities=14%  Similarity=0.051  Sum_probs=53.9

Q ss_pred             eEEEEEEEEEeeeCCCC-c-EEEEcCCeeEEEEecc---cccc-----ccccCCcccccceeEEEEEeeEeeccC-----
Q 044496           35 QRVWLQGVLVSPPDDDG-R-LLLDDGTGVVQIYLSG---DFRI-----RRWNTGVFFFDFWMYVMVVGGFVIRTD-----   99 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~-~-~~LdDgTG~~~v~~~~---~~~~-----~~~~~G~~~~~~~~YVmViG~~~~~~~-----   99 (142)
                      +.||+.|+|.++..-++ . +.|.|+||.+++..+.   ..+.     ..+..|       ..|-|-|.+.++..     
T Consensus        63 ~~V~v~Gwv~~~R~~gkl~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~~  135 (548)
T 3i7f_A           63 KTVTIRARVQAVRGKGNMVFLFLRKGIYTCQALVMKSETISKEFVQFCQKISAE-------SICDITGIVKAVEKPIEKA  135 (548)
T ss_dssp             CEEEEEEEEEEEEECSSEEEEEEEETTEEEEEEEECSSSSCHHHHHHHHTCCTT-------EEEEEEEEEEECSSCCTTS
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEECCCccCHHHHHHHhCCCCC-------CEEEEEEEEEeCCcccccC
Confidence            67999999999865444 3 3499999999998743   1111     248899       99999999988422     


Q ss_pred             --CCceEEEEEEeeCCCC
Q 044496          100 --DIPVIKVHKIVDLSAF  115 (142)
Q Consensus       100 --~~p~i~a~K~~DLS~~  115 (142)
                        .+-.|+|-++.=||.+
T Consensus       136 ~~~~~El~~~~i~vls~a  153 (548)
T 3i7f_A          136 TQQDVEIHVTSIAVVSLA  153 (548)
T ss_dssp             SSCSEEEEEEEEEEEECC
T ss_pred             CCCcEEEEEeEEEEEecC
Confidence              3567888777666664

>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum}

Probab=92.79  E-value=0.8  Score=32.13  Aligned_cols=62  Identities=18%  Similarity=0.169  Sum_probs=42.4

Q ss_pred             EEEEEEEEeeeCC----CC------cEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEE
Q 044496           37 VWLQGVLVSPPDD----DG------RLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKV  106 (142)
Q Consensus        37 VWlQG~vv~~~~~----~~------~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a  106 (142)
                      |-+.|.|+++.+.    +|      .++|-|.||.+.+.+=.+.    +++|       +.|.+-++........+.|.+
T Consensus        16 v~v~~~V~~~~~~~~~k~G~~~~v~~~~l~DeTG~I~~tlW~~~----l~~G-------dvv~i~ng~v~~~~g~~~L~v   84 (106)
T 2k75_A           16 VSVIGKITGIHKKEYESDGTTKSVYQGYIEDDTARIRISSFGKQ----LQDS-------DVVRIDNARVAQFNGYLSLSV   84 (106)
T ss_dssp             EEEEEEEEEEEEEEEEETTEEEEEEEEEEECSSCEEEEEEESSC----CCTT-------EEEEEEEEEEEEETTEEEEEE
T ss_pred             EEEEEEEEEccccccccCCCeeEEEEEEEEcCCCeEEEEEEcCc----cCCC-------CEEEEEeeEEeEECCEEEEEE
Confidence            4455666555321    33      5899999999999982222    9999       999999555444677777775


Q ss_pred             EEE
Q 044496          107 HKI  109 (142)
Q Consensus       107 ~K~  109 (142)
                      -+.
T Consensus        85 ~~~   87 (106)
T 2k75_A           85 GDS   87 (106)
T ss_dssp             CTT
T ss_pred             CCc
Confidence            543

>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=92.53  E-value=0.44  Score=41.15  Aligned_cols=74  Identities=22%  Similarity=0.264  Sum_probs=54.2

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc------cc-cccccCCcccccceeEEEEEeeEeeccCC--Cce
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD------FR-IRRWNTGVFFFDFWMYVMVVGGFVIRTDD--IPV  103 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~------~~-~~~~~~G~~~~~~~~YVmViG~~~~~~~~--~p~  103 (142)
                      +.|++.|.|.++..-++  =+.|.|+||.+++..+..      .+ -..+..|       ..|.|.|.+..+...  +-.
T Consensus        17 ~~V~v~G~v~~~R~~g~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~~-------~~v~v~G~v~~~~~~~~~~e   89 (434)
T 1x54_A           17 KKVRLAGWVYTNMRVGKKIFLWIRDSTGIVQAVVAKNVVGEETFEKAKKLGRE-------SSVIVEGIVKADERAPGGAE   89 (434)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEECHHHHCHHHHHHHHTCCTT-------CEEEEEEEEEECTTSGGGEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCEEEEEEEECCcCCHHHHHHHhcCCCC-------CEEEEEEEEEecCCCCccEE
Confidence            35899999999865444  266889999999987321      11 1258999       999999999884332  678


Q ss_pred             EEEEEEeeCCCC
Q 044496          104 IKVHKIVDLSAF  115 (142)
Q Consensus       104 i~a~K~~DLS~~  115 (142)
                      |.|.++.=||.+
T Consensus        90 l~~~~~~vl~~~  101 (434)
T 1x54_A           90 VHVEKLEVIQAV  101 (434)
T ss_dssp             EEEEEEEEEECC
T ss_pred             EEEeEEEEeecC
Confidence            888887777754

>3au7_A TIAS, putative uncharacterized protein; ATP hydrolysis, RNA binding protein; 2.60A {Archaeoglobus fulgidus} PDB: 3amt_A* 3amu_A*

Probab=92.18  E-value=0.48  Score=41.32  Aligned_cols=67  Identities=24%  Similarity=0.249  Sum_probs=50.0

Q ss_pred             eEEeEEEEEEEEEeee--CCC--CcEEEEcCCeeEEEEe-c--cccccc--cccCCcccccceeEEEEEeeEeeccCCCc
Q 044496           32 ILFQRVWLQGVLVSPP--DDD--GRLLLDDGTGVVQIYL-S--GDFRIR--RWNTGVFFFDFWMYVMVVGGFVIRTDDIP  102 (142)
Q Consensus        32 l~~~~VWlQG~vv~~~--~~~--~~~~LdDgTG~~~v~~-~--~~~~~~--~~~~G~~~~~~~~YVmViG~~~~~~~~~p  102 (142)
                      ...+.+|+.|+|.+.+  ..+  .-|.|.|++|.+.|-- .  +.++..  .+.+|       +.|.|.|.+..  +   
T Consensus       282 ~~~~~~~v~G~V~~~P~~~~GGHV~f~l~d~~~~i~c~ayeptk~fr~~vr~L~~G-------D~V~v~G~v~~--g---  349 (402)
T 3au7_A          282 ENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAAFEPTKQFRNVIRLLRKG-------DVVEVYGSMKK--D---  349 (402)
T ss_dssp             CTTCEEEEEEEEEEEEEEETTTEEEEEEEETTEEEEEEECGGGTTHHHHHTTCCTT-------CEEEEEEEEET--T---
T ss_pred             ccCceEEEEEEEecCcEeccCceEEEEEEcCCCEEEEEEEccchHHHHHHhcCCCC-------CEEEEEEeecC--C---
Confidence            4578999999999882  223  4899999999998874 2  344432  48999       99999999855  2   


Q ss_pred             eEEEEEEe
Q 044496          103 VIKVHKIV  110 (142)
Q Consensus       103 ~i~a~K~~  110 (142)
                      .|.+-|+-
T Consensus       350 tLnvEk~~  357 (402)
T 3au7_A          350 TINLEKIQ  357 (402)
T ss_dssp             EEEEEEEE
T ss_pred             EEEEEEEE
Confidence            77766654

>4ah6_A Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo sapiens}

Probab=87.14  E-value=2.2  Score=38.87  Aligned_cols=73  Identities=27%  Similarity=0.217  Sum_probs=51.5

Q ss_pred             eEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEeccccc-------cccccCCcccccceeEEEEEeeEeeccC--------
Q 044496           35 QRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFR-------IRRWNTGVFFFDFWMYVMVVGGFVIRTD--------   99 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~-------~~~~~~G~~~~~~~~YVmViG~~~~~~~--------   99 (142)
                      +.|.+.|.|-.... .-=+.|.|+||.+++..+....       ...+..|       ..|.|-|.+.++..        
T Consensus        25 ~~V~l~GwV~~~R~-~~Fi~LrD~~g~iQvv~~~~~~~~~~~~~~~~l~~e-------~~V~V~G~v~~~~~~~~n~~~~   96 (617)
T 4ah6_A           25 QEVTLCGWIQYRRQ-NTFLVLRDFDGLVQVIIPQDESAASVKKILCEAPVE-------SVVQVSGTVISRPAGQENPKMP   96 (617)
T ss_dssp             CEEEEEEEECCCCT-TTEEEEECSSCEEEEECCCSSSSHHHHHHHHHCCSS-------CEEEEEEEEEECSTTCCCTTST
T ss_pred             CEEEEEEEeeeecC-eEEEEEEeCCcCEEEEEeCCcCcHHHHHHHhcCCCC-------CEEEEEEEEEeCCccccCccCC
Confidence            47899999998742 3345699999999998743211       1248899       99999999986321        


Q ss_pred             -CCceEEEEEEeeCCCC
Q 044496          100 -DIPVIKVHKIVDLSAF  115 (142)
Q Consensus       100 -~~p~i~a~K~~DLS~~  115 (142)
                       .+-.|+|.++.=||.+
T Consensus        97 tgeiEl~~~~i~vL~~a  113 (617)
T 4ah6_A           97 TGEIEIKVKTAELLNAC  113 (617)
T ss_dssp             TTTEEEEEEEEEEEECB
T ss_pred             CCcEEEEEeEEEEeecC
Confidence             2457777766656553

>3e0j_A DNA polymerase subunit delta-2; DNA polymerase delta, P66 subunit, P50 subunit, human, DNA replication, DNA-directed DNA polymerase; HET: DNA; 3.00A {Homo sapiens}

Probab=85.78  E-value=5.6  Score=35.21  Aligned_cols=38  Identities=21%  Similarity=0.348  Sum_probs=28.7

Q ss_pred             CCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496           49 DDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV   95 (142)
Q Consensus        49 ~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~   95 (142)
                      +++.+.|-|.||++++.+.  .+...+-+|       .-|.|.|...
T Consensus       136 ~~D~l~LEDesGRv~L~g~--~~~~~lVTG-------~VvaV~G~~~  173 (476)
T 3e0j_A          136 PDDELVLEDELQRIKLKGT--IDVSKLVTG-------TVLAVFGSVR  173 (476)
T ss_dssp             SSCEEEEECSSCEEEEEES--CCTTTCCTT-------CEEEEEEEEC
T ss_pred             CCceEEEECCCCEEEEEEE--cccccccCC-------cEEEEEEEEc
Confidence            3568999999999999871  222347888       8888888764

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3

Probab=85.74  E-value=3  Score=29.26  Aligned_cols=48  Identities=15%  Similarity=0.185  Sum_probs=34.5

Q ss_pred             cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496           52 RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK  108 (142)
Q Consensus        52 ~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K  108 (142)
                      .++|-|.||.+++.+ +...  ..+++|       ++|.+-++.....+..+.|...+
T Consensus        41 ~~~l~D~TG~I~~tlW~~~~--~~~~~G-------~vv~i~~g~v~~~~g~~qL~i~~   89 (119)
T 1o7i_A           41 EAIVGDETGRVKLTLWGKHA--GSIKEG-------QVVKIENAWTTAFKGQVQLNAGS   89 (119)
T ss_dssp             EEEEEETTEEEEEEEEGGGT--TCCCTT-------CEEEEEEEEEEEETTEEEEEECT
T ss_pred             EEEEEeCCCEEEEEEECChh--hcCCCC-------CEEEEEeEEEEEeCCEEEEEECC
Confidence            689999999999988 3322  248999       99999944434366667776554

>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=85.18  E-value=1.4  Score=43.20  Aligned_cols=71  Identities=15%  Similarity=0.305  Sum_probs=45.6

Q ss_pred             eEEEEEEEEEeeeCC---CC----cEEEEcCCeeEEEEe-ccccc-ccc-ccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496           35 QRVWLQGVLVSPPDD---DG----RLLLDDGTGVVQIYL-SGDFR-IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVI  104 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~---~~----~~~LdDgTG~~~v~~-~~~~~-~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i  104 (142)
                      ++|.+-|.|+++...   .|    -++|.|.||.+.+.. +...+ -+. +..|       ..|.|-|.++. .+ ...+
T Consensus      1043 ~~v~v~G~v~~~~~~~Tk~G~~maf~tleD~tg~~evvvf~~~~~~~~~~l~~~-------~~~~v~G~v~~-~~-~~~l 1113 (1220)
T 2hpi_A         1043 PKVLLSGMVEEVVRKPTRSGGMMARFTLSDETGALEVVVFGRAYEGVSPKLKED-------IPLLVLAEVEK-GE-ELRV 1113 (1220)
T ss_dssp             CEEEEEEEECCC------------CEEEEETTEEEEEC-------------CTT-------CEEEEEEEEC-------CE
T ss_pred             CeEEEEEEEEEEEEeecCCCCeEEEEEEEECCCCEEEEEcHHHHHHHHHHhccC-------CEEEEEEEEEE-CC-CcEE
Confidence            457789999988432   33    799999999999986 55443 334 8999       99999999976 34 6789


Q ss_pred             EEEEEeeCCC
Q 044496          105 KVHKIVDLSA  114 (142)
Q Consensus       105 ~a~K~~DLS~  114 (142)
                      .|.++.||++
T Consensus      1114 ~~~~i~~l~~ 1123 (1220)
T 2hpi_A         1114 LAQAVWTLEE 1123 (1220)
T ss_dssp             EEEEEEEHHH
T ss_pred             EEeeeecHHH
Confidence            9999999975

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	142
d2pi2a1	128	Replication protein A 32 KDa subunit (RPA32) fragm	99.47
d1nnxa_	106	Hypothetical protein YgiW {Escherichia coli [TaxId	97.91
d1eova1	134	Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S	96.88
d1n9wa1	93	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	96.73
d1b8aa1	103	Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ	95.57
d2pi2e1	115	Replication protein A 14 KDa (RPA14) subunit {Huma	95.44
d1l0wa1	104	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	95.41
d1c0aa1	106	Aspartyl-tRNA synthetase (AspRS) {Escherichia coli	94.27
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	92.94
d3d3ra1	76	Hydrogenase expression/formation protein HypC {She	88.6
d1o7ia_	115	Archaeal ssDNA-binding protein {Archaeon Sulfolobu	86.38
d1sr3a_	114	Heme chaperone CcmE {Escherichia coli [TaxId: 562]	82.1
d1wjja_	145	Hypothetical protein At4g28440 (F20O9.120) {Thale	81.2
d1j6qa_	100	Heme chaperone CcmE {Shewanella putrefaciens [TaxI	80.55

>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=99.47  E-value=4.4e-13  Score=97.15  Aligned_cols=111  Identities=19%  Similarity=0.200  Sum_probs=90.9

Q ss_pred             HHHHhhccCCCCCCceeecCeEEeEEEEEEEEEeeeCC--CCcEEEEcCCe-eEEEEe---ccc-cccc-cccCCccccc
Q 044496           12 CVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDD--DGRLLLDDGTG-VVQIYL---SGD-FRIR-RWNTGVFFFD   83 (142)
Q Consensus        12 ~~QL~~a~~~~s~~~~~l~gl~~~~VWlQG~vv~~~~~--~~~~~LdDgTG-~~~v~~---~~~-~~~~-~~~~G~~~~~   83 (142)
                      ++||.+|.+.  .+.|.++|.++++|.+.|.|+++.+.  .-.+.|||||| .+++..   +.. .... +++.|     
T Consensus         8 I~ql~~a~~~--~~~f~i~g~~v~~V~iVG~V~~i~~~~t~~~y~idDgTG~~i~v~~w~~~~~~~~~~~~i~~g-----   80 (128)
T d2pi2a1           8 ISQLLSATLV--DEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPE-----   80 (128)
T ss_dssp             HHHHHHCEEE--TTEEEETTEEESEEEEEEEEEEEEECSSEEEEEEECSSSSCEEEEEECC-------CCCCCTT-----
T ss_pred             HHHHhcCcCC--CCCEEECCEEEEEEEEEEEEEEEEecCCEEEEEEECCCCCcEEEEEECCCCCCccccccccCC-----
Confidence            7899999653  35799999999999999999999655  45899999999 598886   222 2222 59999     


Q ss_pred             ceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHH
Q 044496           84 FWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLF  133 (142)
Q Consensus        84 ~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~  133 (142)
                        +||.|.|.++. -+..+.|.|.+|.-+.+ ++...+=.|||..+|..+
T Consensus        81 --~yVrV~G~lk~-f~~~~~i~~~~i~~v~d-~Nei~~H~Levi~~hL~~  126 (128)
T d2pi2a1          81 --TYVKVAGHLRS-FQNKKSLVAFKIMPLED-MNEFTTHILEVINAHMVL  126 (128)
T ss_dssp             --CEEEEEEEEEE-ETTEEEEEEEEEEECSC-THHHHHHHHHHHHHHHHH
T ss_pred             --CEEEEEEEEEe-eCCeEEEEEEEEEEeCC-cCHHHHHHHHHHHHHHhh
Confidence              99999999987 67788999999999987 888889999999998764

>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=97.91  E-value=3.6e-05  Score=54.59  Aligned_cols=68  Identities=18%  Similarity=0.164  Sum_probs=58.2

Q ss_pred             eEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEee
Q 044496           35 QRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVD  111 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~D  111 (142)
                      +.|-|.|.|++. -+++.+++.|+||.+.|.. +...++.++.++       .-|.+.|.+-+ ....|.|.+.+|.-
T Consensus        37 t~V~L~G~Iv~~-l~~d~Y~F~D~TG~I~VeId~~~w~g~~v~p~-------~kV~i~GevDk-~~~~~eIdV~~I~~  105 (106)
T d1nnxa_          37 TWVTLRGNIVER-ISDDLYVFKDASGTINVDIDHKRWNGVTVTPK-------DTVEIQGEVDK-DWNSVEIDVKQIRK  105 (106)
T ss_dssp             EEEEEEEEEEEE-EETTEEEEEETTEEEEEECCGGGSTTCCCCTT-------SCEEEEEEEEE-ETTEEEEEEEEEEE
T ss_pred             CeEEEEEEEEEE-eCCceEEEECCCCcEEEEEChhhcCCcccCCC-------CEEEEEEEEcC-CCCceEEEEEEEEE
Confidence            568899999995 4789999999999999998 566688899999       99999999987 45678888887754

>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=96.88  E-value=0.0066  Score=42.76  Aligned_cols=75  Identities=16%  Similarity=0.115  Sum_probs=53.5

Q ss_pred             EeEEEEEEEEEeeeCCCC---cEEEEcCCeeEEEEeccccc----------cccccCCcccccceeEEEEEeeEeeccCC
Q 044496           34 FQRVWLQGVLVSPPDDDG---RLLLDDGTGVVQIYLSGDFR----------IRRWNTGVFFFDFWMYVMVVGGFVIRTDD  100 (142)
Q Consensus        34 ~~~VWlQG~vv~~~~~~~---~~~LdDgTG~~~v~~~~~~~----------~~~~~~G~~~~~~~~YVmViG~~~~~~~~  100 (142)
                      =+.||+.|+|.....-++   =+.|.|+||.+++.......          ...+..|       ..|.|-|.+..+..+
T Consensus        36 g~~V~v~GwV~~~R~~G~kl~F~~LrD~sg~iQ~~v~~~~~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~  108 (134)
T d1eova1          36 DKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLE-------SIVLVRGIVKKVDEP  108 (134)
T ss_dssp             TCEEEEEEEEEEEEECSSSEEEEEEEETTEEEEEEEECCSSSSSCHHHHHHHTTCCTT-------CEEEEEEEEEECSSC
T ss_pred             CCEEEEEEEEEEEEeCCCcEEEEEEEcCCCcEEEEEEeccccchhHHHHHHHhcCCCC-------CEEEEEEEEEeCCcc
Confidence            468999999999965443   36799999999888632211          1247899       999999999873222


Q ss_pred             -------CceEEEEEEeeCCCC
Q 044496          101 -------IPVIKVHKIVDLSAF  115 (142)
Q Consensus       101 -------~p~i~a~K~~DLS~~  115 (142)
                             .-.|++.++.=||.+
T Consensus       109 ~~~~~~~~~Ei~v~~i~vls~a  130 (134)
T d1eova1         109 IKSATVQNLEIHITKIYTISET  130 (134)
T ss_dssp             CTTSSEEEEEEEEEEEEEEECC
T ss_pred             CCCCCCCcEEEEEEEEEEEeCC
Confidence                   237777777666654

>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=96.73  E-value=0.011  Score=39.26  Aligned_cols=71  Identities=28%  Similarity=0.165  Sum_probs=53.0

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeecc--CCCceEEEEEEe
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPVIKVHKIV  110 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~i~a~K~~  110 (142)
                      +.|+++|.|.+....++  =+.|.||||.+++..+..   .....|       ..|.|-|.+..+.  ..+-.|.|.++.
T Consensus        14 ~~V~v~GwV~~~R~~gk~~Fi~LrD~sg~iQ~v~~~~---~~~~~e-------~~v~v~G~v~~~~~~~~~~Ei~v~~i~   83 (93)
T d1n9wa1          14 QEVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGGL---KLPLPE-------SALRVRGLVVENAKAPGGLEVQAKEVE   83 (93)
T ss_dssp             SEEEEEEEEEEEEECSSEEEEEEEETTEEEEEEEESC---CCCCTT-------CEEEEEEEEEECTTSTTSEEEEEEEEE
T ss_pred             CEEEEEEEEEeEEeCCCcEEEEEEcCCccceEEeccc---cccccc-------eEEEEEEEEEECCCCCCCEEEEEeEEE
Confidence            46899999999865444  457899999999987442   235678       9999999998732  246688888777


Q ss_pred             eCCCC
Q 044496          111 DLSAF  115 (142)
Q Consensus       111 DLS~~  115 (142)
                      =||.+
T Consensus        84 il~~a   88 (93)
T d1n9wa1          84 VLSPA   88 (93)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            67653

>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=95.57  E-value=0.056  Score=36.34  Aligned_cols=73  Identities=29%  Similarity=0.302  Sum_probs=49.4

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc------cc-cccccCCcccccceeEEEEEeeEeecc-CCC-ce
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD------FR-IRRWNTGVFFFDFWMYVMVVGGFVIRT-DDI-PV  103 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~------~~-~~~~~~G~~~~~~~~YVmViG~~~~~~-~~~-p~  103 (142)
                      +.|++.|.|.+...-++  =+.|.|+||.+++..+..      ++ -..++.|       ..|-|-|.+..+. .+. -.
T Consensus        17 ~~V~v~Gwv~~~R~~g~i~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~l~~e-------s~v~V~G~v~~~~~~~~~iE   89 (103)
T d1b8aa1          17 QKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSE-------DVVAVEGVVNFTPKAKLGFE   89 (103)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSCHHHHHHGGGCCTT-------CEEEEEEEEEECTTSTTSEE
T ss_pred             CEEEEEEEEehhccCCCcEEEEEEcCCEeeeEEEeccccchhhhhHHhhCCcc-------eEEEEEEEEEECCCCCccEE
Confidence            35889999999864443  345999999999987332      11 1258899       9999999997732 121 24


Q ss_pred             EEEEEEeeCCC
Q 044496          104 IKVHKIVDLSA  114 (142)
Q Consensus       104 i~a~K~~DLS~  114 (142)
                      |.|-++.=||.
T Consensus        90 i~v~~i~ils~  100 (103)
T d1b8aa1          90 ILPEKIVVLNR  100 (103)
T ss_dssp             EEEEEEEEEEC
T ss_pred             EEeeEEEEEEe
Confidence            66666554443

>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=95.44  E-value=0.095  Score=36.24  Aligned_cols=65  Identities=23%  Similarity=0.198  Sum_probs=51.8

Q ss_pred             EEEEEEEEEeeeCCCCcEEEEcCCe-eEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCC
Q 044496           36 RVWLQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSA  114 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~  114 (142)
                      .|.+.|+|.++..++.++++.++-| .++|.++...   ....+       .||=|+|.+..    .-.|+|...+++..
T Consensus        22 ~V~ivGkV~~v~~~g~~~~~~s~D~~~V~v~l~~~~---~~~~~-------~~vEViG~V~~----~~sI~~~~~~~fg~   87 (115)
T d2pi2e1          22 PVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPL---DEEIS-------GIVEVVGRVTA----KATILCTSYVQFKE   87 (115)
T ss_dssp             EEEEEEEEEEECTTSSEEEEECTTSCEEEEECSSCC---SSCCC-------SEEEEEEEECT----TSCEEEEEEEECCC
T ss_pred             eEEEEEEEEEEcCCCCEEEEEcCCCCEEEEEeCCCC---CCccC-------CeEEEEEEECC----CCcEEEEEEEEcCC
Confidence            6889999999877888999998866 6999986632   23567       89999998843    45699999998854

>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=95.41  E-value=0.077  Score=36.01  Aligned_cols=73  Identities=22%  Similarity=0.198  Sum_probs=50.2

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccc---c-cccccCCcccccceeEEEEEeeEeeccCC-------C
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDF---R-IRRWNTGVFFFDFWMYVMVVGGFVIRTDD-------I  101 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~---~-~~~~~~G~~~~~~~~YVmViG~~~~~~~~-------~  101 (142)
                      +.|.+.|.|-.....++  =+.|.|+||.+++......   . ...+..+       ..|.|-|.+.++...       +
T Consensus        17 ~~V~l~GWV~~~R~~g~i~Fi~LRD~~G~iQ~v~~~~~~~~~~~~~l~~E-------s~I~V~G~V~~r~~~n~~~~tG~   89 (104)
T d1l0wa1          17 EEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPE-------WVVRAKGLVRLRPEPNPRLATGR   89 (104)
T ss_dssp             CEEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECTTSTTHHHHTTCCTT-------CEEEEEEEEEECSSCCTTSTTTT
T ss_pred             CEEEEEEEEEehhcCCCeEEEEEECCCCceEEecccchhHHHHHhhcCcc-------cEEEEEEEEeeCCccCCCCCCCC
Confidence            46889999988864444  4569999999999873322   2 2358889       999999999863221       2


Q ss_pred             ceEEEEEEeeCCC
Q 044496          102 PVIKVHKIVDLSA  114 (142)
Q Consensus       102 p~i~a~K~~DLS~  114 (142)
                      -.|.|-++.=||.
T Consensus        90 iEi~v~~i~iL~~  102 (104)
T d1l0wa1          90 VEVELSALEVLAE  102 (104)
T ss_dssp             EEEEEEEEEEEEC
T ss_pred             EEEEEeEEEEEEc
Confidence            3677766654443

>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=94.27  E-value=0.26  Score=33.18  Aligned_cols=56  Identities=23%  Similarity=0.292  Sum_probs=41.1

Q ss_pred             eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccccc-----cccccCCcccccceeEEEEEeeEeec
Q 044496           35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFR-----IRRWNTGVFFFDFWMYVMVVGGFVIR   97 (142)
Q Consensus        35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~-----~~~~~~G~~~~~~~~YVmViG~~~~~   97 (142)
                      +.|.+.|-|-....-++  =+.|.|+||.+++....+..     ...++.+       ..|.|-|.++++
T Consensus        16 ~~V~v~GWv~~~R~~g~i~Fi~LRD~~G~~Q~v~~~~~~~~~~~~~~l~~E-------s~v~V~G~V~~r   78 (106)
T d1c0aa1          16 QQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNE-------FCIQVTGTVRAR   78 (106)
T ss_dssp             CEEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECGGGHHHHHHHTTCCTT-------CEEEEEEEEEEC
T ss_pred             CEEEEEEEEEEeeeCCCcEEEEEEcCCeEEeEEecccchhHHHHHHhhCcc-------ceEEEEeEEecc
Confidence            56889999988754433  44599999999998733211     1247888       999999999863

>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=92.94  E-value=0.53  Score=33.24  Aligned_cols=73  Identities=18%  Similarity=0.299  Sum_probs=55.5

Q ss_pred             EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc------cc--cccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496           36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD------FR--IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK  105 (142)
Q Consensus        36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~------~~--~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~  105 (142)
                      .|-+-|+|.++..-+.  =+.|.|.||.+++..+.+      +.  ...+..|       +.|-|-|.+......+..|.
T Consensus        56 ~V~vaGRI~~~R~~Gk~~F~~i~D~~g~iQi~~~~~~~~~~~~~~~~k~ld~G-------DiIgv~G~~~~TktGElsi~  128 (143)
T d1e1oa1          56 EVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLG-------DIIGARGTLFKTQTGELSIH  128 (143)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSSTTHHHHTGGGCCTT-------CEEEEEEEEEECTTCCEEEE
T ss_pred             eEEEEEEEEEEcccCCeeEEEEEeCCceEEEEEccccchhhhHHHHHhcCCcc-------cEEEeecccEECCCCcEEEE
Confidence            3678999999864333  567899999999987321      11  1247888       99999999988666799999


Q ss_pred             EEEEeeCCCC
Q 044496          106 VHKIVDLSAF  115 (142)
Q Consensus       106 a~K~~DLS~~  115 (142)
                      |..+.=||.+
T Consensus       129 ~~~~~lLsK~  138 (143)
T d1e1oa1         129 CTELRLLTKA  138 (143)
T ss_dssp             EEEEEEEECC
T ss_pred             eeEEEEeccc
Confidence            9998777764

>d3d3ra1 b.40.14.1 (A:1-76) Hydrogenase expression/formation protein HypC {Shewanella oneidensis [TaxId: 70863]}

class: All beta proteins
fold: OB-fold
superfamily: HupF/HypC-like
family: HupF/HypC-like
domain: Hydrogenase expression/formation protein HypC
species: Shewanella oneidensis [TaxId: 70863]

Probab=88.60  E-value=0.97  Score=29.20  Aligned_cols=47  Identities=17%  Similarity=0.140  Sum_probs=31.0

Q ss_pred             EEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496           40 QGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV   95 (142)
Q Consensus        40 QG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~   95 (142)
                      =|+|+++.++....+.|=+.-+-++++.-.+.  +.++|       +||+|+-++-
T Consensus         6 P~kVvei~~~~~~a~vd~~G~~r~v~l~lv~e--~v~vG-------DyVLVH~G~A   52 (76)
T d3d3ra1           6 PSQVVAVDNERQSVTVDTLGVRRDVSSHLMTE--PLAIG-------DYVLIHIGFV   52 (76)
T ss_dssp             CEEEEEEETTTTEEEEEETTEEEEEECTTBSS--CCCTT-------CEEEEEEEEE
T ss_pred             cEEEEEEcCCCcEEEEECCCeEEEEEEEeccC--CCCCC-------CEEEEecchh
Confidence            37888875444455555554445666544432  57899       9999999883

>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=86.38  E-value=3.1  Score=27.48  Aligned_cols=61  Identities=15%  Similarity=0.219  Sum_probs=43.5

Q ss_pred             EEEEEEEEeeeCC------CC-----cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496           37 VWLQGVLVSPPDD------DG-----RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVI  104 (142)
Q Consensus        37 VWlQG~vv~~~~~------~~-----~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i  104 (142)
                      |-+.|+|+++.+.      ++     .++|-|.||++.+.+ +...  ..+++|       ++|.+-+......+..+.|
T Consensus        15 v~i~~~V~~~~~~r~~~~~~g~~~v~~~~i~DeTG~i~~~~W~~~~--~~l~~G-------dvv~i~na~v~~~~g~~el   85 (115)
T d1o7ia_          15 VNVTVRVLEASEARQIQTKNGVRTISEAIVGDETGRVKLTLWGKHA--GSIKEG-------QVVKIENAWTTAFKGQVQL   85 (115)
T ss_dssp             EEEEEEEEEECCCEEECCTTCCEEEEEEEEEETTEEEEEEEEGGGT--TCCCTT-------CEEEEEEEEEEEETTEEEE
T ss_pred             EEEEEEEEECCCCceeecCCCCEEEEEEEEEcCCCeEEEEEecccc--ccCCCC-------CEEEEeeEEEEEECCeEEE
Confidence            5577888887331      22     678999999999987 3322  258999       9999888776656666766


Q ss_pred             EE
Q 044496          105 KV  106 (142)
Q Consensus       105 ~a  106 (142)
                      ..
T Consensus        86 ~~   87 (115)
T d1o7ia_          86 NA   87 (115)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>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=82.10  E-value=2.2  Score=29.21  Aligned_cols=54  Identities=22%  Similarity=0.324  Sum_probs=39.3

Q ss_pred             eEEEEEEEEEe--ee-CCC---CcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEee
Q 044496           35 QRVWLQGVLVS--PP-DDD---GRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVI   96 (142)
Q Consensus        35 ~~VWlQG~vv~--~~-~~~---~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~   96 (142)
                      +++.+.|.|+.  +. +++   -+|.+-|+.+.+.|.+++.... -++.|       .-|.|-|.+..
T Consensus        29 ~~iRvgG~V~~gSi~~~~~~~~~~F~itD~~~~i~V~Y~GilPd-lF~eg-------~~VVveG~~~~   88 (114)
T d1sr3a_          29 QRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVSYEGILPD-LFREG-------QGVVVQGELEK   88 (114)
T ss_dssp             SEEEEEEEECTTTCEECSSSSEEEEEEECSSCEEEEEEESCCCT-TCCTT-------SEEEEEEEECS
T ss_pred             cEEEEeeEEEEeEEEeecCcceEEEEEccCCcEEEEEecCCCCh-hhcCC-------CeEEEEEEECC
Confidence            36778898864  21 222   3699999999999998764421 27889       99999998854

>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=81.20  E-value=1.8  Score=30.28  Aligned_cols=68  Identities=13%  Similarity=0.005  Sum_probs=49.2

Q ss_pred             EeEEEEEEEEEeeeCC---------------------CCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEE
Q 044496           34 FQRVWLQGVLVSPPDD---------------------DGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVV   91 (142)
Q Consensus        34 ~~~VWlQG~vv~~~~~---------------------~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmVi   91 (142)
                      -.+|-+.+.|+++.+.                     =-.+++-|.||++.+.+ +....  .+++|       +.|.+.
T Consensus        26 ~~~vnl~vkVl~~~~~~~~~r~~~~~~~~~~~g~~~~v~~~~v~DeTG~i~~tlW~~~~~--~l~~G-------d~v~i~   96 (145)
T d1wjja_          26 TTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFTARNDQVD--LMKPG-------ATVILR   96 (145)
T ss_dssp             CCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEEECTTHHH--HTCTT-------CEEEEE
T ss_pred             CCCceEEEEEEEcccceeecccccccccccccCCCcEEEEEEEEccCCeEEEEEEecccc--ccCcC-------CEEEEe
Confidence            3556688999987421                     11468999999999998 33221  38999       999999


Q ss_pred             eeEeeccCCCceEEEEEEe
Q 044496           92 GGFVIRTDDIPVIKVHKIV  110 (142)
Q Consensus        92 G~~~~~~~~~p~i~a~K~~  110 (142)
                      +.+.......+.|..-|-.
T Consensus        97 na~v~~~~G~~~L~vg~~g  115 (145)
T d1wjja_          97 NSRIDMFKGTMRLGVDKWG  115 (145)
T ss_dssp             EEEEEEETTEEEEEECTTC
T ss_pred             eEEEEEECCEEEEEECCCE
Confidence            9888766777777776533

>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=80.55  E-value=6  Score=26.28  Aligned_cols=63  Identities=13%  Similarity=0.177  Sum_probs=43.6

Q ss_pred             eEEEEEEEEEe--e-eCCC---CcEEEEcCCe-eEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496           35 QRVWLQGVLVS--P-PDDD---GRLLLDDGTG-VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH  107 (142)
Q Consensus        35 ~~VWlQG~vv~--~-~~~~---~~~~LdDgTG-~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~  107 (142)
                      +++.+-|.|+.  + ..++   -+|.+.|+++ .+.|.+++.... -++.|       .-|.|-|.+..    .-++.|.
T Consensus        27 ~~iRvGG~V~~gSi~~~~~~~~~~F~itD~~~~~i~V~Y~G~lPd-lF~eg-------~gVVveG~~~~----~g~F~A~   94 (100)
T d1j6qa_          27 QRIRVGGMVTVGSMVRDPNSLHVQFAVHDSLGGEILVTYDDLLPD-LFREG-------QGIVAQGVLGE----DGKLAAT   94 (100)
T ss_dssp             CEEEEEEEECTTCCEECTTSSCEEEEEECTTCCCEEEEECSCCTT-SCCSS-------SEEEEEEEECS----TTSEEEE
T ss_pred             CEEEEeeEEeeeEEEecCCccEEEEEEcCCceeEEEEEeCCCCCc-hhcCC-------CeEEEEEEECC----CCEEEEE
Confidence            46778888874  2 2223   3799999976 599998774321 28889       99999998843    3466666


Q ss_pred             EE
Q 044496          108 KI  109 (142)
Q Consensus       108 K~  109 (142)
                      .+
T Consensus        95 ~v   96 (100)
T d1j6qa_          95 EV   96 (100)
T ss_dssp             EE
T ss_pred             EE
Confidence            54