Psyllid ID: psy8456

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350---
Protein Sequence
MSFIERDDRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVRIE
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHHHcccEEEEEEEcccccccccccccccccEEEcEEccHHHHHHHccccccEEEEccccccHHHHHHHHHHHHcccEEEEEEccHHHccccHHHHHHHHHHcccEEEccEEEcccccccccEEEEccccccccccccccccHHHHHHHHHHHHcccEEEEEEEccccccccccEEEccccccccEEcccHHHHHHHcccccEEEEccccEEEEEcccccEEEEEEEcccccccccccccccccccccccccccccccccccHHHHHHHHcccEEEEEEEcccccccccHHHHHHHccccEEEEEEEEccccccccccEEEEccccEEEEc
Secondary Structure Prediction (SSPRO)
cccEEccccccHHHHHHHHHHHHHHHHcccEEEEEcccccccccccEEEccccEEEEEEcccHHHHHHHHccccEEEEEcccHcHHHHHHHHHHHHcccEEEEEEEcccccccccccHHHHHHHHHHHHHHEEEHHHcccccHHHHHccccEEEEEEcccccccHEHHccHHHHEHHHcEEEEEccccccccccccEEEccccEEEEEEcccHHHHHHHHccccEEEEEccEEcHHccccccccEcccccccEEHHHHccccHHHHHcccEEEEccccccHHHHHHHHHHHHcccEEEEEEEcccccccccccHHHHHHHHHHHHHHEEEHHHccccccHHHHHccccccEcc
Coil and Loop (DISEMBL)
msfierddrinpyIVHFCRRIRRYQYANYRCMIVRYakddrydtekvathdqQKLTAVSAVELnkliphtkdidvigidegqffpDVVSFAESMANAGKIVVVAALdgtfqrtgfndilslIPLAECVEKLTAVCMSCFRDAAFTKRIGqekevilgpmfsgktTELIRRIRRYQYANYRCMIVRYakddrydtekvsthdqQKLTAVSAVELnkliphtkdidvigidegqfveviggsdKYMAVCRECykqkapikrspfktlanenaalnvppppefpdvVSFAESMANAGKIVVVAALdgtfqrtgfndilslIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVRIE
Flexible Loop (DISEMBL)
msfierddrinpyivhfcrrirryqyANYRCMIVRYAKDDRYDTEKVathdqqkltaVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFtkrigqekevilgpmfsgktteLIRRIRRYQYANYRCMIVRYAKDDRYDTEKvsthdqqkltaVSAVELNKLIphtkdidvigiDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAftkrigqekevrie
Low Complexity Region (SEG)
MSFIERDDRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVRIE
Disordered region (IsUnstruct)
*******DRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIK***********************DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRI*********
Disordered Region (DISOPRED)
*****RDDRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEK*V*******GKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQ*******
Disordered Region (DISEMBL)
MSFIERDDRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR***********QKLTAVSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVRIE
Disordered Region (DISPRO)
*SFIERDDRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEV***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSFIERDDRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVRIE
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	353	2.2.26 [Sep-21-2011]
A5D7R8	238	Thymidine kinase, cytosol	yes	N/A	0.433	0.642	0.475	2e-45
P68563	177	Thymidine kinase OS=Vacci	no	N/A	0.444	0.887	0.455	1e-44
P68564	177	Thymidine kinase OS=Vacci	yes	N/A	0.444	0.887	0.455	1e-44
P04184	233	Thymidine kinase, cytosol	yes	N/A	0.433	0.656	0.47	1e-44
O57203	177	Thymidine kinase OS=Vacci	yes	N/A	0.444	0.887	0.455	1e-44
P04183	234	Thymidine kinase, cytosol	yes	N/A	0.433	0.653	0.47	1e-44
Q9JFB7	177	Thymidine kinase OS=Vacci	no	N/A	0.444	0.887	0.450	2e-44
P04047	224	Thymidine kinase, cytosol	yes	N/A	0.436	0.687	0.465	4e-44
P04364	177	Thymidine kinase OS=Vario	no	N/A	0.444	0.887	0.450	1e-43
P09768	234	Thymidine kinase, cytosol	yes	N/A	0.433	0.653	0.47	2e-43

>sp|A5D7R8|KITH_BOVIN Thymidine kinase, cytosolic OS=Bos taurus GN=TK1 PE=2 SV=1

 Score =  182 bits (463), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 95/200 (47%), Positives = 122/200 (61%), Gaps = 47/200 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY +   STHD+  + A+ A  
Sbjct: 22  QVILGPMFSGKSTELMRRVRRFQVAQYKCLVIKYAKDTRYSS-LFSTHDRNTMEALPACL 80

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +I   + + VIGIDEGQF                                       
Sbjct: 81  LRDVIQDAQRVAVIGIDEGQF--------------------------------------- 101

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E+MAN+GK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 102 -------FPDIVEFCENMANSGKTVIVAALDGTFQRKAFGTILNLVPLAESVVKLTAVCM 154

Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            CFR+AA+TKR+G EKEV +
Sbjct: 155 ECFREAAYTKRLGVEKEVEV 174

Bos taurus (taxid: 9913)
EC: 2EC: .EC: 7EC: .EC: 1EC: .EC: 2EC: 1

>sp|P68563|KITH_VACCW Thymidine kinase OS=Vaccinia virus (strain Western Reserve) GN=TK PE=1 SV=1

 Score =  181 bits (458), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 93/204 (45%), Positives = 122/204 (59%), Gaps = 47/204 (23%)

Query: 149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV 208
           G   ++I+GPMFSGK+TELIRR+RRYQ A Y+C+ ++Y+ D+RY T  + THD+    A+
Sbjct: 3   GGHIQLIIGPMFSGKSTELIRRVRRYQIAQYKCVTIKYSNDNRYGT-GLWTHDKNNFEAL 61

Query: 209 SAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANE 268
            A +L  ++    D  VIGIDEGQF                                   
Sbjct: 62  EATKLCDVLESITDFSVIGIDEGQF----------------------------------- 86

Query: 269 NAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 328
                      FPD+V F E MAN GKIV+VAALDGTFQR  FN+IL+LIPL+E V KLT
Sbjct: 87  -----------FPDIVEFCERMANEGKIVIVAALDGTFQRKPFNNILNLIPLSEMVVKLT 135

Query: 329 AVCMSCFRDAAFTKRIGQEKEVRI 352
           AVCM CF++A+F+KR+G+E E+ I
Sbjct: 136 AVCMKCFKEASFSKRLGEETEIEI 159

Phosphorylates thymidine and thymidine analogs, such as azidothymidine (AZT). Part of the salvage pathway for pyrimidine deoxyribonucleotide synthesis.

Bos taurus (taxid: 9913)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|P68564|KITH_VACCC Thymidine kinase OS=Vaccinia virus (strain Copenhagen) GN=TK PE=3 SV=1

 Score =  181 bits (458), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 93/204 (45%), Positives = 122/204 (59%), Gaps = 47/204 (23%)

Query: 149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV 208
           G   ++I+GPMFSGK+TELIRR+RRYQ A Y+C+ ++Y+ D+RY T  + THD+    A+
Sbjct: 3   GGHIQLIIGPMFSGKSTELIRRVRRYQIAQYKCVTIKYSNDNRYGT-GLWTHDKNNFEAL 61

Query: 209 SAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANE 268
            A +L  ++    D  VIGIDEGQF                                   
Sbjct: 62  EATKLCDVLESITDFSVIGIDEGQF----------------------------------- 86

Query: 269 NAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 328
                      FPD+V F E MAN GKIV+VAALDGTFQR  FN+IL+LIPL+E V KLT
Sbjct: 87  -----------FPDIVEFCERMANEGKIVIVAALDGTFQRKPFNNILNLIPLSEMVVKLT 135

Query: 329 AVCMSCFRDAAFTKRIGQEKEVRI 352
           AVCM CF++A+F+KR+G+E E+ I
Sbjct: 136 AVCMKCFKEASFSKRLGEETEIEI 159

Phosphorylates thymidine and thymidine analogs, such as azidothymidine (AZT). Part of the salvage pathway for pyrimidine deoxyribonucleotide synthesis.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|P04184|KITH_MOUSE Thymidine kinase, cytosolic OS=Mus musculus GN=Tk1 PE=2 SV=3

 Score =  181 bits (458), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 94/200 (47%), Positives = 119/200 (59%), Gaps = 47/200 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY +   STHD+  + A+ A  
Sbjct: 22  QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRY-SNSFSTHDRNTMDALPACM 80

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +   +  + VIGIDEGQF                                       
Sbjct: 81  LRDVTQESLGVAVIGIDEGQF--------------------------------------- 101

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E MAN GK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 102 -------FPDIVDFCEMMANEGKTVIVAALDGTFQRKAFGSILNLVPLAESVVKLTAVCM 154

Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            CFR+AA+TKR+G EKEV +
Sbjct: 155 ECFREAAYTKRLGLEKEVEV 174

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|O57203|KITH_VACCA Thymidine kinase OS=Vaccinia virus (strain Ankara) GN=TK PE=1 SV=1

 Score =  181 bits (458), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 93/204 (45%), Positives = 122/204 (59%), Gaps = 47/204 (23%)

Query: 149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV 208
           G   ++I+GPMFSGK+TELIRR+RRYQ A Y+C+ ++Y+ D+RY T  + THD+    A+
Sbjct: 3   GGHIQLIIGPMFSGKSTELIRRVRRYQIAQYKCVTIKYSNDNRYGT-GLWTHDKNNFEAL 61

Query: 209 SAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANE 268
            A +L  ++    D  VIGIDEGQF                                   
Sbjct: 62  EATKLCDVLESITDFSVIGIDEGQF----------------------------------- 86

Query: 269 NAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 328
                      FPD+V F E MAN GKIV+VAALDGTFQR  FN+IL+LIPL+E V KLT
Sbjct: 87  -----------FPDIVEFCERMANEGKIVIVAALDGTFQRKPFNNILNLIPLSEMVVKLT 135

Query: 329 AVCMSCFRDAAFTKRIGQEKEVRI 352
           AVCM CF++A+F+KR+G+E E+ I
Sbjct: 136 AVCMKCFKEASFSKRLGEETEIEI 159

Phosphorylates thymidine and thymidine analogs, such as azidothymidine (AZT). Part of the salvage pathway for pyrimidine deoxyribonucleotide synthesis.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|P04183|KITH_HUMAN Thymidine kinase, cytosolic OS=Homo sapiens GN=TK1 PE=1 SV=2

 Score =  180 bits (456), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 94/200 (47%), Positives = 119/200 (59%), Gaps = 47/200 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  
Sbjct: 22  QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACL 80

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +      + VIGIDEGQF                                       
Sbjct: 81  LRDVAQEALGVAVIGIDEGQF--------------------------------------- 101

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 102 -------FPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCM 154

Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            CFR+AA+TKR+G EKEV +
Sbjct: 155 ECFREAAYTKRLGTEKEVEV 174

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|Q9JFB7|KITH_VACCT Thymidine kinase OS=Vaccinia virus (strain Tian Tan) GN=TK PE=3 SV=1

 Score =  179 bits (455), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/204 (45%), Positives = 122/204 (59%), Gaps = 47/204 (23%)

Query: 149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV 208
           G   ++++GPMFSGK+TELIRR+RRYQ A Y+C+ ++Y+ D+RY T  + THD+    A+
Sbjct: 3   GGHIQLMIGPMFSGKSTELIRRVRRYQIAQYKCVTIKYSNDNRYGT-GLWTHDKNNFEAL 61

Query: 209 SAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANE 268
            A +L  ++    D  VIGIDEGQF                                   
Sbjct: 62  EATKLCDVLESITDFSVIGIDEGQF----------------------------------- 86

Query: 269 NAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 328
                      FPD+V F E MAN GKIV+VAALDGTFQR  FN+IL+LIPL+E V KLT
Sbjct: 87  -----------FPDIVEFCERMANEGKIVIVAALDGTFQRKPFNNILNLIPLSEMVVKLT 135

Query: 329 AVCMSCFRDAAFTKRIGQEKEVRI 352
           AVCM CF++A+F+KR+G+E E+ I
Sbjct: 136 AVCMKCFKEASFSKRLGEETEIEI 159

Phosphorylates thymidine and thymidine analogs, such as azidothymidine (AZT). Part of the salvage pathway for pyrimidine deoxyribonucleotide synthesis.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|P04047|KITH_CHICK Thymidine kinase, cytosolic OS=Gallus gallus GN=TK1 PE=3 SV=1

 Score =  178 bits (452), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 93/200 (46%), Positives = 115/200 (57%), Gaps = 46/200 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VI GPMFSGK+TEL+RR+RR+Q A YRC++V+YAKD RY T  VSTHD+  + A  A  
Sbjct: 22  QVIFGPMFSGKSTELMRRVRRFQLAQYRCLLVKYAKDTRYCTTGVSTHDRNTMEARPACA 81

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +        VIGIDEGQF                                       
Sbjct: 82  LQDVYQEALGSAVIGIDEGQF--------------------------------------- 102

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E MAN GK V+VAALDGTFQR  F  IL+L+PLAE V KL AVCM
Sbjct: 103 -------FPDIVEFCEKMANTGKTVIVAALDGTFQRKAFGSILNLVPLAESVVKLNAVCM 155

Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            C+R+A++TKR+G E+EV +
Sbjct: 156 ECYREASYTKRLGAEREVEV 175

Gallus gallus (taxid: 9031)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|P04364|KITH_VAR67 Thymidine kinase OS=Variola virus (isolate Human/India/Ind3/1967) GN=TK PE=3 SV=2

 Score =  177 bits (448), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 92/204 (45%), Positives = 120/204 (58%), Gaps = 47/204 (23%)

Query: 149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV 208
           G   ++I+GPMFSGK+TELIRR+RRYQ A Y+C+ ++Y+ D+RY T  + THD+    A+
Sbjct: 3   GGHIQLIIGPMFSGKSTELIRRVRRYQIAQYKCVTIKYSNDNRYGT-GLWTHDKNNFEAL 61

Query: 209 SAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANE 268
            A +L  ++    D  VIGIDEGQF                                   
Sbjct: 62  EATKLCDVLEAITDFSVIGIDEGQF----------------------------------- 86

Query: 269 NAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 328
                      FPD+V F E MAN GKIV+VAALDGTFQR  FN+IL LIPL+E V KLT
Sbjct: 87  -----------FPDIVEFCERMANEGKIVIVAALDGTFQRKPFNNILDLIPLSEMVVKLT 135

Query: 329 AVCMSCFRDAAFTKRIGQEKEVRI 352
           AVCM CF++A+F+KR+G E ++ I
Sbjct: 136 AVCMKCFKEASFSKRLGTETKIEI 159

Phosphorylates thymidine and thymidine analogs, such as azidothymidine (AZT). Part of the salvage pathway for pyrimidine deoxyribonucleotide synthesis.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|P09768|KITH_CRIGR Thymidine kinase, cytosolic OS=Cricetulus griseus GN=TK1 PE=3 SV=1

 Score =  177 bits (448), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 94/200 (47%), Positives = 117/200 (58%), Gaps = 47/200 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A  +C++++YAKD RY +   STHD+  + A+ A  
Sbjct: 22  QVILGPMFSGKSTELMRRVRRFQIAQNKCLVIKYAKDTRYSSS-FSTHDRNTMDALPACL 80

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +        VIGIDEGQF                                       
Sbjct: 81  LRDVAQEALGAAVIGIDEGQF--------------------------------------- 101

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 102 -------FPDIVEFCEVMANAGKTVIVAALDGTFQRKAFGSILNLVPLAESVVKLTAVCM 154

Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            CFR+AA+TKR+G EKEV +
Sbjct: 155 ECFREAAYTKRLGLEKEVEV 174

Cricetulus griseus (taxid: 10029)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: .

EC: 2

EC: 1

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	353
342183833	637	unnamed protein product, partial [Trypan	0.804	0.445	0.377	8e-60
342183835	849	unnamed protein product [Trypanosoma con	0.804	0.334	0.377	1e-57
324504589	405	Thymidine kinase [Ascaris suum]	0.815	0.711	0.370	3e-57
261332022	455	thymidine kinase, putative [Trypanosoma	0.813	0.630	0.334	5e-51
22324517	455	thymidine kinase [Trypanosoma brucei]	0.813	0.630	0.334	1e-50
71746582	455	thymidine kinase [Trypanosoma brucei bru	0.813	0.630	0.331	3e-50
324503582	375	Thymidine kinase [Ascaris suum]	0.691	0.650	0.360	6e-48
212373999	220	thymidine kinase [Suberites domuncula]	0.436	0.7	0.5	3e-47
340368544	226	PREDICTED: thymidine kinase, cytosolic-l	0.470	0.734	0.481	1e-46
391334485	202	PREDICTED: thymidine kinase, cytosolic-l	0.436	0.762	0.49	5e-46

>gi|342183833|emb|CCC93313.1| unnamed protein product, partial [Trypanosoma congolense IL3000]

 Score =  236 bits (603), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 142/376 (37%), Positives = 193/376 (51%), Gaps = 92/376 (24%)

Query: 20  RIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTA-VSAVELNKLIPHTKDIDVIGI 78
           R+ R   A+  C +++Y+KD RY  E ++THDQ+ LTA VS  +L+++     + DVI +
Sbjct: 221 RVNRNYLASQSCYVIKYSKDVRYSKEIISTHDQRTLTATVSVSKLSEIGNAWCEHDVIAV 280

Query: 79  DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
           D GQFFPD++ F    ANAGK V+V+ALDG ++   F DI  LIP AE V KL+AVCMSC
Sbjct: 281 DGGQFFPDILQFCSMAANAGKKVIVSALDGDYRNEPFEDIAKLIPAAESVTKLSAVCMSC 340

Query: 139 FR---DAAFTKRIGQEK-----------------------------------------EV 154
                DA +T R  Q +                                         EV
Sbjct: 341 NLQSCDACYTHRTVQSEQRELIGGADMYIATCRACYNRLNNQGGSLVENPQSPQSGRIEV 400

Query: 155 ILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA-VSAVEL 213
           ++GPMF+GKTTEL+ R+ RY  A Y C +++Y++D RY  E +STHD++ L A VS  +L
Sbjct: 401 VIGPMFAGKTTELMSRVNRYSLARYSCYVIKYSEDKRYSKENISTHDRRTLPATVSVTKL 460

Query: 214 NKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALN 273
           +++     D DVI +DEGQF                                        
Sbjct: 461 SEVGEKWCDYDVIAVDEGQF---------------------------------------- 480

Query: 274 VPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMS 333
                 FPD++ F    ANAGK V+VAALDG ++   F DI  LIP AE V KL+AVCM 
Sbjct: 481 ------FPDILEFCSMAANAGKKVIVAALDGDYRNEPFEDIAKLIPAAESVTKLSAVCML 534

Query: 334 CFRDAAFTKRIGQEKE 349
           C  DA +T R  Q ++
Sbjct: 535 CGCDAYYTHRTVQSEQ 550

Source: Trypanosoma congolense IL3000

Species: Trypanosoma congolense

Genus: Trypanosoma

Family: Trypanosomatidae

Order: Kinetoplastida

Superkingdom: Eukaryota

>gi|342183835|emb|CCC93315.1| unnamed protein product [Trypanosoma congolense IL3000]

 Score =  229 bits (584), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 141/374 (37%), Positives = 190/374 (50%), Gaps = 90/374 (24%)

Query: 20  RIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTA-VSAVELNKLIPHTKDIDVIGI 78
           R+ R   A Y C ++ Y+KD RY  E + T+D++ L A VS  +L+++     D DVI +
Sbjct: 413 RVNRNYLARYSCYVIEYSKDMRYSKEIIPTYDRRTLPATVSVNKLSEVGNAWHDYDVIAV 472

Query: 79  DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
           DEGQFFPD++ F   +ANAGK V+VAALDG ++   F  I  LIP AE V KL+AVCMSC
Sbjct: 473 DEGQFFPDILEFCSMVANAGKKVIVAALDGDYRNEPFEHIAKLIPAAESVTKLSAVCMSC 532

Query: 139 -FRDAAFTKRIGQEK-----------------------------------------EVIL 156
              +A +T RI Q +                                         E+++
Sbjct: 533 RLSNAYYTHRIVQSEQRELIGGADMYIAACRACYNRLNSQGGSLAENPQSPQSGRIELVI 592

Query: 157 GPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA-VSAVELNK 215
           GPMF+GKTTELI R+ R   A Y C ++ Y+KD RY  E +ST+D++ L A VS  +L++
Sbjct: 593 GPMFAGKTTELISRVNRNYLARYSCYVIEYSKDMRYSKEIISTYDRRTLPATVSVNKLSE 652

Query: 216 LIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVP 275
           +     D DVI +DEGQF                                          
Sbjct: 653 VGNAWHDYDVIAVDEGQF------------------------------------------ 670

Query: 276 PPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCF 335
               FPD++ F    ANAGK V+VAALDG ++   F  I  LIP AE V KL+AVCMSC 
Sbjct: 671 ----FPDILEFCSMAANAGKKVIVAALDGDYRNEPFEHIAKLIPAAESVTKLSAVCMSCG 726

Query: 336 RDAAFTKRIGQEKE 349
            DA +T R  Q ++
Sbjct: 727 CDAHYTHRTVQSEQ 740

Source: Trypanosoma congolense IL3000

Species: Trypanosoma congolense

Genus: Trypanosoma

Family: Trypanosomatidae

Order: Kinetoplastida

Superkingdom: Eukaryota

>gi|324504589|gb|ADY41981.1| Thymidine kinase [Ascaris suum]

 Score =  228 bits (582), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 138/372 (37%), Positives = 179/372 (48%), Gaps = 84/372 (22%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
           RR+ RY+ AN  C IV+Y  D RY  + VATHD Q   A+SAV++  ++    +  V+ I
Sbjct: 23  RRLNRYKLANRTCRIVKYRNDTRYALDHVATHDLQMQEAISAVKVADVMDELSEAHVVAI 82

Query: 79  DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
           DEGQFF D+   +E++AN GKIV+V+ALDG F R  F ++L + P +E + KL AVC  C
Sbjct: 83  DEGQFFDDIAECSENLANQGKIVIVSALDGDFNRKRFKNVLDMCPFSEDIIKLNAVCTGC 142

Query: 139 FRDAAFTKRIGQEK-------------------------------------EVILGPMFS 161
             DA+FTKR+                                         EVILGPMFS
Sbjct: 143 GEDASFTKRLTSNTALELIGGRDVYTAMCRQCYFDASQGFMRPHSPSRGRIEVILGPMFS 202

Query: 162 GKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTK 221
           GKTTE++RR  R+  A   C +++Y  D RYD  KV THDQ     V A  +  +     
Sbjct: 203 GKTTEMLRRYNRHALAGRECRVIKYRGDTRYDANKVVTHDQLMHDGVIATHIADIFDELL 262

Query: 222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFP 281
              VI IDEGQF                                              F 
Sbjct: 263 AYKVIAIDEGQF----------------------------------------------FQ 276

Query: 282 DVVSFAESMANAGKIVVVAALDGTFQRTGF-NDILSLIPLAECVEKLTAVCMSCFRDAAF 340
           D+    E +AN GKIV+VAALDG + R  F + +L L PLAE V KL AVC  C  DA+F
Sbjct: 277 DIAECCERLANMGKIVIVAALDGDYSRKEFASKVLDLCPLAEKVCKLRAVCTECGSDASF 336

Query: 341 TKRIGQEKEVRI 352
           ++R    K   I
Sbjct: 337 SRRTTAHKNQEI 348

Source: Ascaris suum

Species: Ascaris suum

Genus: Ascaris

Family: Ascarididae

Order: Ascaridida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|261332022|emb|CBH15015.1| thymidine kinase, putative [Trypanosoma brucei gambiense DAL972]

 Score =  207 bits (528), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 129/386 (33%), Positives = 192/386 (49%), Gaps = 99/386 (25%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTA-VSAVELNKLIPHTKDIDVIG 77
           RR++R+++A   C I+ Y+++  Y  ++++THDQ  LTA VS  +L+++    +D DVI 
Sbjct: 25  RRVQRHKHAQRSCYIINYSRNS-YQNQRLSTHDQLSLTANVSIAKLSEVCDEWRDYDVIA 83

Query: 78  IDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMS 137
           +D GQFFPDVV F    AN GK V+V+ALD   + T F+++  L+P AE V KL+AVCM 
Sbjct: 84  VDNGQFFPDVVGFCARAANEGKTVIVSALDVDCRETPFDEVCRLVPRAESVLKLSAVCMK 143

Query: 138 CF-RDAAFTKRIGQEKE------------------------------------------- 153
           C   DA  T R  +  E                                           
Sbjct: 144 CHEHDAFLTYRTIESNERELYGGADMYLAVCRWCYKQLTMSHVDAQKTSASTAAVVPNGA 203

Query: 154 -----VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA- 207
                +I+GPMF+GKTTEL+RR++R+++A   C I++Y  D RY    +++HDQ+ LTA 
Sbjct: 204 HGRIELIIGPMFAGKTTELMRRVQRHKHAQRSCYIIKYTGDTRYSEGAITSHDQRALTAN 263

Query: 208 VSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLAN 267
           VS   L+ +    +  DVI +DEGQF                                  
Sbjct: 264 VSVSNLHDVGDEWRKYDVIAVDEGQF---------------------------------- 289

Query: 268 ENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL 327
                       FPDV +F    A++GK+V+V+ALD  + +  F +I  L+  A+ V KL
Sbjct: 290 ------------FPDVAAFCSKAADSGKVVIVSALDADYLQEPFEEICLLVSRADSVVKL 337

Query: 328 TAVCMSCF-RDAAFTKRIGQEKEVRI 352
           +AVCM C  R A+FT R  +  E ++
Sbjct: 338 SAVCMECHNRKASFTYRTVKSDERKL 363

Source: Trypanosoma brucei gambiense DAL972

Species: Trypanosoma brucei

Genus: Trypanosoma

Family: Trypanosomatidae

Order: Kinetoplastida

Superkingdom: Eukaryota

>gi|22324517|gb|AAM95606.1|AF395663_1 thymidine kinase [Trypanosoma brucei]

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 129/386 (33%), Positives = 192/386 (49%), Gaps = 99/386 (25%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTA-VSAVELNKLIPHTKDIDVIG 77
           RR++R+++A   C I+ Y+++  Y  ++++THDQ  LTA VS  +L+++    +D DVI 
Sbjct: 25  RRVQRHKHAQRSCYIINYSRNS-YQNQRLSTHDQLSLTANVSIAKLSEVCDEWRDYDVIA 83

Query: 78  IDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMS 137
           +D GQFFPDVV F    AN GK V+V+ALD   + T F+++  L+P AE V KL+AVCM 
Sbjct: 84  VDNGQFFPDVVGFCARAANEGKTVIVSALDVDCRETPFDEVCRLVPRAESVLKLSAVCMK 143

Query: 138 CF-RDAAFTKRIGQEKE------------------------------------------- 153
           C   DA  T R  +  E                                           
Sbjct: 144 CHEHDAFLTYRTIESNERELYGGADMYLAVCRWCYKQLTMSHVDAQKTSASTAAVVPNGA 203

Query: 154 -----VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA- 207
                +I+GPMF+GKTTEL+RR++R+++A   C I++YA D RY    +++HDQ+ LTA 
Sbjct: 204 HGRIELIIGPMFAGKTTELMRRVQRHKHAQRSCYIIKYAGDTRYSEGAITSHDQRALTAN 263

Query: 208 VSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLAN 267
           VS   L+ +    +  DVI +DEGQF                                  
Sbjct: 264 VSVSNLHDVGDEWRKYDVIAVDEGQF---------------------------------- 289

Query: 268 ENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL 327
                       FP V +F    A++GK+V+V+ALD  + +  F +I  L+  A+ V KL
Sbjct: 290 ------------FPGVAAFCSKAADSGKVVIVSALDADYLQEPFEEICLLVSRADSVVKL 337

Query: 328 TAVCMSCF-RDAAFTKRIGQEKEVRI 352
           +AVCM C  R A+FT R  +  E ++
Sbjct: 338 SAVCMECHNRKASFTYRTVKSDERKL 363

Source: Trypanosoma brucei

Species: Trypanosoma brucei

Genus: Trypanosoma

Family: Trypanosomatidae

Order: Kinetoplastida

Superkingdom: Eukaryota

>gi|71746582|ref|XP_822346.1| thymidine kinase [Trypanosoma brucei brucei strain 927/4 GUTat10.1] gi|70832014|gb|EAN77518.1| thymidine kinase, putative [Trypanosoma brucei brucei strain 927/4 GUTat10.1]

 Score =  205 bits (521), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 128/386 (33%), Positives = 191/386 (49%), Gaps = 99/386 (25%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTA-VSAVELNKLIPHTKDIDVIG 77
           RR++R+++A   C I+ Y+++  Y  ++++THDQ  LTA VS  +L+++    +D DVI 
Sbjct: 25  RRVQRHKHAQRSCYIINYSRNS-YQNQRLSTHDQLSLTANVSIAKLSEVCDEWRDYDVIA 83

Query: 78  IDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMS 137
           +D GQFFPDVV F    AN GK V+V+ALD   + T F+++  L+P AE V KL+AVCM 
Sbjct: 84  VDNGQFFPDVVGFCARAANEGKTVIVSALDVDCRETPFDEVCRLVPRAESVLKLSAVCME 143

Query: 138 CF-RDAAFTKRIGQEKE------------------------------------------- 153
           C   DA  T R  +  E                                           
Sbjct: 144 CHEHDAFLTYRTIESNERELYGGADMYLAVCRWCYKQLTMSHVDAQKTSASTAAVVPNGA 203

Query: 154 -----VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA- 207
                +I+GPMF+GKTTEL+RR++R+++A   C I++Y  D RY    +++HDQ+ LTA 
Sbjct: 204 HGRIELIIGPMFAGKTTELMRRVQRHKHAQRSCYIIKYTGDTRYSEGAITSHDQRALTAN 263

Query: 208 VSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLAN 267
           VS   L+ +    +  DVI +DEGQF                                  
Sbjct: 264 VSVSNLHDVGDEWRKYDVIAVDEGQF---------------------------------- 289

Query: 268 ENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL 327
                       FP V +F    A++GK+V+V+ALD  + +  F +I  L+  A+ V KL
Sbjct: 290 ------------FPGVAAFCSKAADSGKVVIVSALDADYLQEPFEEICLLVSRADSVVKL 337

Query: 328 TAVCMSCF-RDAAFTKRIGQEKEVRI 352
           +AVCM C  R A+FT R  +  E ++
Sbjct: 338 SAVCMECHNRKASFTYRTVKSDERKL 363

Source: Trypanosoma brucei brucei strain 927/4 GUTat10.1

Species: Trypanosoma brucei

Genus: Trypanosoma

Family: Trypanosomatidae

Order: Kinetoplastida

Superkingdom: Eukaryota

>gi|324503582|gb|ADY41554.1| Thymidine kinase [Ascaris suum]

 Score =  197 bits (501), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 118/327 (36%), Positives = 154/327 (47%), Gaps = 83/327 (25%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
           RR+ RY+ AN  C IV+Y  D RY  + VATHD Q   A+SAV++  ++    +  V+ I
Sbjct: 36  RRLNRYKLANRTCRIVKYRNDTRYALDHVATHDLQMQEAISAVKVADVMDELSEAHVVAI 95

Query: 79  DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
           DEGQFF D+   +E++AN GKIV+V+ALDG F R  F ++L + P +E + KL AVC  C
Sbjct: 96  DEGQFFDDIAECSENLANQGKIVIVSALDGDFNRKRFKNVLDMCPFSEDIIKLNAVCTGC 155

Query: 139 FRDAAFTKRIGQEK-------------------------------------EVILGPMFS 161
             DA+FTKR+                                         EVILGPMFS
Sbjct: 156 GEDASFTKRLTSNTALELIGGRDVYTAMCRQCYFDASQGFVRPHSPSRGRIEVILGPMFS 215

Query: 162 GKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTK 221
           GKTTE++RR  R+  A   C +++Y  D RYD  KV THDQ     V A  +  +     
Sbjct: 216 GKTTEMLRRYNRHALAGRECRVIKYRGDTRYDANKVVTHDQLMHDGVIATHIADIFDELL 275

Query: 222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFP 281
              VI IDEGQF                                              F 
Sbjct: 276 AYKVIAIDEGQF----------------------------------------------FQ 289

Query: 282 DVVSFAESMANAGKIVVVAALDGTFQR 308
           D+    E +AN GKIV+VAALDG + R
Sbjct: 290 DIAECCERLANMGKIVIVAALDGDYSR 316

Source: Ascaris suum

Species: Ascaris suum

Genus: Ascaris

Family: Ascarididae

Order: Ascaridida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|212373999|emb|CAP19646.1| thymidine kinase [Suberites domuncula]

 Score =  195 bits (495), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 100/200 (50%), Positives = 122/200 (61%), Gaps = 46/200 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           ++ILGPMFSGKTTELIRR+RR+Q ANY C+IV+YAKDDRY  + VSTHD+Q    +SA E
Sbjct: 20  QLILGPMFSGKTTELIRRMRRFQVANYACLIVKYAKDDRYSNQDVSTHDKQMTAGISATE 79

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L ++    K   VIGIDEGQF                                       
Sbjct: 80  LTEVKKKAKKYGVIGIDEGQF--------------------------------------- 100

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E MANAGK V+VAALDGTFQR  F  IL+L+P+AE V KL AVCM
Sbjct: 101 -------FPDIVDFCEEMANAGKTVIVAALDGTFQRKPFGPILNLVPMAESVVKLKAVCM 153

Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            C++DAAFTKR+G EK++ +
Sbjct: 154 VCYKDAAFTKRLGAEKQIEV 173

Source: Suberites domuncula

Species: Suberites domuncula

Genus: Suberites

Family: Suberitidae

Order: Hadromerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|340368544|ref|XP_003382811.1| PREDICTED: thymidine kinase, cytosolic-like [Amphimedon queenslandica]

 Score =  193 bits (490), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 104/216 (48%), Positives = 127/216 (58%), Gaps = 50/216 (23%)

Query: 137 SCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEK 196
           SC   A    +I    +VILGPMFSGKTTEL+RR+RRYQ AN  C+I++Y+KDDRYD   
Sbjct: 9   SCISGALSKGQI----QVILGPMFSGKTTELMRRMRRYQVANQSCLIIKYSKDDRYDKNG 64

Query: 197 VSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAP 256
           V+THD+Q  +A++A +L +L     D  VIGIDEGQF                       
Sbjct: 65  VATHDKQVSSAMAATKLYELKKTVGDYGVIGIDEGQF----------------------- 101

Query: 257 IKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILS 316
                                  FPD+V F E MANAGK V+VAALDGTFQR  F  +L+
Sbjct: 102 -----------------------FPDLVEFCEDMANAGKTVIVAALDGTFQRKAFGSVLN 138

Query: 317 LIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVRI 352
           LIP+AE V KL AVCM CF DAAFTKR+G EKE+ +
Sbjct: 139 LIPMAESVVKLKAVCMMCFNDAAFTKRLGSEKEIEV 174

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|391334485|ref|XP_003741634.1| PREDICTED: thymidine kinase, cytosolic-like [Metaseiulus occidentalis]

 Score =  191 bits (484), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 98/200 (49%), Positives = 122/200 (61%), Gaps = 46/200 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           ++I+GPMFSGKTTELIRR+RRY  +N+RC +++YAKDDRYD E VSTHDQ K+TA   + 
Sbjct: 24  QLIVGPMFSGKTTELIRRMRRYDVSNHRCYLIKYAKDDRYDAENVSTHDQAKMTASVCLR 83

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +     + DVIG+DEGQF                                       
Sbjct: 84  LADVEAAALNFDVIGVDEGQF--------------------------------------- 104

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPDVV FAE MA  GK+V+VAALDGT+QR GF +I+ L+PL+E + KL AVCM
Sbjct: 105 -------FPDVVCFAEKMAGLGKVVIVAALDGTYQREGFPNIMKLLPLSESIIKLMAVCM 157

Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            C+R+AAFTKRIG E EV I
Sbjct: 158 VCYREAAFTKRIGSETEVEI 177

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

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	353
UNIPROTKB|K7ERV3	267	TK1 "Thymidine kinase" [Homo s	0.382	0.505	0.595	1.6e-47
UNIPROTKB|E2QXP4	242	TK1 "Thymidine kinase" [Canis	0.390	0.570	0.585	5.9e-41
UNIPROTKB|A5D7R8	238	TK1 "Thymidine kinase, cytosol	0.390	0.579	0.585	9.6e-41
MGI|MGI:98763	233	Tk1 "thymidine kinase 1" [Mus	0.390	0.592	0.578	3.3e-40
UNIPROTKB|P04183	234	TK1 "Thymidine kinase, cytosol	0.390	0.589	0.585	2.6e-40
UNIPROTKB|P04047	224	TK1 "Thymidine kinase, cytosol	0.393	0.620	0.578	1.1e-39
UNIPROTKB|K7ES52	180	TK1 "Thymidine kinase" [Homo s	0.388	0.761	0.594	2.6e-40
UNIPROTKB|P09768	234	TK1 "Thymidine kinase, cytosol	0.390	0.589	0.578	4.8e-39
UNIPROTKB|K7ERJ1	187	TK1 "Thymidine kinase" [Homo s	0.390	0.737	0.554	4.3e-38
ZFIN|ZDB-GENE-030131-5801	236	tk1 "thymidine kinase 1, solub	0.393	0.588	0.561	1.6e-38

UNIPROTKB|K7ERV3 TK1 "Thymidine kinase" [Homo sapiens (taxid:9606)]

 Score = 427 (155.4 bits), Expect = 1.6e-47, Sum P(2) = 1.6e-47
 Identities = 81/136 (59%), Positives = 102/136 (75%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
             RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  L  +      + VIGI
Sbjct:    38 RRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACLLRDVAQEALGVAVIGI 96

Query:    79 DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
             DEGQFFPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct:    97 DEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMEC 156

Query:   139 FRDAAFTKRIGQEKEV 154
             FR+AA+TKR+G EKEV
Sbjct:   157 FREAAYTKRLGTEKEV 172

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IEA

UNIPROTKB|E2QXP4 TK1 "Thymidine kinase" [Canis lupus familiaris (taxid:9615)]

 Score = 435 (158.2 bits), Expect = 5.9e-41, P = 5.9e-41
 Identities = 82/140 (58%), Positives = 107/140 (76%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
             RR+RR+Q A Y+C++++YAKD RY +   +THD+  + A+ A  L  +      + VIGI
Sbjct:    38 RRVRRFQIAQYKCLVIKYAKDTRY-SNSFSTHDRNTMEALPACLLRDVAQEALGVAVIGI 96

Query:    79 DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
             DEGQFFPD+V F+E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct:    97 DEGQFFPDIVEFSETMANAGKTVIVAALDGTFQRKAFGTILNLVPLAESVVKLTAVCMEC 156

Query:   139 FRDAAFTKRIGQEKEV-ILG 157
             FR+AA+TKR+G EKEV ++G
Sbjct:   157 FREAAYTKRLGSEKEVEVIG 176

GO:0051289 "protein homotetramerization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|A5D7R8 TK1 "Thymidine kinase, cytosolic" [Bos taurus (taxid:9913)]

 Score = 433 (157.5 bits), Expect = 9.6e-41, P = 9.6e-41
 Identities = 82/140 (58%), Positives = 108/140 (77%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
             RR+RR+Q A Y+C++++YAKD RY +   +THD+  + A+ A  L  +I   + + VIGI
Sbjct:    38 RRVRRFQVAQYKCLVIKYAKDTRYSS-LFSTHDRNTMEALPACLLRDVIQDAQRVAVIGI 96

Query:    79 DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
             DEGQFFPD+V F E+MAN+GK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct:    97 DEGQFFPDIVEFCENMANSGKTVIVAALDGTFQRKAFGTILNLVPLAESVVKLTAVCMEC 156

Query:   139 FRDAAFTKRIGQEKEV-ILG 157
             FR+AA+TKR+G EKEV ++G
Sbjct:   157 FREAAYTKRLGVEKEVEVIG 176

GO:0008270 "zinc ion binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0051289 "protein homotetramerization" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

MGI|MGI:98763 Tk1 "thymidine kinase 1" [Mus musculus (taxid:10090)]

 Score = 428 (155.7 bits), Expect = 3.3e-40, P = 3.3e-40
 Identities = 81/140 (57%), Positives = 105/140 (75%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
             RR+RR+Q A Y+C++++YAKD RY +   +THD+  + A+ A  L  +   +  + VIGI
Sbjct:    38 RRVRRFQIAQYKCLVIKYAKDTRY-SNSFSTHDRNTMDALPACMLRDVTQESLGVAVIGI 96

Query:    79 DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
             DEGQFFPD+V F E MAN GK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct:    97 DEGQFFPDIVDFCEMMANEGKTVIVAALDGTFQRKAFGSILNLVPLAESVVKLTAVCMEC 156

Query:   139 FRDAAFTKRIGQEKEV-ILG 157
             FR+AA+TKR+G EKEV ++G
Sbjct:   157 FREAAYTKRLGLEKEVEVIG 176

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IDA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0008270 "zinc ion binding" evidence=ISO

GO:0009165 "nucleotide biosynthetic process" evidence=IDA

GO:0016301 "kinase activity" evidence=IEA

GO:0016310 "phosphorylation" evidence=IDA

GO:0016740 "transferase activity" evidence=IEA

GO:0046104 "thymidine metabolic process" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0051289 "protein homotetramerization" evidence=ISO

UNIPROTKB|P04183 TK1 "Thymidine kinase, cytosolic" [Homo sapiens (taxid:9606)]

 Score = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 82/140 (58%), Positives = 105/140 (75%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
             RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  L  +      + VIGI
Sbjct:    38 RRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACLLRDVAQEALGVAVIGI 96

Query:    79 DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
             DEGQFFPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct:    97 DEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMEC 156

Query:   139 FRDAAFTKRIGQEKEV-ILG 157
             FR+AA+TKR+G EKEV ++G
Sbjct:   157 FREAAYTKRLGTEKEVEVIG 176

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IEA

GO:0001889 "liver development" evidence=IEA

GO:0009636 "response to toxic substance" evidence=IEA

GO:0014856 "skeletal muscle cell proliferation" evidence=IEA

GO:0031667 "response to nutrient levels" evidence=IEA

GO:0046104 "thymidine metabolic process" evidence=IEA

GO:0046688 "response to copper ion" evidence=IEA

GO:0048565 "digestive tract development" evidence=IEA

GO:0051414 "response to cortisol stimulus" evidence=IEA

GO:0060138 "fetal process involved in parturition" evidence=IEA

GO:0051289 "protein homotetramerization" evidence=IPI

GO:0008270 "zinc ion binding" evidence=IDA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006206 "pyrimidine nucleobase metabolic process" evidence=TAS

GO:0019206 "nucleoside kinase activity" evidence=EXP

GO:0043097 "pyrimidine nucleoside salvage" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

GO:0055086 "nucleobase-containing small molecule metabolic process" evidence=TAS

GO:0009165 "nucleotide biosynthetic process" evidence=EXP

UNIPROTKB|P04047 TK1 "Thymidine kinase, cytosolic" [Gallus gallus (taxid:9031)]

 Score = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 81/140 (57%), Positives = 102/140 (72%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
             RR+RR+Q A YRC++V+YAKD RY T  V+THD+  + A  A  L  +        VIGI
Sbjct:    38 RRVRRFQLAQYRCLLVKYAKDTRYCTTGVSTHDRNTMEARPACALQDVYQEALGSAVIGI 97

Query:    79 DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
             DEGQFFPD+V F E MAN GK V+VAALDGTFQR  F  IL+L+PLAE V KL AVCM C
Sbjct:    98 DEGQFFPDIVEFCEKMANTGKTVIVAALDGTFQRKAFGSILNLVPLAESVVKLNAVCMEC 157

Query:   139 FRDAAFTKRIGQEKEV-ILG 157
             +R+A++TKR+G E+EV ++G
Sbjct:   158 YREASYTKRLGAEREVEVIG 177

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0051289 "protein homotetramerization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=ISS

UNIPROTKB|K7ES52 TK1 "Thymidine kinase" [Homo sapiens (taxid:9606)]

 Score = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 82/138 (59%), Positives = 103/138 (74%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
             RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  L  +      + VIGI
Sbjct:    38 RRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACLLRDVAQEALGVAVIGI 96

Query:    79 DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
             DEGQFFPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct:    97 DEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMEC 156

Query:   139 FRDAAFTKRIGQEKEVIL 156
             FR+AA+TKR+G EKE IL
Sbjct:   157 FREAAYTKRLGTEKEQIL 174

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IEA

UNIPROTKB|P09768 TK1 "Thymidine kinase, cytosolic" [Cricetulus griseus (taxid:10029)]

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 81/140 (57%), Positives = 103/140 (73%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
             RR+RR+Q A  +C++++YAKD RY +   +THD+  + A+ A  L  +        VIGI
Sbjct:    38 RRVRRFQIAQNKCLVIKYAKDTRYSSS-FSTHDRNTMDALPACLLRDVAQEALGAAVIGI 96

Query:    79 DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
             DEGQFFPD+V F E MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct:    97 DEGQFFPDIVEFCEVMANAGKTVIVAALDGTFQRKAFGSILNLVPLAESVVKLTAVCMEC 156

Query:   139 FRDAAFTKRIGQEKEV-ILG 157
             FR+AA+TKR+G EKEV ++G
Sbjct:   157 FREAAYTKRLGLEKEVEVIG 176

GO:0008270 "zinc ion binding" evidence=ISS

UNIPROTKB|K7ERJ1 TK1 "Thymidine kinase" [Homo sapiens (taxid:9606)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 82/148 (55%), Positives = 106/148 (71%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQK--------LTAVSAVELNKLIPHT 70
             RR+RR+Q A Y+C++++YAKD RY +    THD+ +        + A+ A  L  +    
Sbjct:    38 RRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRTRSRIIARNTMEALPACLLRDVAQEA 96

Query:    71 KDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEK 130
               + VIGIDEGQFFPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V K
Sbjct:    97 LGVAVIGIDEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVK 156

Query:   131 LTAVCMSCFRDAAFTKRIGQEKEV-ILG 157
             LTAVCM CFR+AA+TKR+G EKEV ++G
Sbjct:   157 LTAVCMECFREAAYTKRLGTEKEVEVIG 184

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IEA

ZFIN|ZDB-GENE-030131-5801 tk1 "thymidine kinase 1, soluble" [Danio rerio (taxid:7955)]

 Score = 412 (150.1 bits), Expect = 1.6e-38, P = 1.6e-38
 Identities = 82/146 (56%), Positives = 104/146 (71%)

Query:    19 RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHD---QQKLTAVSAVELNKL---IPHTKD 72
             RR+RR+Q A Y C++++YAKD RY    +ATHD   Q+ +  + AV  N+L    P    
Sbjct:    38 RRVRRFQVAQYSCLLIKYAKDTRYSCTGMATHDMYEQEIVNTMEAVPANRLRDVAPLALQ 97

Query:    73 IDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 132
               VIGIDEGQFFPD V F E MAN GK ++VAALDGTFQR  F +IL+L+PLAE V KL 
Sbjct:    98 ACVIGIDEGQFFPDTVEFCEEMANMGKTIIVAALDGTFQRKAFGNILNLVPLAESVVKLN 157

Query:   133 AVCMSCFRDAAFTKRIGQEKEV-ILG 157
             AVCM CF++AA+TKR+G EKEV ++G
Sbjct:   158 AVCMQCFKEAAYTKRLGAEKEVEVIG 183

GO:0005524 "ATP binding" evidence=IEA

GO:0004797 "thymidine kinase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0016740 "transferase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0016301 "kinase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016310 "phosphorylation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	2.7.1.21	LOW CONFIDENCE prediction!
3rd Layer	2.7.1	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	353
PTZ00293	211	PTZ00293, PTZ00293, thymidine kinase; Provisional	4e-65
PTZ00293	211	PTZ00293, PTZ00293, thymidine kinase; Provisional	2e-60
pfam00265	175	pfam00265, TK, Thymidine kinase	1e-58
pfam00265	175	pfam00265, TK, Thymidine kinase	4e-55
PRK04296	190	PRK04296, PRK04296, thymidine kinase; Provisional	8e-27
COG1435	201	COG1435, Tdk, Thymidine kinase [Nucleotide transpo	2e-25
PRK04296	190	PRK04296, PRK04296, thymidine kinase; Provisional	3e-22
COG1435	201	COG1435, Tdk, Thymidine kinase [Nucleotide transpo	3e-20
PTZ00293	211	PTZ00293, PTZ00293, thymidine kinase; Provisional	2e-04

>gnl|CDD|185542 PTZ00293, PTZ00293, thymidine kinase; Provisional

 Score =  204 bits (522), Expect = 4e-65
 Identities = 86/199 (43%), Positives = 120/199 (60%), Gaps = 47/199 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRY-DTEKVSTHDQQKLTAVSAV 211
            VI+GPMFSGKTTEL+R ++R+ Y+  +C++++Y+KD RY D + +S+HD+Q L A+   
Sbjct: 7   SVIIGPMFSGKTTELMRLVKRFTYSEKKCVVIKYSKDTRYSDEQNISSHDKQMLKAIKVS 66

Query: 212 ELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
           +L +++   K+ DVI IDEGQF                                      
Sbjct: 67  KLKEVLETAKNYDVIAIDEGQF-------------------------------------- 88

Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 331
                   FPD+V F+E+ AN GKIV+VAALDGTFQR  F  IL+LIPLAE V KLTAVC
Sbjct: 89  --------FPDLVEFSEAAANLGKIVIVAALDGTFQRKPFGQILNLIPLAERVTKLTAVC 140

Query: 332 MSCFRDAAFTKRIGQEKEV 350
           M C ++A+F+KRI Q +++
Sbjct: 141 MFCGKEASFSKRIVQSEQI 159

Length = 211

>gnl|CDD|185542 PTZ00293, PTZ00293, thymidine kinase; Provisional

 Score =  193 bits (491), Expect = 2e-60
 Identities = 75/142 (52%), Positives = 107/142 (75%), Gaps = 3/142 (2%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRY-DTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIG 77
           R ++R+ Y+  +C++++Y+KD RY D + +++HD+Q L A+   +L +++   K+ DVI 
Sbjct: 23  RLVKRFTYSEKKCVVIKYSKDTRYSDEQNISSHDKQMLKAIKVSKLKEVLETAKNYDVIA 82

Query: 78  IDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMS 137
           IDEGQFFPD+V F+E+ AN GKIV+VAALDGTFQR  F  IL+LIPLAE V KLTAVCM 
Sbjct: 83  IDEGQFFPDLVEFSEAAANLGKIVIVAALDGTFQRKPFGQILNLIPLAERVTKLTAVCMF 142

Query: 138 CFRDAAFTKRIGQEK--EVILG 157
           C ++A+F+KRI Q +  E+I G
Sbjct: 143 CGKEASFSKRIVQSEQIELIGG 164

Length = 211

>gnl|CDD|215828 pfam00265, TK, Thymidine kinase

 Score =  187 bits (476), Expect = 1e-58
 Identities = 87/201 (43%), Positives = 113/201 (56%), Gaps = 49/201 (24%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV--SA 210
           E+I+GPMFSGK+TELIRR+ RYQ A Y+C++++YA D+RY T KV THD   + A     
Sbjct: 4   ELIIGPMFSGKSTELIRRVYRYQLAQYKCVVIKYAIDNRYGTGKVVTHDGISMEAKLIKT 63

Query: 211 VELNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANEN 269
             L+ +    +  I V+GIDE QF                                    
Sbjct: 64  SLLDDIKDIISNTIHVVGIDEAQF------------------------------------ 87

Query: 270 AALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTA 329
                     F D+V F E+MAN GKIV+VA LDG FQR  F +IL+L+PLAE V KL A
Sbjct: 88  ----------FDDIVEFCETMANLGKIVIVAGLDGDFQRKPFGNILNLLPLAEKVTKLKA 137

Query: 330 VCMSCFRDAAFTKRIGQEKEV 350
           VCM C++DA+FTKR+  EKE+
Sbjct: 138 VCMKCYKDASFTKRLNNEKEI 158

Length = 175

>gnl|CDD|215828 pfam00265, TK, Thymidine kinase

 Score =  177 bits (452), Expect = 4e-55
 Identities = 76/141 (53%), Positives = 99/141 (70%), Gaps = 3/141 (2%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAV--SAVELNKLIPH-TKDIDV 75
           RR+ RYQ A Y+C++++YA D+RY T KV THD   + A       L+ +    +  I V
Sbjct: 20  RRVYRYQLAQYKCVVIKYAIDNRYGTGKVVTHDGISMEAKLIKTSLLDDIKDIISNTIHV 79

Query: 76  IGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 135
           +GIDE QFF D+V F E+MAN GKIV+VA LDG FQR  F +IL+L+PLAE V KL AVC
Sbjct: 80  VGIDEAQFFDDIVEFCETMANLGKIVIVAGLDGDFQRKPFGNILNLLPLAEKVTKLKAVC 139

Query: 136 MSCFRDAAFTKRIGQEKEVIL 156
           M C++DA+FTKR+  EKE+IL
Sbjct: 140 MKCYKDASFTKRLNNEKEIIL 160

Length = 175

>gnl|CDD|235272 PRK04296, PRK04296, thymidine kinase; Provisional

 Score =  104 bits (262), Expect = 8e-27
 Identities = 54/205 (26%), Positives = 80/205 (39%), Gaps = 48/205 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV---S 209
           E I G M SGK+TEL++R   Y+    + ++ + A DDRY   KV +       A+   S
Sbjct: 5   EFIYGAMNSGKSTELLQRAYNYEERGMKVLVFKPAIDDRYGEGKVVSRIGLSREAIPVSS 64

Query: 210 AVELNKLI-PHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANE 268
             ++ +LI    + ID + IDE QF                               L  E
Sbjct: 65  DTDIFELIEEEGEKIDCVLIDEAQF-------------------------------LDKE 93

Query: 269 NAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 328
                         VV  AE + + G  V+   LD  F+   F     L+ LA+ V +L 
Sbjct: 94  Q-------------VVQLAEVLDDLGIPVICYGLDTDFRGEPFEGSPYLLALADKVTELK 140

Query: 329 AVCMSCFRDAAFTKRIGQEKEVRIE 353
           A+C+ C R A   +R+        E
Sbjct: 141 AICVHCGRKATMNQRLIDGGPAVYE 165

Length = 190

>gnl|CDD|224352 COG1435, Tdk, Thymidine kinase [Nucleotide transport and metabolism]

 Score =  101 bits (253), Expect = 2e-25
 Identities = 57/207 (27%), Positives = 76/207 (36%), Gaps = 50/207 (24%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV---S 209
           E I GPMFSGKT EL+RR RRY+ A  + ++ + A D RY   KVS+       AV   S
Sbjct: 7   EFIYGPMFSGKTEELLRRARRYKEAGMKVLVFKPAIDTRYGVGKVSSRIGLSSEAVVIPS 66

Query: 210 AVELNKLI---PHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLA 266
             ++   I        +D + IDE QF                                 
Sbjct: 67  DTDIFDEIAALHEKPPVDCVLIDEAQFF-------------------------------- 94

Query: 267 NENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEK 326
                       E   V+   E     G  V+   LD  F+   F     L+ +A+ V K
Sbjct: 95  ----------DEELVYVL--NELADRLGIPVICYGLDTDFRGEPFEGSKYLLAIADKVTK 142

Query: 327 LTAVCMSCFRDAAFTKRIGQEKEVRIE 353
           L A+C  C R A  T R+        E
Sbjct: 143 LKAICNVCGRKATRTLRLINGGPAVYE 169

Length = 201

>gnl|CDD|235272 PRK04296, PRK04296, thymidine kinase; Provisional

 Score = 92.1 bits (230), Expect = 3e-22
 Identities = 41/143 (28%), Positives = 66/143 (46%), Gaps = 6/143 (4%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAV---SAVELNKLI-PHTKDID 74
           +R   Y+    + ++ + A DDRY   KV +       A+   S  ++ +LI    + ID
Sbjct: 21  QRAYNYEERGMKVLVFKPAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEEEGEKID 80

Query: 75  VIGIDEGQFFPD--VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 132
            + IDE QF     VV  AE + + G  V+   LD  F+   F     L+ LA+ V +L 
Sbjct: 81  CVLIDEAQFLDKEQVVQLAEVLDDLGIPVICYGLDTDFRGEPFEGSPYLLALADKVTELK 140

Query: 133 AVCMSCFRDAAFTKRIGQEKEVI 155
           A+C+ C R A   +R+      +
Sbjct: 141 AICVHCGRKATMNQRLIDGGPAV 163

Length = 190

>gnl|CDD|224352 COG1435, Tdk, Thymidine kinase [Nucleotide transport and metabolism]

 Score = 86.9 bits (216), Expect = 3e-20
 Identities = 43/145 (29%), Positives = 66/145 (45%), Gaps = 8/145 (5%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAV---SAVELNKLI---PHTKD 72
           RR RRY+ A  + ++ + A D RY   KV++       AV   S  ++   I        
Sbjct: 23  RRARRYKEAGMKVLVFKPAIDTRYGVGKVSSRIGLSSEAVVIPSDTDIFDEIAALHEKPP 82

Query: 73  IDVIGIDEGQFF-PDVVSFAESMANAGKI-VVVAALDGTFQRTGFNDILSLIPLAECVEK 130
           +D + IDE QFF  ++V     +A+   I V+   LD  F+   F     L+ +A+ V K
Sbjct: 83  VDCVLIDEAQFFDEELVYVLNELADRLGIPVICYGLDTDFRGEPFEGSKYLLAIADKVTK 142

Query: 131 LTAVCMSCFRDAAFTKRIGQEKEVI 155
           L A+C  C R A  T R+      +
Sbjct: 143 LKAICNVCGRKATRTLRLINGGPAV 167

Length = 201

>gnl|CDD|185542 PTZ00293, PTZ00293, thymidine kinase; Provisional

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 228 IDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEF 280
           I + + +E+IGG DKY+A CR+C++ K  +     +       A        F
Sbjct: 153 IVQSEQIELIGGEDKYIATCRKCFRTKQ-LAEKELEKQDLVEFADFSNEENIF 204

Length = 211

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	353
PTZ00293	211	thymidine kinase; Provisional	100.0
PF00265	176	TK: Thymidine kinase; InterPro: IPR001267 Thymidin	100.0
PTZ00293	211	thymidine kinase; Provisional	100.0
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	100.0
PF00265	176	TK: Thymidine kinase; InterPro: IPR001267 Thymidin	100.0
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	100.0
KOG3125|consensus	234		100.0
KOG3125|consensus	234		100.0
PRK04296	190	thymidine kinase; Provisional	100.0
PRK04296	190	thymidine kinase; Provisional	100.0
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.82
PF13173	128	AAA_14: AAA domain	97.49
PRK07413	382	hypothetical protein; Validated	97.35
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.29
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.27
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.14
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.05
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	96.98
PRK08084	235	DNA replication initiation factor; Provisional	96.98
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	96.95
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.92
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.88
smart00382	148	AAA ATPases associated with a variety of cellular	96.87
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.87
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.87
PRK11823	446	DNA repair protein RadA; Provisional	96.86
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.83
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.81
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	96.79
PRK08727	233	hypothetical protein; Validated	96.71
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.71
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	96.59
PRK05642	234	DNA replication initiation factor; Validated	96.57
PRK06893	229	DNA replication initiation factor; Validated	96.57
smart00487	201	DEXDc DEAD-like helicases superfamily.	96.55
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.45
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.36
PRK12422	445	chromosomal replication initiation protein; Provis	96.35
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.35
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.32
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.25
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.24
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.19
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.08
PF13245	76	AAA_19: Part of AAA domain	96.07
PRK00149	450	dnaA chromosomal replication initiation protein; R	95.99
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.87
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.87
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.86
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	95.84
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.83
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	95.82
PRK06526	254	transposase; Provisional	95.74
PRK08903	227	DnaA regulatory inactivator Hda; Validated	95.73
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.69
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.68
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	95.68
PRK05973	237	replicative DNA helicase; Provisional	95.61
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.56
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	95.52
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.51
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.44
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.43
PF13173	128	AAA_14: AAA domain	95.42
PF02702	211	KdpD: Osmosensitive K+ channel His kinase sensor d	95.39
TIGR00595	505	priA primosomal protein N'. All proteins in this f	95.38
PRK08116	268	hypothetical protein; Validated	95.38
PHA00350	399	putative assembly protein	95.35
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.27
PRK06921	266	hypothetical protein; Provisional	95.26
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.25
PRK14974	336	cell division protein FtsY; Provisional	95.23
PRK06620	214	hypothetical protein; Validated	95.21
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.17
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.11
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	95.08
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.04
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	95.03
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	94.97
PRK06067	234	flagellar accessory protein FlaH; Validated	94.97
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.91
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	94.87
PRK10436	462	hypothetical protein; Provisional	94.84
PRK13889	988	conjugal transfer relaxase TraA; Provisional	94.84
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	94.83
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	94.78
PRK14088	440	dnaA chromosomal replication initiation protein; P	94.77
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	94.73
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	94.67
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.66
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	94.65
PRK00411	394	cdc6 cell division control protein 6; Reviewed	94.59
PRK10416	318	signal recognition particle-docking protein FtsY;	94.56
PF13479	213	AAA_24: AAA domain	94.53
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	94.49
PRK13695	174	putative NTPase; Provisional	94.43
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	94.4
PRK10536	262	hypothetical protein; Provisional	94.38
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	94.36
PRK00771	437	signal recognition particle protein Srp54; Provisi	94.31
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.3
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	94.28
PRK13826	1102	Dtr system oriT relaxase; Provisional	94.26
PHA00012	361	I assembly protein	94.21
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	94.21
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	94.15
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	94.14
PRK08084	235	DNA replication initiation factor; Provisional	94.06
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	94.02
TIGR00064	272	ftsY signal recognition particle-docking protein F	94.0
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	93.99
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	93.95
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	93.88
PRK08181	269	transposase; Validated	93.81
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	93.79
PRK14494	229	putative molybdopterin-guanine dinucleotide biosyn	93.74
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	93.66
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	93.52
PRK12377	248	putative replication protein; Provisional	93.51
PRK07952	244	DNA replication protein DnaC; Validated	93.49
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	93.46
TIGR00595	505	priA primosomal protein N'. All proteins in this f	93.44
TIGR02533	486	type_II_gspE general secretory pathway protein E.	93.27
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.22
PRK08727	233	hypothetical protein; Validated	93.2
PRK09183	259	transposase/IS protein; Provisional	93.18
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	93.16
PHA00547	337	hypothetical protein	93.12
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	93.09
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	93.06
PRK05580	679	primosome assembly protein PriA; Validated	93.05
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	92.97
KOG0922|consensus	674		92.94
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	92.91
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	92.87
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	92.86
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	92.84
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	92.79
PRK06835	329	DNA replication protein DnaC; Validated	92.76
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	92.6
PRK14087	450	dnaA chromosomal replication initiation protein; P	92.57
cd03112	158	CobW_like The function of this protein family is u	92.4
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	92.37
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	92.36
PRK11823	446	DNA repair protein RadA; Provisional	92.35
PF12846	304	AAA_10: AAA-like domain	92.32
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	92.28
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	92.25
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	92.22
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	92.15
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	92.13
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	92.07
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	92.07
cd03114	148	ArgK-like The function of this protein family is u	92.06
cd03115	173	SRP The signal recognition particle (SRP) mediates	92.06
PF02492	178	cobW: CobW/HypB/UreG, nucleotide-binding domain; I	91.98
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	91.89
COG2256	436	MGS1 ATPase related to the helicase subunit of the	91.76
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	91.73
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	91.72
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	91.7
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	91.61
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	91.6
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	91.6
PRK04195	482	replication factor C large subunit; Provisional	91.56
PRK00889	175	adenylylsulfate kinase; Provisional	91.4
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	91.3
PRK05541	176	adenylylsulfate kinase; Provisional	91.28
PRK12422	445	chromosomal replication initiation protein; Provis	91.22
smart00487	201	DEXDc DEAD-like helicases superfamily.	91.13
PRK00698	205	tmk thymidylate kinase; Validated	91.09
PRK14738	206	gmk guanylate kinase; Provisional	90.88
PF00004	132	AAA: ATPase family associated with various cellula	90.86
cd01394	218	radB RadB. The archaeal protein radB shares simila	90.67
PRK09087	226	hypothetical protein; Validated	90.66
KOG0953|consensus	700		90.6
TIGR02237	209	recomb_radB DNA repair and recombination protein R	90.54
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	90.5
PRK06893	229	DNA replication initiation factor; Validated	90.41
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	90.4
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	90.35
PHA02558	501	uvsW UvsW helicase; Provisional	90.33
PRK10490	895	sensor protein KdpD; Provisional	90.28
COG1484	254	DnaC DNA replication protein [DNA replication, rec	90.22
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	90.2
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	90.17
PRK08939	306	primosomal protein DnaI; Reviewed	90.14
PRK05642	234	DNA replication initiation factor; Validated	90.13
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	90.07
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	90.01
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	90.0
KOG0923|consensus	902		89.91
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	89.9
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	89.87
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	89.87
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	89.81
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	89.78
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	89.77
KOG1533|consensus	290		89.76
COG1198	730	PriA Primosomal protein N' (replication factor Y)	89.64
PRK14491	597	putative bifunctional molybdopterin-guanine dinucl	89.64
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	89.54
PRK13833	323	conjugal transfer protein TrbB; Provisional	89.49
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	89.47
PRK13764	602	ATPase; Provisional	89.41
PRK13342	413	recombination factor protein RarA; Reviewed	89.35
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	89.2
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	89.11
PRK01184	184	hypothetical protein; Provisional	89.09
TIGR01070	840	mutS1 DNA mismatch repair protein MutS.	89.08
PRK09435	332	membrane ATPase/protein kinase; Provisional	88.95
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	88.84
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	88.79
PRK05399	854	DNA mismatch repair protein MutS; Provisional	88.77
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	88.7
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	88.62
PRK13826	1102	Dtr system oriT relaxase; Provisional	88.59
PF13555	62	AAA_29: P-loop containing region of AAA domain	88.56
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	88.56
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	88.54
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	88.45
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	88.43
cd03109	134	DTBS Dethiobiotin synthetase (DTBS) is the penulti	88.07
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	87.98
PRK13889	988	conjugal transfer relaxase TraA; Provisional	87.96
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	87.87
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	87.76
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	87.7
PRK12402	337	replication factor C small subunit 2; Reviewed	87.64
PRK09519	790	recA DNA recombination protein RecA; Reviewed	87.61
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	87.58
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	87.57
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	87.52
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	87.41
PRK03839	180	putative kinase; Provisional	87.23
PRK13851	344	type IV secretion system protein VirB11; Provision	87.18
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	86.99
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	86.98
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	86.93
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	86.85
cd00983	325	recA RecA is a bacterial enzyme which has roles in	86.84
CHL00181	287	cbbX CbbX; Provisional	86.81
PTZ00424	401	helicase 45; Provisional	86.73
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	86.7
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	86.68
PRK13768	253	GTPase; Provisional	86.63
smart00382	148	AAA ATPases associated with a variety of cellular	86.63
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	86.58
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	86.52
PRK14532	188	adenylate kinase; Provisional	86.52
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	86.51
PRK05580	679	primosome assembly protein PriA; Validated	86.5
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	86.16
PRK00149	450	dnaA chromosomal replication initiation protein; R	86.07
PRK08903	227	DnaA regulatory inactivator Hda; Validated	85.99
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	85.99
PRK08533	230	flagellar accessory protein FlaH; Reviewed	85.98
cd03116	159	MobB Molybdenum is an essential trace element in t	85.97
PRK09354	349	recA recombinase A; Provisional	85.96
PRK07933	213	thymidylate kinase; Validated	85.91
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	85.81
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	85.69
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	85.59
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	85.56
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	85.54
TIGR00376	637	DNA helicase, putative. The gene product may repre	85.43
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	85.38
PRK14495	452	putative molybdopterin-guanine dinucleotide biosyn	85.32
COG0249	843	MutS Mismatch repair ATPase (MutS family) [DNA rep	85.18
PRK10867	433	signal recognition particle protein; Provisional	85.13
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	85.13
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	85.06
PLN02840	421	tRNA dimethylallyltransferase	84.98
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	84.97
PRK13938	196	phosphoheptose isomerase; Provisional	84.91
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	84.85
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	84.84
PRK00440	319	rfc replication factor C small subunit; Reviewed	84.83
KOG0924|consensus	1042		84.81
PRK04328	249	hypothetical protein; Provisional	84.79
PF00154	322	RecA: recA bacterial DNA recombination protein; In	84.74
PRK13695	174	putative NTPase; Provisional	84.74
PHA00729	226	NTP-binding motif containing protein	84.72
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	84.5
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	84.46
PRK14489	366	putative bifunctional molybdopterin-guanine dinucl	84.34
PLN03025	319	replication factor C subunit; Provisional	84.26
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	84.16
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	84.12
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	84.0
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	83.8
PRK06921	266	hypothetical protein; Provisional	83.79
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	83.77
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	83.74
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	83.72
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	83.66
TIGR00767	415	rho transcription termination factor Rho. Members	83.55
PRK10875	615	recD exonuclease V subunit alpha; Provisional	83.45
PHA00350	399	putative assembly protein	83.43
COG3972	660	Superfamily I DNA and RNA helicases [General funct	83.3
PRK07413	382	hypothetical protein; Validated	83.16
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	83.04
PF02702	211	KdpD: Osmosensitive K+ channel His kinase sensor d	82.91
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	82.9
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	82.86
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	82.82
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	82.67
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	82.67
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	82.65
PRK13973	213	thymidylate kinase; Provisional	82.57
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	82.57
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	82.56
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	82.33
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	82.19
PF00005	137	ABC_tran: ABC transporter This structure is on hol	82.18
cd03279	213	ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complex	82.17
PRK14530	215	adenylate kinase; Provisional	82.09
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	82.05
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	82.0
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	81.98
PF05729	166	NACHT: NACHT domain	81.93
PRK06217	183	hypothetical protein; Validated	81.92
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	81.76
PRK14088	440	dnaA chromosomal replication initiation protein; P	81.62
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	81.61
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	81.45
PRK10744	260	pstB phosphate transporter ATP-binding protein; Pr	81.4
PRK14737	186	gmk guanylate kinase; Provisional	81.36
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	81.13
PRK00625	173	shikimate kinase; Provisional	81.08
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	81.05
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	81.04
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	81.03
PTZ00088	229	adenylate kinase 1; Provisional	80.96
PF02223	186	Thymidylate_kin: Thymidylate kinase; InterPro: IPR	80.93
TIGR00347	166	bioD dethiobiotin synthase. Dethiobiotin synthase	80.9
PRK14086	617	dnaA chromosomal replication initiation protein; P	80.85
PHA02653	675	RNA helicase NPH-II; Provisional	80.8
PRK14273	254	phosphate ABC transporter ATP-binding protein; Pro	80.7
PRK08116	268	hypothetical protein; Validated	80.63
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	80.55
PRK14494	229	putative molybdopterin-guanine dinucleotide biosyn	80.55
KOG0926|consensus	1172		80.48
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	80.44
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	80.35
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	80.32
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	80.32
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	80.19
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	80.17
PHA02544	316	44 clamp loader, small subunit; Provisional	80.16
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	80.15
TIGR00959	428	ffh signal recognition particle protein. This mode	80.1

>PTZ00293 thymidine kinase; Provisional

Probab=100.00  E-value=3.5e-50  Score=372.35  Aligned_cols=141  Identities=51%  Similarity=0.898  Sum_probs=135.0

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCC-CCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChHHHH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRY-DTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVV   88 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy-~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~dIv   88 (353)
                      -||||||||++++||.++|+++++|||++|||| +.+.|+||+|+.++|+.++++.++.....++|||+|||||||++|+
T Consensus        14 fSGKTteLLr~i~~y~~ag~kv~~~kp~~DtR~~~~~~I~Sh~g~~~~a~~v~~~~e~~~~~~~~dvI~IDEaQFf~~i~   93 (211)
T PTZ00293         14 FSGKTTELMRLVKRFTYSEKKCVVIKYSKDTRYSDEQNISSHDKQMLKAIKVSKLKEVLETAKNYDVIAIDEGQFFPDLV   93 (211)
T ss_pred             CChHHHHHHHHHHHHHHcCCceEEEEecccccCCCCCcEEecCCCcceeEEcCCHHHHHHhccCCCEEEEEchHhhHhHH
Confidence            489999999999999999999999999999999 7788999999999999999998887656789999999999999999


Q ss_pred             HHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceeccccccccccccccc
Q psy8456          89 SFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQ  150 (353)
Q Consensus        89 ~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~g  150 (353)
                      ++++.+++.|++|||||||+||+++||+++++||++||+|+||+|+|++||++|+||+|+++
T Consensus        94 ~~~~~l~~~g~~VivaGLd~Df~~~~F~~~~~Ll~~AD~V~kl~aiC~~CG~~A~~t~R~~~  155 (211)
T PTZ00293         94 EFSEAAANLGKIVIVAALDGTFQRKPFGQILNLIPLAERVTKLTAVCMFCGKEASFSKRIVQ  155 (211)
T ss_pred             HHHHHHHHCCCeEEEEecCcccccCcCccHHHHHHhhCEEEEcceEchhhCCcceeEEEEcC
Confidence            99999999999999999999999999999999999999999999999999999999999754

>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2

Probab=100.00  E-value=1.2e-49  Score=359.05  Aligned_cols=140  Identities=39%  Similarity=0.616  Sum_probs=125.3

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeee--ecCChhhhcccC-CCccEEEEccccChH-
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAV--SAVELNKLIPHT-KDIDVIGIDEGQFFP-   85 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai--~i~~l~ei~~~~-~~~dvV~IDEaQFF~-   85 (353)
                      -|||||+||++++||+.+|++|++|||++||||+.++|+||+|.+.+|.  .++++.++.... .++|+|+|||||||+ 
T Consensus        11 ~sGKS~eLi~~~~~~~~~~~~v~~~kp~~D~R~~~~~I~s~~g~~~~~~~~~~~~~~~~~~~~~~~~dvI~IDEaQFf~~   90 (176)
T PF00265_consen   11 FSGKSTELIRRIHRYEIAGKKVLVFKPAIDTRYGEDKIVSHDGISLEAIVDPIDNLFEIIDILENDYDVIGIDEAQFFDE   90 (176)
T ss_dssp             TSSHHHHHHHHHHHHHHTT-EEEEEEESTSCCCCSSEEEHTTSCEEEEESSEESSGGGGGGGCCTTCSEEEESSGGGSTT
T ss_pred             CChhHHHHHHHHHHHHhCCCeEEEEEecccCcCCCCeEEecCCCcccccccchhhHHHHHHHhccCCCEEEEechHhhHH
Confidence            5999999999999999999999999999999999889999999999999  788888887544 449999999999998 


Q ss_pred             HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceecccccccccccccc
Q psy8456          86 DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIG  149 (353)
Q Consensus        86 dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~  149 (353)
                      ||+++++.++++|++|+|||||+||+++||+++++||++||+|+||+|+|++||++|++|+|++
T Consensus        91 ~i~~l~~~~~~~g~~Vi~~GL~~df~~~~F~~~~~Ll~~Ad~i~kl~avC~~Cg~~A~~t~R~~  154 (176)
T PF00265_consen   91 QIVQLVEILANKGIPVICAGLDTDFRGEPFGGSPRLLPLADKITKLKAVCEVCGRKATFTQRIV  154 (176)
T ss_dssp             THHHHHHHHHHTT-EEEEEEESB-TTSSB-TTHHHHHHH-SEEEEE-EE-TTTSSEE-EEEEEE
T ss_pred             HHHHHHHHHHhCCCeEEEEeeCCccccCcchhHHHHHhhCCeEEEeccEECCCCCceeEEEEEc
Confidence            9999999999999999999999999999999999999999999999999999999999999975

7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....

>PTZ00293 thymidine kinase; Provisional

Probab=100.00  E-value=7.1e-49  Score=363.59  Aligned_cols=157  Identities=55%  Similarity=0.949  Sum_probs=148.9

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCC-CCCceeeccCcccceeecccHhhhcccCCCccEEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRY-DTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIG  227 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~-~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~  227 (353)
                      .|++++|+|||||||||||||+++||..+|++|+++||+.|+|| +.+.|+||+|..++|+.+.++.++.....++|||+
T Consensus         3 ~G~i~vi~GpMfSGKTteLLr~i~~y~~ag~kv~~~kp~~DtR~~~~~~I~Sh~g~~~~a~~v~~~~e~~~~~~~~dvI~   82 (211)
T PTZ00293          3 RGTISVIIGPMFSGKTTELMRLVKRFTYSEKKCVVIKYSKDTRYSDEQNISSHDKQMLKAIKVSKLKEVLETAKNYDVIA   82 (211)
T ss_pred             ceEEEEEECCCCChHHHHHHHHHHHHHHcCCceEEEEecccccCCCCCcEEecCCCcceeEEcCCHHHHHHhccCCCEEE
Confidence            47899999999999999999999999999999999999999999 77889999999999999998888876667899999


Q ss_pred             EecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEecccccc
Q psy8456         228 IDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQ  307 (353)
Q Consensus       228 IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df~  307 (353)
                      |||+||                                              |++|+++++.+++.|++|||||||+||+
T Consensus        83 IDEaQF----------------------------------------------f~~i~~~~~~l~~~g~~VivaGLd~Df~  116 (211)
T PTZ00293         83 IDEGQF----------------------------------------------FPDLVEFSEAAANLGKIVIVAALDGTFQ  116 (211)
T ss_pred             EEchHh----------------------------------------------hHhHHHHHHHHHHCCCeEEEEecCcccc
Confidence            999999                                              6789999999999999999999999999


Q ss_pred             CCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCeeEE
Q psy8456         308 RTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVR  351 (353)
Q Consensus       308 ~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~~~  351 (353)
                      ++||+++++|||+||+|+||+|+|+.||++|+||+|+++++++.
T Consensus       117 ~~~F~~~~~Ll~~AD~V~kl~aiC~~CG~~A~~t~R~~~~~~~v  160 (211)
T PTZ00293        117 RKPFGQILNLIPLAERVTKLTAVCMFCGKEASFSKRIVQSEQIE  160 (211)
T ss_pred             cCcCccHHHHHHhhCEEEEcceEchhhCCcceeEEEEcCCCCEE
Confidence            99999999999999999999999999999999999999876663

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=100.00  E-value=8.1e-50  Score=365.01  Aligned_cols=142  Identities=29%  Similarity=0.405  Sum_probs=130.4

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhccc---C---CCccEEEEccccC
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH---T---KDIDVIGIDEGQF   83 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~---~---~~~dvV~IDEaQF   83 (353)
                      -||||+|||++++||+++|++|++|||++|+||+.+.|+||.|++.+|+.+.+..++...   .   ..+|||+||||||
T Consensus        14 ~SGKT~eLl~r~~~~~~~g~~v~vfkp~iD~R~~~~~V~Sr~G~~~~A~~i~~~~~i~~~i~~~~~~~~~~~v~IDEaQF   93 (201)
T COG1435          14 FSGKTEELLRRARRYKEAGMKVLVFKPAIDTRYGVGKVSSRIGLSSEAVVIPSDTDIFDEIAALHEKPPVDCVLIDEAQF   93 (201)
T ss_pred             cCcchHHHHHHHHHHHHcCCeEEEEecccccccccceeeeccCCcccceecCChHHHHHHHHhcccCCCcCEEEEehhHh
Confidence            599999999999999999999999999999999999999999999999999887777632   1   2279999999999


Q ss_pred             hH-HHHHHHHHHHhC-CCEEEEEecccccccCCchhHhhhhccccceEeccceecccccccccccccccc
Q psy8456          84 FP-DVVSFAESMANA-GKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQE  151 (353)
Q Consensus        84 F~-dIv~l~~~l~~~-G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~ge  151 (353)
                      |+ ++++.++.+++. |++|||||||+|||+|||+++++||++||+|+||+|||.+||++|++++|+.++
T Consensus        94 ~~~~~v~~l~~lad~lgi~Vi~~GL~~DFrgepFe~s~~Lla~ADkv~kL~aIC~~Cg~~At~~~Rl~~~  163 (201)
T COG1435          94 FDEELVYVLNELADRLGIPVICYGLDTDFRGEPFEGSKYLLAIADKVTKLKAICNVCGRKATRTLRLING  163 (201)
T ss_pred             CCHHHHHHHHHHHhhcCCEEEEeccccccccCCCccHHHHHHHHHHHHHHHHHHHHhCCcceEEEEecCC
Confidence            97 777777777766 999999999999999999999999999999999999999999999999999764

>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2

Probab=100.00  E-value=6.3e-48  Score=347.83  Aligned_cols=154  Identities=45%  Similarity=0.700  Sum_probs=134.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCccccee--ecccHhhhcccC-CCccEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV--SAVELNKLIPHT-KDIDVI  226 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~--~~~~~~~~~~~~-~~~~~i  226 (353)
                      |++++|+|||||||||+||+++++|+.+|++|+++||++|+||+.++|+||+|...+|+  ...++.++.... .++|+|
T Consensus         1 g~l~~i~GpM~sGKS~eLi~~~~~~~~~~~~v~~~kp~~D~R~~~~~I~s~~g~~~~~~~~~~~~~~~~~~~~~~~~dvI   80 (176)
T PF00265_consen    1 GKLEFITGPMFSGKSTELIRRIHRYEIAGKKVLVFKPAIDTRYGEDKIVSHDGISLEAIVDPIDNLFEIIDILENDYDVI   80 (176)
T ss_dssp             -EEEEEEESTTSSHHHHHHHHHHHHHHTT-EEEEEEESTSCCCCSSEEEHTTSCEEEEESSEESSGGGGGGGCCTTCSEE
T ss_pred             CEEEEEECCcCChhHHHHHHHHHHHHhCCCeEEEEEecccCcCCCCeEEecCCCcccccccchhhHHHHHHHhccCCCEE
Confidence            57899999999999999999999999999999999999999999999999999999999  778888887664 349999


Q ss_pred             EEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCc-cHHHHHHHHHhCCCEEEEEecccc
Q psy8456         227 GIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFP-DVVSFAESMANAGKIVVVAALDGT  305 (353)
Q Consensus       227 ~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~-~~~~~~~~~~~~g~~Vi~~gLd~d  305 (353)
                      +|||+||                                              |+ +|+++++.+++.|++|+|||||+|
T Consensus        81 ~IDEaQF----------------------------------------------f~~~i~~l~~~~~~~g~~Vi~~GL~~d  114 (176)
T PF00265_consen   81 GIDEAQF----------------------------------------------FDEQIVQLVEILANKGIPVICAGLDTD  114 (176)
T ss_dssp             EESSGGG----------------------------------------------STTTHHHHHHHHHHTT-EEEEEEESB-
T ss_pred             EEechHh----------------------------------------------hHHHHHHHHHHHHhCCCeEEEEeeCCc
Confidence            9999999                                              54 788888888899999999999999


Q ss_pred             ccCCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCee
Q psy8456         306 FQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKE  349 (353)
Q Consensus       306 f~~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~  349 (353)
                      |+++||+++.+|||+||+|+||+|+|+.||++|+||+|++.+++
T Consensus       115 f~~~~F~~~~~Ll~~Ad~i~kl~avC~~Cg~~A~~t~R~~~~~~  158 (176)
T PF00265_consen  115 FRGEPFGGSPRLLPLADKITKLKAVCEVCGRKATFTQRIVDDGE  158 (176)
T ss_dssp             TTSSB-TTHHHHHHH-SEEEEE-EE-TTTSSEE-EEEEEETTSS
T ss_pred             cccCcchhHHHHHhhCCeEEEeccEECCCCCceeEEEEEcCCCC
Confidence            99999999999999999999999999999999999999986543

7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=100.00  E-value=1.8e-48  Score=356.16  Aligned_cols=156  Identities=33%  Similarity=0.430  Sum_probs=141.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc---C---CC
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH---T---KD  222 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~---~---~~  222 (353)
                      .++++|++|||||||||||||+++||+++|++|+++||++|+||+.+.|+||.|.+.+|+.+.+-.++..+   .   .+
T Consensus         3 ~g~l~~i~gpM~SGKT~eLl~r~~~~~~~g~~v~vfkp~iD~R~~~~~V~Sr~G~~~~A~~i~~~~~i~~~i~~~~~~~~   82 (201)
T COG1435           3 MGWLEFIYGPMFSGKTEELLRRARRYKEAGMKVLVFKPAIDTRYGVGKVSSRIGLSSEAVVIPSDTDIFDEIAALHEKPP   82 (201)
T ss_pred             eEEEEEEEccCcCcchHHHHHHHHHHHHcCCeEEEEecccccccccceeeeccCCcccceecCChHHHHHHHHhcccCCC
Confidence            47899999999999999999999999999999999999999999999999999999999998765555432   1   22


Q ss_pred             ccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEec
Q psy8456         223 IDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAAL  302 (353)
Q Consensus       223 ~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gL  302 (353)
                      +|||+|||+|||                       +++||++|+++++                     +.|++|+||||
T Consensus        83 ~~~v~IDEaQF~-----------------------~~~~v~~l~~lad---------------------~lgi~Vi~~GL  118 (201)
T COG1435          83 VDCVLIDEAQFF-----------------------DEELVYVLNELAD---------------------RLGIPVICYGL  118 (201)
T ss_pred             cCEEEEehhHhC-----------------------CHHHHHHHHHHHh---------------------hcCCEEEEecc
Confidence            899999999997                       5667777766666                     56999999999


Q ss_pred             cccccCCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCe
Q psy8456         303 DGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEK  348 (353)
Q Consensus       303 d~df~~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~  348 (353)
                      |+|||++||+++..||++||+|+||+|+|+.||++|++|+|+.+|+
T Consensus       119 ~~DFrgepFe~s~~Lla~ADkv~kL~aIC~~Cg~~At~~~Rl~~~~  164 (201)
T COG1435         119 DTDFRGEPFEGSKYLLAIADKVTKLKAICNVCGRKATRTLRLINGG  164 (201)
T ss_pred             ccccccCCCccHHHHHHHHHHHHHHHHHHHHhCCcceEEEEecCCC
Confidence            9999999999999999999999999999999999999999999864

>KOG3125|consensus

Probab=100.00  E-value=4.1e-47  Score=346.42  Aligned_cols=160  Identities=49%  Similarity=0.762  Sum_probs=147.8

Q ss_pred             ccccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecc---cHhhhcc--cCC
Q psy8456         147 RIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAV---ELNKLIP--HTK  221 (353)
Q Consensus       147 Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~---~~~~~~~--~~~  221 (353)
                      +..|.++||+|||||||||+||||+++.+.+|++|+++||+.||||..+.|+||+|...++-...   .+.++-.  ...
T Consensus        24 ~t~G~i~vI~gPMfSGKTt~LLrr~r~~~~~grrv~liK~~kDTRy~~~si~Thdg~~~~c~~lp~a~~~s~f~~d~~~~  103 (234)
T KOG3125|consen   24 MTRGTIHVILGPMFSGKTTELLRRIRREIIAGRRVLLIKYAKDTRYESSSIVTHDGIEMPCWALPDASFLSEFGKDALNG  103 (234)
T ss_pred             CCCceEEEEeccccCcchHHHHHHHHHHHhcCceEEEEEecCCcccchheeEeccCCcccccccCCchhHHHHHHHHhcC
Confidence            45689999999999999999999999999999999999999999999999999999988776543   3443332  257


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHh-CCCEEEEE
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMAN-AGKIVVVA  300 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~-~g~~Vi~~  300 (353)
                      ++|||+||||||                                              |+||++||+++|+ .||+|+||
T Consensus       104 ~vdVigIDEaQF----------------------------------------------f~dl~efc~evAd~~Gk~Viva  137 (234)
T KOG3125|consen  104 DVDVIGIDEAQF----------------------------------------------FGDLYEFCREVADVHGKTVIVA  137 (234)
T ss_pred             cceEEEecHHHH----------------------------------------------hHHHHHHHHHHHhccCCEEEEE
Confidence            899999999999                                              8999999999998 99999999


Q ss_pred             eccccccCCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCeeEEe
Q psy8456         301 ALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVRI  352 (353)
Q Consensus       301 gLd~df~~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~~~~  352 (353)
                      ||||||+|+||++++.|+|+||+|+||+++|+.||++|.||.|..++|++++
T Consensus       138 gLdgdF~Rk~Fg~il~Lvplad~v~kLtavC~~Cg~~a~Ft~R~~~~K~ve~  189 (234)
T KOG3125|consen  138 GLDGDFKRKPFGAILDLVPLADSVTKLTAVCEECGADARFTLRKTNDKEVEV  189 (234)
T ss_pred             ecCCchhhCcchhhhhhHhhhhhhhhhhhhhhhhcccceeEeeecCCceeEE
Confidence            9999999999999999999999999999999999999999999999999986

>KOG3125|consensus

Probab=100.00  E-value=5.1e-47  Score=345.80  Aligned_cols=142  Identities=43%  Similarity=0.706  Sum_probs=130.6

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCC---hhhhc--ccCCCccEEEEccccCh
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVE---LNKLI--PHTKDIDVIGIDEGQFF   84 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~---l~ei~--~~~~~~dvV~IDEaQFF   84 (353)
                      .|||||+||||+++...+|++|+++||+.||||..+.|+||+|+++++..+.+   +.++-  ..++++|||+|||||||
T Consensus        37 fSGKTt~LLrr~r~~~~~grrv~liK~~kDTRy~~~si~Thdg~~~~c~~lp~a~~~s~f~~d~~~~~vdVigIDEaQFf  116 (234)
T KOG3125|consen   37 FSGKTTELLRRIRREIIAGRRVLLIKYAKDTRYESSSIVTHDGIEMPCWALPDASFLSEFGKDALNGDVDVIGIDEAQFF  116 (234)
T ss_pred             cCcchHHHHHHHHHHHhcCceEEEEEecCCcccchheeEeccCCcccccccCCchhHHHHHHHHhcCcceEEEecHHHHh
Confidence            59999999999999999999999999999999998899999999999876553   22232  24678999999999999


Q ss_pred             HHHHHHHHHHHh-CCCEEEEEecccccccCCchhHhhhhccccceEeccceecccccccccccccccc
Q psy8456          85 PDVVSFAESMAN-AGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQE  151 (353)
Q Consensus        85 ~dIv~l~~~l~~-~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~ge  151 (353)
                      +|++++|+.+++ +||+|||||||+||+++||+++..|+|+||+|+||+|+|+.||++|.|++|.+.+
T Consensus       117 ~dl~efc~evAd~~Gk~VivagLdgdF~Rk~Fg~il~Lvplad~v~kLtavC~~Cg~~a~Ft~R~~~~  184 (234)
T KOG3125|consen  117 GDLYEFCREVADVHGKTVIVAGLDGDFKRKPFGAILDLVPLADSVTKLTAVCEECGADARFTLRKTND  184 (234)
T ss_pred             HHHHHHHHHHHhccCCEEEEEecCCchhhCcchhhhhhHhhhhhhhhhhhhhhhhcccceeEeeecCC
Confidence            999999999998 9999999999999999999999999999999999999999999999999997653

>PRK04296 thymidine kinase; Provisional

Probab=100.00  E-value=5.6e-38  Score=283.93  Aligned_cols=141  Identities=27%  Similarity=0.413  Sum_probs=128.9

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcc----cCCCccEEEEccccChH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIP----HTKDIDVIGIDEGQFFP   85 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~----~~~~~dvV~IDEaQFF~   85 (353)
                      -+||||+|++.+.|+..+|++|+++||.+|+|++...+.+|.|..+++..+....++..    ...++|+|+|||+|||+
T Consensus        12 GsGKTT~~l~~~~~~~~~g~~v~i~k~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~dvviIDEaq~l~   91 (190)
T PRK04296         12 NSGKSTELLQRAYNYEERGMKVLVFKPAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEEEGEKIDCVLIDEAQFLD   91 (190)
T ss_pred             CCHHHHHHHHHHHHHHHcCCeEEEEeccccccccCCcEecCCCCcccceEeCChHHHHHHHHhhCCCCCEEEEEccccCC
Confidence            58999999999999999999999999999999998889999999888866655555542    23479999999999995


Q ss_pred             --HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceeccccccccccccccc
Q psy8456          86 --DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQ  150 (353)
Q Consensus        86 --dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~g  150 (353)
                        ++.++++.+++.|++|+++||++||+++||+++.+|+++||.|++|+++|++||++|+||+|+++
T Consensus        92 ~~~v~~l~~~l~~~g~~vi~tgl~~~~~~~~f~~~~~L~~~aD~V~~l~~vC~~Cg~~a~~~~r~~~  158 (190)
T PRK04296         92 KEQVVQLAEVLDDLGIPVICYGLDTDFRGEPFEGSPYLLALADKVTELKAICVHCGRKATMNQRLID  158 (190)
T ss_pred             HHHHHHHHHHHHHcCCeEEEEecCcccccCcCchHHHHHHhcCeEEEeeEEccccCCccceEEEEeC
Confidence              69999999999999999999999999999999999999999999999999999999999999874

>PRK04296 thymidine kinase; Provisional

Probab=100.00  E-value=1.7e-34  Score=261.22  Aligned_cols=154  Identities=31%  Similarity=0.478  Sum_probs=134.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc----CCCccE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH----TKDIDV  225 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~----~~~~~~  225 (353)
                      |.+++++|||||||||+|++.+.++..+|++|+++||.+|+|++...+.+|.|..+++.......+++..    ..++|+
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~dv   81 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFKPAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEEEGEKIDC   81 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEeccccccccCCcEecCCCCcccceEeCChHHHHHHHHhhCCCCCE
Confidence            5688999999999999999999999999999999999999999988899999987777555444444322    347999


Q ss_pred             EEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEecccc
Q psy8456         226 IGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGT  305 (353)
Q Consensus       226 i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~d  305 (353)
                      |+|||+||+                       +.+|                     ++++++.|++.|+.|+++||++|
T Consensus        82 viIDEaq~l-----------------------~~~~---------------------v~~l~~~l~~~g~~vi~tgl~~~  117 (190)
T PRK04296         82 VLIDEAQFL-----------------------DKEQ---------------------VVQLAEVLDDLGIPVICYGLDTD  117 (190)
T ss_pred             EEEEccccC-----------------------CHHH---------------------HHHHHHHHHHcCCeEEEEecCcc
Confidence            999999996                       2233                     55566667799999999999999


Q ss_pred             ccCCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCC
Q psy8456         306 FQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQE  347 (353)
Q Consensus       306 f~~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~  347 (353)
                      |++++|+.+..|+++||.|++|+++|+.||++|+||+|+++|
T Consensus       118 ~~~~~f~~~~~L~~~aD~V~~l~~vC~~Cg~~a~~~~r~~~~  159 (190)
T PRK04296        118 FRGEPFEGSPYLLALADKVTELKAICVHCGRKATMNQRLIDG  159 (190)
T ss_pred             cccCcCchHHHHHHhcCeEEEeeEEccccCCccceEEEEeCC
Confidence            999999999999999999999999999999999999999953

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.82  E-value=3.1e-05  Score=70.79  Aligned_cols=78  Identities=24%  Similarity=0.257  Sum_probs=48.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCc--ccceeecccHhhhccc--------
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQ--KLTAVSAVELNKLIPH--------  219 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~--~~~a~~~~~~~~~~~~--------  219 (353)
                      +...++.||-|+|||+-|-.....+..+|++|+++.|+.       +.......  ..++..+..+......        
T Consensus        18 ~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~-------~Aa~~L~~~~~~~a~Ti~~~l~~~~~~~~~~~~~   90 (196)
T PF13604_consen   18 DRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTN-------KAAKELREKTGIEAQTIHSFLYRIPNGDDEGRPE   90 (196)
T ss_dssp             CSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSH-------HHHHHHHHHHTS-EEEHHHHTTEECCEECCSSCC
T ss_pred             CeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcH-------HHHHHHHHhhCcchhhHHHHHhcCCccccccccc
Confidence            457889999999999988777777888899999999854       22111111  1233333332222211        


Q ss_pred             CCCccEEEEeccccc
Q psy8456         220 TKDIDVIGIDEGQFV  234 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~  234 (353)
                      ..+.++|+|||+..+
T Consensus        91 ~~~~~vliVDEasmv  105 (196)
T PF13604_consen   91 LPKKDVLIVDEASMV  105 (196)
T ss_dssp             -TSTSEEEESSGGG-
T ss_pred             CCcccEEEEeccccc
Confidence            355689999999996

>PF13173 AAA_14: AAA domain

Probab=97.49  E-value=0.00027  Score=59.78  Aligned_cols=34  Identities=21%  Similarity=0.228  Sum_probs=25.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      +.+.++.||.++||||-+.+.++.+. ...+++.+
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~-~~~~~~yi   35 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL-PPENILYI   35 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc-ccccceee
Confidence            35678999999999999999887776 34444433

>PRK07413 hypothetical protein; Validated

Probab=97.35  E-value=0.0037  Score=63.55  Aligned_cols=170  Identities=14%  Similarity=0.097  Sum_probs=114.1

Q ss_pred             CchHHHHHHHHHHHHHcCc------eEEEEeeccC-C-CCCCCceeeccC------Cceee------eec-CCh-hhh--
Q psy8456          11 NPYIVHFCRRIRRYQYANY------RCMIVRYAKD-D-RYDTEKVATHDQ------QKLTA------VSA-VEL-NKL--   66 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agk------kvlv~Kp~iD-t-Ry~~~~I~Sr~G------~~~~A------i~i-~~l-~ei--   66 (353)
                      -||||..|..+-|.-=+|+      +|+++.--.. . .|++..+..+.+      +.+..      ..- ... .+.  
T Consensus        30 KGKTTAAlGlalRA~G~G~~~~~~~rV~ivQFlKg~~~~~GE~~~l~~l~~~~~~~i~~~~~g~~~~~~~~~~~~~~~~~  109 (382)
T PRK07413         30 KGKSQAALGVVLRTIGLGICEKRQTRVLLLRFLKGPGRAYDEDAAIEALQRGFPHLIDQVRTGRAEFFGADEITKFDRQE  109 (382)
T ss_pred             CCHHHHHHHHHHHHhcCCCCcCCCCeEEEEEEEcCCCCCCcHHHHHHhccccCCCceEEEECCCCCeeeCCCCcHHHHHH
Confidence            4999999999999999998      9999887776 2 355433222221      11111      110 111 111  


Q ss_pred             ----c----c--cCCCccEEEEccccCh-H----HHHHHHHHHHhC--CCEEEEEecccccccCCchhHhhhhccccceE
Q psy8456          67 ----I----P--HTKDIDVIGIDEGQFF-P----DVVSFAESMANA--GKIVVVAALDGTFQRTGFNDILSLIPLAECVE  129 (353)
Q Consensus        67 ----~----~--~~~~~dvV~IDEaQFF-~----dIv~l~~~l~~~--G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~  129 (353)
                          .    .  ..+.||.|+.||+--- .    +..++.+.+.++  +..||+-|=+         ....|+++||-|+
T Consensus       110 a~~~~~~a~~~i~sg~ydlvILDEi~~Al~~gll~~eevl~~L~~rP~~~evVLTGR~---------ap~~Lie~ADlVT  180 (382)
T PRK07413        110 AQRGWDIAKGAIASGLYSVVVLDELNPVLDLGLLPVDEVVNTLKSRPEGLEIIITGRA---------APQSLLDIADLHS  180 (382)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEeCCC---------CCHHHHHhCCeeE
Confidence                0    0  2468999999998654 1    445556666654  7899999974         3577999999999


Q ss_pred             eccceecccccccc-cccccccceeeeeccCCCCchhHHHHHHHHHHHhCC------EEEEEeeecCCC
Q psy8456         130 KLTAVCMSCFRDAA-FTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANY------RCMIVRYAKDDR  191 (353)
Q Consensus       130 kL~AvC~~CG~~A~-f~~Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~------~~~~~k~~~D~R  191 (353)
                      +++.+=+- ..+.. ..+-..+.+++++|. +=||||..+-.+-|..-+|+      +|+++.--+..+
T Consensus       181 Em~~iKHp-~~~~~~~~~~~~g~i~VYTG~-GKGKTTAAlGlAlRA~G~G~~~~~~~rV~ivQFlKg~~  247 (382)
T PRK07413        181 EMRPHRRP-TASELGVPFNSSGGIEIYTGE-GKGKSTSALGKALQAIGRGISQDKSHRVLILQWLKGGS  247 (382)
T ss_pred             EeceecCC-CcCCCCcccCCCCeEEEEeCC-CCCchHHHHHHHHHHhcCCCCcccCceEEEEEECCCCC
Confidence            99766532 11111 112234678888885 78999999999999999997      999888777663

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.29  E-value=0.0014  Score=59.83  Aligned_cols=81  Identities=22%  Similarity=0.160  Sum_probs=54.2

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEE-EEeeecCCCCCC----Cceee----------ccCccc-----ceeeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCM-IVRYAKDDRYDT----EKVST----------HDQQKL-----TAVSAVE  212 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~-~~k~~~D~R~~~----~~i~s----------~~g~~~-----~a~~~~~  212 (353)
                      -+|+|+.++||||-+++.+...+..|++|- ++.|..  |.+.    -+|++          +.|...     -++....
T Consensus         8 i~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EV--R~gGkR~GF~Ivdl~tg~~~~la~~~~~~~rvGkY~V~v~~   85 (179)
T COG1618           8 IFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEV--REGGKRIGFKIVDLATGEEGILARVGFSRPRVGKYGVNVEG   85 (179)
T ss_pred             EEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeee--ecCCeEeeeEEEEccCCceEEEEEcCCCCcccceEEeeHHH
Confidence            478999999999999999999999999998 777765  3221    12222          222211     1233445


Q ss_pred             Hhhhcc-----cCCCccEEEEecccccc
Q psy8456         213 LNKLIP-----HTKDIDVIGIDEGQFVE  235 (353)
Q Consensus       213 ~~~~~~-----~~~~~~~i~IDE~QF~~  235 (353)
                      ++++..     .....|+|+|||+==+|
T Consensus        86 le~i~~~al~rA~~~aDvIIIDEIGpME  113 (179)
T COG1618          86 LEEIAIPALRRALEEADVIIIDEIGPME  113 (179)
T ss_pred             HHHHhHHHHHHHhhcCCEEEEecccchh
Confidence            555432     24678999999998764

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.27  E-value=0.0011  Score=66.80  Aligned_cols=142  Identities=15%  Similarity=0.079  Sum_probs=83.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCcee---eccCccccee---ecccHhhhccc--CC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVS---THDQQKLTAV---SAVELNKLIPH--TK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~---s~~g~~~~a~---~~~~~~~~~~~--~~  221 (353)
                      +.+.++.|++++||||-+++.+.++...|.+|+.+.....    .+.+.   .+.|...+.+   ...++.++...  ..
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~EEs----~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~~  157 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGEES----PEQIKLRADRLGISTENLYLLAETNLEDILASIEEL  157 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECCcC----HHHHHHHHHHcCCCcccEEEEccCcHHHHHHHHHhc
Confidence            4678899999999999999999999888889998865321    11121   1223221111   12334444332  35


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHH-hCCCEEEEE
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMA-NAGKIVVVA  300 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~-~~g~~Vi~~  300 (353)
                      ++++|+||+.|++..             --.+.+|-+..|+..++.                  ....+| +.|+.|++.
T Consensus       158 ~~~lVVIDSIq~l~~-------------~~~~~~~g~~~qvr~~~~------------------~L~~lak~~~itvilv  206 (372)
T cd01121         158 KPDLVIIDSIQTVYS-------------SELTSAPGSVSQVRECTA------------------ELMRFAKERNIPIFIV  206 (372)
T ss_pred             CCcEEEEcchHHhhc-------------cccccCCCCHHHHHHHHH------------------HHHHHHHHcCCeEEEE
Confidence            799999999998510             001122334455544321                  112222 689999999


Q ss_pred             eccccccCCCchhHHhhhhcccceEEee
Q psy8456         301 ALDGTFQRTGFNDILSLIPLAECVEKLT  328 (353)
Q Consensus       301 gLd~df~~~~F~~~~~L~~~ad~v~kl~  328 (353)
                      |--+. .+. +.+...|--++|.|..+.
T Consensus       207 ghvtk-~g~-~aG~~~leh~vD~Vi~le  232 (372)
T cd01121         207 GHVTK-EGS-IAGPKVLEHMVDTVLYFE  232 (372)
T ss_pred             eeccC-CCc-ccCcccchhhceEEEEEE
Confidence            85432 111 333345666888888765

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.14  E-value=0.0003  Score=64.32  Aligned_cols=91  Identities=11%  Similarity=0.110  Sum_probs=56.3

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcc--------cCCCccEEEEccc
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIP--------HTKDIDVIGIDEG   81 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~--------~~~~~dvV~IDEa   81 (353)
                      =+|||+-|-..+..+..+|.+|+++.|.--..   ..+....|  .+|..+.++.....        ...+.++|+||||
T Consensus        28 GtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa---~~L~~~~~--~~a~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEa  102 (196)
T PF13604_consen   28 GTGKTTLLKALAEALEAAGKRVIGLAPTNKAA---KELREKTG--IEAQTIHSFLYRIPNGDDEGRPELPKKDVLIVDEA  102 (196)
T ss_dssp             TSTHHHHHHHHHHHHHHTT--EEEEESSHHHH---HHHHHHHT--S-EEEHHHHTTEECCEECCSSCC-TSTSEEEESSG
T ss_pred             CCCHHHHHHHHHHHHHhCCCeEEEECCcHHHH---HHHHHhhC--cchhhHHHHHhcCCcccccccccCCcccEEEEecc
Confidence            47999988777788888999999999953111   12222223  34444433322211        1356789999999


Q ss_pred             cChH--HHHHHHHHHHhCCCEEEEEe
Q psy8456          82 QFFP--DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        82 QFF~--dIv~l~~~l~~~G~~VivaG  105 (353)
                      ...+  ++..+.+.+...|..|++.|
T Consensus       103 smv~~~~~~~ll~~~~~~~~klilvG  128 (196)
T PF13604_consen  103 SMVDSRQLARLLRLAKKSGAKLILVG  128 (196)
T ss_dssp             GG-BHHHHHHHHHHS-T-T-EEEEEE
T ss_pred             cccCHHHHHHHHHHHHhcCCEEEEEC
Confidence            9996  77788887778899999998

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.05  E-value=0.0034  Score=52.56  Aligned_cols=36  Identities=22%  Similarity=0.237  Sum_probs=30.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      .+++||.++|||+-+..-+......|.+++++....
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~   37 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEE   37 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCc
Confidence            478999999999999999888888888888776643

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=96.98  E-value=0.001  Score=60.47  Aligned_cols=32  Identities=19%  Similarity=-0.016  Sum_probs=22.2

Q ss_pred             eeeeeccCCCCchhHHHHH-HHHHHHhCCEEEE
Q psy8456         152 KEVILGPMFSGKTTELIRR-IRRYQYANYRCMI  183 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~-~~~~~~~~~~~~~  183 (353)
                      |.+++|.||||||...+.. +..+..+|++|+.
T Consensus         2 I~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t   34 (193)
T PF05707_consen    2 IYLITGKPGSGKSYYAVSYVIIPALKKGRPVYT   34 (193)
T ss_dssp             EEEEE--TTSSHHHHHHHHHHH-GGGS---EEE
T ss_pred             EEEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE
Confidence            5789999999999999998 7777777887775

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.98  E-value=0.0014  Score=61.49  Aligned_cols=63  Identities=10%  Similarity=0.041  Sum_probs=41.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEecc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      .-+++||-|+|||+-+....+.....|++|..+....-.        +            ...++......+|+++|||+
T Consensus        47 ~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~--------~------------~~~~~~~~~~~~dlliiDdi  106 (235)
T PRK08084         47 YIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRA--------W------------FVPEVLEGMEQLSLVCIDNI  106 (235)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHh--------h------------hhHHHHHHhhhCCEEEEeCh
Confidence            458999999999976655566566678887766543200        0            01122223345789999999


Q ss_pred             ccc
Q psy8456         232 QFV  234 (353)
Q Consensus       232 QF~  234 (353)
                      |++
T Consensus       107 ~~~  109 (235)
T PRK08084        107 ECI  109 (235)
T ss_pred             hhh
Confidence            996

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=96.95  E-value=0.0028  Score=57.65  Aligned_cols=21  Identities=29%  Similarity=0.312  Sum_probs=17.9

Q ss_pred             eeeccCCCCchhHHHHHHHHH
Q psy8456         154 VILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +|.|+.||||||.+.+.+...
T Consensus         2 vv~G~pGsGKSt~i~~~~~~~   22 (234)
T PF01443_consen    2 VVHGVPGSGKSTLIKKLLKDR   22 (234)
T ss_pred             EEEcCCCCCHHHHHHHHHHhc
Confidence            689999999999888777664

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=96.92  E-value=0.00085  Score=62.52  Aligned_cols=71  Identities=21%  Similarity=0.286  Sum_probs=43.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHH---hCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQY---ANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGI  228 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~---~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~I  228 (353)
                      .-+|+||-|+|||. |++.+.++-.   .+.+|+.+....   +     ..+   -..++....+.++......+|+++|
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~~~~~~~v~y~~~~~---f-----~~~---~~~~~~~~~~~~~~~~~~~~DlL~i  103 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQKQHPGKRVVYLSAEE---F-----IRE---FADALRDGEIEEFKDRLRSADLLII  103 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHHCTTS-EEEEEHHH---H-----HHH---HHHHHHTTSHHHHHHHHCTSSEEEE
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHhccccccceeecHHH---H-----HHH---HHHHHHcccchhhhhhhhcCCEEEE
Confidence            35899999999986 7777766533   367777655321   0     000   0011111334444444578999999


Q ss_pred             eccccc
Q psy8456         229 DEGQFV  234 (353)
Q Consensus       229 DE~QF~  234 (353)
                      |..|++
T Consensus       104 DDi~~l  109 (219)
T PF00308_consen  104 DDIQFL  109 (219)
T ss_dssp             ETGGGG
T ss_pred             ecchhh
Confidence            999996

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.88  E-value=0.0013  Score=65.09  Aligned_cols=83  Identities=19%  Similarity=0.173  Sum_probs=47.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH--HHhCCEEEEEeeecCCCCC-CCceeeccCcccceeecccHhhhcc-------cCC
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY--QYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTAVSAVELNKLIP-------HTK  221 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~--~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a~~~~~~~~~~~-------~~~  221 (353)
                      +.+|.|..|||||.-++..++.+  ...+.+++++.+...-+.. ...+.........-..+.....++.       ..+
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   82 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNPKLKKSDFRKPTSFINNYSESDKEKN   82 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHHHHHHhhhcccchhhhhhhhhHHHHhhcccccccCC
Confidence            46899999999999999999998  6666666655543322210 0011111100000001112222222       246


Q ss_pred             CccEEEEeccccc
Q psy8456         222 DIDVIGIDEGQFV  234 (353)
Q Consensus       222 ~~~~i~IDE~QF~  234 (353)
                      ++|+|+|||||.+
T Consensus        83 ~~DviivDEAqrl   95 (352)
T PF09848_consen   83 KYDVIIVDEAQRL   95 (352)
T ss_pred             cCCEEEEehhHhh
Confidence            8999999999986

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.87  E-value=0.00064  Score=54.18  Aligned_cols=38  Identities=26%  Similarity=0.162  Sum_probs=29.6

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ...+++||+||||||-+...++.+...+..++.+....
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~   40 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGED   40 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEE
Confidence            45689999999999999888887766665677666654

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=96.87  E-value=0.0021  Score=57.44  Aligned_cols=38  Identities=21%  Similarity=0.120  Sum_probs=28.6

Q ss_pred             cceeeeeccCCCCchhH-HHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTE-LIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~-Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +++.++.-..|||||+. |-+.++.+..++.+|+++.|.
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~rvLvL~PT   42 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIKRRLRVLVLAPT   42 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHHTT--EEEEESS
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHHccCeEEEeccc
Confidence            56788888899999998 556677788899999999995

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=96.87  E-value=0.0039  Score=55.75  Aligned_cols=89  Identities=18%  Similarity=0.218  Sum_probs=45.0

Q ss_pred             CCchHHHH-HHHHHHHHHcCceEEEEeeccCCC----------CCCCceee--------ccCCce-eeeecCChhh-hc-
Q psy8456          10 INPYIVHF-CRRIRRYQYANYRCMIVRYAKDDR----------YDTEKVAT--------HDQQKL-TAVSAVELNK-LI-   67 (353)
Q Consensus        10 ~~GKSteL-Lrr~~ry~~agkkvlv~Kp~iDtR----------y~~~~I~S--------r~G~~~-~Ai~i~~l~e-i~-   67 (353)
                      -||||+.. =+.++.+..++.+|||+.|   ||          .+.. +.-        +.|... ....-..... +. 
T Consensus        14 GaGKTr~vlp~~~~~~i~~~~rvLvL~P---TRvva~em~~aL~~~~-~~~~t~~~~~~~~g~~~i~vMc~at~~~~~~~   89 (148)
T PF07652_consen   14 GAGKTRRVLPEIVREAIKRRLRVLVLAP---TRVVAEEMYEALKGLP-VRFHTNARMRTHFGSSIIDVMCHATYGHFLLN   89 (148)
T ss_dssp             TSSTTTTHHHHHHHHHHHTT--EEEEES---SHHHHHHHHHHTTTSS-EEEESTTSS----SSSSEEEEEHHHHHHHHHT
T ss_pred             CCCCcccccHHHHHHHHHccCeEEEecc---cHHHHHHHHHHHhcCC-cccCceeeeccccCCCcccccccHHHHHHhcC
Confidence            48999984 4556777889999999999   45          0111 111        111111 1110001111 11 


Q ss_pred             -ccCCCccEEEEccccChH--HHH--HHHHHHHhCC-CEEE
Q psy8456          68 -PHTKDIDVIGIDEGQFFP--DVV--SFAESMANAG-KIVV  102 (353)
Q Consensus        68 -~~~~~~dvV~IDEaQFF~--dIv--~l~~~l~~~G-~~Vi  102 (353)
                       ....+||+|++||+||.+  .|.  -+...++..| ..|+
T Consensus        90 p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~~~~g~~~~i  130 (148)
T PF07652_consen   90 PCRLKNYDVIIMDECHFTDPTSIAARGYLRELAESGEAKVI  130 (148)
T ss_dssp             SSCTTS-SEEEECTTT--SHHHHHHHHHHHHHHHTTS-EEE
T ss_pred             cccccCccEEEEeccccCCHHHHhhheeHHHhhhccCeeEE
Confidence             234679999999999996  443  4556666676 3343

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.86  E-value=0.0034  Score=64.64  Aligned_cols=81  Identities=17%  Similarity=0.160  Sum_probs=53.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCcee---eccCccccee---ecccHhhhccc--CC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVS---THDQQKLTAV---SAVELNKLIPH--TK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~---s~~g~~~~a~---~~~~~~~~~~~--~~  221 (353)
                      +.+.++.|++++||||-+++.+.+....|.+|+.+.....    .+.+.   .+.|.....+   ...++.+++..  ..
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ees----~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i~~~  155 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEES----ASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEE  155 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcccc----HHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHHHhh
Confidence            4578899999999999999999998878999998875321    11121   1222211111   12344444432  35


Q ss_pred             CccEEEEeccccc
Q psy8456         222 DIDVIGIDEGQFV  234 (353)
Q Consensus       222 ~~~~i~IDE~QF~  234 (353)
                      ++++|+||+.|++
T Consensus       156 ~~~lVVIDSIq~l  168 (446)
T PRK11823        156 KPDLVVIDSIQTM  168 (446)
T ss_pred             CCCEEEEechhhh
Confidence            7899999999975

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=96.83  E-value=0.0089  Score=52.46  Aligned_cols=138  Identities=12%  Similarity=0.038  Sum_probs=79.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCC--------CCCCceee--ccCc-cc-ce----eecc-----
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR--------YDTEKVST--HDQQ-KL-TA----VSAV-----  211 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R--------~~~~~i~s--~~g~-~~-~a----~~~~-----  211 (353)
                      .++.||.++|||+-.++-++.....|.+|+++......+        .+-+ +.-  ..|. .. ..    .+..     
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~e~~~~~~~~~~~~~g~~-~~~l~~~g~l~~~d~~~~~~s~~~~~~~   80 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAESLGWD-LERLEDEGLLAIVDADPDEIGPAESSLR   80 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEECCCCHHHHHHHHHHcCCC-hHHHHhcCCeEEEecCccccchhhhhhh
Confidence            578999999999999999999888999999987643221        1110 000  0010 00 00    0000     


Q ss_pred             -c-Hhhhcc--cCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCC-ccHHHH
Q psy8456         212 -E-LNKLIP--HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEF-PDVVSF  286 (353)
Q Consensus       212 -~-~~~~~~--~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f-~~~~~~  286 (353)
                       + +..+..  ...++++++|||.+-+.                      ..+.                +.. ..+.++
T Consensus        81 ~~~~~~i~~~~~~~~~~~lviD~~~~~~----------------------~~~~----------------~~~~~~i~~l  122 (187)
T cd01124          81 LELIQRLKDAIEEFKAKRVVIDSVSGLL----------------------LMEQ----------------STARLEIRRL  122 (187)
T ss_pred             HHHHHHHHHHHHHhCCCEEEEeCcHHHh----------------------hcCh----------------HHHHHHHHHH
Confidence             0 111211  13578999999999530                      0000                001 234556


Q ss_pred             HHHHHhCCCEEEEEeccccccCCCchhHHhhhhcccceEEeeee
Q psy8456         287 AESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  330 (353)
Q Consensus       287 ~~~~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~  330 (353)
                      ...+++.|+.|++..=+...... ......+-.+||.|..|...
T Consensus       123 ~~~l~~~g~tvi~v~~~~~~~~~-~~~~~~~~~~aD~ii~l~~~  165 (187)
T cd01124         123 LFALKRFGVTTLLTSEQSGLEGT-GFGGGDVEYLVDGVIRLRLD  165 (187)
T ss_pred             HHHHHHCCCEEEEEeccccCCCc-ccCcCceeEeeeEEEEEEEE
Confidence            66777889998887655544322 12234567889999888765

A related protein is found in archaea.

>TIGR00416 sms DNA repair protein RadA

Probab=96.81  E-value=0.0034  Score=64.85  Aligned_cols=143  Identities=13%  Similarity=0.054  Sum_probs=82.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceee---ccCcccc---eeecccHhhhccc--CC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVST---HDQQKLT---AVSAVELNKLIPH--TK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s---~~g~~~~---a~~~~~~~~~~~~--~~  221 (353)
                      +.+.++.|++++||||-+++.+.+....|.+|+.+.... ++   ..+..   +.|...+   .....++.++...  ..
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~EE-s~---~qi~~ra~rlg~~~~~l~~~~e~~~~~I~~~i~~~  169 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEE-SL---QQIKMRAIRLGLPEPNLYVLSETNWEQICANIEEE  169 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECcC-CH---HHHHHHHHHcCCChHHeEEcCCCCHHHHHHHHHhc
Confidence            467899999999999999999999888888999887542 11   11211   1222111   1112344444322  35


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHH-hCCCEEEEE
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMA-NAGKIVVVA  300 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~-~~g~~Vi~~  300 (353)
                      ++++|+||..|.+.. .            -...+|-+..|+..++.                  ....+| ..|+.|++.
T Consensus       170 ~~~~vVIDSIq~l~~-~------------~~~~~~g~~~q~r~~~~------------------~L~~~ak~~giTvllt  218 (454)
T TIGR00416       170 NPQACVIDSIQTLYS-P------------DISSAPGSVSQVRECTA------------------ELMRLAKTRGIAIFIV  218 (454)
T ss_pred             CCcEEEEecchhhcc-c------------ccccCCCCHHHHHHHHH------------------HHHHHHHHhCCEEEEE
Confidence            789999999997510 0            00122334445544321                  122222 689999998


Q ss_pred             eccccccCCCchhHHhhhhcccceEEeee
Q psy8456         301 ALDGTFQRTGFNDILSLIPLAECVEKLTA  329 (353)
Q Consensus       301 gLd~df~~~~F~~~~~L~~~ad~v~kl~a  329 (353)
                      |=.+. .+ .+.+...|--++|.|..|..
T Consensus       219 ~hvtk-eg-~~aG~~~le~lvD~VI~Le~  245 (454)
T TIGR00416       219 GHVTK-EG-SIAGPKVLEHMVDTVLYFEG  245 (454)
T ss_pred             ecccc-CC-ccCCcccEeeeceEEEEEec
Confidence            74322 11 12233345567898888864

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=96.79  E-value=0.00043  Score=57.19  Aligned_cols=38  Identities=34%  Similarity=0.304  Sum_probs=26.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh-----CCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA-----NYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~-----~~~~~~~k~~  187 (353)
                      +..-+++||-|+|||+-+-+.++.+...     +.+++.+...
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~   46 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCP   46 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeC
Confidence            3456899999999999988888887654     5666644443

>PRK08727 hypothetical protein; Validated

Probab=96.71  E-value=0.0037  Score=58.56  Aligned_cols=63  Identities=14%  Similarity=0.090  Sum_probs=42.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEecc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      .-+++||-|+|||.-+--..+.....|+++..+....   .                 ...+.+++....++|+++|||+
T Consensus        43 ~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~---~-----------------~~~~~~~~~~l~~~dlLiIDDi  102 (233)
T PRK08727         43 WLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQA---A-----------------AGRLRDALEALEGRSLVALDGL  102 (233)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHH---h-----------------hhhHHHHHHHHhcCCEEEEeCc
Confidence            3689999999999655555666677788777665311   0                 0112233344567899999999


Q ss_pred             ccc
Q psy8456         232 QFV  234 (353)
Q Consensus       232 QF~  234 (353)
                      |++
T Consensus       103 ~~l  105 (233)
T PRK08727        103 ESI  105 (233)
T ss_pred             ccc
Confidence            986

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.71  E-value=0.001  Score=68.48  Aligned_cols=73  Identities=22%  Similarity=0.282  Sum_probs=43.9

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHH---hCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQY---ANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGI  228 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~---~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~I  228 (353)
                      .-+++|+.|+||| .|++.+.++-.   .+.+|+.+.+..   +. ..+....+.     ....+.++.....++|+++|
T Consensus       143 pl~i~G~~G~GKT-HLl~Ai~~~l~~~~~~~~v~yv~~~~---f~-~~~~~~l~~-----~~~~~~~~~~~~~~~dvLiI  212 (450)
T PRK14087        143 PLFIYGESGMGKT-HLLKAAKNYIESNFSDLKVSYMSGDE---FA-RKAVDILQK-----THKEIEQFKNEICQNDVLII  212 (450)
T ss_pred             ceEEECCCCCcHH-HHHHHHHHHHHHhCCCCeEEEEEHHH---HH-HHHHHHHHH-----hhhHHHHHHHHhccCCEEEE
Confidence            3579999999999 67788777533   367777655421   00 011110000     00223344444678999999


Q ss_pred             eccccc
Q psy8456         229 DEGQFV  234 (353)
Q Consensus       229 DE~QF~  234 (353)
                      ||+||+
T Consensus       213 DDiq~l  218 (450)
T PRK14087        213 DDVQFL  218 (450)
T ss_pred             eccccc
Confidence            999996

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=96.59  E-value=0.0032  Score=69.05  Aligned_cols=83  Identities=27%  Similarity=0.290  Sum_probs=53.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH-HHhCCEEEEEeee------cCCCCCCC----ceeecc--Cc-------ccceee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY-QYANYRCMIVRYA------KDDRYDTE----KVSTHD--QQ-------KLTAVS  209 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~-~~~~~~~~~~k~~------~D~R~~~~----~i~s~~--g~-------~~~a~~  209 (353)
                      ..+.++=.||||||||.|++-++.+ ...+.+|+++...      +-.|+...    -+...+  +.       ..-++.
T Consensus        49 ~~V~vVRSpMGTGKTtaLi~wLk~~l~~~~~~VLvVShRrSL~~sL~~rf~~~~l~gFv~Y~d~~~~~i~~~~~~rLivq  128 (824)
T PF02399_consen   49 RGVLVVRSPMGTGKTTALIRWLKDALKNPDKSVLVVSHRRSLTKSLAERFKKAGLSGFVNYLDSDDYIIDGRPYDRLIVQ  128 (824)
T ss_pred             CCeEEEECCCCCCcHHHHHHHHHHhccCCCCeEEEEEhHHHHHHHHHHHHhhcCCCcceeeeccccccccccccCeEEEE
Confidence            3567899999999999999988887 5678999988653      22232211    111111  11       122344


Q ss_pred             cccHhhhccc-CCCccEEEEeccc
Q psy8456         210 AVELNKLIPH-TKDIDVIGIDEGQ  232 (353)
Q Consensus       210 ~~~~~~~~~~-~~~~~~i~IDE~Q  232 (353)
                      ++++..+... .++||+|+|||+-
T Consensus       129 IdSL~R~~~~~l~~yDvVIIDEv~  152 (824)
T PF02399_consen  129 IDSLHRLDGSLLDRYDVVIIDEVM  152 (824)
T ss_pred             ehhhhhcccccccccCEEEEehHH
Confidence            5566555433 5679999999984

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>PRK05642 DNA replication initiation factor; Validated

Probab=96.57  E-value=0.0043  Score=58.22  Aligned_cols=62  Identities=10%  Similarity=0.176  Sum_probs=40.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHH-HHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRR-YQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDE  230 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~-~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE  230 (353)
                      .-+++||-|+|||. |++.+.+ +...|.+|+.+....        ..++            ..+++....++|+++||+
T Consensus        47 ~l~l~G~~G~GKTH-Ll~a~~~~~~~~~~~v~y~~~~~--------~~~~------------~~~~~~~~~~~d~LiiDD  105 (234)
T PRK05642         47 LIYLWGKDGVGRSH-LLQAACLRFEQRGEPAVYLPLAE--------LLDR------------GPELLDNLEQYELVCLDD  105 (234)
T ss_pred             eEEEECCCCCCHHH-HHHHHHHHHHhCCCcEEEeeHHH--------HHhh------------hHHHHHhhhhCCEEEEec
Confidence            45799999999985 5555544 455678887665421        1111            123334456789999999


Q ss_pred             cccc
Q psy8456         231 GQFV  234 (353)
Q Consensus       231 ~QF~  234 (353)
                      .|++
T Consensus       106 i~~~  109 (234)
T PRK05642        106 LDVI  109 (234)
T ss_pred             hhhh
Confidence            9995

>PRK06893 DNA replication initiation factor; Validated

Probab=96.57  E-value=0.0053  Score=57.29  Aligned_cols=62  Identities=19%  Similarity=0.181  Sum_probs=41.3

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQ  232 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~Q  232 (353)
                      -+++||.|+|||+-+--..+.+..+|.++..+....   ..                 ....+++....++|+++|||+|
T Consensus        42 l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~---~~-----------------~~~~~~~~~~~~~dlLilDDi~  101 (229)
T PRK06893         42 FYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSK---SQ-----------------YFSPAVLENLEQQDLVCLDDLQ  101 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHH---hh-----------------hhhHHHHhhcccCCEEEEeChh
Confidence            478999999999766666666667777776665421   00                 0001233334678999999999


Q ss_pred             cc
Q psy8456         233 FV  234 (353)
Q Consensus       233 F~  234 (353)
                      ++
T Consensus       102 ~~  103 (229)
T PRK06893        102 AV  103 (229)
T ss_pred             hh
Confidence            95

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=96.55  E-value=0.0031  Score=53.66  Aligned_cols=37  Identities=16%  Similarity=0.135  Sum_probs=30.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhC--CEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYAN--YRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~--~~~~~~k~~  187 (353)
                      ...++.||+|||||+.++..+.+....+  ++++++.|.
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~   63 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPT   63 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCC
Confidence            4568999999999998888877775554  889999984

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=96.45  E-value=0.0037  Score=50.53  Aligned_cols=37  Identities=16%  Similarity=0.105  Sum_probs=26.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +..-+++||.|+|||+-+...++.+...+..++.+..
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~   55 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNA   55 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEeh
Confidence            3456899999999998665555555555666666554

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.36  E-value=0.023  Score=51.17  Aligned_cols=132  Identities=18%  Similarity=0.160  Sum_probs=77.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCCCceeecc--------Cccccee---ecc---cHh
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDTEKVSTHD--------QQKLTAV---SAV---ELN  214 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~~~i~s~~--------g~~~~a~---~~~---~~~  214 (353)
                      |-+++++|+ +.||||..+-.+.+..-+|++|+++.--+.. .+|+..+-.+-        |....-.   ...   ...
T Consensus         3 G~i~vy~g~-G~Gkt~~a~g~~~ra~~~g~~v~~vQFlKg~~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~a~   81 (159)
T cd00561           3 GLIQVYTGN-GKGKTTAALGLALRALGHGYRVGVVQFLKGGWKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAAAA   81 (159)
T ss_pred             CEEEEECCC-CCCHHHHHHHHHHHHHHCCCeEEEEEEeCCCCccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHHHH
Confidence            445666666 9999999999999999999999995555443 33432222221        1110000   000   000


Q ss_pred             hhc------ccCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHH
Q psy8456         215 KLI------PHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAE  288 (353)
Q Consensus       215 ~~~------~~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~  288 (353)
                      +..      -...++|++++||+=..-                 ....++.                     .+|+++++
T Consensus        82 ~~~~~a~~~~~~~~~dLlVLDEi~~a~-----------------~~gli~~---------------------~~v~~ll~  123 (159)
T cd00561          82 EGWAFAKEAIASGEYDLVILDEINYAL-----------------GYGLLDV---------------------EEVVDLLK  123 (159)
T ss_pred             HHHHHHHHHHhcCCCCEEEEechHhHh-----------------hCCCCCH---------------------HHHHHHHH
Confidence            111      124789999999987620                 0011111                     23444333


Q ss_pred             HHHhCCCEEEEEeccccccCCCchhHHhhhhcccceEEeeee
Q psy8456         289 SMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  330 (353)
Q Consensus       289 ~~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~  330 (353)
                      + .-.+..||+-|=+         ....|+++||-|++++.+
T Consensus       124 ~-rp~~~evIlTGr~---------~p~~l~e~AD~VTEm~~v  155 (159)
T cd00561         124 A-KPEDLELVLTGRN---------APKELIEAADLVTEMREV  155 (159)
T ss_pred             c-CCCCCEEEEECCC---------CCHHHHHhCceeeeccee
Confidence            2 2346789998853         346799999999998754

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.35  E-value=0.0041  Score=64.12  Aligned_cols=72  Identities=17%  Similarity=0.242  Sum_probs=42.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEecc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      .-+++||-|+|||+-+-...+.+...|.+|+.+....=.+    .+.       .+........+.....++|+++|||+
T Consensus       143 pl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~----~~~-------~~l~~~~~~~f~~~~~~~dvLiIDDi  211 (445)
T PRK12422        143 PIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTE----HLV-------SAIRSGEMQRFRQFYRNVDALFIEDI  211 (445)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHH----HHH-------HHHhcchHHHHHHHcccCCEEEEcch
Confidence            3589999999997655444444556788887666421000    000       00001112223233567899999999


Q ss_pred             ccc
Q psy8456         232 QFV  234 (353)
Q Consensus       232 QF~  234 (353)
                      ||+
T Consensus       212 q~l  214 (445)
T PRK12422        212 EVF  214 (445)
T ss_pred             hhh
Confidence            996

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.35  E-value=0.0036  Score=67.11  Aligned_cols=70  Identities=20%  Similarity=0.314  Sum_probs=41.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHH---hCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEe
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQY---ANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGID  229 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~---~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~ID  229 (353)
                      -+|+|+-|+||| .|++.+-++-.   .|++|+.+....   +. +...       .++......++.....++|+++||
T Consensus       317 L~LyG~sGsGKT-HLL~AIa~~a~~~~~g~~V~Yitaee---f~-~el~-------~al~~~~~~~f~~~y~~~DLLlID  384 (617)
T PRK14086        317 LFIYGESGLGKT-HLLHAIGHYARRLYPGTRVRYVSSEE---FT-NEFI-------NSIRDGKGDSFRRRYREMDILLVD  384 (617)
T ss_pred             EEEECCCCCCHH-HHHHHHHHHHHHhCCCCeEEEeeHHH---HH-HHHH-------HHHHhccHHHHHHHhhcCCEEEEe
Confidence            489999999998 56666655533   377887666421   00 0000       001111223333445779999999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      +.||+
T Consensus       385 DIq~l  389 (617)
T PRK14086        385 DIQFL  389 (617)
T ss_pred             hhccc
Confidence            99996

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=96.32  E-value=0.0082  Score=54.03  Aligned_cols=30  Identities=30%  Similarity=0.225  Sum_probs=25.3

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      -+|+|+.++||||-|.+.+..++..|.++-
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l~~~~~~v~   31 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEELKKKGLPVG   31 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHHHHTCGGEE
T ss_pred             EEEECcCCCCHHHHHHHHHHHhhccCCccc
Confidence            378999999999999999999988777664

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.25  E-value=0.023  Score=51.96  Aligned_cols=131  Identities=15%  Similarity=0.095  Sum_probs=77.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCC-CCCCcee-------eccCcccceee---------cccHh
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR-YDTEKVS-------THDQQKLTAVS---------AVELN  214 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R-~~~~~i~-------s~~g~~~~a~~---------~~~~~  214 (353)
                      ...++++-+-||||..+-.+.|...+|++|+++.--+..+ +++..+.       .+.|..+.-..         +.+..
T Consensus         7 li~v~~g~GkGKtt~a~g~a~ra~~~g~~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~   86 (173)
T TIGR00708         7 IIIVHTGNGKGKTTAAFGMALRALGHGKKVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAKAAW   86 (173)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHHHHH
Confidence            3445555899999999999999999999998776666553 4432111       11121111000         00111


Q ss_pred             hhc-c--cCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHH
Q psy8456         215 KLI-P--HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMA  291 (353)
Q Consensus       215 ~~~-~--~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~  291 (353)
                      +.. .  ...++|+|++||+=-.-                 ...-++.                     .+|++++++ .
T Consensus        87 ~~a~~~l~~~~~DlvVLDEi~~A~-----------------~~gli~~---------------------~~v~~lL~~-r  127 (173)
T TIGR00708        87 QHAKEMLADPELDLVLLDELTYAL-----------------KYGYLDV---------------------EEVVEALQE-R  127 (173)
T ss_pred             HHHHHHHhcCCCCEEEehhhHHHH-----------------HCCCcCH---------------------HHHHHHHHh-C
Confidence            111 1  14789999999987410                 0000111                     244444432 3


Q ss_pred             hCCCEEEEEeccccccCCCchhHHhhhhcccceEEeeee
Q psy8456         292 NAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  330 (353)
Q Consensus       292 ~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~  330 (353)
                      ..+..||+-|=+         ....|+++||.|++++.+
T Consensus       128 p~~~evVlTGR~---------~p~~l~e~AD~VTEm~~v  157 (173)
T TIGR00708       128 PGHQHVIITGRG---------CPQDLLELADLVTEMRPV  157 (173)
T ss_pred             CCCCEEEEECCC---------CCHHHHHhCceeeeeccc
Confidence            457889998853         357899999999998764

Alternate name: corrinoid adenosyltransferase.

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.24  E-value=0.01  Score=60.33  Aligned_cols=67  Identities=30%  Similarity=0.205  Sum_probs=40.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc-CCCccEEEEec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH-TKDIDVIGIDE  230 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~-~~~~~~i~IDE  230 (353)
                      +.+++||+.+||||-|    ..+...+.+..++-...|.|......            .+.+..+... ..+-..|++||
T Consensus        39 i~~i~GpR~~GKTtll----~~l~~~~~~~~iy~~~~d~~~~~~~l------------~d~~~~~~~~~~~~~~yifLDE  102 (398)
T COG1373          39 IILILGPRQVGKTTLL----KLLIKGLLEEIIYINFDDLRLDRIEL------------LDLLRAYIELKEREKSYIFLDE  102 (398)
T ss_pred             EEEEECCccccHHHHH----HHHHhhCCcceEEEEecchhcchhhH------------HHHHHHHHHhhccCCceEEEec
Confidence            7899999999999998    33444454445555556666543211            1112222111 11457999999


Q ss_pred             cccc
Q psy8456         231 GQFV  234 (353)
Q Consensus       231 ~QF~  234 (353)
                      +|++
T Consensus       103 Iq~v  106 (398)
T COG1373         103 IQNV  106 (398)
T ss_pred             ccCc
Confidence            9995

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.19  E-value=0.038  Score=50.54  Aligned_cols=114  Identities=11%  Similarity=0.115  Sum_probs=70.6

Q ss_pred             CchHHHHHHHHHHHHHcCceEEEEeeccCC-CCCCCceeeccCCceeeee-----c-CCh----------hhhc-c--cC
Q psy8456          11 NPYIVHFCRRIRRYQYANYRCMIVRYAKDD-RYDTEKVATHDQQKLTAVS-----A-VEL----------NKLI-P--HT   70 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agkkvlv~Kp~iDt-Ry~~~~I~Sr~G~~~~Ai~-----i-~~l----------~ei~-~--~~   70 (353)
                      -||||..+..+.|..-+|++|+++.--.-. .+++..+-.+.+..+....     . .+.          .+.. .  ..
T Consensus        16 kGKtt~a~g~a~ra~~~g~~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~a~~~l~~   95 (173)
T TIGR00708        16 KGKTTAAFGMALRALGHGKKVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAKAAWQHAKEMLAD   95 (173)
T ss_pred             CChHHHHHHHHHHHHHCCCeEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHHHHHHHHHHHHhc
Confidence            599999999999999999999655443333 2343212111122111100     0 111          1110 1  24


Q ss_pred             CCccEEEEcccc------ChH--HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccce
Q psy8456          71 KDIDVIGIDEGQ------FFP--DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  134 (353)
Q Consensus        71 ~~~dvV~IDEaQ------FF~--dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~Av  134 (353)
                      +.+|+|++||+-      +++  ++.++.+. .-.+..||+-|=+         ....|+++||.|++++.+
T Consensus        96 ~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~-rp~~~evVlTGR~---------~p~~l~e~AD~VTEm~~v  157 (173)
T TIGR00708        96 PELDLVLLDELTYALKYGYLDVEEVVEALQE-RPGHQHVIITGRG---------CPQDLLELADLVTEMRPV  157 (173)
T ss_pred             CCCCEEEehhhHHHHHCCCcCHHHHHHHHHh-CCCCCEEEEECCC---------CCHHHHHhCceeeeeccc
Confidence            689999999998      554  45554421 3457899999973         357799999999998754

Alternate name: corrinoid adenosyltransferase.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.08  E-value=0.023  Score=58.40  Aligned_cols=143  Identities=23%  Similarity=0.310  Sum_probs=82.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH--HhCCEEEEEeeecCC-CCCC-Cceeec---cCccc-ceeecccHhhhcccCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ--YANYRCMIVRYAKDD-RYDT-EKVSTH---DQQKL-TAVSAVELNKLIPHTK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~--~~~~~~~~~k~~~D~-R~~~-~~i~s~---~g~~~-~a~~~~~~~~~~~~~~  221 (353)
                      +...+++||-|+||||-+..-+..+.  ..|++|.++.-  |+ |.+. +.+.+.   .|..+ .+....++...+....
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~--D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~  298 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITL--DTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQLR  298 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEEC--CccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHhC
Confidence            45778999999999999999988886  46789998863  43 2110 111111   11111 0111233444444456


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhc--------cCCCCCCCCccHHHHHHHHHhC
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA--------LNVPPPPEFPDVVSFAESMANA  293 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--------~~~~~~~~f~~~~~~~~~~~~~  293 (353)
                      ++|+|+||-+=+.                     +....++.+|..+.+.        |-++...-..++.+++..+...
T Consensus       299 ~~DlVlIDt~G~~---------------------~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~~~~f~~~  357 (424)
T PRK05703        299 DCDVILIDTAGRS---------------------QRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDIYKHFSRL  357 (424)
T ss_pred             CCCEEEEeCCCCC---------------------CCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHHHHHhCCC
Confidence            7999999988552                     2244556666555541        1122222224666666666655


Q ss_pred             CC-EEEEEeccccccCCCchhHHhhh
Q psy8456         294 GK-IVVVAALDGTFQRTGFNDILSLI  318 (353)
Q Consensus       294 g~-~Vi~~gLd~df~~~~F~~~~~L~  318 (353)
                      +. .||+-=||.+   ..|+.+..++
T Consensus       358 ~~~~vI~TKlDet---~~~G~i~~~~  380 (424)
T PRK05703        358 PLDGLIFTKLDET---SSLGSILSLL  380 (424)
T ss_pred             CCCEEEEeccccc---ccccHHHHHH
Confidence            55 5677777763   4566555543

>PF13245 AAA_19: Part of AAA domain

Probab=96.07  E-value=0.0098  Score=46.94  Aligned_cols=38  Identities=32%  Similarity=0.341  Sum_probs=33.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh----CCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA----NYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~----~~~~~~~k~~  187 (353)
                      +..-++.||.|||||+-+++++..+..+    +++|+++.|.
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t   51 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPT   51 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCC
Confidence            5566779999999999999999999876    8999998875

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=95.99  E-value=0.0067  Score=62.07  Aligned_cols=72  Identities=22%  Similarity=0.179  Sum_probs=40.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHh--CCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYA--NYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGID  229 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~--~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~ID  229 (353)
                      .-+++||-|+|||.-+-...+.....  +.+|+.+.... -.   ..+..       ++......++......+|+++||
T Consensus       150 ~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~-~~---~~~~~-------~~~~~~~~~~~~~~~~~dlLiiD  218 (450)
T PRK00149        150 PLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEK-FT---NDFVN-------ALRNNTMEEFKEKYRSVDVLLID  218 (450)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHH-HH---HHHHH-------HHHcCcHHHHHHHHhcCCEEEEe
Confidence            35899999999986554444444444  56666655421 00   00000       00001223333334579999999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |+||+
T Consensus       219 Di~~l  223 (450)
T PRK00149        219 DIQFL  223 (450)
T ss_pred             hhhhh
Confidence            99996

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.87  E-value=0.027  Score=51.09  Aligned_cols=64  Identities=13%  Similarity=0.089  Sum_probs=39.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDE  230 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE  230 (353)
                      ..-+++||-|+|||+-+...++.....+..++.+.-..-.        .            ...+++......++++|||
T Consensus        39 ~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~--------~------------~~~~~~~~~~~~~lLvIDd   98 (226)
T TIGR03420        39 RFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELA--------Q------------ADPEVLEGLEQADLVCLDD   98 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHH--------H------------hHHHHHhhcccCCEEEEeC
Confidence            4567999999999987666555555556665544321100        0            0012222234568999999


Q ss_pred             cccc
Q psy8456         231 GQFV  234 (353)
Q Consensus       231 ~QF~  234 (353)
                      +|.+
T Consensus        99 i~~l  102 (226)
T TIGR03420        99 VEAI  102 (226)
T ss_pred             hhhh
Confidence            9986

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.87  E-value=0.052  Score=49.55  Aligned_cols=35  Identities=23%  Similarity=0.259  Sum_probs=23.9

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEe
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVR  185 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k  185 (353)
                      ++.+|.||++|||||-|-.-++..... +.+++.+.
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e   37 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIE   37 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEc
Confidence            467899999999999886555554433 34555443

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.86  E-value=0.022  Score=57.99  Aligned_cols=83  Identities=22%  Similarity=0.303  Sum_probs=53.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHH----hCCEEEEEeeecCC-CCCC-Cceeec---cCcccceee-cccHhhhccc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQY----ANYRCMIVRYAKDD-RYDT-EKVSTH---DQQKLTAVS-AVELNKLIPH  219 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~----~~~~~~~~k~~~D~-R~~~-~~i~s~---~g~~~~a~~-~~~~~~~~~~  219 (353)
                      ..+.+++||.|+||||-+...+.+|..    .|++|.++.-  |+ |.+. +...+.   .|..+.... ...+.+.+..
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~--Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~  251 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITI--DNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ  251 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEec--cCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH
Confidence            457789999999999999999988864    4788988764  33 4332 122221   122221111 1234443445


Q ss_pred             CCCccEEEEeccccc
Q psy8456         220 TKDIDVIGIDEGQFV  234 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~  234 (353)
                      ..++|+|+||++-..
T Consensus       252 ~~~~DlVLIDTaGr~  266 (388)
T PRK12723        252 SKDFDLVLVDTIGKS  266 (388)
T ss_pred             hCCCCEEEEcCCCCC
Confidence            678999999999884

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.84  E-value=0.055  Score=55.87  Aligned_cols=117  Identities=19%  Similarity=0.210  Sum_probs=75.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCcee---eccCcc---cceeecccHhhhccc--CC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVS---THDQQK---LTAVSAVELNKLIPH--TK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~---s~~g~~---~~a~~~~~~~~~~~~--~~  221 (353)
                      +...+|-|..+-||||-|+|.+.++..++ +|+.+.-..    +..+|.   .|.|..   +.-....++.+|+.+  ..
T Consensus        93 Gs~iLIgGdPGIGKSTLLLQva~~lA~~~-~vLYVsGEE----S~~QiklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~  167 (456)
T COG1066          93 GSVILIGGDPGIGKSTLLLQVAARLAKRG-KVLYVSGEE----SLQQIKLRADRLGLPTNNLYLLAETNLEDIIAELEQE  167 (456)
T ss_pred             ccEEEEccCCCCCHHHHHHHHHHHHHhcC-cEEEEeCCc----CHHHHHHHHHHhCCCccceEEehhcCHHHHHHHHHhc
Confidence            34678899999999999999999998888 898876422    111121   122321   222234567777654  58


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHH-hCCCEEEEE
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMA-NAGKIVVVA  300 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~-~~g~~Vi~~  300 (353)
                      ++++++||=+|=+        |.+     -.+.+|-+-+||.+-+..              |+    ++| ..|+.+++.
T Consensus       168 ~p~lvVIDSIQT~--------~s~-----~~~SapGsVsQVRe~t~~--------------L~----~~AK~~~i~~fiV  216 (456)
T COG1066         168 KPDLVVIDSIQTL--------YSE-----EITSAPGSVSQVREVAAE--------------LM----RLAKTKNIAIFIV  216 (456)
T ss_pred             CCCEEEEecccee--------ecc-----cccCCCCcHHHHHHHHHH--------------HH----HHHHHcCCeEEEE
Confidence            8999999999953        100     124566788888776532              22    233 478888877


Q ss_pred             ec
Q psy8456         301 AL  302 (353)
Q Consensus       301 gL  302 (353)
                      |=
T Consensus       217 GH  218 (456)
T COG1066         217 GH  218 (456)
T ss_pred             EE
Confidence            74

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.83  E-value=0.036  Score=49.15  Aligned_cols=35  Identities=31%  Similarity=0.447  Sum_probs=30.9

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      ..++|+.+|||||-+.+.+.....+|++|-++|+.
T Consensus         2 i~i~G~~gsGKTtl~~~l~~~l~~~G~~V~viK~~   36 (155)
T TIGR00176         2 LQIVGPKNSGKTTLIERLVKALKARGYRVATIKHD   36 (155)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecc
Confidence            35789999999999888888888889999999974

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=95.82  E-value=0.0082  Score=60.39  Aligned_cols=72  Identities=19%  Similarity=0.154  Sum_probs=39.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHh--CCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYA--NYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGID  229 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~--~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~ID  229 (353)
                      .-+++||-|+|||.-+-...+.....  +.+|+.+.... -.   ..+....+       .....++.....++|+++||
T Consensus       138 ~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~-~~---~~~~~~~~-------~~~~~~~~~~~~~~dlLiiD  206 (405)
T TIGR00362       138 PLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEK-FT---NDFVNALR-------NNKMEEFKEKYRSVDLLLID  206 (405)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHH-HH---HHHHHHHH-------cCCHHHHHHHHHhCCEEEEe
Confidence            45899999999986554444444433  56677665321 00   00100000       01122333334568999999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |+|++
T Consensus       207 Di~~l  211 (405)
T TIGR00362       207 DIQFL  211 (405)
T ss_pred             hhhhh
Confidence            99996

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PRK06526 transposase; Provisional

Probab=95.74  E-value=0.011  Score=56.68  Aligned_cols=72  Identities=24%  Similarity=0.158  Sum_probs=45.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEecc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      --+++||.|+|||+-+....+....+|++|.++....        +......   +.....+...+....++|+++|||.
T Consensus       100 nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~--------l~~~l~~---~~~~~~~~~~l~~l~~~dlLIIDD~  168 (254)
T PRK06526        100 NVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQ--------WVARLAA---AHHAGRLQAELVKLGRYPLLIVDEV  168 (254)
T ss_pred             eEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHH--------HHHHHHH---HHhcCcHHHHHHHhccCCEEEEccc
Confidence            3589999999999887777777788899887654320        0000000   0011122333344567899999999


Q ss_pred             ccc
Q psy8456         232 QFV  234 (353)
Q Consensus       232 QF~  234 (353)
                      +.+
T Consensus       169 g~~  171 (254)
T PRK06526        169 GYI  171 (254)
T ss_pred             ccC
Confidence            984

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=95.73  E-value=0.065  Score=49.23  Aligned_cols=60  Identities=12%  Similarity=0.092  Sum_probs=39.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDE  230 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE  230 (353)
                      ..-+++||-|+|||+-+-...+.....|..+.++......                        +........++++|||
T Consensus        43 ~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~~------------------------~~~~~~~~~~~liiDd   98 (227)
T PRK08903         43 RFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPL------------------------LAFDFDPEAELYAVDD   98 (227)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHhH------------------------HHHhhcccCCEEEEeC
Confidence            4568999999999975555445445667777666543211                        0011234578999999


Q ss_pred             cccc
Q psy8456         231 GQFV  234 (353)
Q Consensus       231 ~QF~  234 (353)
                      +|.+
T Consensus        99 i~~l  102 (227)
T PRK08903         99 VERL  102 (227)
T ss_pred             hhhc
Confidence            9996

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.69  E-value=0.079  Score=44.24  Aligned_cols=123  Identities=11%  Similarity=0.004  Sum_probs=69.9

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCc--eeeccCCceee-e--e---cCChhh------hcccCCCccE
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEK--VATHDQQKLTA-V--S---AVELNK------LIPHTKDIDV   75 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~--I~Sr~G~~~~A-i--~---i~~l~e------i~~~~~~~dv   75 (353)
                      =+|||+-+...+......|.+++++......+.....  ...+.+..-.. .  .   ......      ......++++
T Consensus         9 G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (165)
T cd01120           9 GSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATADDPAAARLLSKAERLRERGGDDL   88 (165)
T ss_pred             CCCHHHHHHHHHHHHHhcCCEEEEEECCcchHHHHHHHhhhhhccccccEEEEEcCCCCCcHHHHHHHHHHHHhCCCCEE
Confidence            4899999999999888888999888764332200000  00000100000 0  0   011111      1123467999


Q ss_pred             EEEccccCh---------------H-HHHHHHHHHHhCCCEEEEEecccccccCCc---hhHhhhhccccceEecc
Q psy8456          76 IGIDEGQFF---------------P-DVVSFAESMANAGKIVVVAALDGTFQRTGF---NDILSLIPLAECVEKLT  132 (353)
Q Consensus        76 V~IDEaQFF---------------~-dIv~l~~~l~~~G~~VivaGLd~DFr~~pF---~~~~~Ll~lAD~I~kL~  132 (353)
                      ++|||.|.+               . .+.++.+.+.+.|++|++.+=........+   .+...|.-+||.+..|.
T Consensus        89 lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~l~  164 (165)
T cd01120          89 IILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVLS  164 (165)
T ss_pred             EEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCccccCcccccCccceeeecceEEEEe
Confidence            999999966               1 344556666667888887776555443333   13355667777776654

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=95.68  E-value=0.043  Score=51.80  Aligned_cols=79  Identities=24%  Similarity=0.242  Sum_probs=43.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCccccee-ecccHhhhccc--CCCccEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV-SAVELNKLIPH--TKDIDVI  226 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~-~~~~~~~~~~~--~~~~~~i  226 (353)
                      +...++.|+++|||||-|-.-+......+.+++.+-....-+....     +...+... ...+..+++..  -.++|+|
T Consensus       127 ~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~~l~~~-----~~~~~~~~~~~~~~~~~l~~~LR~~pD~i  201 (270)
T PF00437_consen  127 RGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPELRLPGP-----NQIQIQTRRDEISYEDLLKSALRQDPDVI  201 (270)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S--SCS-----SEEEEEEETTTBSHHHHHHHHTTS--SEE
T ss_pred             ceEEEEECCCccccchHHHHHhhhccccccceEEeccccceeeccc-----ceEEEEeecCcccHHHHHHHHhcCCCCcc
Confidence            4567899999999999986555544444478887764433332211     01111111 12234444432  3689999


Q ss_pred             EEecccc
Q psy8456         227 GIDEGQF  233 (353)
Q Consensus       227 ~IDE~QF  233 (353)
                      +|+|..=
T Consensus       202 iigEiR~  208 (270)
T PF00437_consen  202 IIGEIRD  208 (270)
T ss_dssp             EESCE-S
T ss_pred             cccccCC
Confidence            9999986

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=95.68  E-value=0.03  Score=61.37  Aligned_cols=78  Identities=23%  Similarity=0.265  Sum_probs=50.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeecc--CcccceeecccH-hhhc---ccCCCc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHD--QQKLTAVSAVEL-NKLI---PHTKDI  223 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~--g~~~~a~~~~~~-~~~~---~~~~~~  223 (353)
                      +++.++.|+-|+||||-|-....-++..|++|+++-|+-       +..-+.  ....++..+..+ ...-   ....+.
T Consensus       368 ~~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~ApTg-------~Aa~~L~~~~g~~a~Ti~~~~~~~~~~~~~~~~~  440 (744)
T TIGR02768       368 GDIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSG-------KAAEGLQAESGIESRTLASLEYAWANGRDLLSDK  440 (744)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeCcH-------HHHHHHHhccCCceeeHHHHHhhhccCcccCCCC
Confidence            457899999999999887777677788899999998852       111111  111222232222 1111   113578


Q ss_pred             cEEEEeccccc
Q psy8456         224 DVIGIDEGQFV  234 (353)
Q Consensus       224 ~~i~IDE~QF~  234 (353)
                      |+++|||+..+
T Consensus       441 ~llIvDEasMv  451 (744)
T TIGR02768       441 DVLVIDEAGMV  451 (744)
T ss_pred             cEEEEECcccC
Confidence            99999999997

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK05973 replicative DNA helicase; Provisional

Probab=95.61  E-value=0.054  Score=51.73  Aligned_cols=89  Identities=13%  Similarity=0.038  Sum_probs=59.7

Q ss_pred             HHHHH-hCCCEEEEEecccccccCCchhHhhhhccccceEeccceecccccccccccccccceeeeeccCCCCchhHHHH
Q psy8456          91 AESMA-NAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus        91 ~~~l~-~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~geI~vi~G~M~sGKt~~Li~  169 (353)
                      ++.+. ..|++-. -+||.=-..+-|...+.|-+-+...+....+         ..-=..+.+.+|.|+.++|||+-.++
T Consensus        14 a~~~~~~~~~~~~-~~~~~~a~~~g~~~w~~~~~~~~~~~p~~~l---------~GGl~~Gsl~LIaG~PG~GKT~lalq   83 (237)
T PRK05973         14 AKLLSRAQNIPLH-EALDRIAAEEGFSSWSLLAAKAAATTPAEEL---------FSQLKPGDLVLLGARPGHGKTLLGLE   83 (237)
T ss_pred             HHHHHHhcCCcHH-HHHHHHHHHhccchHHHHHHhccCCCCHHHh---------cCCCCCCCEEEEEeCCCCCHHHHHHH
Confidence            44444 3455533 3567777788888888776644333332110         00001356889999999999999999


Q ss_pred             HHHHHHHhCCEEEEEeeecC
Q psy8456         170 RIRRYQYANYRCMIVRYAKD  189 (353)
Q Consensus       170 ~~~~~~~~~~~~~~~k~~~D  189 (353)
                      -+.+...+|++|++|....+
T Consensus        84 fa~~~a~~Ge~vlyfSlEes  103 (237)
T PRK05973         84 LAVEAMKSGRTGVFFTLEYT  103 (237)
T ss_pred             HHHHHHhcCCeEEEEEEeCC
Confidence            99998888999999987654

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.56  E-value=0.042  Score=52.80  Aligned_cols=79  Identities=18%  Similarity=0.183  Sum_probs=44.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc--CCCccEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVIG  227 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i~  227 (353)
                      .++.+|+||++|||||-|-..+......+.+++.+--...-+.. +...+.....    .-....+.+..  -.++|+|+
T Consensus        80 ~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~~~-~~~q~~v~~~----~~~~~~~~l~~~lR~~PD~i~  154 (264)
T cd01129          80 HGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQIP-GINQVQVNEK----AGLTFARGLRAILRQDPDIIM  154 (264)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceecCC-CceEEEeCCc----CCcCHHHHHHHHhccCCCEEE
Confidence            46789999999999998865555443346677665432222221 1110000000    00123333322  36899999


Q ss_pred             Eecccc
Q psy8456         228 IDEGQF  233 (353)
Q Consensus       228 IDE~QF  233 (353)
                      |+|+.=
T Consensus       155 vgEiR~  160 (264)
T cd01129         155 VGEIRD  160 (264)
T ss_pred             eccCCC
Confidence            999875

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=95.52  E-value=0.04  Score=52.06  Aligned_cols=147  Identities=16%  Similarity=0.167  Sum_probs=71.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec-CCCCC-CCce--eeccCcccceeecccHhhhcccCCCccEE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK-DDRYD-TEKV--STHDQQKLTAVSAVELNKLIPHTKDIDVI  226 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~-D~R~~-~~~i--~s~~g~~~~a~~~~~~~~~~~~~~~~~~i  226 (353)
                      ...+++|++|+||||-.-. +     ++ +.+++..-. ..+.. ...+  ...+--.......+.+..+-....+|+.|
T Consensus        13 ~~~liyG~~G~GKtt~a~~-~-----~~-~~~~~~~d~~~~~l~g~~~~~v~~~d~~~~~~~~~d~l~~~~~~~~~ydtV   85 (220)
T TIGR01618        13 NMYLIYGKPGTGKTSTIKY-L-----PG-KTLVLSFDMSSKVLIGDENVDIADHDDMPPIQAMVEFYVMQNIQAVKYDNI   85 (220)
T ss_pred             cEEEEECCCCCCHHHHHHh-c-----CC-CCEEEeccccchhccCCCCCceeecCCCCCHHHHHHHHHHHHhccccCCEE
Confidence            4589999999999984332 2     34 344444321 22211 1111  00000000000011122222345789999


Q ss_pred             EEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCC----ccHHHHHHHHHhCCCEEEEEec
Q psy8456         227 GIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEF----PDVVSFAESMANAGKIVVVAAL  302 (353)
Q Consensus       227 ~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f----~~~~~~~~~~~~~g~~Vi~~gL  302 (353)
                      +||.+.-++-    .-+...||++   ++                 ..|+.+.|    ..+.+++..|.+.|+.|++.|-
T Consensus        86 VIDsI~~l~~----~~~~~~~r~~---k~-----------------~~~~~~~yg~~~~~fl~~l~~L~~~g~nII~tAh  141 (220)
T TIGR01618        86 VIDNISALQN----LWLENIGRAA---KN-----------------GQPELQHYQKLDLWFLDLLTVLKESNKNIYATAW  141 (220)
T ss_pred             EEecHHHHHH----HHHHHHhhhc---CC-----------------CCcccccHHHHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            9999997620    1111222221   11                 11222223    2366677788889999998886


Q ss_pred             ccc-----ccCCCch--------hHH-hhhhcccceEEee
Q psy8456         303 DGT-----FQRTGFN--------DIL-SLIPLAECVEKLT  328 (353)
Q Consensus       303 d~d-----f~~~~F~--------~~~-~L~~~ad~v~kl~  328 (353)
                      ..+     ..+.++.        .+. .++.++|-|-++.
T Consensus       142 e~~~~~~de~G~~~~r~~P~i~~K~~n~l~G~~DvV~rl~  181 (220)
T TIGR01618       142 ELTNQSSGESGQIYNRYQPDIREKVLNAFLGLTDVVGRIV  181 (220)
T ss_pred             eccccccCCCCCCcceechhhhhhHHHhhcccccEEEEEE
Confidence            532     2233221        112 2666788887774

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=95.51  E-value=0.069  Score=54.16  Aligned_cols=83  Identities=13%  Similarity=0.082  Sum_probs=42.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHH--hCCEEEEEeeecCCCCC-CCceeeccCcccceeecccHhhhccc--CCCcc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQY--ANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTAVSAVELNKLIPH--TKDID  224 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~--~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~  224 (353)
                      +++.+++||++|||||-|-.-+.....  .+.+++.+-....-... .+.+..-.+... ........+.+..  -.++|
T Consensus       149 ~GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~~~~~~~~~~~q~ev-g~~~~~~~~~l~~aLR~~PD  227 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYILGSPDDLLPPAQSQI-GRDVDSFANGIRLALRRAPK  227 (372)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhccCCCceeeccccccc-CCCccCHHHHHHHhhccCCC
Confidence            457799999999999988554444332  24566655322221111 111110000000 0011123333322  36899


Q ss_pred             EEEEecccc
Q psy8456         225 VIGIDEGQF  233 (353)
Q Consensus       225 ~i~IDE~QF  233 (353)
                      +|+|.|..=
T Consensus       228 ~I~vGEiRd  236 (372)
T TIGR02525       228 IIGVGEIRD  236 (372)
T ss_pred             EEeeCCCCC
Confidence            999999885

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.44  E-value=0.01  Score=57.43  Aligned_cols=80  Identities=25%  Similarity=0.326  Sum_probs=50.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh-C-CEEEEEeeecCC-CCCC-Cceeec---cCcccce-eecccHhhhcccCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA-N-YRCMIVRYAKDD-RYDT-EKVSTH---DQQKLTA-VSAVELNKLIPHTK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~-~-~~~~~~k~~~D~-R~~~-~~i~s~---~g~~~~a-~~~~~~~~~~~~~~  221 (353)
                      +.+..++||-||||||-+...+..+... | ++|.++.  .|+ |.+. +.+.+.   .|..+.. ....++.+.+....
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~--~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~~  271 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALIT--TDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRLR  271 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEE--CCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHcc
Confidence            4577899999999999999999988776 5 8999887  344 2111 111111   1211111 11123445555557


Q ss_pred             CccEEEEecc
Q psy8456         222 DIDVIGIDEG  231 (353)
Q Consensus       222 ~~~~i~IDE~  231 (353)
                      ++|+|+||.+
T Consensus       272 ~~d~vliDt~  281 (282)
T TIGR03499       272 DKDLILIDTA  281 (282)
T ss_pred             CCCEEEEeCC
Confidence            7999999964

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.43  E-value=0.04  Score=55.75  Aligned_cols=118  Identities=9%  Similarity=0.010  Sum_probs=73.7

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCcee---eccCCceeeee---cCChhhhcc--cCCCccEEEEcc
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVA---THDQQKLTAVS---AVELNKLIP--HTKDIDVIGIDE   80 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~---Sr~G~~~~Ai~---i~~l~ei~~--~~~~~dvV~IDE   80 (353)
                      .=+|||+-+++.+.++...|.+|+.+...-    +.+.+.   .|.|...+.+.   ..++.++..  ...++++|+||+
T Consensus        91 pG~GKStLllq~a~~~a~~g~~VlYvs~EE----s~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~~~~~lVVIDS  166 (372)
T cd01121          91 PGIGKSTLLLQVAARLAKRGGKVLYVSGEE----SPEQIKLRADRLGISTENLYLLAETNLEDILASIEELKPDLVIIDS  166 (372)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEEEECCc----CHHHHHHHHHHcCCCcccEEEEccCcHHHHHHHHHhcCCcEEEEcc
Confidence            457999999999999988888999886531    111222   23444333321   223444432  234799999999


Q ss_pred             ccChH------------HHH----HHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEecc
Q psy8456          81 GQFFP------------DVV----SFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT  132 (353)
Q Consensus        81 aQFF~------------dIv----~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~  132 (353)
                      +|++-            |+.    ++.+.+.+.|++|++.|--+. .+. +.+...|--++|.|..+.
T Consensus       167 Iq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~itvilvghvtk-~g~-~aG~~~leh~vD~Vi~le  232 (372)
T cd01121         167 IQTVYSSELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHVTK-EGS-IAGPKVLEHMVDTVLYFE  232 (372)
T ss_pred             hHHhhccccccCCCCHHHHHHHHHHHHHHHHHcCCeEEEEeeccC-CCc-ccCcccchhhceEEEEEE
Confidence            99872            222    244556678999999986432 122 333345556788888664

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PF13173 AAA_14: AAA domain

Probab=95.42  E-value=0.025  Score=47.76  Aligned_cols=85  Identities=15%  Similarity=0.162  Sum_probs=51.8

Q ss_pred             CCCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhh-ccc-CCCccEEEEccccChH
Q psy8456           8 DRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKL-IPH-TKDIDVIGIDEGQFFP   85 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei-~~~-~~~~dvV~IDEaQFF~   85 (353)
                      .|-+||||-|.+.++.+. .+.+++.+.= -|.+...  ...           .++.+. ... .++..+|+|||+|..+
T Consensus        10 ~R~vGKTtll~~~~~~~~-~~~~~~yi~~-~~~~~~~--~~~-----------~~~~~~~~~~~~~~~~~i~iDEiq~~~   74 (128)
T PF13173_consen   10 PRGVGKTTLLKQLAKDLL-PPENILYINF-DDPRDRR--LAD-----------PDLLEYFLELIKPGKKYIFIDEIQYLP   74 (128)
T ss_pred             CCCCCHHHHHHHHHHHhc-ccccceeecc-CCHHHHH--Hhh-----------hhhHHHHHHhhccCCcEEEEehhhhhc
Confidence            477999999999988776 4444444432 1222200  000           001111 111 2356789999999999


Q ss_pred             HHHHHHHHHHhCC--CEEEEEecc
Q psy8456          86 DVVSFAESMANAG--KIVVVAALD  107 (353)
Q Consensus        86 dIv~l~~~l~~~G--~~VivaGLd  107 (353)
                      +..+.++.+.+.+  ..|++.|=.
T Consensus        75 ~~~~~lk~l~d~~~~~~ii~tgS~   98 (128)
T PF13173_consen   75 DWEDALKFLVDNGPNIKIILTGSS   98 (128)
T ss_pred             cHHHHHHHHHHhccCceEEEEccc
Confidence            7777777777665  788888753

>PF02702 KdpD: Osmosensitive K+ channel His kinase sensor domain; InterPro: IPR003852 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []

Probab=95.39  E-value=0.082  Score=49.87  Aligned_cols=35  Identities=20%  Similarity=0.261  Sum_probs=28.7

Q ss_pred             cceeeeecc-CCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         150 QEKEVILGP-MFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       150 geI~vi~G~-M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      |.+.+++|. .|.|||-.+|+.++....+|..|++=
T Consensus         4 GrLkIflG~apGVGKTy~ML~ea~~l~~~G~DVViG   39 (211)
T PF02702_consen    4 GRLKIFLGAAPGVGKTYAMLQEAHRLKEQGVDVVIG   39 (211)
T ss_dssp             --EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE
T ss_pred             ccEEEEEecCCCCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            678889998 99999999999999999999999863

Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the N-terminal domain found in KdpD sensor kinase proteins, which regulate the kdpFABC operon responsible for potassium transport []. The N-terminal domain forms part of the cytoplasmic region of the protein, which may be the sensor domain responsible for sensing turgor pressure [].; GO: 0000155 two-component sensor activity, 0004673 protein histidine kinase activity, 0000160 two-component signal transduction system (phosphorelay), 0016020 membrane; PDB: 2R8R_B.

>TIGR00595 priA primosomal protein N'

Probab=95.38  E-value=0.028  Score=58.89  Aligned_cols=80  Identities=18%  Similarity=0.171  Sum_probs=53.2

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecC----------CCCCCCceeeccCcccc--------------eee
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKD----------DRYDTEKVSTHDQQKLT--------------AVS  209 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D----------~R~~~~~i~s~~g~~~~--------------a~~  209 (353)
                      ++.||.|||||.-.++.+......|++++++-|.+.          .+++.....-|.+..-.              -+.
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IV   80 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV   80 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEE
Confidence            468999999999999988888888999999999753          23443333445433110              011


Q ss_pred             cccHhhhcccCCCccEEEEecccc
Q psy8456         210 AVELNKLIPHTKDIDVIGIDEGQF  233 (353)
Q Consensus       210 ~~~~~~~~~~~~~~~~i~IDE~QF  233 (353)
                      +..-..+....++.+.|+|||.|-
T Consensus        81 VGTrsalf~p~~~l~lIIVDEeh~  104 (505)
T TIGR00595        81 IGTRSALFLPFKNLGLIIVDEEHD  104 (505)
T ss_pred             ECChHHHcCcccCCCEEEEECCCc
Confidence            222222333357899999999985

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK08116 hypothetical protein; Validated

Probab=95.38  E-value=0.036  Score=53.39  Aligned_cols=73  Identities=14%  Similarity=0.141  Sum_probs=41.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCcee-eccCcccceeecccHhhhcccCCCccEEEEec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVS-THDQQKLTAVSAVELNKLIPHTKDIDVIGIDE  230 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~-s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE  230 (353)
                      .-+++|+.|+|||.-+.-.++....+|+.|+++.... -   -..+. +.++.     .-....+++....++|+++||+
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~-l---l~~i~~~~~~~-----~~~~~~~~~~~l~~~dlLviDD  186 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQ-L---LNRIKSTYKSS-----GKEDENEIIRSLVNADLLILDD  186 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHH-H---HHHHHHHHhcc-----ccccHHHHHHHhcCCCEEEEec
Confidence            3589999999997655555555566688887665311 0   00010 00000     0012233444567889999999


Q ss_pred             ccc
Q psy8456         231 GQF  233 (353)
Q Consensus       231 ~QF  233 (353)
                      .+.
T Consensus       187 lg~  189 (268)
T PRK08116        187 LGA  189 (268)
T ss_pred             ccC
Confidence            975

>PHA00350 putative assembly protein

Probab=95.35  E-value=0.042  Score=56.32  Aligned_cols=31  Identities=19%  Similarity=0.030  Sum_probs=26.8

Q ss_pred             eeeeeccCCCCchhHHHH-HHHHHHHhCCEEE
Q psy8456         152 KEVILGPMFSGKTTELIR-RIRRYQYANYRCM  182 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~-~~~~~~~~~~~~~  182 (353)
                      +.+++|.+|||||.+.+. .+..+..+|++|+
T Consensus         3 I~l~tG~pGSGKT~~aV~~~i~palk~GR~V~   34 (399)
T PHA00350          3 IYAIVGRPGSYKSYEAVVYHIIPALKDGRKVI   34 (399)
T ss_pred             eEEEecCCCCchhHHHHHHHHHHHHHCCCEEE
Confidence            678999999999999998 6788888898664

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.27  E-value=0.069  Score=48.16  Aligned_cols=114  Identities=14%  Similarity=0.121  Sum_probs=74.6

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEE---EeeccCCCCCCCceeecc-CCceeeee------cCChhh-hc------c----
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMI---VRYAKDDRYDTEKVATHD-QQKLTAVS------AVELNK-LI------P----   68 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv---~Kp~iDtRy~~~~I~Sr~-G~~~~Ai~------i~~l~e-i~------~----   68 (353)
                      -.|||+..+..+.|.--+|++|++   +|...  .+|+..+-.+. +...-...      -.+..+ ..      .    
T Consensus        12 G~Gkt~~a~g~~~ra~~~g~~v~~vQFlKg~~--~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~a~~~~~~a~~   89 (159)
T cd00561          12 GKGKTTAALGLALRALGHGYRVGVVQFLKGGW--KYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAAAAEGWAFAKE   89 (159)
T ss_pred             CCCHHHHHHHHHHHHHHCCCeEEEEEEeCCCC--ccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHHHHHHHHHHHH
Confidence            469999999999999999999999   66531  23432222222 22111100      011111 10      0    


Q ss_pred             --cCCCccEEEEccccCh-H----HHHHHHHHHHhC--CCEEEEEecccccccCCchhHhhhhccccceEeccce
Q psy8456          69 --HTKDIDVIGIDEGQFF-P----DVVSFAESMANA--GKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  134 (353)
Q Consensus        69 --~~~~~dvV~IDEaQFF-~----dIv~l~~~l~~~--G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~Av  134 (353)
                        ....||.|++||+=.- +    +..++.+.+.++  +..||+-|=+         ....|+++||-|++++.+
T Consensus        90 ~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~---------~p~~l~e~AD~VTEm~~v  155 (159)
T cd00561          90 AIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRN---------APKELIEAADLVTEMREV  155 (159)
T ss_pred             HHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCC---------CCHHHHHhCceeeeccee
Confidence              2468999999998776 3    455666666654  7889999974         357799999999998754

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK06921 hypothetical protein; Provisional

Probab=95.26  E-value=0.032  Score=53.75  Aligned_cols=70  Identities=17%  Similarity=0.096  Sum_probs=44.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEe
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGID  229 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~ID  229 (353)
                      .--+++||.|+|||.-+...++....+ |..|+.+....        ...+...   +  .....+.+....+.|+++||
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~--------l~~~l~~---~--~~~~~~~~~~~~~~dlLiID  184 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVE--------GFGDLKD---D--FDLLEAKLNRMKKVEVLFID  184 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHH--------HHHHHHH---H--HHHHHHHHHHhcCCCEEEEe
Confidence            345899999999997776666666666 88888766411        0000000   0  01222333445789999999


Q ss_pred             cccc
Q psy8456         230 EGQF  233 (353)
Q Consensus       230 E~QF  233 (353)
                      +.|+
T Consensus       185 Dl~~  188 (266)
T PRK06921        185 DLFK  188 (266)
T ss_pred             cccc
Confidence            9977

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.25  E-value=0.012  Score=60.28  Aligned_cols=71  Identities=25%  Similarity=0.336  Sum_probs=42.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCC---EEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANY---RCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIG  227 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~---~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~  227 (353)
                      +.-+|+||-|+||| +|++.+-++..+..   +++-+.+.   .+. ...+       ++.......++-... ..|+++
T Consensus       114 nplfi~G~~GlGKT-HLl~Aign~~~~~~~~a~v~y~~se---~f~-~~~v-------~a~~~~~~~~Fk~~y-~~dlll  180 (408)
T COG0593         114 NPLFIYGGVGLGKT-HLLQAIGNEALANGPNARVVYLTSE---DFT-NDFV-------KALRDNEMEKFKEKY-SLDLLL  180 (408)
T ss_pred             CcEEEECCCCCCHH-HHHHHHHHHHHhhCCCceEEeccHH---HHH-HHHH-------HHHHhhhHHHHHHhh-ccCeee
Confidence            45689999999997 88999988865533   23322211   110 0001       111112333343445 799999


Q ss_pred             Eeccccc
Q psy8456         228 IDEGQFV  234 (353)
Q Consensus       228 IDE~QF~  234 (353)
                      ||-+||+
T Consensus       181 IDDiq~l  187 (408)
T COG0593         181 IDDIQFL  187 (408)
T ss_pred             echHhHh
Confidence            9999995

>PRK14974 cell division protein FtsY; Provisional

Probab=95.23  E-value=0.036  Score=55.46  Aligned_cols=81  Identities=21%  Similarity=0.253  Sum_probs=50.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCC-Cceeec---cCcccceeec---ccHh----hhc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDT-EKVSTH---DQQKLTAVSA---VELN----KLI  217 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~-~~i~s~---~g~~~~a~~~---~~~~----~~~  217 (353)
                      ....+++||.|+||||-+...++.+...|.+|.++.  .|+ |.+. +...++   .|.  +.+..   .++.    +.+
T Consensus       140 ~~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~--~Dt~R~~a~eqL~~~a~~lgv--~v~~~~~g~dp~~v~~~ai  215 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAA--GDTFRAGAIEQLEEHAERLGV--KVIKHKYGADPAAVAYDAI  215 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEec--CCcCcHHHHHHHHHHHHHcCC--ceecccCCCCHHHHHHHHH
Confidence            346788999999999999999999988899998865  453 3221 122211   121  11111   1111    211


Q ss_pred             c--cCCCccEEEEeccccc
Q psy8456         218 P--HTKDIDVIGIDEGQFV  234 (353)
Q Consensus       218 ~--~~~~~~~i~IDE~QF~  234 (353)
                      .  ...++|+|+||.++.+
T Consensus       216 ~~~~~~~~DvVLIDTaGr~  234 (336)
T PRK14974        216 EHAKARGIDVVLIDTAGRM  234 (336)
T ss_pred             HHHHhCCCCEEEEECCCcc
Confidence            1  2467899999999985

>PRK06620 hypothetical protein; Validated

Probab=95.21  E-value=0.045  Score=50.93  Aligned_cols=18  Identities=44%  Similarity=0.471  Sum_probs=14.0

Q ss_pred             eeeeccCCCCchhHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~  171 (353)
                      -+++||-|||||+ |++.+
T Consensus        47 l~l~Gp~G~GKTh-Ll~a~   64 (214)
T PRK06620         47 LLIKGPSSSGKTY-LTKIW   64 (214)
T ss_pred             EEEECCCCCCHHH-HHHHH
Confidence            4899999999985 44543

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=95.17  E-value=0.14  Score=47.96  Aligned_cols=40  Identities=18%  Similarity=0.189  Sum_probs=27.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhC--CEEEEEeeecC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYAN--YRCMIVRYAKD  189 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~--~~~~~~k~~~D  189 (353)
                      ..+.++.||.|+|||.-.+..+...-..|  .++++++|...
T Consensus        19 ~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~   60 (205)
T PF02562_consen   19 NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVE   60 (205)
T ss_dssp             -SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCC
Confidence            45788999999999988887777665555  58999999885

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.11  E-value=0.1  Score=51.90  Aligned_cols=80  Identities=20%  Similarity=0.191  Sum_probs=42.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHH-hCCEEEEEeeecCCCCC-CCceeeccCcccceeecccHhhhccc--CCCccE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQY-ANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDV  225 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~-~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~  225 (353)
                      +++-++.||++|||||-|-.-++.... .+.+++.+.....-.+. ...+.++......   .....+.+..  -.++|+
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~~~~~~~~i~q~evg~~---~~~~~~~l~~~lr~~pd~  198 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVHRNKRSLINQREVGLD---TLSFANALRAALREDPDV  198 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhhccCccceEEccccCCC---CcCHHHHHHHhhccCCCE
Confidence            567899999999999988655544432 24566655332211111 0111111100000   1123333322  378999


Q ss_pred             EEEeccc
Q psy8456         226 IGIDEGQ  232 (353)
Q Consensus       226 i~IDE~Q  232 (353)
                      |++||.-
T Consensus       199 i~vgEir  205 (343)
T TIGR01420       199 ILIGEMR  205 (343)
T ss_pred             EEEeCCC
Confidence            9999984

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.08  E-value=0.032  Score=56.01  Aligned_cols=79  Identities=22%  Similarity=0.170  Sum_probs=56.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCC-C-----------ceeeccCcccceeecccHhhhc
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDT-E-----------KVSTHDQQKLTAVSAVELNKLI  217 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~-~-----------~i~s~~g~~~~a~~~~~~~~~~  217 (353)
                      ...+++|..|+||||-+-.-++.|+..|++|++.-  -|| |.+. +           .+.+|.   .-+.++.-.++-+
T Consensus       140 ~Vil~vGVNG~GKTTTIaKLA~~l~~~g~~VllaA--~DTFRAaAiEQL~~w~er~gv~vI~~~---~G~DpAaVafDAi  214 (340)
T COG0552         140 FVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAA--GDTFRAAAIEQLEVWGERLGVPVISGK---EGADPAAVAFDAI  214 (340)
T ss_pred             EEEEEEecCCCchHhHHHHHHHHHHHCCCeEEEEe--cchHHHHHHHHHHHHHHHhCCeEEccC---CCCCcHHHHHHHH
Confidence            35578999999999999999999999999999864  355 6441 1           234432   1233343344444


Q ss_pred             cc--CCCccEEEEeccccc
Q psy8456         218 PH--TKDIDVIGIDEGQFV  234 (353)
Q Consensus       218 ~~--~~~~~~i~IDE~QF~  234 (353)
                      .+  ..++|+++||=|=.+
T Consensus       215 ~~Akar~~DvvliDTAGRL  233 (340)
T COG0552         215 QAAKARGIDVVLIDTAGRL  233 (340)
T ss_pred             HHHHHcCCCEEEEeCcccc
Confidence            33  588999999999876

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.04  E-value=0.051  Score=56.11  Aligned_cols=142  Identities=13%  Similarity=0.178  Sum_probs=83.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCC-CCceeecc-Ccccceeecc---cHhhhcccC---C
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYD-TEKVSTHD-QQKLTAVSAV---ELNKLIPHT---K  221 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~-~~~i~s~~-g~~~~a~~~~---~~~~~~~~~---~  221 (353)
                      ....++||.||||||-+..-+..+..+|++|.++..  |+ |.+ .+...+.. -..++.+...   .+.+.+...   .
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~a--Dt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~~~  319 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITT--DHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEEA  319 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEec--CCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHhcc
Confidence            466899999999999999999999888999998764  33 322 12222210 0112222222   233333222   3


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccC-------CCCCCCCccHHHHHHHHHhCC
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALN-------VPPPPEFPDVVSFAESMANAG  294 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------~~~~~~f~~~~~~~~~~~~~g  294 (353)
                      ++|+|+||-+=..                     +....++.+|..+..+..       ++..---.|+.++++.....|
T Consensus       320 ~~DvVLIDTaGRs---------------------~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~~F~~~~  378 (436)
T PRK11889        320 RVDYILIDTAGKN---------------------YRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNFKDIH  378 (436)
T ss_pred             CCCEEEEeCcccc---------------------CcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHHHhcCCC
Confidence            6899999988552                     124556677766554311       111111136777777777666


Q ss_pred             CE-EEEEeccccccCCCchhHHhhh
Q psy8456         295 KI-VVVAALDGTFQRTGFNDILSLI  318 (353)
Q Consensus       295 ~~-Vi~~gLd~df~~~~F~~~~~L~  318 (353)
                      +. +|+-=||.+-   .+|.+..++
T Consensus       379 idglI~TKLDET~---k~G~iLni~  400 (436)
T PRK11889        379 IDGIVFTKFDETA---SSGELLKIP  400 (436)
T ss_pred             CCEEEEEcccCCC---CccHHHHHH
Confidence            54 6777788765   355555543

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=95.03  E-value=0.26  Score=45.30  Aligned_cols=21  Identities=33%  Similarity=0.328  Sum_probs=17.1

Q ss_pred             cceeeeeccCCCCchhHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRR  170 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~  170 (353)
                      +++.+++||.+|||||-|=..
T Consensus        25 g~~~~ltGpNg~GKSTllr~i   45 (199)
T cd03283          25 KNGILITGSNMSGKSTFLRTI   45 (199)
T ss_pred             CcEEEEECCCCCChHHHHHHH
Confidence            468899999999999876443

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=94.97  E-value=0.1  Score=48.51  Aligned_cols=115  Identities=14%  Similarity=0.136  Sum_probs=75.8

Q ss_pred             CchHHHHHHHHHHHHHcCceEEEEeeccCC-CCCCCceeecc-CCceeeee-----c-CCh-hhhc----------c--c
Q psy8456          11 NPYIVHFCRRIRRYQYANYRCMIVRYAKDD-RYDTEKVATHD-QQKLTAVS-----A-VEL-NKLI----------P--H   69 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agkkvlv~Kp~iDt-Ry~~~~I~Sr~-G~~~~Ai~-----i-~~l-~ei~----------~--~   69 (353)
                      -|||+..+..+.|.--+|.+|+++.--... .+|+...-++. +..+....     . .+. .+..          .  .
T Consensus        33 kGKtt~a~g~a~ra~g~G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~~~~~~~a~~~l~  112 (191)
T PRK05986         33 KGKSTAAFGMALRAVGHGKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAAREGWEEAKRMLA  112 (191)
T ss_pred             CChHHHHHHHHHHHHHCCCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHHHHHHHHHHHHHh
Confidence            599999999999999999999998887766 34443333332 22222110     0 111 1111          0  2


Q ss_pred             CCCccEEEEccccCh-H----HHHHHHHHHHh--CCCEEEEEecccccccCCchhHhhhhccccceEeccce
Q psy8456          70 TKDIDVIGIDEGQFF-P----DVVSFAESMAN--AGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  134 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF-~----dIv~l~~~l~~--~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~Av  134 (353)
                      .+.||+|+.||+--- .    +..++.+.+.+  .+..||+-|=+         ....|+++||-|++++.+
T Consensus       113 ~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~---------~p~~Lie~ADlVTEm~~v  175 (191)
T PRK05986        113 DESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRG---------APRELIEAADLVTEMRPV  175 (191)
T ss_pred             CCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCC---------CCHHHHHhCchheecccc
Confidence            468999999998654 1    34455555554  47899999974         356799999999998764

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=94.97  E-value=0.11  Score=48.15  Aligned_cols=38  Identities=11%  Similarity=0.011  Sum_probs=33.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +.+.++.|+.+||||+-..+-+.....+|.+|+++.-.
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e   62 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE   62 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcC
Confidence            46788999999999999999988887889999988864

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.91  E-value=0.07  Score=54.25  Aligned_cols=82  Identities=18%  Similarity=0.191  Sum_probs=51.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh-C-CEEEEEeeecCC-CCCC-Cceee---ccCcccceee-cccHhhhcccCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA-N-YRCMIVRYAKDD-RYDT-EKVST---HDQQKLTAVS-AVELNKLIPHTK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~-~-~~~~~~k~~~D~-R~~~-~~i~s---~~g~~~~a~~-~~~~~~~~~~~~  221 (353)
                      +++.+++||.|+||||-+.+-+.++... | ++|.++..  |+ |.+. +.+.+   .-|..+..+. ..++...+....
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~--D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~  214 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTT--DSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELR  214 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEec--ccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhc
Confidence            5678899999999999999999988644 5 57877763  33 5432 11211   1122211111 123444445567


Q ss_pred             CccEEEEecccc
Q psy8456         222 DIDVIGIDEGQF  233 (353)
Q Consensus       222 ~~~~i~IDE~QF  233 (353)
                      +.|+|+||++=+
T Consensus       215 ~~DlVLIDTaG~  226 (374)
T PRK14722        215 NKHMVLIDTIGM  226 (374)
T ss_pred             CCCEEEEcCCCC
Confidence            889999999965

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.87  E-value=0.097  Score=55.75  Aligned_cols=144  Identities=24%  Similarity=0.275  Sum_probs=83.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh--CCEEEEEeeecCC-CCCC-Cceeec---cCcccce-eecccHhhhcccCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA--NYRCMIVRYAKDD-RYDT-EKVSTH---DQQKLTA-VSAVELNKLIPHTK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~--~~~~~~~k~~~D~-R~~~-~~i~s~---~g~~~~a-~~~~~~~~~~~~~~  221 (353)
                      +++..++||-|+||||-+..-+..+...  +++|.++.-  |+ |-+. +...+.   .|..+.. .....+.+++....
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdt--DtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~  427 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTT--DTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERLR  427 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEec--ccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHhc
Confidence            5677899999999999998888877554  578887763  43 3221 111111   1211111 11234555555567


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHh------hccCCCCCCCCccHHHHHHHHHhCC-
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANEN------AALNVPPPPEFPDVVSFAESMANAG-  294 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~------~~~~~~~~~~f~~~~~~~~~~~~~g-  294 (353)
                      ++|+|+||.+=..                     +.......+|..+.      .-|-+|..+.+.++.++++.+...+ 
T Consensus       428 ~~DLVLIDTaG~s---------------------~~D~~l~eeL~~L~aa~~~a~lLVLpAtss~~Dl~eii~~f~~~~~  486 (559)
T PRK12727        428 DYKLVLIDTAGMG---------------------QRDRALAAQLNWLRAARQVTSLLVLPANAHFSDLDEVVRRFAHAKP  486 (559)
T ss_pred             cCCEEEecCCCcc---------------------hhhHHHHHHHHHHHHhhcCCcEEEEECCCChhHHHHHHHHHHhhCC
Confidence            8999999998762                     11223333333222      1234455555667777777776543 


Q ss_pred             CEEEEEeccccccCCCchhHHhhhh
Q psy8456         295 KIVVVAALDGTFQRTGFNDILSLIP  319 (353)
Q Consensus       295 ~~Vi~~gLd~df~~~~F~~~~~L~~  319 (353)
                      .-+|+-.||.+   ..++.++.++.
T Consensus       487 ~gvILTKlDEt---~~lG~aLsv~~  508 (559)
T PRK12727        487 QGVVLTKLDET---GRFGSALSVVV  508 (559)
T ss_pred             eEEEEecCcCc---cchhHHHHHHH
Confidence            34777778774   34566666543

>PRK10436 hypothetical protein; Provisional

Probab=94.84  E-value=0.079  Score=55.20  Aligned_cols=80  Identities=20%  Similarity=0.229  Sum_probs=45.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc--CCCccEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVI  226 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i  226 (353)
                      ..++-++.||+||||||-|-..+......+++++-+-.-..-+..  .+.   +..+....-.+..+.+..  -.++|+|
T Consensus       217 ~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE~~l~--gi~---Q~~v~~~~g~~f~~~lr~~LR~dPDvI  291 (462)
T PRK10436        217 PQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVEIPLA--GIN---QTQIHPKAGLTFQRVLRALLRQDPDVI  291 (462)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCccccCC--Ccc---eEeeCCccCcCHHHHHHHHhcCCCCEE
Confidence            467889999999999999866665544445666654433322211  110   001100000123333332  3789999


Q ss_pred             EEecccc
Q psy8456         227 GIDEGQF  233 (353)
Q Consensus       227 ~IDE~QF  233 (353)
                      .|.|+-=
T Consensus       292 ~vGEIRD  298 (462)
T PRK10436        292 MVGEIRD  298 (462)
T ss_pred             EECCCCC
Confidence            9999875

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=94.84  E-value=0.067  Score=60.48  Aligned_cols=78  Identities=18%  Similarity=0.170  Sum_probs=46.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccC--cccceeecccHhhhc----ccCCCc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQ--QKLTAVSAVELNKLI----PHTKDI  223 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g--~~~~a~~~~~~~~~~----~~~~~~  223 (353)
                      .++.++.|+-|+||||-|-....-++..|++|+.+-|+-       +...+.+  ...++..+..+..-.    ....+.
T Consensus       362 ~~v~vv~G~AGTGKTT~l~~~~~~~e~~G~~V~~~ApTG-------kAA~~L~e~tGi~a~TI~sll~~~~~~~~~l~~~  434 (988)
T PRK13889        362 RDLGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSG-------IAAENLEGGSGIASRTIASLEHGWGQGRDLLTSR  434 (988)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEecCcH-------HHHHHHhhccCcchhhHHHHHhhhcccccccccC
Confidence            357889999999999965444444577799999988842       2111111  111122221211000    113567


Q ss_pred             cEEEEeccccc
Q psy8456         224 DVIGIDEGQFV  234 (353)
Q Consensus       224 ~~i~IDE~QF~  234 (353)
                      ++++|||+-.+
T Consensus       435 ~vlIVDEASMv  445 (988)
T PRK13889        435 DVLVIDEAGMV  445 (988)
T ss_pred             cEEEEECcccC
Confidence            89999999996

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=94.83  E-value=0.065  Score=51.24  Aligned_cols=61  Identities=21%  Similarity=0.121  Sum_probs=34.5

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQ  232 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~Q  232 (353)
                      -+++||.|+|||+-+...++..   +..+........                  .....+.+.+......++++|||+|
T Consensus        33 ~ll~Gp~G~GKT~la~~ia~~~---~~~~~~~~~~~~------------------~~~~~l~~~l~~~~~~~vl~iDEi~   91 (305)
T TIGR00635        33 LLLYGPPGLGKTTLAHIIANEM---GVNLKITSGPAL------------------EKPGDLAAILTNLEEGDVLFIDEIH   91 (305)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh---CCCEEEeccchh------------------cCchhHHHHHHhcccCCEEEEehHh
Confidence            5899999999997665554432   222222111000                  0112233333334567899999999


Q ss_pred             cc
Q psy8456         233 FV  234 (353)
Q Consensus       233 F~  234 (353)
                      ++
T Consensus        92 ~l   93 (305)
T TIGR00635        92 RL   93 (305)
T ss_pred             hh
Confidence            96

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=94.78  E-value=0.035  Score=50.71  Aligned_cols=115  Identities=17%  Similarity=0.170  Sum_probs=63.4

Q ss_pred             CchHHHHHHHHHHHHHcCceEEEEeeccCCCC-CCCceeeccC-Cceee-----eecCChh--hh------cc------c
Q psy8456          11 NPYIVHFCRRIRRYQYANYRCMIVRYAKDDRY-DTEKVATHDQ-QKLTA-----VSAVELN--KL------IP------H   69 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy-~~~~I~Sr~G-~~~~A-----i~i~~l~--ei------~~------~   69 (353)
                      -||||..+..+-|.--.|++|+++.--...++ ++-..-.+.+ .....     +.-.+..  +.      ..      .
T Consensus        14 KGKTTAAlGlalRA~G~G~rV~ivQFlKg~~~~GE~~~l~~l~~~~~~~~g~~f~~~~~~~~~~~~~~~~~~~~a~~~i~   93 (172)
T PF02572_consen   14 KGKTTAALGLALRAAGHGMRVLIVQFLKGGRYSGELKALKKLPNVEIERFGKGFVWRMNEEEEDRAAAREGLEEAKEAIS   93 (172)
T ss_dssp             S-HHHHHHHHHHHHHCTT--EEEEESS--SS--HHHHHHGGGT--EEEE--TT----GGGHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCchHHHHHHHHHHHhCCCEEEEEEEecCCCCcCHHHHHHhCCeEEEEEcCCcccccCCCcHHHHHHHHHHHHHHHHHHh
Confidence            49999999999999999999999988777443 3322222222 22211     1111111  11      00      2


Q ss_pred             CCCccEEEEccccCh-H----HHHHHHHHHHh--CCCEEEEEecccccccCCchhHhhhhccccceEeccce
Q psy8456          70 TKDIDVIGIDEGQFF-P----DVVSFAESMAN--AGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  134 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF-~----dIv~l~~~l~~--~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~Av  134 (353)
                      ...+|+|++||+=-- .    +..++.+.+.+  .+..|++-|=+         ....|+++||-|++++.+
T Consensus        94 ~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~---------~~~~l~e~ADlVTem~~v  156 (172)
T PF02572_consen   94 SGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRN---------APEELIEAADLVTEMREV  156 (172)
T ss_dssp             -TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS-----------HHHHHH-SEEEEEEEC
T ss_pred             CCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCC---------CCHHHHHhCCeeeeecee
Confidence            468999999998432 1    33344444554  68899999973         357899999999998765

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=94.77  E-value=0.039  Score=56.79  Aligned_cols=71  Identities=28%  Similarity=0.399  Sum_probs=38.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH-HHh--CCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccC-CCccEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY-QYA--NYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHT-KDIDVIG  227 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~-~~~--~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~-~~~~~i~  227 (353)
                      .-+++||-|+|||. |++.+.++ ...  +.+|+.+...-   +- ..+.+.       +......++.... .++|+++
T Consensus       132 ~l~lyG~~G~GKTH-Ll~ai~~~l~~~~~~~~v~yi~~~~---f~-~~~~~~-------~~~~~~~~f~~~~~~~~dvLl  199 (440)
T PRK14088        132 PLFIYGGVGLGKTH-LLQSIGNYVVQNEPDLRVMYITSEK---FL-NDLVDS-------MKEGKLNEFREKYRKKVDVLL  199 (440)
T ss_pred             eEEEEcCCCCcHHH-HHHHHHHHHHHhCCCCeEEEEEHHH---HH-HHHHHH-------HhcccHHHHHHHHHhcCCEEE
Confidence            35899999999985 55555544 333  56777665421   00 001000       0001122222222 3689999


Q ss_pred             Eeccccc
Q psy8456         228 IDEGQFV  234 (353)
Q Consensus       228 IDE~QF~  234 (353)
                      |||+||+
T Consensus       200 IDDi~~l  206 (440)
T PRK14088        200 IDDVQFL  206 (440)
T ss_pred             Eechhhh
Confidence            9999995

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=94.73  E-value=0.032  Score=55.24  Aligned_cols=116  Identities=13%  Similarity=0.078  Sum_probs=63.5

Q ss_pred             CCCCchHHHHHHHHHHH--HHcCceEEEEeeccCCCCC-CCceeecc-CCceeeeecCChhhhcc-------cCCCccEE
Q psy8456           8 DRINPYIVHFCRRIRRY--QYANYRCMIVRYAKDDRYD-TEKVATHD-QQKLTAVSAVELNKLIP-------HTKDIDVI   76 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry--~~agkkvlv~Kp~iDtRy~-~~~I~Sr~-G~~~~Ai~i~~l~ei~~-------~~~~~dvV   76 (353)
                      ..=+|||.-++..++.+  ...+.+++++.+..--+.. ...+.... +..... .+..+..++.       ....+|+|
T Consensus         9 ~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~Dvi   87 (352)
T PF09848_consen    9 GAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNPKLKKS-DFRKPTSFINNYSESDKEKNKYDVI   87 (352)
T ss_pred             cCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHHHHHHhhhcccchhhh-hhhhhHHHHhhcccccccCCcCCEE
Confidence            45689999999999999  6677777777664322210 01121111 000000 0112222221       23679999


Q ss_pred             EEccccChHH----------HHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhcc
Q psy8456          77 GIDEGQFFPD----------VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPL  124 (353)
Q Consensus        77 ~IDEaQFF~d----------Iv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~l  124 (353)
                      +|||||-+.+          ..++-+.+....+.|++++=....+..-.+....|-.+
T Consensus        88 ivDEAqrl~~~~~~~~~~~~~~~L~~i~~~~kv~v~f~D~~Q~i~~~e~~~~~~l~~~  145 (352)
T PF09848_consen   88 IVDEAQRLRTKGDQYNNFSEPNQLDEIIKRAKVVVFFYDENQSIRPSEIGTLENLEEI  145 (352)
T ss_pred             EEehhHhhhhccccccccccHHHHHHHHhcCCEEEEEEccccEeecccCCCHHHHHHH
Confidence            9999999953          23444555555566666766666655554444433333

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=94.67  E-value=0.15  Score=49.58  Aligned_cols=36  Identities=28%  Similarity=0.204  Sum_probs=25.5

Q ss_pred             ccce-eeeeccCCCCchhHHHHHHHHHHH-----hCCEEEEE
Q psy8456         149 GQEK-EVILGPMFSGKTTELIRRIRRYQY-----ANYRCMIV  184 (353)
Q Consensus       149 ~geI-~vi~G~M~sGKt~~Li~~~~~~~~-----~~~~~~~~  184 (353)
                      .+++ .+++||.++||||.|-.-++....     .++||.++
T Consensus       135 ~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~Ii  176 (308)
T COG3854         135 NGWLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGII  176 (308)
T ss_pred             cCceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEE
Confidence            3566 889999999999977555554432     35677765

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.66  E-value=0.2  Score=51.56  Aligned_cols=144  Identities=16%  Similarity=0.173  Sum_probs=84.9

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCC-CceeeccC-cccceeeccc---Hhhhccc---
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDT-EKVSTHDQ-QKLTAVSAVE---LNKLIPH---  219 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~-~~i~s~~g-~~~~a~~~~~---~~~~~~~---  219 (353)
                      .+.+.+++||-||||||-+...+..+..+|++|.++.-  |+ |.+. +...++.. ..++-....+   +.+.+..   
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lIta--DtyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~~l~~  282 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITT--DTFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQYMTY  282 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeC--CccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHHHHHh
Confidence            35678899999999999999999888888999998764  44 4321 12222111 1122222223   3332322   


Q ss_pred             CCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCC------C-CCCccHHHHHHHHHh
Q psy8456         220 TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPP------P-PEFPDVVSFAESMAN  292 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~------~-~~f~~~~~~~~~~~~  292 (353)
                      ..++|+|+||=+-..                     |...+++.+|..+.+.++.+.      | .-..|+.++++....
T Consensus       283 ~~~~D~VLIDTAGr~---------------------~~d~~~l~EL~~l~~~~~p~~~~LVLsag~~~~d~~~i~~~f~~  341 (407)
T PRK12726        283 VNCVDHILIDTVGRN---------------------YLAEESVSEISAYTDVVHPDLTCFTFSSGMKSADVMTILPKLAE  341 (407)
T ss_pred             cCCCCEEEEECCCCC---------------------ccCHHHHHHHHHHhhccCCceEEEECCCcccHHHHHHHHHhcCc
Confidence            257999999988772                     335677777777666432211      1 111355555544443


Q ss_pred             CCC-EEEEEeccccccCCCchhHHhhh
Q psy8456         293 AGK-IVVVAALDGTFQRTGFNDILSLI  318 (353)
Q Consensus       293 ~g~-~Vi~~gLd~df~~~~F~~~~~L~  318 (353)
                      .+. -+|+-=||.+   ..||.+..++
T Consensus       342 l~i~glI~TKLDET---~~~G~~Lsv~  365 (407)
T PRK12726        342 IPIDGFIITKMDET---TRIGDLYTVM  365 (407)
T ss_pred             CCCCEEEEEcccCC---CCccHHHHHH
Confidence            333 3677777776   4466666554

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=94.65  E-value=0.15  Score=46.17  Aligned_cols=37  Identities=35%  Similarity=0.443  Sum_probs=33.8

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD  190 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~  190 (353)
                      =|+|+-+|||||-+-+.+.+...+|++|-++|.+-.+
T Consensus         6 ~ivG~k~SGKTTLie~lv~~L~~~G~rVa~iKH~hh~   42 (161)
T COG1763           6 GIVGYKNSGKTTLIEKLVRKLKARGYRVATVKHAHHD   42 (161)
T ss_pred             EEEecCCCChhhHHHHHHHHHHhCCcEEEEEEecCCC
Confidence            3799999999999999999999999999999988765

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=94.59  E-value=0.024  Score=56.11  Aligned_cols=32  Identities=22%  Similarity=0.285  Sum_probs=24.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhC--CEEEEE
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYAN--YRCMIV  184 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~--~~~~~~  184 (353)
                      -+|+||-|+|||+-+-..++.....+  ..++.+
T Consensus        58 ~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         58 VLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            48999999999998888888776655  344444

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.56  E-value=0.05  Score=53.89  Aligned_cols=37  Identities=16%  Similarity=0.178  Sum_probs=33.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+..++||.||||||-+..-+..+...|++|+++.-
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~  150 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAG  150 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEec
Confidence            5677889999999999999999999989999998863

>PF13479 AAA_24: AAA domain

Probab=94.53  E-value=0.08  Score=48.88  Aligned_cols=71  Identities=23%  Similarity=0.227  Sum_probs=41.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeec-cCcccceeecccHhhhc----ccCCCccEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTH-DQQKLTAVSAVELNKLI----PHTKDIDVI  226 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~-~g~~~~a~~~~~~~~~~----~~~~~~~~i  226 (353)
                      .-+|+|+.++||||-+...        .+++++....-+.    .+... ++...+..+..++.+.+    ....+|++|
T Consensus         5 ~~lIyG~~G~GKTt~a~~~--------~k~l~id~E~g~~----~~~~~~~~~~i~i~s~~~~~~~~~~l~~~~~~y~ti   72 (213)
T PF13479_consen    5 KILIYGPPGSGKTTLAASL--------PKPLFIDTENGSD----SLKFLDDGDVIPITSWEDFLEALDELEEDEADYDTI   72 (213)
T ss_pred             EEEEECCCCCCHHHHHHhC--------CCeEEEEeCCCcc----chhhhcCCCeeCcCCHHHHHHHHHHHHhccCCCCEE
Confidence            4589999999999876654        6677666533211    11111 22222222333333322    235799999


Q ss_pred             EEeccccc
Q psy8456         227 GIDEGQFV  234 (353)
Q Consensus       227 ~IDE~QF~  234 (353)
                      +||-+..+
T Consensus        73 VIDsis~~   80 (213)
T PF13479_consen   73 VIDSISWL   80 (213)
T ss_pred             EEECHHHH
Confidence            99988875

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=94.49  E-value=0.11  Score=47.27  Aligned_cols=97  Identities=12%  Similarity=0.090  Sum_probs=49.5

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChH-HHH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFP-DVV   88 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~-dIv   88 (353)
                      -||||+.+.+.+...    ..+...+|...-.-..  .  ..........+++...-......++.++|||+|-++ .-.
T Consensus         8 GsGKSt~i~~~~~~~----~~~~~~~~~~~~~~~~--~--~~~~~~~~~~v~s~~~~~~~~~~~~~liiDE~~~~~~g~l   79 (234)
T PF01443_consen    8 GSGKSTLIKKLLKDR----LVVTVISPTIELYTEW--L--PDPPSKSVRTVDSFLKALVKPKSYDTLIIDEAQLLPPGYL   79 (234)
T ss_pred             CCCHHHHHHHHHHhc----cccccccccceecccc--c--cccCCccccEEeEhhhcccccCcCCEEEEeccccCChHHH
Confidence            489999888887765    3334445533322110  0  011111111122221110011358999999999997 333


Q ss_pred             HHHHHHHhCC-CEEEEEecccccccCCchhHh
Q psy8456          89 SFAESMANAG-KIVVVAALDGTFQRTGFNDIL  119 (353)
Q Consensus        89 ~l~~~l~~~G-~~VivaGLd~DFr~~pF~~~~  119 (353)
                      .++  +...+ ..++++   +|..+-+|....
T Consensus        80 ~~l--~~~~~~~~~~l~---GDp~Q~~~~~~~  106 (234)
T PF01443_consen   80 LLL--LSLSPAKNVILF---GDPLQIPYISRN  106 (234)
T ss_pred             HHH--HhhccCcceEEE---ECchhccCCccc
Confidence            332  22222 467776   588777777543

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PRK13695 putative NTPase; Provisional

Probab=94.43  E-value=0.29  Score=43.25  Aligned_cols=30  Identities=27%  Similarity=0.255  Sum_probs=23.9

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      .+++|+.+|||||-|-..++.+...|.++.
T Consensus         3 i~ltG~~G~GKTTll~~i~~~l~~~G~~~~   32 (174)
T PRK13695          3 IGITGPPGVGKTTLVLKIAELLKEEGYKVG   32 (174)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEE
Confidence            468999999999998877777666677654

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=94.40  E-value=0.78  Score=42.47  Aligned_cols=82  Identities=20%  Similarity=0.174  Sum_probs=44.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCC-CceeeccCcccc---eee-----cccHhhhcccC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDT-EKVSTHDQQKLT---AVS-----AVELNKLIPHT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~-~~i~s~~g~~~~---a~~-----~~~~~~~~~~~  220 (353)
                      ++..+++||.+|||||-|-........++.-+.+  |+.-.+.+. +.+.++-+..-.   ..+     ...+..++...
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~~~la~~G~~v--pa~~~~l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~~il~~~  106 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFV--PAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYA  106 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHHcCCCc--chhhcCccChhheeEecCCccccchhhhHHHHHHHHHHHHHHhc
Confidence            4788999999999998654433333333322222  555444432 356666543211   111     11233333334


Q ss_pred             CCccEEEEecccc
Q psy8456         221 KDIDVIGIDEGQF  233 (353)
Q Consensus       221 ~~~~~i~IDE~QF  233 (353)
                      .+.+++++||.--
T Consensus       107 ~~~~lvllDE~~~  119 (204)
T cd03282         107 DGDSLVLIDELGR  119 (204)
T ss_pred             CCCcEEEeccccC
Confidence            6678999999754

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PRK10536 hypothetical protein; Provisional

Probab=94.38  E-value=0.18  Score=49.16  Aligned_cols=42  Identities=14%  Similarity=0.027  Sum_probs=30.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH-HhC-CEEEEEeeecCCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ-YAN-YRCMIVRYAKDDR  191 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~-~~~-~~~~~~k~~~D~R  191 (353)
                      ..+.+++||-|+|||+-.+......- ... .++++.+|...-.
T Consensus        74 ~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~~g  117 (262)
T PRK10536         74 KQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQAD  117 (262)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCCch
Confidence            35788999999999988777666433 222 5677888887543

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=94.36  E-value=0.24  Score=46.09  Aligned_cols=132  Identities=14%  Similarity=0.083  Sum_probs=82.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCCCceeecc--------Ccccceeecc------cHhh
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDTEKVSTHD--------QQKLTAVSAV------ELNK  215 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~~~i~s~~--------g~~~~a~~~~------~~~~  215 (353)
                      +.-.++++-+-||||..+-.+.|..-+|.+|+++.--+.. .+|+..+..+.        |....-....      ...+
T Consensus        23 g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~~~  102 (191)
T PRK05986         23 GLLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAARE  102 (191)
T ss_pred             CeEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHHHH
Confidence            4556777789999999999999999999999999888877 45543332221        2111100000      0111


Q ss_pred             hc----c--cCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHH
Q psy8456         216 LI----P--HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAES  289 (353)
Q Consensus       216 ~~----~--~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~  289 (353)
                      .+    .  ...++|+|+.||.=..-                 ..--++.                     .+|++++++
T Consensus       103 ~~~~a~~~l~~~~ydlvVLDEi~~Al-----------------~~gli~~---------------------eevi~~L~~  144 (191)
T PRK05986        103 GWEEAKRMLADESYDLVVLDELTYAL-----------------KYGYLDV---------------------EEVLEALNA  144 (191)
T ss_pred             HHHHHHHHHhCCCCCEEEEehhhHHH-----------------HCCCccH---------------------HHHHHHHHc
Confidence            11    1  14789999999987520                 0000111                     345555533


Q ss_pred             HHhCCCEEEEEeccccccCCCchhHHhhhhcccceEEeeee
Q psy8456         290 MANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  330 (353)
Q Consensus       290 ~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~  330 (353)
                       .-.+..||+-|=+         ....|+++||-|++++.+
T Consensus       145 -rp~~~evVlTGR~---------~p~~Lie~ADlVTEm~~v  175 (191)
T PRK05986        145 -RPGMQHVVITGRG---------APRELIEAADLVTEMRPV  175 (191)
T ss_pred             -CCCCCEEEEECCC---------CCHHHHHhCchheecccc
Confidence             3457889998853         346799999999998764

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=94.31  E-value=0.075  Score=54.99  Aligned_cols=82  Identities=17%  Similarity=0.164  Sum_probs=50.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-C-Cce---eeccCcccceee-ccc----Hhhhccc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-T-EKV---STHDQQKLTAVS-AVE----LNKLIPH  219 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~-~~i---~s~~g~~~~a~~-~~~----~~~~~~~  219 (353)
                      ....+++|+.||||||-+..-++.+...|++|.++..  |+.-. . +..   ..+.|....... ..+    +.+.+..
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~--D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al~~  172 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAA--DTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGLEK  172 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecC--CCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHH
Confidence            4567889999999999999999999888999998854  44311 0 111   111122111110 112    2233334


Q ss_pred             CCCccEEEEecccc
Q psy8456         220 TKDIDVIGIDEGQF  233 (353)
Q Consensus       220 ~~~~~~i~IDE~QF  233 (353)
                      ..+.|+|+||.+=.
T Consensus       173 ~~~~DvVIIDTAGr  186 (437)
T PRK00771        173 FKKADVIIVDTAGR  186 (437)
T ss_pred             hhcCCEEEEECCCc
Confidence            45679999999943

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=94.30  E-value=0.017  Score=53.76  Aligned_cols=27  Identities=26%  Similarity=0.293  Sum_probs=20.9

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQ  175 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~  175 (353)
                      ..+.-+++||.||||||-+-..++.+.
T Consensus        42 ~~~~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        42 REGFILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHhcC
Confidence            355778999999999988776665544

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=94.28  E-value=0.068  Score=46.79  Aligned_cols=39  Identities=23%  Similarity=0.153  Sum_probs=31.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD  190 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~  190 (353)
                      +.++.|+++|||||.+=+-...+...|.+|..+.....+
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~~~g~~v~~~~~~~~~   40 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEARGYEVVLTREPGGT   40 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCCCC
Confidence            357899999999998888888888889999877654433

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=94.26  E-value=0.1  Score=59.64  Aligned_cols=78  Identities=18%  Similarity=0.172  Sum_probs=50.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccC--cccceeecccH-hhhc---ccCCCc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQ--QKLTAVSAVEL-NKLI---PHTKDI  223 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g--~~~~a~~~~~~-~~~~---~~~~~~  223 (353)
                      +.+.++.|+-|+||||-|-....-++..|++|+..-|+-       +.....+  .-+++..+..+ ...-   .....-
T Consensus       397 ~r~~~v~G~AGTGKTt~l~~~~~~~e~~G~~V~g~ApTg-------kAA~~L~e~~Gi~a~TIas~ll~~~~~~~~l~~~  469 (1102)
T PRK13826        397 ARIAAVVGRAGAGKTTMMKAAREAWEAAGYRVVGGALAG-------KAAEGLEKEAGIQSRTLSSWELRWNQGRDQLDNK  469 (1102)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEcCcH-------HHHHHHHHhhCCCeeeHHHHHhhhccCccCCCCC
Confidence            568899999999999998888888889999999888842       2211110  01122222221 1110   113456


Q ss_pred             cEEEEeccccc
Q psy8456         224 DVIGIDEGQFV  234 (353)
Q Consensus       224 ~~i~IDE~QF~  234 (353)
                      ++++|||+-.+
T Consensus       470 ~vlVIDEAsMv  480 (1102)
T PRK13826        470 TVFVLDEAGMV  480 (1102)
T ss_pred             cEEEEECcccC
Confidence            89999999996

>PHA00012 I assembly protein

Probab=94.21  E-value=0.35  Score=48.87  Aligned_cols=31  Identities=23%  Similarity=0.193  Sum_probs=28.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      +++|.|-++||||-+.+..+..+..+|++|.
T Consensus         3 iylITGkPGSGKSl~aV~~I~~~L~~Gr~Va   33 (361)
T PHA00012          3 VYVVTGKLGAGKTLVAVSRIQDKLVKGCIVA   33 (361)
T ss_pred             eEEEecCCCCCchHHHHHHHHHHHHcCCEEE
Confidence            6789999999999999999999999998665

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=94.21  E-value=0.14  Score=50.19  Aligned_cols=62  Identities=21%  Similarity=0.149  Sum_probs=36.7

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEecc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      --+++||-|+|||+-+...++..   |.++.........                  ....+..++......++++|||+
T Consensus        53 ~~ll~GppG~GKT~la~~ia~~l---~~~~~~~~~~~~~------------------~~~~l~~~l~~l~~~~vl~IDEi  111 (328)
T PRK00080         53 HVLLYGPPGLGKTTLANIIANEM---GVNIRITSGPALE------------------KPGDLAAILTNLEEGDVLFIDEI  111 (328)
T ss_pred             cEEEECCCCccHHHHHHHHHHHh---CCCeEEEeccccc------------------ChHHHHHHHHhcccCCEEEEecH
Confidence            35889999999998766554443   3333222111000                  01233444444567889999999


Q ss_pred             ccc
Q psy8456         232 QFV  234 (353)
Q Consensus       232 QF~  234 (353)
                      |.+
T Consensus       112 ~~l  114 (328)
T PRK00080        112 HRL  114 (328)
T ss_pred             hhc
Confidence            986

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=94.15  E-value=0.067  Score=49.27  Aligned_cols=80  Identities=19%  Similarity=0.242  Sum_probs=47.7

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCC-Cceeec---cCcccceee-cccHhh----hcc--c
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDT-EKVSTH---DQQKLTAVS-AVELNK----LIP--H  219 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~-~~i~s~---~g~~~~a~~-~~~~~~----~~~--~  219 (353)
                      ..+++||-|+||||-+.+-+.+|...|++|.++.-  |+ |-+. +++.+.   .|..+.... ..+..+    .+.  .
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis~--D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~~~   80 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLKGKKVALISA--DTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEKFR   80 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE--STSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhccccceeecC--CCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHHHh
Confidence            46789999999999999999999988999999884  54 4331 112111   121111110 111222    222  2


Q ss_pred             CCCccEEEEecccc
Q psy8456         220 TKDIDVIGIDEGQF  233 (353)
Q Consensus       220 ~~~~~~i~IDE~QF  233 (353)
                      .+++|+|+||-+=.
T Consensus        81 ~~~~D~vlIDT~Gr   94 (196)
T PF00448_consen   81 KKGYDLVLIDTAGR   94 (196)
T ss_dssp             HTTSSEEEEEE-SS
T ss_pred             hcCCCEEEEecCCc
Confidence            46799999999865

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=94.14  E-value=0.49  Score=43.65  Aligned_cols=114  Identities=11%  Similarity=0.131  Sum_probs=75.4

Q ss_pred             CchHHHHHHHHHHHHHcCceEEEEeeccCCC-CCCCceeecc-CCceee------eecCChh--hh------cc------
Q psy8456          11 NPYIVHFCRRIRRYQYANYRCMIVRYAKDDR-YDTEKVATHD-QQKLTA------VSAVELN--KL------IP------   68 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agkkvlv~Kp~iDtR-y~~~~I~Sr~-G~~~~A------i~i~~l~--ei------~~------   68 (353)
                      -||||..+..+-|.-=+|++|+++.--...+ +|+..+..+. +..+..      ..-.++.  +.      ..      
T Consensus        32 KGKTTAAlGlalRAaG~G~rV~iiQFlKg~~~~GE~~~l~~~~~v~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~a~~~l  111 (178)
T PRK07414         32 RNFFTSVMAQALRIAGQGTPVLIVQFLKGGIQQGPDRPIQLGQNLDWVRCDLPRCLDTPHLDESEKKALQELWQYTQAVV  111 (178)
T ss_pred             CCchHHHHHHHHHHhcCCCEEEEEEEecCCCcchHHHHHHhCCCcEEEECCCCCeeeCCCcCHHHHHHHHHHHHHHHHHH
Confidence            4999999999999999999999998877764 4543222222 222211      1111211  11      00      


Q ss_pred             cCCCccEEEEccccCh-H----HHHHHHHHHHh--CCCEEEEEecccccccCCchhHhhhhccccceEeccc
Q psy8456          69 HTKDIDVIGIDEGQFF-P----DVVSFAESMAN--AGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTA  133 (353)
Q Consensus        69 ~~~~~dvV~IDEaQFF-~----dIv~l~~~l~~--~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~A  133 (353)
                      ....||.|+.||+-.- .    +..++.+.+.+  .+..||+-|=+         ..+.|+++||.|++++.
T Consensus       112 ~~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~---------~p~~Lie~AD~VTEm~~  174 (178)
T PRK07414        112 DEGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPE---------MPESLLAIADQITELRR  174 (178)
T ss_pred             hCCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCC---------CCHHHHHhCCeeeeeec
Confidence            1367999999998654 1    34455555554  47899999963         45789999999999863

>PRK08084 DNA replication initiation factor; Provisional

Probab=94.06  E-value=0.14  Score=48.00  Aligned_cols=37  Identities=8%  Similarity=0.298  Sum_probs=26.6

Q ss_pred             CCCccEEEEccccChH-------HHHHHHHHHHhCCC-EEEEEec
Q psy8456          70 TKDIDVIGIDEGQFFP-------DVVSFAESMANAGK-IVVVAAL  106 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~-~VivaGL  106 (353)
                      ...+|+++|||+|+++       .+.++.+.+.+.|+ .++++|=
T Consensus        95 ~~~~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~  139 (235)
T PRK08084         95 MEQLSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGD  139 (235)
T ss_pred             hhhCCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCC
Confidence            3457899999999994       24466666666775 7887764

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=94.02  E-value=0.069  Score=42.53  Aligned_cols=37  Identities=16%  Similarity=0.189  Sum_probs=30.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHH--hCCEEEEEeeecC
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQY--ANYRCMIVRYAKD  189 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~--~~~~~~~~k~~~D  189 (353)
                      -++.||+|||||+.++..+.+...  ..++++++-|..+
T Consensus         3 ~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~   41 (144)
T cd00046           3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRE   41 (144)
T ss_pred             EEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHH
Confidence            478999999999999999888765  5678888888653

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=94.00  E-value=0.08  Score=51.19  Aligned_cols=36  Identities=14%  Similarity=0.179  Sum_probs=31.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      .....++||.|+||||-+..-+..+...|++|+++.
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~  107 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAA  107 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEe
Confidence            346677899999999999999999999999999986

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=93.99  E-value=0.4  Score=41.93  Aligned_cols=124  Identities=10%  Similarity=-0.008  Sum_probs=74.4

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCC--------CCCCceee--ccCCc-e-eeee--cC--C-------hhh
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDR--------YDTEKVAT--HDQQK-L-TAVS--AV--E-------LNK   65 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtR--------y~~~~I~S--r~G~~-~-~Ai~--i~--~-------l~e   65 (353)
                      .-+|||+-.++-++.....|.+|+++...-+.+        .+-+ +.-  ..|.. . +..+  ..  .       ...
T Consensus         8 ~G~GKT~l~~~~~~~~~~~g~~v~~~s~e~~~~~~~~~~~~~g~~-~~~l~~~g~l~~~d~~~~~~s~~~~~~~~~~~~~   86 (187)
T cd01124           8 PGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAESLGWD-LERLEDEGLLAIVDADPDEIGPAESSLRLELIQR   86 (187)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCcEEEEECCCCHHHHHHHHHHcCCC-hHHHHhcCCeEEEecCccccchhhhhhhHHHHHH
Confidence            458999999999999989999999997643221        1111 000  01110 0 0000  00  0       011


Q ss_pred             hcc--cCCCccEEEEccccCh-H--------HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccce
Q psy8456          66 LIP--HTKDIDVIGIDEGQFF-P--------DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  134 (353)
Q Consensus        66 i~~--~~~~~dvV~IDEaQFF-~--------dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~Av  134 (353)
                      +..  ...++++|+|||.+-+ +        .+.++...+...|++|++..=.....+.+ .....+-.+||.|..|...
T Consensus        87 i~~~~~~~~~~~lviD~~~~~~~~~~~~~~~~i~~l~~~l~~~g~tvi~v~~~~~~~~~~-~~~~~~~~~aD~ii~l~~~  165 (187)
T cd01124          87 LKDAIEEFKAKRVVIDSVSGLLLMEQSTARLEIRRLLFALKRFGVTTLLTSEQSGLEGTG-FGGGDVEYLVDGVIRLRLD  165 (187)
T ss_pred             HHHHHHHhCCCEEEEeCcHHHhhcChHHHHHHHHHHHHHHHHCCCEEEEEeccccCCCcc-cCcCceeEeeeEEEEEEEE
Confidence            111  2347899999999965 2        34567777778899988887655443322 2335567889999888755

A related protein is found in archaea.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.95  E-value=0.1  Score=54.07  Aligned_cols=142  Identities=14%  Similarity=0.210  Sum_probs=82.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH-HHhCCEEEEEeeecCC-CCCC-Cceeec-cCcccceeecccHhhhccc--CCCc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY-QYANYRCMIVRYAKDD-RYDT-EKVSTH-DQQKLTAVSAVELNKLIPH--TKDI  223 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~-~~~~~~~~~~k~~~D~-R~~~-~~i~s~-~g~~~~a~~~~~~~~~~~~--~~~~  223 (353)
                      +.+.+++||.||||||-+.+-+..+ ...|++|.++.-  |+ |-+. +...+. ....++......+.++...  ..++
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~--Dt~R~aA~eQLk~yAe~lgvp~~~~~~~~~l~~~l~~~~~  300 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTT--DNYRIAAIEQLKRYADTMGMPFYPVKDIKKFKETLARDGS  300 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecc--cchhhhHHHHHHHHHHhcCCCeeehHHHHHHHHHHHhCCC
Confidence            3467899999999999999999877 567899998873  44 2221 111111 1111222333333333322  3689


Q ss_pred             cEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCC--CCC--------ccHHHHHHHHHhC
Q psy8456         224 DVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPP--PEF--------PDVVSFAESMANA  293 (353)
Q Consensus       224 ~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~f--------~~~~~~~~~~~~~  293 (353)
                      |+|+||=+=+.                     +-...|++.|.++.+..+-+.|  .++        .++.+++......
T Consensus       301 D~VLIDTaGr~---------------------~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f~~~  359 (432)
T PRK12724        301 ELILIDTAGYS---------------------HRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAYESL  359 (432)
T ss_pred             CEEEEeCCCCC---------------------ccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHhcCC
Confidence            99999976552                     2356788888777664322221  112        2555655555545


Q ss_pred             CCE-EEEEeccccccCCCchhHHhh
Q psy8456         294 GKI-VVVAALDGTFQRTGFNDILSL  317 (353)
Q Consensus       294 g~~-Vi~~gLd~df~~~~F~~~~~L  317 (353)
                      |.. +|+-=||.+   ..++.+..+
T Consensus       360 ~~~glIlTKLDEt---~~~G~il~i  381 (432)
T PRK12724        360 NYRRILLTKLDEA---DFLGSFLEL  381 (432)
T ss_pred             CCCEEEEEcccCC---CCccHHHHH
Confidence            543 677777776   334444444

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=93.88  E-value=0.16  Score=54.01  Aligned_cols=80  Identities=16%  Similarity=0.155  Sum_probs=43.7

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc--CCCccEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVI  226 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i  226 (353)
                      ..++-+++||+||||||-|-..++.....+++++-+-.-..-+.. + +.   +.......-.+..+.+..  -.++|+|
T Consensus       315 ~~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE~~~~-~-~~---q~~v~~~~g~~~~~~l~~~LR~dPDvI  389 (564)
T TIGR02538       315 PQGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEINLP-G-IN---QVNVNPKIGLTFAAALRSFLRQDPDII  389 (564)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCceecCC-C-ce---EEEeccccCCCHHHHHHHHhccCCCEE
Confidence            356889999999999999866665543334555543332222221 0 10   000000000122333322  3789999


Q ss_pred             EEecccc
Q psy8456         227 GIDEGQF  233 (353)
Q Consensus       227 ~IDE~QF  233 (353)
                      .|.|.-=
T Consensus       390 ~vGEiRd  396 (564)
T TIGR02538       390 MVGEIRD  396 (564)
T ss_pred             EeCCCCC
Confidence            9999875

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>PRK08181 transposase; Validated

Probab=93.81  E-value=0.061  Score=52.14  Aligned_cols=71  Identities=18%  Similarity=0.240  Sum_probs=44.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQ  232 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~Q  232 (353)
                      -+++||.|+|||.-+.-..+....+|++|+.++...        +.....   .+.....+.+++....++|+++|||.+
T Consensus       109 lll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~--------L~~~l~---~a~~~~~~~~~l~~l~~~dLLIIDDlg  177 (269)
T PRK08181        109 LLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTD--------LVQKLQ---VARRELQLESAIAKLDKFDLLILDDLA  177 (269)
T ss_pred             EEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHH--------HHHHHH---HHHhCCcHHHHHHHHhcCCEEEEeccc
Confidence            589999999999766666666677899887765311        111000   000112233444456789999999999


Q ss_pred             cc
Q psy8456         233 FV  234 (353)
Q Consensus       233 F~  234 (353)
                      ..
T Consensus       178 ~~  179 (269)
T PRK08181        178 YV  179 (269)
T ss_pred             cc
Confidence            84

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=93.79  E-value=0.17  Score=48.51  Aligned_cols=60  Identities=28%  Similarity=0.278  Sum_probs=31.2

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceee-cccHhhhcccCCCccEEEEecc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVS-AVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~-~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      -+.+||.|.||||- .+.+.+.  -|.....+.                |   +++. ..++..++...++-++++|||+
T Consensus        53 ~lf~GPPG~GKTTL-A~IIA~e--~~~~~~~~s----------------g---~~i~k~~dl~~il~~l~~~~ILFIDEI  110 (233)
T PF05496_consen   53 MLFYGPPGLGKTTL-ARIIANE--LGVNFKITS----------------G---PAIEKAGDLAAILTNLKEGDILFIDEI  110 (233)
T ss_dssp             EEEESSTTSSHHHH-HHHHHHH--CT--EEEEE----------------C---CC--SCHHHHHHHHT--TT-EEEECTC
T ss_pred             EEEECCCccchhHH-HHHHHhc--cCCCeEecc----------------c---hhhhhHHHHHHHHHhcCCCcEEEEech
Confidence            36799999999864 4444333  222222111                1   0111 2344455555567789999999


Q ss_pred             ccc
Q psy8456         232 QFV  234 (353)
Q Consensus       232 QF~  234 (353)
                      |.|
T Consensus       111 HRl  113 (233)
T PF05496_consen  111 HRL  113 (233)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            986

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK14494 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional

Probab=93.74  E-value=0.2  Score=47.69  Aligned_cols=36  Identities=22%  Similarity=0.268  Sum_probs=32.1

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      -.++|+-+|||||-+.+.+.++..+|++|.++|+..
T Consensus         4 i~ivG~~gsGKTtl~~~l~~~L~~~G~~V~viK~~~   39 (229)
T PRK14494          4 IGVIGFKDSGKTTLIEKILKNLKERGYRVATAKHTH   39 (229)
T ss_pred             EEEECCCCChHHHHHHHHHHHHHhCCCeEEEEEecc
Confidence            357899999999999999999999999999999744

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=93.66  E-value=0.16  Score=55.55  Aligned_cols=39  Identities=15%  Similarity=0.005  Sum_probs=32.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhC--CEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYAN--YRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~--~~~~~~k~~  187 (353)
                      .+...++.|+.|+||||-+-..+.-++..|  .++++.-|+
T Consensus       337 ~~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApT  377 (720)
T TIGR01448       337 QHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPT  377 (720)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCc
Confidence            356889999999999998777777777777  788888875

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=93.52  E-value=0.25  Score=49.76  Aligned_cols=37  Identities=24%  Similarity=0.209  Sum_probs=24.9

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHH---hCCEEEEEe
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQY---ANYRCMIVR  185 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~---~~~~~~~~k  185 (353)
                      .+++.+++||+||||||-|---++.+..   .+.+++.+.
T Consensus       133 ~~glilI~GpTGSGKTTtL~aLl~~i~~~~~~~~~Ivt~E  172 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLLAAIIRELAEAPDSHRKILTYE  172 (358)
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHHhhcCCCCcEEEEeC
Confidence            4678899999999999977444443322   345666543

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>PRK12377 putative replication protein; Provisional

Probab=93.51  E-value=0.089  Score=50.46  Aligned_cols=72  Identities=17%  Similarity=0.135  Sum_probs=44.9

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEecc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      --+++||.|+|||.-+...++.....|+.|+++... |       +.........  .-....+++....++|+++|||.
T Consensus       103 ~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~-~-------l~~~l~~~~~--~~~~~~~~l~~l~~~dLLiIDDl  172 (248)
T PRK12377        103 NFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVP-D-------VMSRLHESYD--NGQSGEKFLQELCKVDLLVLDEI  172 (248)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHH-H-------HHHHHHHHHh--ccchHHHHHHHhcCCCEEEEcCC
Confidence            347899999999987777777777788888765432 1       1111100000  00112344555688999999999


Q ss_pred             cc
Q psy8456         232 QF  233 (353)
Q Consensus       232 QF  233 (353)
                      .-
T Consensus       173 g~  174 (248)
T PRK12377        173 GI  174 (248)
T ss_pred             CC
Confidence            54

>PRK07952 DNA replication protein DnaC; Validated

Probab=93.49  E-value=0.057  Score=51.62  Aligned_cols=73  Identities=15%  Similarity=0.165  Sum_probs=46.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEecc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      .-+++|+.|+|||+-+...++.+...|++|+++...        .+.++...... .......+++....++|+++|||.
T Consensus       101 ~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~--------~l~~~l~~~~~-~~~~~~~~~l~~l~~~dlLvIDDi  171 (244)
T PRK07952        101 SFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVA--------DIMSAMKDTFS-NSETSEEQLLNDLSNVDLLVIDEI  171 (244)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHH--------HHHHHHHHHHh-hccccHHHHHHHhccCCEEEEeCC
Confidence            458999999999988777777777789999877431        11111100000 001122344445678999999999


Q ss_pred             cc
Q psy8456         232 QF  233 (353)
Q Consensus       232 QF  233 (353)
                      .-
T Consensus       172 g~  173 (244)
T PRK07952        172 GV  173 (244)
T ss_pred             CC
Confidence            87

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=93.46  E-value=0.1  Score=46.47  Aligned_cols=41  Identities=24%  Similarity=0.097  Sum_probs=32.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD  190 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~  190 (353)
                      +.+-++.|+++|||||..-+-...+...|++|.++....++
T Consensus         3 g~~IvieG~~GsGKsT~~~~L~~~l~~~g~~v~~~~~~~~~   43 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTTQANLLKKLLQENGYDVLFTREPGGT   43 (195)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCCCC
Confidence            45678999999999998888888888889999866543333

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>TIGR00595 priA primosomal protein N'

Probab=93.44  E-value=2.3  Score=44.79  Aligned_cols=162  Identities=16%  Similarity=0.045  Sum_probs=87.5

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccC----------CCCCCCceeeccCCcee-------------e-eecCChh
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKD----------DRYDTEKVATHDQQKLT-------------A-VSAVELN   64 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iD----------tRy~~~~I~Sr~G~~~~-------------A-i~i~~l~   64 (353)
                      .-||||+-.++.+.....+|++++++-|.+.          .+++....+-|.+..-.             + +.+....
T Consensus         6 TGsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrs   85 (505)
T TIGR00595         6 TGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRS   85 (505)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChH
Confidence            4599999999999888889999999999642          23443333445443211             1 1222222


Q ss_pred             hhcccCCCccEEEEccccChH---------HHHHHHHHHH-hCCCEEEEEecccccccCCchhHhhhhcccc-ceEeccc
Q psy8456          65 KLIPHTKDIDVIGIDEGQFFP---------DVVSFAESMA-NAGKIVVVAALDGTFQRTGFNDILSLIPLAE-CVEKLTA  133 (353)
Q Consensus        65 ei~~~~~~~dvV~IDEaQFF~---------dIv~l~~~l~-~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD-~I~kL~A  133 (353)
                      -+..-..+.+.|+|||.|=++         +..+++...+ ..|.+|+...=      .|-..+..+...-. ....|+.
T Consensus        86 alf~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~~~~~vil~SA------TPsles~~~~~~g~~~~~~l~~  159 (505)
T TIGR00595        86 ALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSA------TPSLESYHNAKQKAYRLLVLTR  159 (505)
T ss_pred             HHcCcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHhcCCCEEEEeC------CCCHHHHHHHhcCCeEEeechh
Confidence            222234678999999997764         2344444444 35777765432      12222222211000 0111110


Q ss_pred             eecccccccccccccccceeeeeccCC-----CCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         134 VCMSCFRDAAFTKRIGQEKEVILGPMF-----SGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       134 vC~~CG~~A~f~~Ri~geI~vi~G~M~-----sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      .         ++.+....++++  .|.     +.=|.+|++.+++...+|+.|++|-+.
T Consensus       160 r---------~~~~~~p~v~vi--d~~~~~~~~~ls~~l~~~i~~~l~~g~qvLvflnr  207 (505)
T TIGR00595       160 R---------VSGRKPPEVKLI--DMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNR  207 (505)
T ss_pred             h---------hcCCCCCeEEEE--ecccccccCCccHHHHHHHHHHHHcCCcEEEEEeC
Confidence            0         000000112221  121     234678999999999999999998764

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=93.27  E-value=0.16  Score=53.07  Aligned_cols=77  Identities=19%  Similarity=0.201  Sum_probs=43.5

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCc--eeeccCcccceeecccHhhhccc--CCCc
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEK--VSTHDQQKLTAVSAVELNKLIPH--TKDI  223 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~--i~s~~g~~~~a~~~~~~~~~~~~--~~~~  223 (353)
                      ..++.+++||+||||||-|-..++.....+++++.+--...-+.. ...  +..+.|        .+..+.+..  -.++
T Consensus       241 ~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE~~~~~~~q~~v~~~~g--------~~f~~~lr~~LR~dP  312 (486)
T TIGR02533       241 PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEYQIEGIGQIQVNPKIG--------LTFAAGLRAILRQDP  312 (486)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCeeeecCCCceEEEccccC--------ccHHHHHHHHHhcCC
Confidence            346789999999999999866666554445666644322211111 000  000111        122222222  3789


Q ss_pred             cEEEEecccc
Q psy8456         224 DVIGIDEGQF  233 (353)
Q Consensus       224 ~~i~IDE~QF  233 (353)
                      |+|.|.|..=
T Consensus       313 DvI~vGEiRd  322 (486)
T TIGR02533       313 DIIMVGEIRD  322 (486)
T ss_pred             CEEEEeCCCC
Confidence            9999999875

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.22  E-value=0.41  Score=49.78  Aligned_cols=36  Identities=17%  Similarity=0.164  Sum_probs=32.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      ..++.||.++||||-+++-+++...+|.+|+++.-.
T Consensus       265 ~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s~e  300 (484)
T TIGR02655       265 IILATGATGTGKTLLVSKFLENACANKERAILFAYE  300 (484)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEee
Confidence            678999999999999999999998899999988754

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK08727 hypothetical protein; Validated

Probab=93.20  E-value=0.27  Score=46.09  Aligned_cols=39  Identities=15%  Similarity=0.230  Sum_probs=28.8

Q ss_pred             ccCCCccEEEEccccChH----H---HHHHHHHHHhCCCEEEEEec
Q psy8456          68 PHTKDIDVIGIDEGQFFP----D---VVSFAESMANAGKIVVVAAL  106 (353)
Q Consensus        68 ~~~~~~dvV~IDEaQFF~----d---Iv~l~~~l~~~G~~VivaGL  106 (353)
                      ....++|+|+|||+|++.    +   +.++.+...+.|+.|++.+=
T Consensus        89 ~~l~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~  134 (233)
T PRK08727         89 EALEGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTAR  134 (233)
T ss_pred             HHHhcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECC
Confidence            345678999999999984    1   44556666677888888775

>PRK09183 transposase/IS protein; Provisional

Probab=93.18  E-value=0.1  Score=50.03  Aligned_cols=114  Identities=19%  Similarity=0.071  Sum_probs=62.6

Q ss_pred             HHHHHhCCCEEEEEecc-cccccCCchhHhhhhccccceEeccceecccccccccccccccceeeeeccCCCCchhHHHH
Q psy8456          91 AESMANAGKIVVVAALD-GTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus        91 ~~~l~~~G~~VivaGLd-~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~geI~vi~G~M~sGKt~~Li~  169 (353)
                      ...+...+.|+. ..|+ -||.-.|...-..+..+++        |.       | .. .+..-+++||.|+|||+-+.-
T Consensus        60 ~~~~k~a~~p~~-~~l~~fd~~~~~~~~~~~i~~L~~--------~~-------~-i~-~~~~v~l~Gp~GtGKThLa~a  121 (259)
T PRK09183         60 AMYTRMAAFPAV-KTFEEYDFTFATGAPQKQLQSLRS--------LS-------F-IE-RNENIVLLGPSGVGKTHLAIA  121 (259)
T ss_pred             HHHHHhCCCCCC-CcHhhcccccCCCCCHHHHHHHhc--------CC-------c-hh-cCCeEEEEeCCCCCHHHHHHH
Confidence            334445677765 4442 4555555555444444432        21       1 10 134567999999999987777


Q ss_pred             HHHHHHHhCCEEEEEeee-cCCCCCCCceeeccCcccceeecccHhhhccc-CCCccEEEEeccccc
Q psy8456         170 RIRRYQYANYRCMIVRYA-KDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH-TKDIDVIGIDEGQFV  234 (353)
Q Consensus       170 ~~~~~~~~~~~~~~~k~~-~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~-~~~~~~i~IDE~QF~  234 (353)
                      ..+.+..+|++|.++... .-...    ..++..        ..+..++.. ...+|+++|||.++.
T Consensus       122 l~~~a~~~G~~v~~~~~~~l~~~l----~~a~~~--------~~~~~~~~~~~~~~dlLiiDdlg~~  176 (259)
T PRK09183        122 LGYEAVRAGIKVRFTTAADLLLQL----STAQRQ--------GRYKTTLQRGVMAPRLLIIDEIGYL  176 (259)
T ss_pred             HHHHHHHcCCeEEEEeHHHHHHHH----HHHHHC--------CcHHHHHHHHhcCCCEEEEcccccC
Confidence            666667789999876521 10000    000100        112222222 356799999999984

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=93.16  E-value=0.5  Score=43.52  Aligned_cols=95  Identities=17%  Similarity=0.137  Sum_probs=62.6

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEE-EEeeccCCCCCCC----cee----------eccCCcee-----eeecCChhhhc-
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCM-IVRYAKDDRYDTE----KVA----------THDQQKLT-----AVSAVELNKLI-   67 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvl-v~Kp~iDtRy~~~----~I~----------Sr~G~~~~-----Ai~i~~l~ei~-   67 (353)
                      .=+||||-+++.+..++..|.+|- ++.|.+  |.+..    .|+          ++.|.+.+     .+.++.++++. 
T Consensus        14 PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EV--R~gGkR~GF~Ivdl~tg~~~~la~~~~~~~rvGkY~V~v~~le~i~~   91 (179)
T COG1618          14 PGVGKTTLVLKIAEKLREKGYKVGGFITPEV--REGGKRIGFKIVDLATGEEGILARVGFSRPRVGKYGVNVEGLEEIAI   91 (179)
T ss_pred             CCccHHHHHHHHHHHHHhcCceeeeEEeeee--ecCCeEeeeEEEEccCCceEEEEEcCCCCcccceEEeeHHHHHHHhH
Confidence            348999999999999999998876 455654  43211    122          22222221     12345566554 


Q ss_pred             ----ccCCCccEEEEccccCh---H-HHHHHHHHHHhCCCEEEEEec
Q psy8456          68 ----PHTKDIDVIGIDEGQFF---P-DVVSFAESMANAGKIVVVAAL  106 (353)
Q Consensus        68 ----~~~~~~dvV~IDEaQFF---~-dIv~l~~~l~~~G~~VivaGL  106 (353)
                          ......|+|+|||+==.   + .+.+.++.+.+.++|+ ++.|
T Consensus        92 ~al~rA~~~aDvIIIDEIGpMElks~~f~~~ve~vl~~~kpl-iatl  137 (179)
T COG1618          92 PALRRALEEADVIIIDEIGPMELKSKKFREAVEEVLKSGKPL-IATL  137 (179)
T ss_pred             HHHHHHhhcCCEEEEecccchhhccHHHHHHHHHHhcCCCcE-EEEE
Confidence                12356899999999654   3 7888899999999994 4555

>PHA00547 hypothetical protein

Probab=93.12  E-value=0.37  Score=47.55  Aligned_cols=30  Identities=23%  Similarity=0.239  Sum_probs=24.5

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhC
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYAN  178 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~  178 (353)
                      .+-+.++.||||||||+-+---++.|+..+
T Consensus        74 ~spis~i~G~LGsGKTlLMT~LA~~~K~K~  103 (337)
T PHA00547         74 DNPLSVIIGKLGTGKTLLLTYLSQTMKLLT  103 (337)
T ss_pred             cCCceEEeccCCCchhHHHHHHHHHHHhhh
Confidence            356899999999999988777777777655

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=93.09  E-value=0.081  Score=54.34  Aligned_cols=132  Identities=19%  Similarity=0.219  Sum_probs=75.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH--HhCCEEEEEeeecCC-CCCC-Cceeecc-CcccceeecccHhh---hcccCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ--YANYRCMIVRYAKDD-RYDT-EKVSTHD-QQKLTAVSAVELNK---LIPHTK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~--~~~~~~~~~k~~~D~-R~~~-~~i~s~~-g~~~~a~~~~~~~~---~~~~~~  221 (353)
                      +++-.++||-|.||||-|..-+.+|.  ...++|-+++-  |+ |-|. +.+.+-. -..++-..+....+   -+....
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITt--DtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l~  280 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITT--DTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEALR  280 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEe--ccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHHHhh
Confidence            56778999999999999999999997  56677877764  33 3221 2222211 01122222333333   344568


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhcc-------CCCCCCCCccHHHHHHHHHhCC
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL-------NVPPPPEFPDVVSFAESMANAG  294 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-------~~~~~~~f~~~~~~~~~~~~~g  294 (353)
                      ++|+|+||=+=.                  .|.   ...++++|....+..       -++----..|+-+..+..+.-+
T Consensus       281 ~~d~ILVDTaGr------------------s~~---D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~~f~~~~  339 (407)
T COG1419         281 DCDVILVDTAGR------------------SQY---DKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQFSLFP  339 (407)
T ss_pred             cCCEEEEeCCCC------------------Ccc---CHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHHHhccCC
Confidence            899999997754                  122   344444444444321       1111111246777777777655


Q ss_pred             CE-EEEEeccc
Q psy8456         295 KI-VVVAALDG  304 (353)
Q Consensus       295 ~~-Vi~~gLd~  304 (353)
                      +. +|+-=||-
T Consensus       340 i~~~I~TKlDE  350 (407)
T COG1419         340 IDGLIFTKLDE  350 (407)
T ss_pred             cceeEEEcccc
Confidence            54 55556663

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=93.06  E-value=0.24  Score=37.60  Aligned_cols=32  Identities=22%  Similarity=0.170  Sum_probs=29.0

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      ++.|..++||||-....+..+...|++++++.
T Consensus         3 ~~~g~~G~Gktt~~~~l~~~l~~~g~~v~~~~   34 (99)
T cd01983           3 VVTGKGGVGKTTLAANLAAALAKRGKRVLLID   34 (99)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCeEEEEC
Confidence            56788899999999999999998999999988

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK05580 primosome assembly protein PriA; Validated

Probab=93.05  E-value=0.21  Score=54.17  Aligned_cols=83  Identities=17%  Similarity=0.099  Sum_probs=54.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC----------CCCCCceeeccCcccc--------------
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD----------RYDTEKVSTHDQQKLT--------------  206 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~----------R~~~~~i~s~~g~~~~--------------  206 (353)
                      ...++.||.|||||.-.+..+.....+|++++++-|...-          +++.....-|.|....              
T Consensus       163 ~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~  242 (679)
T PRK05580        163 SPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEA  242 (679)
T ss_pred             CcEEEECCCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCC
Confidence            4568899999999999998888888889999999997543          2333233344432210              


Q ss_pred             eeecccHhhhcccCCCccEEEEecccc
Q psy8456         207 AVSAVELNKLIPHTKDIDVIGIDEGQF  233 (353)
Q Consensus       207 a~~~~~~~~~~~~~~~~~~i~IDE~QF  233 (353)
                      -+.+..-..+....++...|+|||+|-
T Consensus       243 ~IVVgTrsal~~p~~~l~liVvDEeh~  269 (679)
T PRK05580        243 KVVIGARSALFLPFKNLGLIIVDEEHD  269 (679)
T ss_pred             CEEEeccHHhcccccCCCEEEEECCCc
Confidence            111221222222357889999999995

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=92.97  E-value=0.24  Score=54.92  Aligned_cols=112  Identities=18%  Similarity=0.193  Sum_probs=67.2

Q ss_pred             CCCchHHHHHHHHHHH-HHcCceEEEEeec------cCCCCCCC---ceee-c--cCCc-------eeeeecCChhhhcc
Q psy8456           9 RINPYIVHFCRRIRRY-QYANYRCMIVRYA------KDDRYDTE---KVAT-H--DQQK-------LTAVSAVELNKLIP   68 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry-~~agkkvlv~Kp~------iDtRy~~~---~I~S-r--~G~~-------~~Ai~i~~l~ei~~   68 (353)
                      --+||||.|++-++.+ ...+.+|+++.+.      +-.|....   ..++ .  .+..       .=++-++++.-+..
T Consensus        58 MGTGKTtaLi~wLk~~l~~~~~~VLvVShRrSL~~sL~~rf~~~~l~gFv~Y~d~~~~~i~~~~~~rLivqIdSL~R~~~  137 (824)
T PF02399_consen   58 MGTGKTTALIRWLKDALKNPDKSVLVVSHRRSLTKSLAERFKKAGLSGFVNYLDSDDYIIDGRPYDRLIVQIDSLHRLDG  137 (824)
T ss_pred             CCCCcHHHHHHHHHHhccCCCCeEEEEEhHHHHHHHHHHHHhhcCCCcceeeeccccccccccccCeEEEEehhhhhccc
Confidence            3589999999988776 4778999999872      22232111   0111 1  1111       11244667655542


Q ss_pred             -cCCCccEEEEccc-----cChH-------HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhh
Q psy8456          69 -HTKDIDVIGIDEG-----QFFP-------DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLI  122 (353)
Q Consensus        69 -~~~~~dvV~IDEa-----QFF~-------dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll  122 (353)
                       ..++||+|+|||+     |||+       ++.++...+...-+.||++  |.|-....++-+..+-
T Consensus       138 ~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~--DA~ln~~tvdFl~~~R  202 (824)
T PF02399_consen  138 SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVM--DADLNDQTVDFLASCR  202 (824)
T ss_pred             ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEe--cCCCCHHHHHHHHHhC
Confidence             3456999999997     8884       3445455555667777774  5555555565555543

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>KOG0922|consensus

Probab=92.94  E-value=0.18  Score=54.58  Aligned_cols=84  Identities=19%  Similarity=0.232  Sum_probs=49.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCE-EEEEeee--------------cCCCCCCCc---eeeccCc-ccceee-
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYR-CMIVRYA--------------KDDRYDTEK---VSTHDQQ-KLTAVS-  209 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~-~~~~k~~--------------~D~R~~~~~---i~s~~g~-~~~a~~-  209 (353)
                      ++.-+++|..||||||++=+-+...-++.+. +-+..|.              ...++|++.   |---|-. +-+-+. 
T Consensus        66 nqvlIviGeTGsGKSTQipQyL~eaG~~~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~IRFed~ts~~Triky  145 (674)
T KOG0922|consen   66 NQVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYTIRFEDSTSKDTRIKY  145 (674)
T ss_pred             CCEEEEEcCCCCCccccHhHHHHhcccccCCcEEeecCchHHHHHHHHHHHHHhCCCcCceeeeEEEecccCCCceeEEE
Confidence            4577899999999999999999887555432 4455553              122233211   0000000 011111 


Q ss_pred             cc---cHhhhc--ccCCCccEEEEecccc
Q psy8456         210 AV---ELNKLI--PHTKDIDVIGIDEGQF  233 (353)
Q Consensus       210 ~~---~~~~~~--~~~~~~~~i~IDE~QF  233 (353)
                      .+   -|.+++  +...+|+||+|||||-
T Consensus       146 mTDG~LLRE~l~Dp~LskYsvIIlDEAHE  174 (674)
T KOG0922|consen  146 MTDGMLLREILKDPLLSKYSVIILDEAHE  174 (674)
T ss_pred             ecchHHHHHHhcCCccccccEEEEechhh
Confidence            11   266665  4578999999999996

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=92.91  E-value=0.17  Score=53.30  Aligned_cols=79  Identities=22%  Similarity=0.221  Sum_probs=48.6

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCC-C--ceeeccCcccceeecccHhhhcccCCCccE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDT-E--KVSTHDQQKLTAVSAVELNKLIPHTKDIDV  225 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~-~--~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~  225 (353)
                      ..++.+++||.||||||-|-..+.......++++-+---+.-.... .  .|....|..+    +.-+..++  -.|+|+
T Consensus       257 p~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPVE~~~~gI~Q~qVN~k~gltf----a~~LRa~L--RqDPDv  330 (500)
T COG2804         257 PQGLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPVEYQLPGINQVQVNPKIGLTF----ARALRAIL--RQDPDV  330 (500)
T ss_pred             CCeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCeeeecCCcceeecccccCCCH----HHHHHHHh--ccCCCe
Confidence            5678999999999999999999999888888766443222111110 0  1111112111    11122222  368999


Q ss_pred             EEEecccc
Q psy8456         226 IGIDEGQF  233 (353)
Q Consensus       226 i~IDE~QF  233 (353)
                      |.|.|..=
T Consensus       331 ImVGEIRD  338 (500)
T COG2804         331 IMVGEIRD  338 (500)
T ss_pred             EEEeccCC
Confidence            99999986

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=92.87  E-value=0.3  Score=44.63  Aligned_cols=132  Identities=20%  Similarity=0.199  Sum_probs=68.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeecc--------Ccccceeecc------cHh
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHD--------QQKLTAVSAV------ELN  214 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~--------g~~~~a~~~~------~~~  214 (353)
                      |-+++++|+ +=||||..+-.+-|..-.|++|+++.--+..++. +-.+..+.        |..+.-..-.      ...
T Consensus         4 G~i~vytG~-GKGKTTAAlGlalRA~G~G~rV~ivQFlKg~~~~GE~~~l~~l~~~~~~~~g~~f~~~~~~~~~~~~~~~   82 (172)
T PF02572_consen    4 GLIQVYTGD-GKGKTTAALGLALRAAGHGMRVLIVQFLKGGRYSGELKALKKLPNVEIERFGKGFVWRMNEEEEDRAAAR   82 (172)
T ss_dssp             --EEEEESS-SS-HHHHHHHHHHHHHCTT--EEEEESS--SS--HHHHHHGGGT--EEEE--TT----GGGHHHHHHHHH
T ss_pred             cEEEEEeCC-CCCchHHHHHHHHHHHhCCCEEEEEEEecCCCCcCHHHHHHhCCeEEEEEcCCcccccCCCcHHHHHHHH
Confidence            457888886 6699999999999999999999999988885533 22221111        1111000000      011


Q ss_pred             hhc----c--cCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHH
Q psy8456         215 KLI----P--HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAE  288 (353)
Q Consensus       215 ~~~----~--~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~  288 (353)
                      +.+    .  ....+|+|++||+=-.-                 ..--++.                     .+|+++++
T Consensus        83 ~~~~~a~~~i~~~~~dlvILDEi~~a~-----------------~~gll~~---------------------~~v~~~l~  124 (172)
T PF02572_consen   83 EGLEEAKEAISSGEYDLVILDEINYAV-----------------DYGLLSE---------------------EEVLDLLE  124 (172)
T ss_dssp             HHHHHHHHHTT-TT-SEEEEETHHHHH-----------------HTTSS-H---------------------HHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCEEEEcchHHHh-----------------HCCCccH---------------------HHHHHHHH
Confidence            111    1  14789999999986410                 0000122                     23444443


Q ss_pred             HHHhCCCEEEEEeccccccCCCchhHHhhhhcccceEEeeee
Q psy8456         289 SMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  330 (353)
Q Consensus       289 ~~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~  330 (353)
                      + ...+..||+-|=+         ....|+++||.|++++.+
T Consensus       125 ~-rp~~~evVlTGR~---------~~~~l~e~ADlVTem~~v  156 (172)
T PF02572_consen  125 N-RPESLEVVLTGRN---------APEELIEAADLVTEMREV  156 (172)
T ss_dssp             T-S-TT-EEEEE-SS-----------HHHHHH-SEEEEEEEC
T ss_pred             c-CCCCeEEEEECCC---------CCHHHHHhCCeeeeecee
Confidence            1 2467889998853         257899999999999765

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=92.86  E-value=0.16  Score=44.43  Aligned_cols=36  Identities=28%  Similarity=0.465  Sum_probs=29.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      -.++|+-+|||||-+-.-++.+..+|++|.++|..-
T Consensus         3 v~VvG~~~sGKTTl~~~Li~~l~~~g~~v~~ik~~~   38 (140)
T PF03205_consen    3 VQVVGPKNSGKTTLIRKLINELKRRGYRVAVIKHTD   38 (140)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE-S
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhHcCCceEEEEEcc
Confidence            368999999999999888999999999999888754

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=92.84  E-value=0.028  Score=46.31  Aligned_cols=100  Identities=14%  Similarity=0.186  Sum_probs=54.4

Q ss_pred             CCCchHHHHHHHHHHHHHc-----CceEEEEeeccCCCCCCC----ceeeccCCceee-eecCChhhhc-c--cCCCccE
Q psy8456           9 RINPYIVHFCRRIRRYQYA-----NYRCMIVRYAKDDRYDTE----KVATHDQQKLTA-VSAVELNKLI-P--HTKDIDV   75 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~a-----gkkvlv~Kp~iDtRy~~~----~I~Sr~G~~~~A-i~i~~l~ei~-~--~~~~~dv   75 (353)
                      .-+|||+-+-+-++.+...     +.+++.+.-.-..  +..    .+..-.|..... .....+.+.. .  ......+
T Consensus        13 ~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~~~~~~   90 (131)
T PF13401_consen   13 PGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSR--TPRDFAQEILEALGLPLKSRQTSDELRSLLIDALDRRRVVL   90 (131)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHS--SHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHHCTEEE
T ss_pred             CCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCC--CHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHhcCCeE
Confidence            3489999988888887654     5666655543322  111    122222222211 1111111111 1  1123469


Q ss_pred             EEEccccCh-H-HHHHHHHHH-HhCCCEEEEEecccccc
Q psy8456          76 IGIDEGQFF-P-DVVSFAESM-ANAGKIVVVAALDGTFQ  111 (353)
Q Consensus        76 V~IDEaQFF-~-dIv~l~~~l-~~~G~~VivaGLd~DFr  111 (353)
                      |+|||+|.+ + +..+....+ ...+++|+++|.. .++
T Consensus        91 lviDe~~~l~~~~~l~~l~~l~~~~~~~vvl~G~~-~l~  128 (131)
T PF13401_consen   91 LVIDEADHLFSDEFLEFLRSLLNESNIKVVLVGTP-ELE  128 (131)
T ss_dssp             EEEETTHHHHTHHHHHHHHHHTCSCBEEEEEEESS-TTT
T ss_pred             EEEeChHhcCCHHHHHHHHHHHhCCCCeEEEEECh-hhH
Confidence            999999999 7 444444444 4679999999986 443

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=92.79  E-value=0.2  Score=49.93  Aligned_cols=78  Identities=24%  Similarity=0.113  Sum_probs=44.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCC--CCCce--ee-ccCcccceeecccHhhhccc--CCCcc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRY--DTEKV--ST-HDQQKLTAVSAVELNKLIPH--TKDID  224 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~--~~~~i--~s-~~g~~~~a~~~~~~~~~~~~--~~~~~  224 (353)
                      .-+|.|+++|||||-| +.+-++-..+.+++.+--...-..  ..+.+  .+ ..+...   ......+++..  -.++|
T Consensus       162 nili~G~tgSGKTTll-~aL~~~ip~~~ri~tiEd~~El~l~~~~n~~~~~~~~~~~~~---~~~~~~~ll~~~LR~~PD  237 (332)
T PRK13900        162 NIIISGGTSTGKTTFT-NAALREIPAIERLITVEDAREIVLSNHPNRVHLLASKGGQGR---AKVTTQDLIEACLRLRPD  237 (332)
T ss_pred             cEEEECCCCCCHHHHH-HHHHhhCCCCCeEEEecCCCccccccCCCEEEEEecCCCCCc---CcCcHHHHHHHHhccCCC
Confidence            4589999999999877 556666666777776532221111  11211  11 111111   11234444432  36799


Q ss_pred             EEEEecccc
Q psy8456         225 VIGIDEGQF  233 (353)
Q Consensus       225 ~i~IDE~QF  233 (353)
                      +|+|.|..=
T Consensus       238 ~IivGEiR~  246 (332)
T PRK13900        238 RIIVGELRG  246 (332)
T ss_pred             eEEEEecCC
Confidence            999999874

>PRK06835 DNA replication protein DnaC; Validated

Probab=92.76  E-value=0.35  Score=48.22  Aligned_cols=73  Identities=14%  Similarity=0.055  Sum_probs=43.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCc-ccceeecccHhhhcccCCCccEEEEe
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQ-KLTAVSAVELNKLIPHTKDIDVIGID  229 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~-~~~a~~~~~~~~~~~~~~~~~~i~ID  229 (353)
                      .--+++||.|+|||.-+.-.++.+...|++|+.+....        +...... ....  ..+....+....++|+++||
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~--------l~~~l~~~~~~~--~~~~~~~~~~l~~~DLLIID  253 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADE--------LIEILREIRFNN--DKELEEVYDLLINCDLLIID  253 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHH--------HHHHHHHHHhcc--chhHHHHHHHhccCCEEEEe
Confidence            34589999999999866666666777888887665421        0000000 0000  00111113345688999999


Q ss_pred             cccc
Q psy8456         230 EGQF  233 (353)
Q Consensus       230 E~QF  233 (353)
                      +.+.
T Consensus       254 DlG~  257 (329)
T PRK06835        254 DLGT  257 (329)
T ss_pred             ccCC
Confidence            9987

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=92.60  E-value=0.2  Score=48.95  Aligned_cols=83  Identities=18%  Similarity=0.073  Sum_probs=41.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCC-CceeeccCcccceeecccHhhhccc--CCCccEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDT-EKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVI  226 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~-~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i  226 (353)
                      +...+|+||++|||||-|-- +-.+.....+++.+.....-.... +.+.-..+............+++..  ..++|+|
T Consensus       144 ~~~ili~G~tGsGKTTll~a-l~~~~~~~~~iv~ied~~El~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~Lr~~pd~i  222 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKS-LVDEIPKDERIITIEDTREIFLPHPNYVHLFYSKGGQGLAKVTPKDLLQSCLRMRPDRI  222 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHH-HHccCCccccEEEEcCccccCCCCCCEEEEEecCCCCCcCccCHHHHHHHHhcCCCCeE
Confidence            45678999999999997643 333333444555553211111111 1111000000011111234444432  4689999


Q ss_pred             EEecccc
Q psy8456         227 GIDEGQF  233 (353)
Q Consensus       227 ~IDE~QF  233 (353)
                      ++||..=
T Consensus       223 i~gE~r~  229 (308)
T TIGR02788       223 ILGELRG  229 (308)
T ss_pred             EEeccCC
Confidence            9999874

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=92.57  E-value=0.091  Score=54.35  Aligned_cols=87  Identities=14%  Similarity=0.177  Sum_probs=51.2

Q ss_pred             CCCchHHHHHHHHHHHHH---cCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChH
Q psy8456           9 RINPYIVHFCRRIRRYQY---ANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFP   85 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~---agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~   85 (353)
                      .-.||| .|++.+-++-.   .+.+|+.+.+. |  .. ..+....+..     ...+.++.....++|+++|||+||+.
T Consensus       150 ~G~GKT-HLl~Ai~~~l~~~~~~~~v~yv~~~-~--f~-~~~~~~l~~~-----~~~~~~~~~~~~~~dvLiIDDiq~l~  219 (450)
T PRK14087        150 SGMGKT-HLLKAAKNYIESNFSDLKVSYMSGD-E--FA-RKAVDILQKT-----HKEIEQFKNEICQNDVLIIDDVQFLS  219 (450)
T ss_pred             CCCcHH-HHHHHHHHHHHHhCCCCeEEEEEHH-H--HH-HHHHHHHHHh-----hhHHHHHHHHhccCCEEEEecccccc
Confidence            347999 66677766432   45777655542 1  10 1122111100     01233343445679999999999994


Q ss_pred             -------HHHHHHHHHHhCCCEEEEEe
Q psy8456          86 -------DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        86 -------dIv~l~~~l~~~G~~VivaG  105 (353)
                             .+..+.+.+.+.|+.+++.+
T Consensus       220 ~k~~~~e~lf~l~N~~~~~~k~iIlts  246 (450)
T PRK14087        220 YKEKTNEIFFTIFNNFIENDKQLFFSS  246 (450)
T ss_pred             CCHHHHHHHHHHHHHHHHcCCcEEEEC
Confidence                   25666777788899887774

>cd03112 CobW_like The function of this protein family is unkown

Probab=92.40  E-value=0.26  Score=43.45  Aligned_cols=35  Identities=20%  Similarity=0.172  Sum_probs=25.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ..+++|+++|||||-+-+.+...  .+.++.++....
T Consensus         2 ~~~l~G~~GsGKTtl~~~l~~~~--~~~~~~~i~~~~   36 (158)
T cd03112           2 VTVLTGFLGAGKTTLLNHILTEQ--HGRKIAVIENEF   36 (158)
T ss_pred             EEEEEECCCCCHHHHHHHHHhcc--cCCcEEEEecCC
Confidence            45789999999998776665542  477777766554

The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=92.37  E-value=0.067  Score=42.59  Aligned_cols=32  Identities=3%  Similarity=-0.095  Sum_probs=25.6

Q ss_pred             CCCCchHHHHHHHHHHHHH--cCceEEEEeeccC
Q psy8456           8 DRINPYIVHFCRRIRRYQY--ANYRCMIVRYAKD   39 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry~~--agkkvlv~Kp~iD   39 (353)
                      ..-+|||+.++..+.+...  ..++++++-|..+
T Consensus         8 ~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~   41 (144)
T cd00046           8 PTGSGKTLAALLPILELLDSLKGGQVLVLAPTRE   41 (144)
T ss_pred             CCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHH
Confidence            3458999999999988776  5689999999643

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=92.36  E-value=0.11  Score=46.18  Aligned_cols=37  Identities=27%  Similarity=0.312  Sum_probs=27.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH--------HHhCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY--------QYANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~--------~~~~~~~~~~k~~~  188 (353)
                      +.+|.||.|+|||+-|...+...        ...+.+++++.|+.
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN   63 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSN   63 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSH
T ss_pred             CEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCc
Confidence            68999999999999999888887        45577777777643

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.35  E-value=0.36  Score=49.90  Aligned_cols=118  Identities=12%  Similarity=0.045  Sum_probs=71.7

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCce---eeccCCceeeee---cCChhhhccc--CCCccEEEEcc
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKV---ATHDQQKLTAVS---AVELNKLIPH--TKDIDVIGIDE   80 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I---~Sr~G~~~~Ai~---i~~l~ei~~~--~~~~dvV~IDE   80 (353)
                      .=+|||+-+++.+.++..+|.+|+.+.-.-    +...+   ..|.|...+.+.   ..++.++...  ..++++|+||+
T Consensus        89 pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ee----s~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i~~~~~~lVVIDS  164 (446)
T PRK11823         89 PGIGKSTLLLQVAARLAAAGGKVLYVSGEE----SASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEEKPDLVVIDS  164 (446)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEEEEccc----cHHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHHHhhCCCEEEEec
Confidence            347999999999999887899999887532    11223   223443333222   2344444422  34789999999


Q ss_pred             ccChH------------HHH----HHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEecc
Q psy8456          81 GQFFP------------DVV----SFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT  132 (353)
Q Consensus        81 aQFF~------------dIv----~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~  132 (353)
                      .|++-            ++.    +|.+.+.+.|++|++.|--+. .+. +.+...|--++|.|..+.
T Consensus       165 Iq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~itvilv~hvtk-~~~-~ag~~~lehlvD~Vi~le  230 (446)
T PRK11823        165 IQTMYSPELESAPGSVSQVRECAAELMRLAKQRGIAVFLVGHVTK-EGA-IAGPRVLEHMVDTVLYFE  230 (446)
T ss_pred             hhhhccccccCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEeeccC-CCC-cCCcchhhhhCeEEEEEE
Confidence            99762            233    345556688999999985321 111 222233445678877663

>PF12846 AAA_10: AAA-like domain

Probab=92.32  E-value=0.15  Score=47.38  Aligned_cols=37  Identities=32%  Similarity=0.290  Sum_probs=32.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecC
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKD  189 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D  189 (353)
                      .+|+|++|||||+.+...+......|..++++-|.-|
T Consensus         4 ~~i~G~tGsGKT~~~~~l~~~~~~~g~~~~i~D~~g~   40 (304)
T PF12846_consen    4 TLILGKTGSGKTTLLKNLLEQLIRRGPRVVIFDPKGD   40 (304)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHcCCCEEEEcCCch
Confidence            4799999999999999999999999999999976543

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=92.28  E-value=0.23  Score=53.21  Aligned_cols=39  Identities=21%  Similarity=0.158  Sum_probs=30.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhC-----CEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYAN-----YRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~-----~~~~~~k~~  187 (353)
                      .+...+|.|+.|+||||-+.+.+..+...+     .++.+.-|+
T Consensus       159 ~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APT  202 (586)
T TIGR01447       159 KSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPT  202 (586)
T ss_pred             hCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCc
Confidence            357899999999999998888777665432     468888874

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=92.25  E-value=0.21  Score=47.13  Aligned_cols=39  Identities=18%  Similarity=0.111  Sum_probs=35.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +...+|+|+++||||+-.++-+.+...+|.+|+.+....
T Consensus        23 g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e   61 (260)
T COG0467          23 GSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEE   61 (260)
T ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecC
Confidence            457899999999999999999999999999999988654

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=92.22  E-value=0.32  Score=43.77  Aligned_cols=34  Identities=26%  Similarity=0.297  Sum_probs=22.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      +...+++||++|||||-| +.+-.+.....+++.+
T Consensus        25 g~~i~I~G~tGSGKTTll-~aL~~~i~~~~~~i~i   58 (186)
T cd01130          25 RKNILISGGTGSGKTTLL-NALLAFIPPDERIITI   58 (186)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHhhcCCCCCEEEE
Confidence            567799999999999865 4444443344444444

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PF00488 MutS_V: MutS domain V C-terminus

Probab=92.15  E-value=0.66  Score=43.89  Aligned_cols=81  Identities=20%  Similarity=0.192  Sum_probs=44.7

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCcccc---ee-----ecccHhhhcccCC
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLT---AV-----SAVELNKLIPHTK  221 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~---a~-----~~~~~~~~~~~~~  221 (353)
                      +..+|+||..|||||-|=...-..-.|+.-+.  -|+...+.+ -+.|-||.+..-.   ..     ....+..++....
T Consensus        44 ~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~--VPA~~~~i~~~d~I~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~  121 (235)
T PF00488_consen   44 RIIIITGPNMSGKSTFLKQIGLIVILAQIGCF--VPAESAEIPIFDRIFTRIGDDDSIESGLSTFMAEMKRLSSILRNAT  121 (235)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHHHHHTTT----BSSSEEEEE--SEEEEEES---SSTTSSSHHHHHHHHHHHHHHH--
T ss_pred             eEEEEeCCCccchhhHHHHHHHHhhhhhcCce--eeecccccccccEEEeecccccccccccccHHHhHHHHHhhhhhcc
Confidence            57899999999999988777777666653222  233322222 1345555442211   11     1233444554444


Q ss_pred             CccEEEEecccc
Q psy8456         222 DIDVIGIDEGQF  233 (353)
Q Consensus       222 ~~~~i~IDE~QF  233 (353)
                      +-..|+|||.=.
T Consensus       122 ~~sLvliDE~g~  133 (235)
T PF00488_consen  122 EKSLVLIDELGR  133 (235)
T ss_dssp             TTEEEEEESTTT
T ss_pred             cceeeecccccC
Confidence            566899999766

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=92.13  E-value=0.24  Score=51.37  Aligned_cols=36  Identities=25%  Similarity=0.226  Sum_probs=32.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      ....++|+-||||||-+..-+..+...|++|+++..
T Consensus       101 ~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~  136 (429)
T TIGR01425       101 NVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCA  136 (429)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcC
Confidence            467899999999999999999999989999998853

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=92.07  E-value=0.14  Score=47.70  Aligned_cols=44  Identities=16%  Similarity=0.385  Sum_probs=33.5

Q ss_pred             hhhhcccCCCccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEec
Q psy8456          63 LNKLIPHTKDIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAAL  106 (353)
Q Consensus        63 l~ei~~~~~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaGL  106 (353)
                      ..++......+|+++||.+|++.       .+..+.+.+.+.|+++++++=
T Consensus        88 ~~~~~~~~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~  138 (219)
T PF00308_consen   88 IEEFKDRLRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSD  138 (219)
T ss_dssp             HHHHHHHHCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEES
T ss_pred             chhhhhhhhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeC
Confidence            34444445689999999999994       255777888889999998874

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.07  E-value=0.089  Score=57.99  Aligned_cols=82  Identities=20%  Similarity=0.171  Sum_probs=50.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH-HhC-CEEEEEeeecCC-CCCC-Cceee---ccCcccce-eecccHhhhcccCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ-YAN-YRCMIVRYAKDD-RYDT-EKVST---HDQQKLTA-VSAVELNKLIPHTK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~-~~~-~~~~~~k~~~D~-R~~~-~~i~s---~~g~~~~a-~~~~~~~~~~~~~~  221 (353)
                      +++..++||.|+||||-+..-+..|. ..| ++|.++..  |+ |-+. +...+   ..|..... ....++.+.+...+
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~--Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~~~  262 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTT--DSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALAALG  262 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecC--cccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHHHhc
Confidence            56788999999999999999999884 555 58877663  32 3211 11111   11221111 11223444455567


Q ss_pred             CccEEEEecccc
Q psy8456         222 DIDVIGIDEGQF  233 (353)
Q Consensus       222 ~~~~i~IDE~QF  233 (353)
                      ++|+|+||=+=.
T Consensus       263 ~~D~VLIDTAGR  274 (767)
T PRK14723        263 DKHLVLIDTVGM  274 (767)
T ss_pred             CCCEEEEeCCCC
Confidence            889999998765

>cd03114 ArgK-like The function of this protein family is unkown

Probab=92.06  E-value=0.51  Score=41.41  Aligned_cols=39  Identities=18%  Similarity=0.147  Sum_probs=32.8

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCC
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRY  192 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~  192 (353)
                      .++|+-+|||||-+..-...+...|.+++++.-....++
T Consensus         3 ~~~G~~GsGKTt~~~~l~~~~~~~g~~v~ii~~D~~~~~   41 (148)
T cd03114           3 GITGVPGAGKSTLIDALITALRARGKRVAVLAIDPSSPF   41 (148)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeCCCCCC
Confidence            468999999999999998889999999999886554444

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=92.06  E-value=0.23  Score=43.59  Aligned_cols=81  Identities=15%  Similarity=0.157  Sum_probs=49.9

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCC--Cce---eeccCccccee-ecccHhhh----cc--c
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDT--EKV---STHDQQKLTAV-SAVELNKL----IP--H  219 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~--~~i---~s~~g~~~~a~-~~~~~~~~----~~--~  219 (353)
                      +.++.|+.+|||||-....+..+...|++|+++.  .|.+...  +..   ..+.|..+... ...++.++    +.  .
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~--~D~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVA--ADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHAR   79 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE--cCCCChHHHHHHHHhcccCCeEEEecCCCCCHHHHHHHHHHHHH
Confidence            4578999999999999999988888899999877  3544321  001   11222111110 01122222    11  2


Q ss_pred             CCCccEEEEeccccc
Q psy8456         220 TKDIDVIGIDEGQFV  234 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~  234 (353)
                      ..++|+|+||..+..
T Consensus        80 ~~~~d~viiDt~g~~   94 (173)
T cd03115          80 EENFDVVIVDTAGRL   94 (173)
T ss_pred             hCCCCEEEEECcccc
Confidence            468999999999873

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt

Probab=91.98  E-value=0.19  Score=44.92  Aligned_cols=36  Identities=22%  Similarity=0.169  Sum_probs=29.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +.++.|..+|||||-|.+.+. ....|.++.++.-..
T Consensus         2 v~ii~GfLGsGKTTli~~ll~-~~~~~~~~~vI~ne~   37 (178)
T PF02492_consen    2 VIIITGFLGSGKTTLINHLLK-RNRQGERVAVIVNEF   37 (178)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH-HHTTTS-EEEEECST
T ss_pred             EEEEEcCCCCCHHHHHHHHHH-HhcCCceeEEEEccc
Confidence            468999999999999988888 777889999887543

Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=91.89  E-value=0.36  Score=47.33  Aligned_cols=77  Identities=18%  Similarity=0.177  Sum_probs=42.0

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHH--hCCEEEEEeeecCCCC-CCCceeeccCcccceeecccHhhhccc--CCCccEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQY--ANYRCMIVRYAKDDRY-DTEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVI  226 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~--~~~~~~~~k~~~D~R~-~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i  226 (353)
                      .-+|+|+++|||||-|-.-+.....  .+.+++.+.....-.. ..+.+.-+.+.     ....+.+++..  -.++|.|
T Consensus       134 ~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~~~~~v~~~~~~-----~~~~~~~~l~~aLR~~pD~i  208 (299)
T TIGR02782       134 NILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVVQLRTSD-----DAISMTRLLKATLRLRPDRI  208 (299)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCCCCCEEEEEecC-----CCCCHHHHHHHHhcCCCCEE
Confidence            4589999999999987544443332  2567766543221111 11111111010     01245555432  3689999


Q ss_pred             EEecccc
Q psy8456         227 GIDEGQF  233 (353)
Q Consensus       227 ~IDE~QF  233 (353)
                      ++.|..=
T Consensus       209 ivGEiR~  215 (299)
T TIGR02782       209 IVGEVRG  215 (299)
T ss_pred             EEeccCC
Confidence            9999874

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=91.76  E-value=0.35  Score=49.93  Aligned_cols=44  Identities=25%  Similarity=0.271  Sum_probs=24.3

Q ss_pred             hccccceEeccceeccccccc-----cccccccc--ce--eeeeccCCCCchhH
Q psy8456         122 IPLAECVEKLTAVCMSCFRDA-----AFTKRIGQ--EK--EVILGPMFSGKTTE  166 (353)
Q Consensus       122 l~lAD~I~kL~AvC~~CG~~A-----~f~~Ri~g--eI--~vi~G~M~sGKt~~  166 (353)
                      +|+|+++.. +.+=...|.+-     -.-.|...  .+  -+.+||.|+||||-
T Consensus        12 ~PLA~rmRP-~~lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTl   64 (436)
T COG2256          12 MPLAERLRP-KSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTL   64 (436)
T ss_pred             cChHHHhCC-CCHHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHH
Confidence            677777663 34444555431     11122221  22  35799999999973

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=91.73  E-value=0.21  Score=46.92  Aligned_cols=38  Identities=24%  Similarity=0.317  Sum_probs=31.5

Q ss_pred             eeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC
Q psy8456         155 ILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD  193 (353)
Q Consensus       155 i~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~  193 (353)
                      +.||.+||||+-|.+.++.++.. +++-+++--+-+..+
T Consensus        18 v~Gp~GSGKTaLie~~~~~L~~~-~~~aVI~~Di~t~~D   55 (202)
T COG0378          18 VGGPPGSGKTALIEKTLRALKDE-YKIAVITGDIYTKED   55 (202)
T ss_pred             ecCCCCcCHHHHHHHHHHHHHhh-CCeEEEeceeechhh
Confidence            68999999999999999998777 888888876666444

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=91.72  E-value=0.23  Score=55.18  Aligned_cols=39  Identities=13%  Similarity=0.111  Sum_probs=30.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ++..++.|+.||||||.+...+-.....+.+++++.|..
T Consensus        17 ~~~vIi~a~TGSGKTT~vpl~lL~~~~~~~~ilvlqPrR   55 (819)
T TIGR01970        17 HPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRR   55 (819)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhhccCCeEEEEeCcH
Confidence            446688999999999999988765544566888888853

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>TIGR00416 sms DNA repair protein RadA

Probab=91.70  E-value=0.36  Score=50.09  Aligned_cols=119  Identities=7%  Similarity=-0.014  Sum_probs=73.1

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCcee---eccCCceeeee---cCChhhhcc--cCCCccEEEEcc
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVA---THDQQKLTAVS---AVELNKLIP--HTKDIDVIGIDE   80 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~---Sr~G~~~~Ai~---i~~l~ei~~--~~~~~dvV~IDE   80 (353)
                      .=+||||-+++.+.+....|.+|+.+...- ++   ..+.   .|.|...+...   -.++.++..  ...++++|+||.
T Consensus       103 pGsGKTTL~lq~a~~~a~~g~kvlYvs~EE-s~---~qi~~ra~rlg~~~~~l~~~~e~~~~~I~~~i~~~~~~~vVIDS  178 (454)
T TIGR00416       103 PGIGKSTLLLQVACQLAKNQMKVLYVSGEE-SL---QQIKMRAIRLGLPEPNLYVLSETNWEQICANIEEENPQACVIDS  178 (454)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCcEEEEECcC-CH---HHHHHHHHHcCCChHHeEEcCCCCHHHHHHHHHhcCCcEEEEec
Confidence            357999999999999888888999887642 22   1222   23333222211   223444432  234789999999


Q ss_pred             ccChH------------HHHH----HHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccc
Q psy8456          81 GQFFP------------DVVS----FAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTA  133 (353)
Q Consensus        81 aQFF~------------dIv~----l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~A  133 (353)
                      .|.+.            |+.+    |.+.+.+.|++|++.|=.+. .+ .+.+...|--++|.|..|.-
T Consensus       179 Iq~l~~~~~~~~~g~~~q~r~~~~~L~~~ak~~giTvllt~hvtk-eg-~~aG~~~le~lvD~VI~Le~  245 (454)
T TIGR00416       179 IQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTK-EG-SIAGPKVLEHMVDTVLYFEG  245 (454)
T ss_pred             chhhcccccccCCCCHHHHHHHHHHHHHHHHHhCCEEEEEecccc-CC-ccCCcccEeeeceEEEEEec
Confidence            99862            2333    44455678999999984332 11 23333345568999988864

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=91.61  E-value=0.29  Score=44.71  Aligned_cols=36  Identities=22%  Similarity=0.048  Sum_probs=30.9

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +..++|+.+|||||-+-+.+......|.+|-.+|..
T Consensus         8 ii~ivG~sgsGKTTLi~~li~~l~~~g~~vg~Ik~~   43 (173)
T PRK10751          8 LLAIAAWSGTGKTTLLKKLIPALCARGIRPGLIKHT   43 (173)
T ss_pred             EEEEECCCCChHHHHHHHHHHHHhhcCCeEEEEEEc
Confidence            567899999999998888888888889999999873

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=91.60  E-value=0.48  Score=44.87  Aligned_cols=20  Identities=25%  Similarity=0.044  Sum_probs=14.4

Q ss_pred             eeeeccCCCCchhHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~  172 (353)
                      -+++||.|+||||-.--.++
T Consensus        45 vll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881        45 MIFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            36899999999975433333

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=91.60  E-value=0.55  Score=42.87  Aligned_cols=33  Identities=18%  Similarity=0.182  Sum_probs=25.6

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      .++|+++|||||-+-+.++++. .+.++.+++-.
T Consensus        26 ~~~G~~gsGKTTli~~l~~~~~-~~~~v~v~~~~   58 (207)
T TIGR00073        26 NFMSSPGSGKTTLIEKLIDNLK-DEVKIAVIEGD   58 (207)
T ss_pred             EEECCCCCCHHHHHHHHHHHHh-cCCeEEEEECC
Confidence            4899999999998888777653 35788877743

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK04195 replication factor C large subunit; Provisional

Probab=91.56  E-value=0.33  Score=50.34  Aligned_cols=33  Identities=18%  Similarity=0.250  Sum_probs=22.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      ..-+++||.|+||||-+-..++.+   |..++-+..
T Consensus        40 ~~lLL~GppG~GKTtla~ala~el---~~~~ielna   72 (482)
T PRK04195         40 KALLLYGPPGVGKTSLAHALANDY---GWEVIELNA   72 (482)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc---CCCEEEEcc
Confidence            456899999999998665554443   555555543

>PRK00889 adenylylsulfate kinase; Provisional

Probab=91.40  E-value=0.29  Score=43.06  Aligned_cols=36  Identities=19%  Similarity=0.098  Sum_probs=28.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +.+-++.|+|+|||||-.-.....+...|.++.++.
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~id   39 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVLD   39 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEc
Confidence            567789999999999877666667777788887774

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=91.30  E-value=0.41  Score=52.61  Aligned_cols=91  Identities=16%  Similarity=0.183  Sum_probs=60.4

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChh-hhc---ccCCCccEEEEccccChH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELN-KLI---PHTKDIDVIGIDEGQFFP   85 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~-ei~---~~~~~~dvV~IDEaQFF~   85 (353)
                      =.||||-|-...+-++..|.+|+++-|.  .|.. ..+.  ....++|..+.++. ...   ....+.++|+|||+...+
T Consensus       378 GTGKTtll~~i~~~~~~~g~~V~~~ApT--g~Aa-~~L~--~~~g~~a~Ti~~~~~~~~~~~~~~~~~~llIvDEasMv~  452 (744)
T TIGR02768       378 GTGKSTMLKAAREAWEAAGYRVIGAALS--GKAA-EGLQ--AESGIESRTLASLEYAWANGRDLLSDKDVLVIDEAGMVG  452 (744)
T ss_pred             CCCHHHHHHHHHHHHHhCCCeEEEEeCc--HHHH-HHHH--hccCCceeeHHHHHhhhccCcccCCCCcEEEEECcccCC
Confidence            3799998777777788889999999884  2321 1111  11223344433331 111   123568999999999996


Q ss_pred             --HHHHHHHHHHhCCCEEEEEe
Q psy8456          86 --DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        86 --dIv~l~~~l~~~G~~VivaG  105 (353)
                        ++.++.+.+...|..|++.|
T Consensus       453 ~~~~~~Ll~~~~~~~~kliLVG  474 (744)
T TIGR02768       453 SRQMARVLKEAEEAGAKVVLVG  474 (744)
T ss_pred             HHHHHHHHHHHHhcCCEEEEEC
Confidence              67777777777899999999

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=91.28  E-value=0.29  Score=43.12  Aligned_cols=35  Identities=23%  Similarity=0.047  Sum_probs=26.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      +...++.|+|+|||||-.-...+++...+..+.++
T Consensus         7 ~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~   41 (176)
T PRK05541          7 GYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYL   41 (176)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            44678999999999988766666666666666555

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=91.22  E-value=0.26  Score=50.97  Aligned_cols=86  Identities=13%  Similarity=0.259  Sum_probs=47.7

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChH---
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFP---   85 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~---   85 (353)
                      .-+|||.-+-..++.+...|.+|+.+.+.-   .. +.+.+.       .......++......+|+++|||+||+.   
T Consensus       150 ~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~---f~-~~~~~~-------l~~~~~~~f~~~~~~~dvLiIDDiq~l~~k~  218 (445)
T PRK12422        150 EGSGKTHLMQAAVHALRESGGKILYVRSEL---FT-EHLVSA-------IRSGEMQRFRQFYRNVDALFIEDIEVFSGKG  218 (445)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCEEEeeHHH---HH-HHHHHH-------HhcchHHHHHHHcccCCEEEEcchhhhcCCh
Confidence            346786655544555555666666555421   00 011110       0001122222335679999999999993   


Q ss_pred             ----HHHHHHHHHHhCCCEEEEEe
Q psy8456          86 ----DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        86 ----dIv~l~~~l~~~G~~VivaG  105 (353)
                          ++..+.+.+.+.|+.+++.+
T Consensus       219 ~~qeelf~l~N~l~~~~k~IIlts  242 (445)
T PRK12422        219 ATQEEFFHTFNSLHTEGKLIVISS  242 (445)
T ss_pred             hhHHHHHHHHHHHHHCCCcEEEec
Confidence                24455566667899988887

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=91.13  E-value=0.51  Score=39.96  Aligned_cols=31  Identities=3%  Similarity=-0.189  Sum_probs=24.6

Q ss_pred             cCCCCchHHHHHHHHHHHHHcC--ceEEEEeec
Q psy8456           7 DDRINPYIVHFCRRIRRYQYAN--YRCMIVRYA   37 (353)
Q Consensus         7 ~~~~~GKSteLLrr~~ry~~ag--kkvlv~Kp~   37 (353)
                      ...-+|||+.++..+.+....+  ++++++.|.
T Consensus        31 ~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~   63 (201)
T smart00487       31 APTGSGKTLAALLPALEALKRGKGKRVLVLVPT   63 (201)
T ss_pred             CCCCCchhHHHHHHHHHHhcccCCCcEEEEeCC
Confidence            3456899998888887776655  889999994

>PRK00698 tmk thymidylate kinase; Validated

Probab=91.09  E-value=0.26  Score=43.92  Aligned_cols=37  Identities=16%  Similarity=-0.006  Sum_probs=28.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+.++.|+++|||||.+-.-...+...|..+.+.+.
T Consensus         3 ~~~I~ieG~~gsGKsT~~~~L~~~l~~~~~~~~~~~~   39 (205)
T PRK00698          3 GMFITIEGIDGAGKSTQIELLKELLEQQGRDVVFTRE   39 (205)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCceeEeeC
Confidence            4567899999999999877766777777877776544

>PRK14738 gmk guanylate kinase; Provisional

Probab=90.88  E-value=0.61  Score=42.79  Aligned_cols=29  Identities=34%  Similarity=0.437  Sum_probs=21.3

Q ss_pred             ccccccccceeeeeccCCCCchhHHHHHHH
Q psy8456         143 AFTKRIGQEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       143 ~f~~Ri~geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      -++..-.+.+.+++||.+||||| |++.+.
T Consensus         6 ~~~~~~~~~~ivi~GpsG~GK~t-l~~~L~   34 (206)
T PRK14738          6 LFNKPAKPLLVVISGPSGVGKDA-VLARMR   34 (206)
T ss_pred             ccCCCCCCeEEEEECcCCCCHHH-HHHHHH
Confidence            34544556778899999999998 555554

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=90.86  E-value=0.086  Score=43.03  Aligned_cols=65  Identities=18%  Similarity=0.154  Sum_probs=35.7

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCCCceeeccCcccceeecccHhhhccc--CC-CccEEEEe
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDTEKVSTHDQQKLTAVSAVELNKLIPH--TK-DIDVIGID  229 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~-~~~~i~ID  229 (353)
                      +++||.|+|||+-+-..++..   +..++-+...... .+             .......+.+++..  .. ...+++||
T Consensus         2 ll~G~~G~GKT~l~~~la~~l---~~~~~~i~~~~~~~~~-------------~~~~~~~i~~~~~~~~~~~~~~vl~iD   65 (132)
T PF00004_consen    2 LLHGPPGTGKTTLARALAQYL---GFPFIEIDGSELISSY-------------AGDSEQKIRDFFKKAKKSAKPCVLFID   65 (132)
T ss_dssp             EEESSTTSSHHHHHHHHHHHT---TSEEEEEETTHHHTSS-------------TTHHHHHHHHHHHHHHHTSTSEEEEEE
T ss_pred             EEECcCCCCeeHHHHHHHhhc---cccccccccccccccc-------------ccccccccccccccccccccceeeeec
Confidence            689999999996554444433   5555544432211 10             00111233444332  12 36899999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |++-+
T Consensus        66 e~d~l   70 (132)
T PF00004_consen   66 EIDKL   70 (132)
T ss_dssp             TGGGT
T ss_pred             cchhc
Confidence            99964

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>cd01394 radB RadB

Probab=90.67  E-value=0.4  Score=43.68  Aligned_cols=36  Identities=17%  Similarity=0.120  Sum_probs=32.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +.+..++|+.+||||+-.++.+.+....|.+|+++.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            567889999999999999999999988899999885

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK09087 hypothetical protein; Validated

Probab=90.66  E-value=0.56  Score=44.00  Aligned_cols=19  Identities=37%  Similarity=0.321  Sum_probs=14.4

Q ss_pred             eeeeeccCCCCchhHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~  171 (353)
                      .-+|+||-|||||+- ++.+
T Consensus        46 ~l~l~G~~GsGKThL-l~~~   64 (226)
T PRK09087         46 VVVLAGPVGSGKTHL-ASIW   64 (226)
T ss_pred             eEEEECCCCCCHHHH-HHHH
Confidence            358999999999854 4443

>KOG0953|consensus

Probab=90.60  E-value=0.25  Score=52.83  Aligned_cols=149  Identities=19%  Similarity=0.291  Sum_probs=75.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHH--------------------HHHhCCEEEEEeeecCCCCCCCceeeccCcccceeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRR--------------------YQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSA  210 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~--------------------~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~  210 (353)
                      .+-+.+||.|||||-..|+++..                    .+.+|-.|=+++-.. -|+.     --+|.  +|-..
T Consensus       192 kIi~H~GPTNSGKTy~ALqrl~~aksGvycGPLrLLA~EV~~r~na~gipCdL~TGeE-~~~~-----~~~~~--~a~hv  263 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYRALQRLKSAKSGVYCGPLRLLAHEVYDRLNALGIPCDLLTGEE-RRFV-----LDNGN--PAQHV  263 (700)
T ss_pred             eEEEEeCCCCCchhHHHHHHHhhhccceecchHHHHHHHHHHHhhhcCCCccccccce-eeec-----CCCCC--cccce
Confidence            46778999999999988876543                    344555555544221 1111     01111  11000


Q ss_pred             ccHhhhcccCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCC---ccHHHHH
Q psy8456         211 VELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEF---PDVVSFA  287 (353)
Q Consensus       211 ~~~~~~~~~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f---~~~~~~~  287 (353)
                      .---+....+..|||..|||+|-+.  -++-||..            |+.=+---|.++.         .   |.+++.+
T Consensus       264 ScTVEM~sv~~~yeVAViDEIQmm~--Dp~RGwAW------------TrALLGl~AdEiH---------LCGepsvldlV  320 (700)
T KOG0953|consen  264 SCTVEMVSVNTPYEVAVIDEIQMMR--DPSRGWAW------------TRALLGLAADEIH---------LCGEPSVLDLV  320 (700)
T ss_pred             EEEEEEeecCCceEEEEehhHHhhc--CcccchHH------------HHHHHhhhhhhhh---------ccCCchHHHHH
Confidence            0001112234679999999999862  22223310            1111111122222         3   6788999


Q ss_pred             HHHHh-CCCEEEEEeccccccCCCchhHHhhhhcccceEEe-eeecccccc
Q psy8456         288 ESMAN-AGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL-TAVCMSCFR  336 (353)
Q Consensus       288 ~~~~~-~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl-~a~C~~Cg~  336 (353)
                      +++.. -|=.|.|.-    |.|  +++..-+=.+-+++..| ++-|.+|+.
T Consensus       321 ~~i~k~TGd~vev~~----YeR--l~pL~v~~~~~~sl~nlk~GDCvV~FS  365 (700)
T KOG0953|consen  321 RKILKMTGDDVEVRE----YER--LSPLVVEETALGSLSNLKPGDCVVAFS  365 (700)
T ss_pred             HHHHhhcCCeeEEEe----ecc--cCcceehhhhhhhhccCCCCCeEEEee
Confidence            88885 477777643    322  22222111334445555 566888874

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=90.54  E-value=0.42  Score=43.13  Aligned_cols=38  Identities=18%  Similarity=0.093  Sum_probs=34.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +.+..|+||.+||||+-.++.+.+....|.+|+.+...
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e   49 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE   49 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            56788999999999999999999988889999988775

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=90.50  E-value=0.78  Score=55.60  Aligned_cols=38  Identities=16%  Similarity=0.024  Sum_probs=33.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +.+.++.|+-|+||||-|-..+.-++..|++|+++-|+
T Consensus       446 ~~v~ii~G~aGTGKTt~l~~l~~~~~~~G~~V~~lAPT  483 (1960)
T TIGR02760       446 KRFIIINGFGGTGSTEIAQLLLHLASEQGYEIQIITAG  483 (1960)
T ss_pred             CCeEEEEECCCCCHHHHHHHHHHHHHhcCCeEEEEeCC
Confidence            46889999999999998888888888899999999885

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK06893 DNA replication initiation factor; Validated

Probab=90.41  E-value=0.86  Score=42.52  Aligned_cols=38  Identities=13%  Similarity=0.280  Sum_probs=26.6

Q ss_pred             cCCCccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEec
Q psy8456          69 HTKDIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAAL  106 (353)
Q Consensus        69 ~~~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaGL  106 (353)
                      ...++|+++|||+|+..       .+.++.+.+.+.|.++++.+=
T Consensus        88 ~~~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits  132 (229)
T PRK06893         88 NLEQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISA  132 (229)
T ss_pred             hcccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeC
Confidence            34568999999999973       244566666677877655443

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=90.40  E-value=0.45  Score=43.18  Aligned_cols=79  Identities=19%  Similarity=0.120  Sum_probs=42.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH--HhCCEEEEEeeecCCCCCC-CceeeccCccc---ceee-----cccHhhhcc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ--YANYRCMIVRYAKDDRYDT-EKVSTHDQQKL---TAVS-----AVELNKLIP  218 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~--~~~~~~~~~k~~~D~R~~~-~~i~s~~g~~~---~a~~-----~~~~~~~~~  218 (353)
                      ++..+++||.+|||||-|-......-  ..|.    +.|+...+.+. +.+-+|-+..-   ...+     ...+..++.
T Consensus        29 ~~~~~l~G~Ng~GKStll~~i~~~~~~~~~g~----~~~~~~~~i~~~dqi~~~~~~~d~i~~~~s~~~~e~~~l~~i~~  104 (202)
T cd03243          29 GRLLLITGPNMGGKSTYLRSIGLAVLLAQIGC----FVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILS  104 (202)
T ss_pred             CeEEEEECCCCCccHHHHHHHHHHHHHHHcCC----CccccccccCCcCEEEEEecCcccccCCceeHHHHHHHHHHHHH
Confidence            46789999999999987766553332  2232    22333333331 23333332211   1111     122444444


Q ss_pred             cCCCccEEEEeccc
Q psy8456         219 HTKDIDVIGIDEGQ  232 (353)
Q Consensus       219 ~~~~~~~i~IDE~Q  232 (353)
                      ...+.+++++||.=
T Consensus       105 ~~~~~~llllDEp~  118 (202)
T cd03243         105 LATPRSLVLIDELG  118 (202)
T ss_pred             hccCCeEEEEecCC
Confidence            45789999999974

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=90.35  E-value=0.42  Score=43.82  Aligned_cols=38  Identities=24%  Similarity=0.213  Sum_probs=31.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k~~  187 (353)
                      +...++.||.+||||+-.++-+.+...+ |.+|+.+.-.
T Consensus        19 gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~e   57 (226)
T PF06745_consen   19 GSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFE   57 (226)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESS
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEec
Confidence            4578999999999999999999999888 9999988853

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PHA02558 uvsW UvsW helicase; Provisional

Probab=90.33  E-value=2.1  Score=44.61  Aligned_cols=82  Identities=12%  Similarity=0.114  Sum_probs=45.1

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCC-EEEEEeeecCCC---------CCC---Cce-eeccCccc---ceeecccHhh
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANY-RCMIVRYAKDDR---------YDT---EKV-STHDQQKL---TAVSAVELNK  215 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~-~~~~~k~~~D~R---------~~~---~~i-~s~~g~~~---~a~~~~~~~~  215 (353)
                      -++..|.+||||.-....++.+...+. +++++-|..+=-         +..   ..+ .-..|...   ..+.+.....
T Consensus       132 ~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~~i~~g~~~~~~~~I~VaT~qs  211 (501)
T PHA02558        132 RLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMHKIYSGTAKDTDAPIVVSTWQS  211 (501)
T ss_pred             eEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHHHHHHHHHHHHhccccccceeEEecCcccCCCCCEEEeeHHH
Confidence            488999999999755444444444445 899988863211         110   111 01111111   1233333333


Q ss_pred             hcc----cCCCccEEEEeccccc
Q psy8456         216 LIP----HTKDIDVIGIDEGQFV  234 (353)
Q Consensus       216 ~~~----~~~~~~~i~IDE~QF~  234 (353)
                      +..    ..+++++|+|||+|-+
T Consensus       212 l~~~~~~~~~~~~~iIvDEaH~~  234 (501)
T PHA02558        212 AVKQPKEWFDQFGMVIVDECHLF  234 (501)
T ss_pred             HhhchhhhccccCEEEEEchhcc
Confidence            322    2478999999999974

>PRK10490 sensor protein KdpD; Provisional

Probab=90.28  E-value=1.5  Score=49.09  Aligned_cols=35  Identities=14%  Similarity=0.314  Sum_probs=32.4

Q ss_pred             ccceeeeecc-CCCCchhHHHHHHHHHHHhCCEEEE
Q psy8456         149 GQEKEVILGP-MFSGKTTELIRRIRRYQYANYRCMI  183 (353)
Q Consensus       149 ~geI~vi~G~-M~sGKt~~Li~~~~~~~~~~~~~~~  183 (353)
                      .|.+.+++|. .|.|||..+|+.++....+|..|++
T Consensus        22 ~g~l~i~~g~~~gvgkt~~ml~~a~~~~~~g~dvv~   57 (895)
T PRK10490         22 RGKLKIFFGACAGVGKTYAMLQEAQRLRAQGLDVLV   57 (895)
T ss_pred             CCcEEEEeecCCCCCHHHHHHHHHHHHHhCCCcEEE
Confidence            4889999998 8999999999999999999999984

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=90.22  E-value=0.23  Score=47.58  Aligned_cols=72  Identities=24%  Similarity=0.277  Sum_probs=46.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccH-hhhcccCCCccEEEEe
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVEL-NKLIPHTKDIDVIGID  229 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~-~~~~~~~~~~~~i~ID  229 (353)
                      .--+++||.|.|||.-+.--.++...+|.+|++++..-        ..+.......   .... .++......+|+++||
T Consensus       106 ~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~e--------l~~~Lk~~~~---~~~~~~~l~~~l~~~dlLIiD  174 (254)
T COG1484         106 ENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPD--------LLSKLKAAFD---EGRLEEKLLRELKKVDLLIID  174 (254)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHH--------HHHHHHHHHh---cCchHHHHHHHhhcCCEEEEe
Confidence            34589999999999887777787787799999887531        1221111110   0111 2233336789999999


Q ss_pred             cccc
Q psy8456         230 EGQF  233 (353)
Q Consensus       230 E~QF  233 (353)
                      |.=.
T Consensus       175 DlG~  178 (254)
T COG1484         175 DIGY  178 (254)
T ss_pred             cccC
Confidence            9765

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=90.20  E-value=0.14  Score=46.36  Aligned_cols=70  Identities=17%  Similarity=0.252  Sum_probs=44.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQ  232 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~Q  232 (353)
                      -+++||.|.|||.-..-.++.+...|++|+.++..-        +..+....   ..-....+++....++|+++|||.=
T Consensus        50 l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~--------L~~~l~~~---~~~~~~~~~~~~l~~~dlLilDDlG  118 (178)
T PF01695_consen   50 LILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASD--------LLDELKQS---RSDGSYEELLKRLKRVDLLILDDLG  118 (178)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHH--------HHHHHHCC---HCCTTHCHHHHHHHTSSCEEEETCT
T ss_pred             EEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCc--------eecccccc---ccccchhhhcCccccccEecccccc
Confidence            589999999999888888888888999999876531        11110000   0011233444455689999999964


Q ss_pred             c
Q psy8456         233 F  233 (353)
Q Consensus       233 F  233 (353)
                      .
T Consensus       119 ~  119 (178)
T PF01695_consen  119 Y  119 (178)
T ss_dssp             S
T ss_pred             e
Confidence            3

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=90.17  E-value=2  Score=39.71  Aligned_cols=132  Identities=15%  Similarity=0.110  Sum_probs=82.1

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCC-CCCCceeec--------cCcccceee--cc-----c
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR-YDTEKVSTH--------DQQKLTAVS--AV-----E  212 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R-~~~~~i~s~--------~g~~~~a~~--~~-----~  212 (353)
                      .|-+++++|. |=||||..+-.+-|..-+|++|+++.--+..+ +|+..+..+        -|....-..  ..     .
T Consensus        21 ~Gli~VYtGd-GKGKTTAAlGlalRAaG~G~rV~iiQFlKg~~~~GE~~~l~~~~~v~~~~~g~~~~~~~~~~~~~~~~~   99 (178)
T PRK07414         21 EGLVQVFTSS-QRNFFTSVMAQALRIAGQGTPVLIVQFLKGGIQQGPDRPIQLGQNLDWVRCDLPRCLDTPHLDESEKKA   99 (178)
T ss_pred             CCEEEEEeCC-CCCchHHHHHHHHHHhcCCCEEEEEEEecCCCcchHHHHHHhCCCcEEEECCCCCeeeCCCcCHHHHHH
Confidence            3567888886 77999999999999999999999998888874 553322222        221110000  00     0


Q ss_pred             Hhhhcc------cCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHH
Q psy8456         213 LNKLIP------HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSF  286 (353)
Q Consensus       213 ~~~~~~------~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~  286 (353)
                      ..+.+.      ...++|+|+.||+=..-                 ..--++.                     .+++++
T Consensus       100 ~~~~~~~a~~~l~~~~~dlvVLDEi~~Al-----------------~~gli~~---------------------eeVl~~  141 (178)
T PRK07414        100 LQELWQYTQAVVDEGRYSLVVLDELSLAI-----------------QFGLIPE---------------------TEVLEF  141 (178)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEehhHHHH-----------------HCCCccH---------------------HHHHHH
Confidence            111111      14789999999987520                 0000011                     245554


Q ss_pred             HHHHHhCCCEEEEEeccccccCCCchhHHhhhhcccceEEeee
Q psy8456         287 AESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTA  329 (353)
Q Consensus       287 ~~~~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a  329 (353)
                      .+. ...+..||+-|=         +....|+++||.|++++.
T Consensus       142 L~~-rp~~~evILTGR---------~~p~~Lie~AD~VTEm~~  174 (178)
T PRK07414        142 LEK-RPSHVDVILTGP---------EMPESLLAIADQITELRR  174 (178)
T ss_pred             HHh-CCCCCEEEEECC---------CCCHHHHHhCCeeeeeec
Confidence            443 245788999874         245789999999999863

>PRK08939 primosomal protein DnaI; Reviewed

Probab=90.14  E-value=0.21  Score=49.20  Aligned_cols=71  Identities=13%  Similarity=0.184  Sum_probs=47.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEecc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEG  231 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~  231 (353)
                      --+++||.|+|||.-+.-.++.+...|++|.++....   . -..+..       +.....+.+.+....++|+++|||.
T Consensus       158 gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~---l-~~~lk~-------~~~~~~~~~~l~~l~~~dlLiIDDi  226 (306)
T PRK08939        158 GLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPE---F-IRELKN-------SISDGSVKEKIDAVKEAPVLMLDDI  226 (306)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHH---H-HHHHHH-------HHhcCcHHHHHHHhcCCCEEEEecC
Confidence            4589999999999888877788888899988775421   0 000110       0011234455556789999999998


Q ss_pred             cc
Q psy8456         232 QF  233 (353)
Q Consensus       232 QF  233 (353)
                      ..
T Consensus       227 G~  228 (306)
T PRK08939        227 GA  228 (306)
T ss_pred             CC
Confidence            76

>PRK05642 DNA replication initiation factor; Validated

Probab=90.13  E-value=0.8  Score=42.98  Aligned_cols=39  Identities=10%  Similarity=0.314  Sum_probs=29.2

Q ss_pred             ccCCCccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEec
Q psy8456          68 PHTKDIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAAL  106 (353)
Q Consensus        68 ~~~~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaGL  106 (353)
                      ....++|+++||++||+.       .+.++.+.+.+.|+.+++.+=
T Consensus        93 ~~~~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~  138 (234)
T PRK05642         93 DNLEQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAAS  138 (234)
T ss_pred             HhhhhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCC
Confidence            344568999999999983       266677777778888777664

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=90.07  E-value=0.36  Score=45.25  Aligned_cols=33  Identities=18%  Similarity=0.136  Sum_probs=27.3

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      .++.|+|+|||||-.-+-.+.+...|.++.++.
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i~   34 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILG   34 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEc
Confidence            578999999999988777777777788887764

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=90.01  E-value=0.55  Score=47.84  Aligned_cols=82  Identities=18%  Similarity=0.102  Sum_probs=50.4

Q ss_pred             CCCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcc-cCCCccEEEEccccChHH
Q psy8456           8 DRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIP-HTKDIDVIGIDEGQFFPD   86 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~-~~~~~dvV~IDEaQFF~d   86 (353)
                      .|-+||||-|    +.+...+.+..++-..-|.|......            .+.+..... ...+-..|++||+|+.++
T Consensus        45 pR~~GKTtll----~~l~~~~~~~~iy~~~~d~~~~~~~l------------~d~~~~~~~~~~~~~~yifLDEIq~v~~  108 (398)
T COG1373          45 PRQVGKTTLL----KLLIKGLLEEIIYINFDDLRLDRIEL------------LDLLRAYIELKEREKSYIFLDEIQNVPD  108 (398)
T ss_pred             CccccHHHHH----HHHHhhCCcceEEEEecchhcchhhH------------HHHHHHHHHhhccCCceEEEecccCchh
Confidence            4679999998    44445555545665656666542211            111111111 111457999999999998


Q ss_pred             HHHHHHHHHhCCC-EEEEEe
Q psy8456          87 VVSFAESMANAGK-IVVVAA  105 (353)
Q Consensus        87 Iv~l~~~l~~~G~-~VivaG  105 (353)
                      -...++.+.+.|. .|++.|
T Consensus       109 W~~~lk~l~d~~~~~v~itg  128 (398)
T COG1373         109 WERALKYLYDRGNLDVLITG  128 (398)
T ss_pred             HHHHHHHHHccccceEEEEC
Confidence            7777888888877 466665

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=90.00  E-value=0.49  Score=43.38  Aligned_cols=38  Identities=18%  Similarity=0.135  Sum_probs=34.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +.+..++|+.+||||+-.++-+.+....|.+|+++.-.
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            56789999999999999999999998889999988754

>KOG0923|consensus

Probab=89.91  E-value=0.12  Score=56.15  Aligned_cols=80  Identities=21%  Similarity=0.199  Sum_probs=50.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHH--HhCCEEEEEeeecCCCCCCCceeecc----Cccc--------c---eeec---
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQ--YANYRCMIVRYAKDDRYDTEKVSTHD----QQKL--------T---AVSA---  210 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~--~~~~~~~~~k~~~D~R~~~~~i~s~~----g~~~--------~---a~~~---  210 (353)
                      ..-+|.|..||||||+|=+-++..-  ..|+++-+..|.   |-..-.|.+|.    |.++        .   |.+.   
T Consensus       281 QVLiI~GeTGSGKTTQiPQyL~EaGytk~gk~IgcTQPR---RVAAmSVAaRVA~EMgvkLG~eVGYsIRFEdcTSekTv  357 (902)
T KOG0923|consen  281 QVLIIVGETGSGKTTQIPQYLYEAGYTKGGKKIGCTQPR---RVAAMSVAARVAEEMGVKLGHEVGYSIRFEDCTSEKTV  357 (902)
T ss_pred             cEEEEEcCCCCCccccccHHHHhcccccCCceEeecCcc---hHHHHHHHHHHHHHhCcccccccceEEEeccccCccee
Confidence            4567999999999999999988764  445666666663   32223344443    1111        1   1110   


Q ss_pred             -------ccHhhhcc--cCCCccEEEEecccc
Q psy8456         211 -------VELNKLIP--HTKDIDVIGIDEGQF  233 (353)
Q Consensus       211 -------~~~~~~~~--~~~~~~~i~IDE~QF  233 (353)
                             .-+.+++.  ....|.||+|||||-
T Consensus       358 lKYMTDGmLlREfL~epdLasYSViiiDEAHE  389 (902)
T KOG0923|consen  358 LKYMTDGMLLREFLSEPDLASYSVIIVDEAHE  389 (902)
T ss_pred             eeeecchhHHHHHhccccccceeEEEeehhhh
Confidence                   01555553  367899999999995

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=89.90  E-value=0.5  Score=38.52  Aligned_cols=27  Identities=30%  Similarity=0.352  Sum_probs=20.2

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      .+|.||++|||||-.-+-..++   |..++
T Consensus         2 I~I~G~~gsGKST~a~~La~~~---~~~~i   28 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL---GFPVI   28 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH---TCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHH---CCeEE
Confidence            4789999999999776666655   55443

...

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=89.87  E-value=0.53  Score=42.49  Aligned_cols=78  Identities=18%  Similarity=0.190  Sum_probs=46.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCC---CceeeccCcc---cceeec-ccHhhhcccCCCcc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDT---EKVSTHDQQK---LTAVSA-VELNKLIPHTKDID  224 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~---~~i~s~~g~~---~~a~~~-~~~~~~~~~~~~~~  224 (353)
                      +.+|+|+.+||||+--.+.+..   .+.+++.+..+.  -++.   ..|..|....   ...+.. .++.+.+...+..+
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~---~~~~~~y~at~~--~~d~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~   75 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAE---LGGPVTYIATAE--AFDDEMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGD   75 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHh---cCCCeEEEEccC--cCCHHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCC
Confidence            4689999999999987777654   566777664432  2232   1233343222   222221 34555554444678


Q ss_pred             EEEEeccccc
Q psy8456         225 VIGIDEGQFV  234 (353)
Q Consensus       225 ~i~IDE~QF~  234 (353)
                      +|+||=.-.+
T Consensus        76 ~VLIDclt~~   85 (169)
T cd00544          76 VVLIDCLTLW   85 (169)
T ss_pred             EEEEEcHhHH
Confidence            9999987753

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=89.87  E-value=0.74  Score=44.61  Aligned_cols=26  Identities=23%  Similarity=0.139  Sum_probs=17.0

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhC
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYAN  178 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~  178 (353)
                      -+++||.|+|||+-.-...+.+...|
T Consensus        61 vll~G~pGTGKT~lA~~ia~~l~~~g   86 (284)
T TIGR02880        61 MSFTGNPGTGKTTVALRMAQILHRLG   86 (284)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence            57889999999975443334343333

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=89.81  E-value=0.58  Score=46.28  Aligned_cols=24  Identities=42%  Similarity=0.517  Sum_probs=18.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+.+|+||++||||+-..+-+..+
T Consensus         5 ~~i~i~GptgsGKt~la~~la~~~   28 (307)
T PRK00091          5 KVIVIVGPTASGKTALAIELAKRL   28 (307)
T ss_pred             eEEEEECCCCcCHHHHHHHHHHhC
Confidence            367899999999998777665543

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=89.78  E-value=4.8  Score=37.44  Aligned_cols=21  Identities=33%  Similarity=0.472  Sum_probs=16.8

Q ss_pred             cceeeeeccCCCCchhHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRR  170 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~  170 (353)
                      .+..+++||.+|||||-|=..
T Consensus        30 ~~~~~l~Gpn~sGKstllr~i   50 (216)
T cd03284          30 RQILLITGPNMAGKSTYLRQV   50 (216)
T ss_pred             ceEEEEECCCCCChHHHHHHH
Confidence            367799999999999865444

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=89.77  E-value=0.44  Score=44.22  Aligned_cols=79  Identities=20%  Similarity=0.083  Sum_probs=41.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHH--HhCCEEEEEeeecCCCCC-CCceeeccCccc---ceee-----cccHhhhccc
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQ--YANYRCMIVRYAKDDRYD-TEKVSTHDQQKL---TAVS-----AVELNKLIPH  219 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~--~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~---~a~~-----~~~~~~~~~~  219 (353)
                      +..+++||.+|||||-|-.......  ..|.-    .|+...+.+ -+.+.++.+..-   ...+     ...+..+...
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~~~~la~~G~~----v~a~~~~~~~~d~i~~~l~~~~si~~~~S~f~~el~~l~~~l~~  105 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVALIVFLAHIGSF----VPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRL  105 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHHHhCCCe----eEcCCcEEeeeeeeeeeeCCccChhhccchHHHHHHHHHHHHHh
Confidence            5678999999999987766554332  23332    222222211 122333332211   1111     1122223333


Q ss_pred             CCCccEEEEecccc
Q psy8456         220 TKDIDVIGIDEGQF  233 (353)
Q Consensus       220 ~~~~~~i~IDE~QF  233 (353)
                      ..+..++++||..-
T Consensus       106 ~~~~slvllDE~~~  119 (213)
T cd03281         106 ATRRSLVLIDEFGK  119 (213)
T ss_pred             CCCCcEEEeccccC
Confidence            56789999999876

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>KOG1533|consensus

Probab=89.76  E-value=0.35  Score=47.06  Aligned_cols=39  Identities=26%  Similarity=0.226  Sum_probs=32.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe--eecCCC
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVR--YAKDDR  191 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k--~~~D~R  191 (353)
                      ++++||.+|||||.-.-...-+...|+++.++.  |+.|+=
T Consensus         5 qvVIGPPgSGKsTYc~g~~~fls~~gr~~~vVNLDPaNd~~   45 (290)
T KOG1533|consen    5 QVVIGPPGSGKSTYCNGMSQFLSAIGRPVAVVNLDPANDNL   45 (290)
T ss_pred             eEEEcCCCCCccchhhhHHHHHHHhCCceEEEecCCcccCC
Confidence            689999999999999888888888999877764  777664

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=89.64  E-value=1.5  Score=48.51  Aligned_cols=82  Identities=17%  Similarity=0.133  Sum_probs=57.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecC----------CCCCCCceeeccCcccce--------------
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKD----------DRYDTEKVSTHDQQKLTA--------------  207 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D----------~R~~~~~i~s~~g~~~~a--------------  207 (353)
                      -.++.|..|||||+-+++.+..+-.+|+.++++-|.+-          .|++....+-|.|..-.-              
T Consensus       219 ~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~  298 (730)
T COG1198         219 PFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEAR  298 (730)
T ss_pred             ceeEeCCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCce
Confidence            45789999999999999999999999999999999874          345544445555532110              


Q ss_pred             eecccHhhhcccCCCccEEEEecccc
Q psy8456         208 VSAVELNKLIPHTKDIDVIGIDEGQF  233 (353)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~i~IDE~QF  233 (353)
                      +.+..=..+..-.++...|+|||-|=
T Consensus       299 vVIGtRSAlF~Pf~~LGLIIvDEEHD  324 (730)
T COG1198         299 VVIGTRSALFLPFKNLGLIIVDEEHD  324 (730)
T ss_pred             EEEEechhhcCchhhccEEEEecccc
Confidence            11111111222257888999999996

>PRK14491 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional

Probab=89.64  E-value=1.5  Score=47.15  Aligned_cols=35  Identities=20%  Similarity=0.076  Sum_probs=32.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +--|+|+-+|||||-+-+-+.++..+|++|-++|.
T Consensus        12 vi~ivG~s~sGKTTlie~li~~L~~~G~rVavIKh   46 (597)
T PRK14491         12 LLGFCAYSGTGKTTLLEQLIPELNQRGLRLAVIKH   46 (597)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhCCceEEEEEc
Confidence            45589999999999999999999999999999998

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=89.54  E-value=0.47  Score=36.15  Aligned_cols=31  Identities=19%  Similarity=0.174  Sum_probs=21.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      -.+.|+++|||||-.-.-..++  .+.++.++.
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l--~~~~~~~i~   32 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL--GGRSVVVLD   32 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh--cCCCEEEEe
Confidence            3679999999998766655555  455555554

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=89.49  E-value=0.5  Score=47.14  Aligned_cols=75  Identities=23%  Similarity=0.180  Sum_probs=40.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHH---HhCCEEEEEeeecCCCC-CCCceeeccCcccceeecccHhhhccc--CCCccE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQ---YANYRCMIVRYAKDDRY-DTEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDV  225 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~---~~~~~~~~~k~~~D~R~-~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~  225 (353)
                      .-+|.|+++|||||-| +.+-.+.   ..+.+++.+.....-.. ..+.+..+      .-...+..+++..  -.++|.
T Consensus       146 nilI~G~tGSGKTTll-~aL~~~i~~~~~~~rivtiEd~~El~~~~~n~v~l~------~~~~~~~~~lv~~aLR~~PD~  218 (323)
T PRK13833        146 NIVISGGTGSGKTTLA-NAVIAEIVASAPEDRLVILEDTAEIQCAAENAVALH------TSDTVDMARLLKSTMRLRPDR  218 (323)
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHHhcCCCCceEEEecCCcccccCCCCEEEec------cCCCcCHHHHHHHHhCCCCCE
Confidence            3489999999999877 4444443   23556665442211111 11111111      1111235555432  378999


Q ss_pred             EEEecccc
Q psy8456         226 IGIDEGQF  233 (353)
Q Consensus       226 i~IDE~QF  233 (353)
                      |++.|+.=
T Consensus       219 IivGEiRg  226 (323)
T PRK13833        219 IIVGEVRD  226 (323)
T ss_pred             EEEeecCC
Confidence            99999863

>cd00268 DEADc DEAD-box helicases

Probab=89.47  E-value=0.99  Score=40.09  Aligned_cols=38  Identities=18%  Similarity=0.155  Sum_probs=26.5

Q ss_pred             cceeeeeccCCCCchhH-HHHHHHHHHH----hCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTE-LIRRIRRYQY----ANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~-Li~~~~~~~~----~~~~~~~~k~~  187 (353)
                      ++..++.+|-++|||.- ++-.+.....    .+.+++++.|.
T Consensus        36 ~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~   78 (203)
T cd00268          36 GRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPT   78 (203)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCC
Confidence            44568999999999966 3444444433    35688988884

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>PRK13764 ATPase; Provisional

Probab=89.41  E-value=1.2  Score=48.14  Aligned_cols=34  Identities=21%  Similarity=0.049  Sum_probs=24.7

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      ..-+++||.+|||||-|-.-+..+...++.|..+
T Consensus       258 ~~ILIsG~TGSGKTTll~AL~~~i~~~~riV~Ti  291 (602)
T PRK13764        258 EGILIAGAPGAGKSTFAQALAEFYADMGKIVKTM  291 (602)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhCCCEEEEE
Confidence            3468999999999998766555556566655444

>PRK13342 recombination factor protein RarA; Reviewed

Probab=89.35  E-value=0.84  Score=46.36  Aligned_cols=19  Identities=32%  Similarity=0.249  Sum_probs=14.3

Q ss_pred             eeeeccCCCCchhHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~  171 (353)
                      -+++||.|+||||-+-...
T Consensus        39 ilL~GppGtGKTtLA~~ia   57 (413)
T PRK13342         39 MILWGPPGTGKTTLARIIA   57 (413)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4679999999997554443

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=89.20  E-value=0.58  Score=43.04  Aligned_cols=41  Identities=10%  Similarity=-0.002  Sum_probs=35.9

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEeeecC
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVRYAKD  189 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k~~~D  189 (353)
                      .+++.+|.|+.++|||+-+++-+.++... |.+|+++.....
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~~   53 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMS   53 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCCC
Confidence            46789999999999999999999999777 999999986543

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=89.11  E-value=0.21  Score=48.86  Aligned_cols=24  Identities=21%  Similarity=0.221  Sum_probs=18.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQ  175 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~  175 (353)
                      .-+|+||-|+|||+-+-..++...
T Consensus        42 ~i~I~G~~GtGKT~l~~~~~~~l~   65 (365)
T TIGR02928        42 NVFIYGKTGTGKTAVTKYVMKELE   65 (365)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHH
Confidence            458999999999977665555544

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK01184 hypothetical protein; Provisional

Probab=89.09  E-value=0.27  Score=43.54  Aligned_cols=27  Identities=15%  Similarity=0.015  Sum_probs=18.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      +-+++|||+||||| +.+.   .+..|..++
T Consensus         3 ~i~l~G~~GsGKsT-~a~~---~~~~g~~~i   29 (184)
T PRK01184          3 IIGVVGMPGSGKGE-FSKI---AREMGIPVV   29 (184)
T ss_pred             EEEEECCCCCCHHH-HHHH---HHHcCCcEE
Confidence            45789999999999 5553   334465544

>TIGR01070 mutS1 DNA mismatch repair protein MutS

Probab=89.08  E-value=4.4  Score=45.40  Aligned_cols=81  Identities=16%  Similarity=0.112  Sum_probs=53.7

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCcccce---ee-----cccHhhhcccCC
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTA---VS-----AVELNKLIPHTK  221 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a---~~-----~~~~~~~~~~~~  221 (353)
                      ...+|+||..+||||-|=+..-..-.|+.-+.  -|+...+-+ -+.|-||.|..-.-   .+     ..+...++....
T Consensus       593 ~~~iITGPNmgGKSt~lrqvali~imAq~G~~--VPA~~a~i~~~D~Iftrig~~d~i~~g~STF~~Em~e~a~IL~~at  670 (840)
T TIGR01070       593 RMLLITGPNMGGKSTYMRQTALIALLAQIGSF--VPAESAELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNAT  670 (840)
T ss_pred             cEEEEECCCCCCchHHHHHHHHHHHHHhcCCC--ccchheEeccccEEEEecCcccchhcCcchHHHHHHHHHHHHhhCC
Confidence            46799999999999998887766655554333  355545544 35788887753211   11     234555666556


Q ss_pred             CccEEEEecccc
Q psy8456         222 DIDVIGIDEGQF  233 (353)
Q Consensus       222 ~~~~i~IDE~QF  233 (353)
                      .-.+|++||.=.
T Consensus       671 ~~sLvllDE~Gr  682 (840)
T TIGR01070       671 ENSLVLFDEIGR  682 (840)
T ss_pred             CCEEEEEccCCC
Confidence            778999999765

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=88.95  E-value=0.9  Score=45.53  Aligned_cols=35  Identities=14%  Similarity=-0.037  Sum_probs=29.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      .--+.||.||||||-+-.-+..+...|.+|.++.-
T Consensus        58 ~igi~G~~GaGKSTl~~~l~~~l~~~g~~v~vi~~   92 (332)
T PRK09435         58 RIGITGVPGVGKSTFIEALGMHLIEQGHKVAVLAV   92 (332)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEe
Confidence            34579999999999888888888888999887765

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=88.84  E-value=1.7  Score=34.75  Aligned_cols=94  Identities=12%  Similarity=-0.081  Sum_probs=46.8

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChH---
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFP---   85 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~---   85 (353)
                      .=+|||+-+-..++.+...+.+++.+...-. ... .....-.+..     ............+..++++||+|.++   
T Consensus        28 ~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~-~~~-~~~~~~~~~~-----~~~~~~~~~~~~~~~~lilDe~~~~~~~~  100 (151)
T cd00009          28 PGTGKTTLARAIANELFRPGAPFLYLNASDL-LEG-LVVAELFGHF-----LVRLLFELAEKAKPGVLFIDEIDSLSRGA  100 (151)
T ss_pred             CCCCHHHHHHHHHHHhhcCCCCeEEEehhhh-hhh-hHHHHHhhhh-----hHhHHHHhhccCCCeEEEEeChhhhhHHH
Confidence            4589998555555555555666666654221 111 0000000000     00000011223467899999999873   


Q ss_pred             --HHHHHHHHHHh-----CCCEEEEEecccc
Q psy8456          86 --DVVSFAESMAN-----AGKIVVVAALDGT  109 (353)
Q Consensus        86 --dIv~l~~~l~~-----~G~~VivaGLd~D  109 (353)
                        .+.++.+...+     .+..|++.+-+.+
T Consensus       101 ~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009         101 QNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             HHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence              33444444332     4777877776544

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=88.79  E-value=0.24  Score=44.36  Aligned_cols=20  Identities=30%  Similarity=0.323  Sum_probs=15.7

Q ss_pred             cceeeeeccCCCCchhHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~  169 (353)
                      +.+.+++|||+|||||-+-.
T Consensus         2 g~~i~l~G~sGsGKsTl~~~   21 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLAA   21 (186)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45678999999999985433

>PRK05399 DNA mismatch repair protein MutS; Provisional

Probab=88.77  E-value=4.7  Score=45.20  Aligned_cols=82  Identities=17%  Similarity=0.156  Sum_probs=52.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCcccc---eee-----cccHhhhcccC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLT---AVS-----AVELNKLIPHT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~---a~~-----~~~~~~~~~~~  220 (353)
                      ++..+|+||..+||||-|-+..-..-.|+.-+.  -|+...+-+ -+.|-||.|..-.   ..+     ..++..++...
T Consensus       607 ~~~~iiTGpN~~GKSt~lr~v~l~~ilAq~G~~--VPa~~a~i~~~d~I~triga~d~i~~g~STF~~E~~~~~~il~~a  684 (854)
T PRK05399        607 RRLLLITGPNMAGKSTYMRQVALIVLLAQIGSF--VPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMTETANILNNA  684 (854)
T ss_pred             CcEEEEECCCCCCcHHHHHHHHHHHHHHhcCCc--eeccceEecccCeeeeccCcccccccCcccHHHHHHHHHHHHHhC
Confidence            457899999999999998877766555544333  355544444 3567888774321   111     23444555555


Q ss_pred             CCccEEEEecccc
Q psy8456         221 KDIDVIGIDEGQF  233 (353)
Q Consensus       221 ~~~~~i~IDE~QF  233 (353)
                      .+..+|++||.=.
T Consensus       685 t~~sLvllDE~Gr  697 (854)
T PRK05399        685 TERSLVLLDEIGR  697 (854)
T ss_pred             CCCcEEEEecCCC
Confidence            5679999999755

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=88.70  E-value=0.74  Score=46.10  Aligned_cols=84  Identities=18%  Similarity=0.209  Sum_probs=45.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHH-HHHhCCEEEEEeeecCCCCCC-Cceeecc--Ccccceee-----cccHhhhcccC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRR-YQYANYRCMIVRYAKDDRYDT-EKVSTHD--QQKLTAVS-----AVELNKLIPHT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~-~~~~~~~~~~~k~~~D~R~~~-~~i~s~~--g~~~~a~~-----~~~~~~~~~~~  220 (353)
                      +..-++.||-|+|||+ ||+.+.. +...++.|+++-|+-=.=..- +-..-|.  +..+.-..     ......+....
T Consensus        22 ~~~~fv~G~~GtGKs~-l~~~i~~~~~~~~~~~~~~a~tg~AA~~i~~G~T~hs~f~i~~~~~~~~~~~~~~~~~~~~~l  100 (364)
T PF05970_consen   22 GLNFFVTGPAGTGKSF-LIKAIIDYLRSRGKKVLVTAPTGIAAFNIPGGRTIHSFFGIPINNNEKSQCKISKNSRLRERL  100 (364)
T ss_pred             CcEEEEEcCCCCChhH-HHHHHHHHhccccceEEEecchHHHHHhccCCcchHHhcCccccccccccccccccchhhhhh
Confidence            4456899999999985 4555544 466678888887742110000 1112221  11111000     01111222335


Q ss_pred             CCccEEEEeccccc
Q psy8456         221 KDIDVIGIDEGQFV  234 (353)
Q Consensus       221 ~~~~~i~IDE~QF~  234 (353)
                      .+.++++|||+-.+
T Consensus       101 ~~~~~lIiDEism~  114 (364)
T PF05970_consen  101 RKADVLIIDEISMV  114 (364)
T ss_pred             hhheeeecccccch
Confidence            78899999999985

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=88.62  E-value=0.59  Score=42.05  Aligned_cols=79  Identities=18%  Similarity=0.124  Sum_probs=40.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCccccee---e-----cccHhhhcccCCCc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTAV---S-----AVELNKLIPHTKDI  223 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a~---~-----~~~~~~~~~~~~~~  223 (353)
                      .+++||.+|||||-|-...-....++.-+  +.|+.-.+.+ .+.+.++-+..-...   +     ...+..++....+.
T Consensus         2 ~~ltG~N~~GKst~l~~i~~~~~la~~G~--~v~a~~~~~~~~d~il~~~~~~d~~~~~~s~fs~~~~~l~~~l~~~~~~   79 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGLIVIMAQIGS--FVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATEN   79 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHHHhCC--CeeehheEecccceEEEEeCCCCchhccccHHHHHHHHHHHHHHhCCCC
Confidence            36899999999998766664443332222  2222222222 123344433211110   0     11233334444578


Q ss_pred             cEEEEecccc
Q psy8456         224 DVIGIDEGQF  233 (353)
Q Consensus       224 ~~i~IDE~QF  233 (353)
                      +++++||.--
T Consensus        80 ~llllDEp~~   89 (185)
T smart00534       80 SLVLLDELGR   89 (185)
T ss_pred             eEEEEecCCC
Confidence            9999999753

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=88.59  E-value=0.75  Score=52.82  Aligned_cols=108  Identities=15%  Similarity=0.144  Sum_probs=70.5

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCCh-hhhc---ccCCCccEEEEccccChH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVEL-NKLI---PHTKDIDVIGIDEGQFFP   85 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l-~ei~---~~~~~~dvV~IDEaQFF~   85 (353)
                      -+||||-|-....-++..|.+|+.+-|+  .|.. ..+..-.|+  ++..+.++ ....   ......++|+|||+...+
T Consensus       407 GTGKTt~l~~~~~~~e~~G~~V~g~ApT--gkAA-~~L~e~~Gi--~a~TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~  481 (1102)
T PRK13826        407 GAGKTTMMKAAREAWEAAGYRVVGGALA--GKAA-EGLEKEAGI--QSRTLSSWELRWNQGRDQLDNKTVFVLDEAGMVA  481 (1102)
T ss_pred             CCCHHHHHHHHHHHHHHcCCeEEEEcCc--HHHH-HHHHHhhCC--CeeeHHHHHhhhccCccCCCCCcEEEEECcccCC
Confidence            3799999888888888999999999884  2321 112222233  34434332 1111   123457899999999996


Q ss_pred             --HHHHHHHHHHhCCCEEEEEeccccc----ccCCchhHhhhh
Q psy8456          86 --DVVSFAESMANAGKIVVVAALDGTF----QRTGFNDILSLI  122 (353)
Q Consensus        86 --dIv~l~~~l~~~G~~VivaGLd~DF----r~~pF~~~~~Ll  122 (353)
                        ++..+.+.+...|..|++.|=..=.    .|.||.....-+
T Consensus       482 ~~~m~~Ll~~~~~~garvVLVGD~~QL~~V~aG~~f~~l~~~i  524 (1102)
T PRK13826        482 SRQMALFVEAVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRI  524 (1102)
T ss_pred             HHHHHHHHHHHHhcCCEEEEECCHHHcCCCCCCcHHHHHHhhc
Confidence              7778888888889999999821111    367776655433

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=88.56  E-value=0.4  Score=36.93  Aligned_cols=18  Identities=44%  Similarity=0.527  Sum_probs=15.5

Q ss_pred             cceeeeeccCCCCchhHH
Q psy8456         150 QEKEVILGPMFSGKTTEL  167 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~L  167 (353)
                      +...+|+|+.+|||||-|
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            457999999999999854

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=88.56  E-value=0.66  Score=43.36  Aligned_cols=39  Identities=10%  Similarity=-0.037  Sum_probs=33.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +...++.||.+||||+-.++-+.+...+|.+|+.+.-..
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~ee   59 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALEE   59 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEeeC
Confidence            457889999999999999999988878899999887543

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=88.54  E-value=1.6  Score=44.73  Aligned_cols=80  Identities=19%  Similarity=0.193  Sum_probs=54.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccc----------------e-eecccH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLT----------------A-VSAVEL  213 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~----------------a-~~~~~~  213 (353)
                      +..++...-|||||+-+-+.+.....+|-+|.|..|..|-=-   ++..|.++.+.                + ..+..-
T Consensus       117 ~~~lv~AV~GaGKTEMif~~i~~al~~G~~vciASPRvDVcl---El~~Rlk~aF~~~~I~~Lyg~S~~~fr~plvVaTt  193 (441)
T COG4098         117 EDTLVWAVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDVCL---ELYPRLKQAFSNCDIDLLYGDSDSYFRAPLVVATT  193 (441)
T ss_pred             CcEEEEEecCCCchhhhHHHHHHHHhcCCeEEEecCcccchH---HHHHHHHHhhccCCeeeEecCCchhccccEEEEeh
Confidence            356788889999999999999999999999999999887521   12222222221                1 111122


Q ss_pred             hhhcccCCCccEEEEecccc
Q psy8456         214 NKLIPHTKDIDVIGIDEGQF  233 (353)
Q Consensus       214 ~~~~~~~~~~~~i~IDE~QF  233 (353)
                      ..++...+-+|+++|||+.=
T Consensus       194 HQLlrFk~aFD~liIDEVDA  213 (441)
T COG4098         194 HQLLRFKQAFDLLIIDEVDA  213 (441)
T ss_pred             HHHHHHHhhccEEEEecccc
Confidence            23333457799999999983

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=88.45  E-value=3.5  Score=38.83  Aligned_cols=81  Identities=16%  Similarity=0.129  Sum_probs=46.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCcccc---eee-----cccHhhhcccC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLT---AVS-----AVELNKLIPHT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~---a~~-----~~~~~~~~~~~  220 (353)
                      ++..+++||.++||||-|-...-....+..-+  +.|+...+.+ -+.|-||.|..-.   ..+     ...+..++...
T Consensus        31 g~~~~itG~N~~GKStll~~i~~~~~la~~G~--~v~a~~~~~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~  108 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVALITIMAQIGS--FVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNC  108 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHhCCC--EEEcCceEEeccceEEEEecCccccccccchHHHHHHHHHHHHHhC
Confidence            56789999999999986655544343333322  3344333332 2356666543211   111     23355555555


Q ss_pred             CCccEEEEeccc
Q psy8456         221 KDIDVIGIDEGQ  232 (353)
Q Consensus       221 ~~~~~i~IDE~Q  232 (353)
                      .+.+++++||.=
T Consensus       109 ~~~sLvllDE~~  120 (222)
T cd03287         109 TSRSLVILDELG  120 (222)
T ss_pred             CCCeEEEEccCC
Confidence            678999999953

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=88.43  E-value=0.58  Score=43.71  Aligned_cols=40  Identities=25%  Similarity=0.361  Sum_probs=30.6

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhC----CEEEEEeeec
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYAN----YRCMIVRYAK  188 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~----~~~~~~k~~~  188 (353)
                      ..+..+|.|+-||||||-|+.|+...-..+    .++++++++.
T Consensus        12 ~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~   55 (315)
T PF00580_consen   12 TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTN   55 (315)
T ss_dssp             -SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSH
T ss_pred             CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCH
Confidence            345678899999999999999998876655    6788887753

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms

Probab=88.07  E-value=1.1  Score=38.41  Aligned_cols=35  Identities=20%  Similarity=0.134  Sum_probs=31.3

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecC
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKD  189 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D  189 (353)
                      |+.| .+||||+-.+.-++.++.+|.+|..+||..+
T Consensus         4 ~~~~-~~~Gkt~~~~~l~~~l~~~~~~v~~~kp~~~   38 (134)
T cd03109           4 FGTG-TDIGKTVATAILARALKEKGYRVAPLKPVQT   38 (134)
T ss_pred             EeCC-CCcCHHHHHHHHHHHHHHCCCeEEEEecCCC
Confidence            5566 5699999999999999999999999999875

The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=87.98  E-value=1.2  Score=44.33  Aligned_cols=77  Identities=21%  Similarity=0.172  Sum_probs=41.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHH--HhCCEEEEEeeecCCCCC-CCceeeccCcccceeecccHhhhccc--CCCccE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQ--YANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDV  225 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~--~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~  225 (353)
                      ...+|+|+++|||||-|-.-+..+.  ....+++.+.....-... .+.+..+.+      ....+.+++..  -.++|.
T Consensus       149 ~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El~~~~~~~v~~~~~------~~~~~~~ll~~aLR~~PD~  222 (319)
T PRK13894        149 RNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCAAENYVQYHTS------IDVNMTALLKTTLRMRPDR  222 (319)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCccccCCCCEEEEecC------CCCCHHHHHHHHhcCCCCE
Confidence            3568999999999976654444331  234566654432221111 111111111      11234555432  368999


Q ss_pred             EEEecccc
Q psy8456         226 IGIDEGQF  233 (353)
Q Consensus       226 i~IDE~QF  233 (353)
                      |++.|..=
T Consensus       223 IivGEiR~  230 (319)
T PRK13894        223 ILVGEVRG  230 (319)
T ss_pred             EEEeccCC
Confidence            99999874

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=87.96  E-value=0.76  Score=52.27  Aligned_cols=105  Identities=16%  Similarity=0.122  Sum_probs=63.5

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhc----ccCCCccEEEEccccChH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLI----PHTKDIDVIGIDEGQFFP   85 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~----~~~~~~dvV~IDEaQFF~   85 (353)
                      =+||||-|-....-++..|.+|+++-|+  .+.. ..+.  .+..++|..+.++..-.    ....+.++|+|||+-..+
T Consensus       372 GTGKTT~l~~~~~~~e~~G~~V~~~ApT--GkAA-~~L~--e~tGi~a~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~  446 (988)
T PRK13889        372 GTGKSAMLGVAREAWEAAGYEVRGAALS--GIAA-ENLE--GGSGIASRTIASLEHGWGQGRDLLTSRDVLVIDEAGMVG  446 (988)
T ss_pred             CCCHHHHHHHHHHHHHHcCCeEEEecCc--HHHH-HHHh--hccCcchhhHHHHHhhhcccccccccCcEEEEECcccCC
Confidence            3799996443444566779999999883  1211 1111  11222333333332100    123467899999999996


Q ss_pred             --HHHHHHHHHHhCCCEEEEEecccc-----cccCCchhHhh
Q psy8456          86 --DVVSFAESMANAGKIVVVAALDGT-----FQRTGFNDILS  120 (353)
Q Consensus        86 --dIv~l~~~l~~~G~~VivaGLd~D-----Fr~~pF~~~~~  120 (353)
                        ++..+.+.+...|..|++.| |.+     =.|.+|.....
T Consensus       447 ~~~m~~LL~~a~~~garvVLVG-D~~QLpsV~aG~~f~~L~~  487 (988)
T PRK13889        447 TRQLERVLSHAADAGAKVVLVG-DPQQLQAIEAGAAFRSIHE  487 (988)
T ss_pred             HHHHHHHHHhhhhCCCEEEEEC-CHHHcCCCCCCchHHHHHH
Confidence              67788777778899999998 222     13667765533

>TIGR02012 tigrfam_recA protein RecA

Probab=87.87  E-value=0.65  Score=46.37  Aligned_cols=37  Identities=30%  Similarity=0.219  Sum_probs=33.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+..|+||.+|||||-.++.+...+..|.+|+++..
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~   91 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDA   91 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcc
Confidence            4578899999999999999999999999999998744

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=87.76  E-value=0.87  Score=41.74  Aligned_cols=38  Identities=13%  Similarity=-0.081  Sum_probs=32.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +...++.|+.+||||+-+++.+.+....|.+|+++...
T Consensus        20 G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~e   57 (229)
T TIGR03881        20 GFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTTE   57 (229)
T ss_pred             CeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            56788999999999999999888777789999888753

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=87.70  E-value=1.6  Score=39.59  Aligned_cols=95  Identities=12%  Similarity=0.150  Sum_probs=48.4

Q ss_pred             cCCCCchHHHHHHHHHHHHH--cCceEEEEeeccCCCCCCCc--eeeccC-----Cceeee--ecCCh----hhhcccCC
Q psy8456           7 DDRINPYIVHFCRRIRRYQY--ANYRCMIVRYAKDDRYDTEK--VATHDQ-----QKLTAV--SAVEL----NKLIPHTK   71 (353)
Q Consensus         7 ~~~~~GKSteLLrr~~ry~~--agkkvlv~Kp~iDtRy~~~~--I~Sr~G-----~~~~Ai--~i~~l----~ei~~~~~   71 (353)
                      |+-+.|+..+++.+++++..  .+..++++-|.     |.++  +.....     ...+.+  ...++    .++.....
T Consensus        15 ~~~~~~~~~~~~~~l~~~~~~~~~~~lll~G~~-----G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~   89 (226)
T TIGR03420        15 DNFYAGGNAELLAALRQLAAGKGDRFLYLWGES-----GSGKSHLLQAACAAAEERGKSAIYLPLAELAQADPEVLEGLE   89 (226)
T ss_pred             cCcCcCCcHHHHHHHHHHHhcCCCCeEEEECCC-----CCCHHHHHHHHHHHHHhcCCcEEEEeHHHHHHhHHHHHhhcc
Confidence            34445667777777777632  33456666652     3331  111100     011121  11111    22223345


Q ss_pred             CccEEEEccccChH--H-----HHHHHHHHHhCCCEEEEEec
Q psy8456          72 DIDVIGIDEGQFFP--D-----VVSFAESMANAGKIVVVAAL  106 (353)
Q Consensus        72 ~~dvV~IDEaQFF~--d-----Iv~l~~~l~~~G~~VivaGL  106 (353)
                      +.++++|||+|.++  .     +..+.+.+...+..+++.+=
T Consensus        90 ~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~  131 (226)
T TIGR03420        90 QADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGR  131 (226)
T ss_pred             cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECC
Confidence            67899999999985  2     44444444556677776543

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=87.64  E-value=0.83  Score=43.89  Aligned_cols=23  Identities=30%  Similarity=0.311  Sum_probs=17.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQ  175 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~  175 (353)
                      -+++||.|+||||-+...++.+.
T Consensus        39 lll~Gp~GtGKT~la~~~~~~l~   61 (337)
T PRK12402         39 LLVQGPPGSGKTAAVRALARELY   61 (337)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            47899999999987766655543

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=87.61  E-value=4.3  Score=45.28  Aligned_cols=82  Identities=16%  Similarity=0.102  Sum_probs=52.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceee---c---ccHhhhcc---cC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVS---A---VELNKLIP---HT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~---~---~~~~~~~~---~~  220 (353)
                      +.+..|+||.+||||+-+++.+.+.+.+|.+|+.+.....-+-   ....+.|..+.-+.   .   .....++.   ..
T Consensus        60 GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~E~t~~~---~~A~~lGvDl~~llv~~~~~~E~~l~~i~~lv~~  136 (790)
T PRK09519         60 GRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDP---DYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRS  136 (790)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchhH---HHHHHcCCChhHeEEecCCCHHHHHHHHHHHhhc
Confidence            4578899999999999999999999999999998876543220   11222232221111   1   11111111   13


Q ss_pred             CCccEEEEeccccc
Q psy8456         221 KDIDVIGIDEGQFV  234 (353)
Q Consensus       221 ~~~~~i~IDE~QF~  234 (353)
                      ..+++|+||-++-+
T Consensus       137 ~~~~LVVIDSI~aL  150 (790)
T PRK09519        137 GALDIVVIDSVAAL  150 (790)
T ss_pred             CCCeEEEEcchhhh
Confidence            57999999999954

>smart00072 GuKc Guanylate kinase homologues

Probab=87.58  E-value=2  Score=38.44  Aligned_cols=19  Identities=37%  Similarity=0.349  Sum_probs=15.0

Q ss_pred             ceeeeeccCCCCchhHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~  169 (353)
                      .+.+++||.+|||+|-.-+
T Consensus         3 r~ivl~Gpsg~GK~tl~~~   21 (184)
T smart00072        3 RPIVLSGPSGVGKGTLLAE   21 (184)
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            4678999999999984333

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=87.57  E-value=0.68  Score=43.24  Aligned_cols=25  Identities=24%  Similarity=0.159  Sum_probs=18.6

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .|.+.+++||.|+||||-+-.-+.+
T Consensus         3 ~G~l~vlsgPSG~GKsTl~k~L~~~   27 (191)
T COG0194           3 KGLLIVLSGPSGVGKSTLVKALLED   27 (191)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhh
Confidence            3678899999999999855444333

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=87.52  E-value=0.29  Score=43.10  Aligned_cols=24  Identities=29%  Similarity=0.239  Sum_probs=17.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+.+|+||++|||||-+=.-...+
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~   25 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARL   25 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            456899999999998665443443

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=87.41  E-value=1.9  Score=37.16  Aligned_cols=20  Identities=40%  Similarity=0.617  Sum_probs=15.4

Q ss_pred             eeeeccCCCCchhHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .+|+||.+||||| |++.+.+
T Consensus         2 i~i~GpsGsGKst-l~~~L~~   21 (137)
T cd00071           2 IVLSGPSGVGKST-LLKRLLE   21 (137)
T ss_pred             EEEECCCCCCHHH-HHHHHHh
Confidence            4789999999998 5555544

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK03839 putative kinase; Provisional

Probab=87.23  E-value=0.44  Score=42.15  Aligned_cols=22  Identities=27%  Similarity=0.075  Sum_probs=17.0

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++|+|||||||---+-++++
T Consensus         3 I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          3 IAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4789999999999655555554

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=87.18  E-value=0.85  Score=45.87  Aligned_cols=79  Identities=20%  Similarity=0.136  Sum_probs=40.6

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCce--e-eccCcccceeecccHhhhccc--CCCcc
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKV--S-THDQQKLTAVSAVELNKLIPH--TKDID  224 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i--~-s~~g~~~~a~~~~~~~~~~~~--~~~~~  224 (353)
                      ..-+|.||++|||||-| +.+-.+.-.+.+++.+.....-... .+.+  . +.++...   ......+++..  -.++|
T Consensus       163 ~nilI~G~tGSGKTTll-~aLl~~i~~~~rivtiEd~~El~l~~~~~v~l~~~~~~~~~---~~~t~~~ll~~~LR~~pD  238 (344)
T PRK13851        163 LTMLLCGPTGSGKTTMS-KTLISAIPPQERLITIEDTLELVIPHENHVRLLYSKNGAGL---GAVTAEHLLQASLRMRPD  238 (344)
T ss_pred             CeEEEECCCCccHHHHH-HHHHcccCCCCCEEEECCCccccCCCCCEEEEEeeccccCc---CccCHHHHHHHHhcCCCC
Confidence            34689999999999876 4444443345555554432211111 1111  1 1111111   11233344332  36799


Q ss_pred             EEEEecccc
Q psy8456         225 VIGIDEGQF  233 (353)
Q Consensus       225 ~i~IDE~QF  233 (353)
                      .|++.|..=
T Consensus       239 ~IivGEiR~  247 (344)
T PRK13851        239 RILLGEMRD  247 (344)
T ss_pred             eEEEEeeCc
Confidence            999999864

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=86.99  E-value=1.1  Score=39.48  Aligned_cols=27  Identities=33%  Similarity=0.140  Sum_probs=20.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA  177 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~  177 (353)
                      +..+|+||.+||||+-|=...-..-.+
T Consensus        22 ~~~~i~G~NgsGKS~~l~~i~~~~~~~   48 (162)
T cd03227          22 SLTIITGPNGSGKSTILDAIGLALGGA   48 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            478999999999998776654444433

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=86.98  E-value=0.28  Score=44.99  Aligned_cols=13  Identities=46%  Similarity=0.593  Sum_probs=11.8

Q ss_pred             eeeeccCCCCchh
Q psy8456         153 EVILGPMFSGKTT  165 (353)
Q Consensus       153 ~vi~G~M~sGKt~  165 (353)
                      -|.+|+|+|||||
T Consensus         5 IvLiG~mGaGKST   17 (172)
T COG0703           5 IVLIGFMGAGKST   17 (172)
T ss_pred             EEEEcCCCCCHhH
Confidence            4789999999998

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=86.93  E-value=1.3  Score=53.89  Aligned_cols=38  Identities=18%  Similarity=0.190  Sum_probs=28.7

Q ss_pred             cceeeeeccCCCCchhHHHHH---H-HHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRR---I-RRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~---~-~~~~~~~~~~~~~k~~  187 (353)
                      +...+|.|+-|+||||-|...   + ..++..|++|+.+-|+
T Consensus      1036 ~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~~g~~v~glApT 1077 (1960)
T TIGR02760      1036 DRFVAVQGLAGVGKTTMLESRYKPVLQAFESEQLQVIGLAPT 1077 (1960)
T ss_pred             CcEEEEEeCCCCCHHHhHHHHHHHHHHHHHhcCCeEEEEeCh
Confidence            356788999999999999432   2 2345678999988775

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=86.85  E-value=11  Score=35.38  Aligned_cols=80  Identities=21%  Similarity=0.166  Sum_probs=44.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCC-CceeeccCccc---ce-----eecccHhhhcccC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDT-EKVSTHDQQKL---TA-----VSAVELNKLIPHT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~-~~i~s~~g~~~---~a-----~~~~~~~~~~~~~  220 (353)
                      ++..+++||.++|||+-|-...-..-.++.-+  +-|+.-.+-+. +.|-||.|..-   ..     .....+..++...
T Consensus        30 ~~~~~itG~n~~gKs~~l~~i~~~~~la~~G~--~vpa~~~~i~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~  107 (218)
T cd03286          30 PRILVLTGPNMGGKSTLLRTVCLAVIMAQMGM--DVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHA  107 (218)
T ss_pred             CcEEEEECCCCCchHHHHHHHHHHHHHHHcCC--ccCccccEeccccEEEEecCcccccccCcchHHHHHHHHHHHHHhC
Confidence            46779999999999986665555543332211  12222222221 34555543211   11     1123455566666


Q ss_pred             CCccEEEEecc
Q psy8456         221 KDIDVIGIDEG  231 (353)
Q Consensus       221 ~~~~~i~IDE~  231 (353)
                      .+..+|++||.
T Consensus       108 ~~~sLvLlDE~  118 (218)
T cd03286         108 TPDSLVILDEL  118 (218)
T ss_pred             CCCeEEEEecc
Confidence            77899999994

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=86.84  E-value=0.8  Score=45.83  Aligned_cols=37  Identities=27%  Similarity=0.182  Sum_probs=33.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+..|+||.+|||||-.++.+.+++..|.+|+++..
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~   91 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDA   91 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECc
Confidence            4578899999999999999999999999999998865

RecA couples ATP hydrolysis to DNA strand exchange.

>CHL00181 cbbX CbbX; Provisional

Probab=86.81  E-value=1.3  Score=43.05  Aligned_cols=24  Identities=21%  Similarity=0.083  Sum_probs=16.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQY  176 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~  176 (353)
                      -+++||.|+|||+-.-..++.+..
T Consensus        62 ill~G~pGtGKT~lAr~la~~~~~   85 (287)
T CHL00181         62 MSFTGSPGTGKTTVALKMADILYK   85 (287)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            467899999999765554444433

>PTZ00424 helicase 45; Provisional

Probab=86.73  E-value=0.56  Score=46.35  Aligned_cols=36  Identities=11%  Similarity=0.189  Sum_probs=24.0

Q ss_pred             eeeeccCCCCchhHHH-HHHHHHH--HhCCEEEEEeeec
Q psy8456         153 EVILGPMFSGKTTELI-RRIRRYQ--YANYRCMIVRYAK  188 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li-~~~~~~~--~~~~~~~~~k~~~  188 (353)
                      .++.+|.|||||.-.+ -.++...  ..+.+++++-|..
T Consensus        68 ~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~  106 (401)
T PTZ00424         68 TIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTR  106 (401)
T ss_pred             EEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCH
Confidence            4688999999997543 3333332  2466788888853

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=86.70  E-value=1  Score=42.31  Aligned_cols=40  Identities=18%  Similarity=0.012  Sum_probs=34.4

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEeeec
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVRYAK  188 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k~~~  188 (353)
                      .+++.++.|+.++|||+-+++-+.++... |.+|+++....
T Consensus        29 ~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~E~   69 (271)
T cd01122          29 KGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEE   69 (271)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEccc
Confidence            35688999999999999999999988766 99999987644

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=86.68  E-value=3.3  Score=37.55  Aligned_cols=31  Identities=19%  Similarity=0.251  Sum_probs=27.9

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCC
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDD   40 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDt   40 (353)
                      =|||||-+=+.+.++..+|.+|.++|+.-..
T Consensus        12 ~SGKTTLie~lv~~L~~~G~rVa~iKH~hh~   42 (161)
T COG1763          12 NSGKTTLIEKLVRKLKARGYRVATVKHAHHD   42 (161)
T ss_pred             CCChhhHHHHHHHHHHhCCcEEEEEEecCCC
Confidence            4899999999999999999999999997554

>PRK13768 GTPase; Provisional

Probab=86.63  E-value=0.86  Score=43.40  Aligned_cols=34  Identities=29%  Similarity=0.197  Sum_probs=30.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +.++.|+-||||||-.......+...|++|+++.
T Consensus         4 ~i~v~G~~G~GKTt~~~~~~~~l~~~g~~v~~i~   37 (253)
T PRK13768          4 IVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVN   37 (253)
T ss_pred             EEEEECCCCccHHHHHHHHHHHHHhcCCceEEEE
Confidence            4688999999999999888888888999999875

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=86.63  E-value=1.3  Score=34.89  Aligned_cols=98  Identities=8%  Similarity=-0.098  Sum_probs=51.4

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCc---eeeccC--CceeeeecCChhhhcccCCCccEEEEccccC
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEK---VATHDQ--QKLTAVSAVELNKLIPHTKDIDVIGIDEGQF   83 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~---I~Sr~G--~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQF   83 (353)
                      .=+|||+-+...+..+...+..++.+.+..........   ......  ............+.. ....+++|+|||++-
T Consensus        11 ~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~viiiDei~~   89 (148)
T smart00382       11 PGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALA-RKLKPDVLILDEITS   89 (148)
T ss_pred             CCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHH-HhcCCCEEEEECCcc
Confidence            34899999999988877776677777775433221100   000000  000000011111111 123379999999999


Q ss_pred             hH-H-HHH----------HHHHHHhCCCEEEEEecc
Q psy8456          84 FP-D-VVS----------FAESMANAGKIVVVAALD  107 (353)
Q Consensus        84 F~-d-Iv~----------l~~~l~~~G~~VivaGLd  107 (353)
                      +. . ...          ........+..|+++...
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  125 (148)
T smart00382       90 LLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             cCCHHHHHHHHhhhhhHHHHHHHhcCCCEEEEEeCC
Confidence            95 1 111          122334567778887775

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=86.58  E-value=12  Score=40.91  Aligned_cols=159  Identities=12%  Similarity=0.071  Sum_probs=0.0

Q ss_pred             CchHHHHHHHHHHHHHcCceEEEEeeccCCC----------------CCCCceeeccCCc--------------eeeeec
Q psy8456          11 NPYIVHFCRRIRRYQYANYRCMIVRYAKDDR----------------YDTEKVATHDQQK--------------LTAVSA   60 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agkkvlv~Kp~iDtR----------------y~~~~I~Sr~G~~--------------~~Ai~i   60 (353)
                      ||||.-.+-.+......|.+++++-|   ||                .+.....-+.|..              -.-+.+
T Consensus       293 SGKT~va~~~il~~~~~g~q~lilaP---T~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvV  369 (681)
T PRK10917        293 SGKTVVAALAALAAIEAGYQAALMAP---TEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVI  369 (681)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEEec---cHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEE


Q ss_pred             CChhhhccc--CCCccEEEEccccChHHHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceeccc
Q psy8456          61 VELNKLIPH--TKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC  138 (353)
Q Consensus        61 ~~l~ei~~~--~~~~dvV~IDEaQFF~dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~C  138 (353)
                      .+..-+...  .++.++|+|||+|-|  -+.....+...|...-+-++..    .|.+.+..+..+.+            
T Consensus       370 gT~~ll~~~v~~~~l~lvVIDE~Hrf--g~~qr~~l~~~~~~~~iL~~SA----Tp~prtl~~~~~g~------------  431 (681)
T PRK10917        370 GTHALIQDDVEFHNLGLVIIDEQHRF--GVEQRLALREKGENPHVLVMTA----TPIPRTLAMTAYGD------------  431 (681)
T ss_pred             chHHHhcccchhcccceEEEechhhh--hHHHHHHHHhcCCCCCEEEEeC----CCCHHHHHHHHcCC------------


Q ss_pred             ccccccccccccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC
Q psy8456         139 FRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD  190 (353)
Q Consensus       139 G~~A~f~~Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~  190 (353)
                      -........-.+...+..-.....+..+++..+.+....|++++++-|.++.
T Consensus       432 ~~~s~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~~~~~g~q~~v~~~~ie~  483 (681)
T PRK10917        432 LDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEE  483 (681)
T ss_pred             CceEEEecCCCCCCCcEEEEeCcccHHHHHHHHHHHHHcCCcEEEEEccccc

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=86.52  E-value=0.9  Score=40.11  Aligned_cols=41  Identities=24%  Similarity=0.220  Sum_probs=31.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHH----------hCCEEEEEeeecC
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQY----------ANYRCMIVRYAKD  189 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~----------~~~~~~~~k~~~D  189 (353)
                      .+++.++.||-++|||+-+++.+..+..          .+.+|+.+....+
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~   81 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS   81 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC
Confidence            4678999999999999999999998865          5678888876554

>PRK14532 adenylate kinase; Provisional

Probab=86.52  E-value=0.46  Score=42.22  Aligned_cols=22  Identities=27%  Similarity=0.454  Sum_probs=17.3

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++|||+|||||.--+-+.+|
T Consensus         3 i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            4789999999999866665554

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=86.51  E-value=1  Score=43.04  Aligned_cols=39  Identities=13%  Similarity=-0.022  Sum_probs=33.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +...+|.|+.++|||+-.++-+.+...+|.+|+++....
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~Ee   74 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVES   74 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEecC
Confidence            457899999999999999999888877899999888653

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK05580 primosome assembly protein PriA; Validated

Probab=86.50  E-value=13  Score=40.52  Aligned_cols=169  Identities=14%  Similarity=0.010  Sum_probs=85.3

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCC----------CCCCCceeeccCCcee-------------e-eecCChh
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDD----------RYDTEKVATHDQQKLT-------------A-VSAVELN   64 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDt----------Ry~~~~I~Sr~G~~~~-------------A-i~i~~l~   64 (353)
                      .-||||.-.+..+.....+|++++++-|.+.-          +.+.....-|.|....             + +.+.+..
T Consensus       171 TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrs  250 (679)
T PRK05580        171 TGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARS  250 (679)
T ss_pred             CCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccH
Confidence            35899999999888888889999999996532          2233223344443211             0 1222222


Q ss_pred             hhcccCCCccEEEEccccChH---------HHHHHHHHHH-hCCCEEEEEecccccccCCchhHhhhhccccce--Eecc
Q psy8456          65 KLIPHTKDIDVIGIDEGQFFP---------DVVSFAESMA-NAGKIVVVAALDGTFQRTGFNDILSLIPLAECV--EKLT  132 (353)
Q Consensus        65 ei~~~~~~~dvV~IDEaQFF~---------dIv~l~~~l~-~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I--~kL~  132 (353)
                      .+..-..+...|+|||+|-+.         +..+++...+ ..|.+++..+=      .|-..+..+.. ..+.  ..|.
T Consensus       251 al~~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~ra~~~~~~~il~SA------Tps~~s~~~~~-~g~~~~~~l~  323 (679)
T PRK05580        251 ALFLPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSA------TPSLESLANAQ-QGRYRLLRLT  323 (679)
T ss_pred             HhcccccCCCEEEEECCCccccccCcCCCCcHHHHHHHHhhccCCCEEEEcC------CCCHHHHHHHh-ccceeEEEec
Confidence            222224678899999998664         1334443333 45777776543      12222222211 1111  1111


Q ss_pred             ceecccccccccccccccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         133 AVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       133 AvC~~CG~~A~f~~Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      ...   +.......++.+-..-.-+..++.=|..|++.+++...+|+.++++-+.
T Consensus       324 ~r~---~~~~~p~v~~id~~~~~~~~~~~~ls~~l~~~i~~~l~~g~qvll~~nr  375 (679)
T PRK05580        324 KRA---GGARLPEVEIIDMRELLRGENGSFLSPPLLEAIKQRLERGEQVLLFLNR  375 (679)
T ss_pred             ccc---ccCCCCeEEEEechhhhhhcccCCCCHHHHHHHHHHHHcCCeEEEEEcC
Confidence            110   0111111111110000000011224578999999999999999988763

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=86.16  E-value=0.85  Score=51.03  Aligned_cols=36  Identities=22%  Similarity=0.131  Sum_probs=27.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCC-EEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANY-RCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~-~~~~~k~  186 (353)
                      ..-+|.|+.||||||.+=+.+...-..+. ++.+.-|
T Consensus        66 ~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~tQP  102 (845)
T COG1643          66 QVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQP  102 (845)
T ss_pred             CEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEecCc
Confidence            46689999999999999988877765333 4445555

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=86.07  E-value=0.65  Score=47.63  Aligned_cols=37  Identities=27%  Similarity=0.486  Sum_probs=26.9

Q ss_pred             cCCCccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEe
Q psy8456          69 HTKDIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        69 ~~~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaG  105 (353)
                      ...++|+++|||+||+.       ++..+.+.+.+.|+.+++.+
T Consensus       208 ~~~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits  251 (450)
T PRK00149        208 KYRSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTS  251 (450)
T ss_pred             HHhcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEEC
Confidence            34579999999999993       24455566667888777654

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=85.99  E-value=3.1  Score=38.13  Aligned_cols=36  Identities=11%  Similarity=0.280  Sum_probs=24.0

Q ss_pred             CCCccEEEEccccChH--H---HHHHHHHHHhCCCE-EEEEe
Q psy8456          70 TKDIDVIGIDEGQFFP--D---VVSFAESMANAGKI-VVVAA  105 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF~--d---Iv~l~~~l~~~G~~-VivaG  105 (353)
                      ..+.++|+|||+|.++  +   +..+.+.....|.. |++++
T Consensus        88 ~~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~  129 (227)
T PRK08903         88 DPEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAG  129 (227)
T ss_pred             cccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeC
Confidence            4467899999999995  3   44445555567775 44443

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=85.99  E-value=0.98  Score=47.24  Aligned_cols=22  Identities=27%  Similarity=0.235  Sum_probs=16.2

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+++||.|+||||-..-.++..
T Consensus        39 ~Lf~GPpGtGKTTlA~~lA~~l   60 (472)
T PRK14962         39 YIFAGPRGTGKTTVARILAKSL   60 (472)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4789999999998655444443

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=85.98  E-value=1.2  Score=41.78  Aligned_cols=38  Identities=18%  Similarity=0.101  Sum_probs=33.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +...++.|+.+|||||-.++.+......|.+++.+...
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e   61 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQ   61 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCC
Confidence            56889999999999999999999887789999887743

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=85.97  E-value=1  Score=40.28  Aligned_cols=35  Identities=26%  Similarity=0.196  Sum_probs=30.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      -.++|+-+|||||-+-+-+..+...|++|-++|+.
T Consensus         4 i~i~G~~gsGKTTli~~L~~~l~~~g~~V~~iK~~   38 (159)
T cd03116           4 IGFVGYSGSGKTTLLEKLIPALSARGLRVAVIKHD   38 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEec
Confidence            45899999999999999888888889999998864

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>PRK09354 recA recombinase A; Provisional

Probab=85.96  E-value=0.97  Score=45.71  Aligned_cols=38  Identities=29%  Similarity=0.220  Sum_probs=33.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +.+..|+||.+|||||-.++.+.+++..|.+|+.+...
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E   97 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAE   97 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCc
Confidence            45788999999999999999999999999999977654

>PRK07933 thymidylate kinase; Validated

Probab=85.91  E-value=1.1  Score=41.66  Aligned_cols=34  Identities=15%  Similarity=-0.022  Sum_probs=29.5

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      -++-|+-||||||.+-.-.+.++.+|++|.+++-
T Consensus         3 IviEG~dGsGKST~~~~L~~~L~~~g~~v~~~~~   36 (213)
T PRK07933          3 IAIEGVDGAGKRTLTEALRAALEARGRSVATLAF   36 (213)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEec
Confidence            4678999999999988888888999999997764

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=85.81  E-value=0.64  Score=44.11  Aligned_cols=31  Identities=29%  Similarity=0.247  Sum_probs=23.5

Q ss_pred             eeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         155 ILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       155 i~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      ++||-||||||---...+.+...|+++.++.
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~~~~~~vN   31 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNGRDVYIVN   31 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT-S-EEEEE
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCceEEE
Confidence            5899999999987777777777889998875

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=85.69  E-value=0.81  Score=50.95  Aligned_cols=37  Identities=16%  Similarity=0.130  Sum_probs=27.7

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      ..-++.|+.||||||.+..-+-.....+.+++++-|.
T Consensus        21 ~~vvv~A~TGSGKTt~~pl~lL~~~~~~~~ilvlqPr   57 (812)
T PRK11664         21 PQVLLKAPTGAGKSTWLPLQLLQHGGINGKIIMLEPR   57 (812)
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHcCCcCCeEEEECCh
Confidence            4568899999999999987665433233478888884

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=85.59  E-value=0.83  Score=46.03  Aligned_cols=86  Identities=12%  Similarity=0.098  Sum_probs=46.4

Q ss_pred             CCCchHHHHHHHHHHHHHc--CceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChH-
Q psy8456           9 RINPYIVHFCRRIRRYQYA--NYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFP-   85 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~a--gkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~-   85 (353)
                      .-+|||.-+-...+.+..+  +.+|+.+... |-  . ..+....+       -....++.....++|+++|||+|++. 
T Consensus       145 ~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~-~~--~-~~~~~~~~-------~~~~~~~~~~~~~~dlLiiDDi~~l~~  213 (405)
T TIGR00362       145 VGLGKTHLLHAIGNEILENNPNAKVVYVSSE-KF--T-NDFVNALR-------NNKMEEFKEKYRSVDLLLIDDIQFLAG  213 (405)
T ss_pred             CCCcHHHHHHHHHHHHHHhCCCCcEEEEEHH-HH--H-HHHHHHHH-------cCCHHHHHHHHHhCCEEEEehhhhhcC
Confidence            4578887665555555444  5666665432 10  0 01111000       01122232234568999999999983 


Q ss_pred             ------HHHHHHHHHHhCCCEEEEEe
Q psy8456          86 ------DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        86 ------dIv~l~~~l~~~G~~VivaG  105 (353)
                            .+..+.+.+.+.|+++++.+
T Consensus       214 ~~~~~~~l~~~~n~~~~~~~~iiits  239 (405)
T TIGR00362       214 KERTQEEFFHTFNALHENGKQIVLTS  239 (405)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCEEEec
Confidence                  24455566667788777654

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=85.56  E-value=1.8  Score=38.64  Aligned_cols=23  Identities=39%  Similarity=0.466  Sum_probs=16.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      +.+-+++||.+|||||-.-+-+.
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~   24 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQ   24 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            35678999999999865443333

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=85.54  E-value=1.5  Score=39.85  Aligned_cols=21  Identities=38%  Similarity=0.308  Sum_probs=16.8

Q ss_pred             ceeeeeccCCCCchhHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~  171 (353)
                      +..+++||.+|||||-|-...
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            368899999999998765543

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a

>TIGR00376 DNA helicase, putative

Probab=85.43  E-value=0.95  Score=49.00  Aligned_cols=37  Identities=27%  Similarity=0.365  Sum_probs=33.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +..+|.||.|+|||+-+...+.....+|++|++..|+
T Consensus       174 ~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~a~s  210 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPS  210 (637)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCc
Confidence            6789999999999999999999888899999998864

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=85.38  E-value=2.9  Score=39.31  Aligned_cols=115  Identities=14%  Similarity=0.113  Sum_probs=71.5

Q ss_pred             CchHHHHHHHHHHHHHcCceEEEEeeccCC-CCCCCceeeccCCcee------eeecC--Ch-hhhc------------c
Q psy8456          11 NPYIVHFCRRIRRYQYANYRCMIVRYAKDD-RYDTEKVATHDQQKLT------AVSAV--EL-NKLI------------P   68 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agkkvlv~Kp~iDt-Ry~~~~I~Sr~G~~~~------Ai~i~--~l-~ei~------------~   68 (353)
                      -||||..+-.+-|.-=.|++|.++.--.=. -+|+....+.-+..++      .+.-+  +. .|+.            -
T Consensus        39 KGKTTAAlG~alRa~GhG~rv~vvQFiKg~~~~GE~~~~~~~~~~v~~~~~~~g~tw~~~~~~~d~~aa~~~w~~a~~~l  118 (198)
T COG2109          39 KGKTTAALGLALRALGHGLRVGVVQFIKGGWKYGEEAALEKFGLGVEFHGMGEGFTWETQDREADIAAAKAGWEHAKEAL  118 (198)
T ss_pred             CChhHHHHHHHHHHhcCCCEEEEEEEeecCcchhHHHHHHhhccceeEEecCCceeCCCcCcHHHHHHHHHHHHHHHHHH
Confidence            489999999999999999999887653321 1233222222111111      11111  00 0111            0


Q ss_pred             cCCCccEEEEccccCh---H--HHHHHHHHHHh--CCCEEEEEecccccccCCchhHhhhhccccceEeccce
Q psy8456          69 HTKDIDVIGIDEGQFF---P--DVVSFAESMAN--AGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  134 (353)
Q Consensus        69 ~~~~~dvV~IDEaQFF---~--dIv~l~~~l~~--~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~Av  134 (353)
                      ..++||+|+.||.---   .  ++.++...+.+  ....||+-|=     +.    -+.|+++||-|++++.+
T Consensus       119 ~~~~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~~~~vIiTGr-----~a----p~~lie~ADlVTEm~~v  182 (198)
T COG2109         119 ADGKYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGR-----GA----PPELIELADLVTEMRLV  182 (198)
T ss_pred             hCCCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECC-----CC----CHHHHHHHHHHhhcccc
Confidence            2467999999998653   2  56666666664  4888999992     22    35699999999999765

>PRK14495 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/unknown domain fusion protein; Provisional

Probab=85.32  E-value=0.98  Score=47.19  Aligned_cols=34  Identities=21%  Similarity=0.167  Sum_probs=31.3

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      -|+|.-||||||-+-+-+..+..+|++|-++|+.
T Consensus         5 ~IvG~sgSGKTTLiekLI~~L~~rG~rVavIKH~   38 (452)
T PRK14495          5 GIIGWKDAGKTGLVERLVAAIAARGFSVSTVKHS   38 (452)
T ss_pred             EEEecCCCCHHHHHHHHHHHHHhCCCeEEEEecc
Confidence            4789999999999999999999999999999964

>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

Probab=85.18  E-value=1.1  Score=50.04  Aligned_cols=82  Identities=18%  Similarity=0.156  Sum_probs=57.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCcccce---ee-----cccHhhhcccC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTA---VS-----AVELNKLIPHT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a---~~-----~~~~~~~~~~~  220 (353)
                      .++-+|+||..|||||-|-+..-..-.|+.-+.  -|+.--+.+ -++|-||.|..-.-   .+     ..+...|+.+.
T Consensus       607 ~~i~lITGPNM~GKSTylRQvali~imAQiGsf--VPA~~A~i~ivD~IfTRiGa~DDL~~G~STFMvEM~Eta~IL~~A  684 (843)
T COG0249         607 RRIILITGPNMGGKSTYLRQVALIVILAQIGSF--VPAEKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNA  684 (843)
T ss_pred             ceEEEEECCCCCccHHHHHHHHHHHHHHHcCCC--eeHHHccccccceeeecccccchhhccccHHHHHHHHHHHHHHhC
Confidence            367899999999999999998888777765544  466656666 36788998853221   11     12455556554


Q ss_pred             CCccEEEEecccc
Q psy8456         221 KDIDVIGIDEGQF  233 (353)
Q Consensus       221 ~~~~~i~IDE~QF  233 (353)
                      .+=..|++||.=.
T Consensus       685 T~~SLvilDEiGR  697 (843)
T COG0249         685 TERSLVILDEIGR  697 (843)
T ss_pred             CCCcEEEEecccC
Confidence            4445999999977

>PRK10867 signal recognition particle protein; Provisional

Probab=85.13  E-value=1.1  Score=46.40  Aligned_cols=134  Identities=18%  Similarity=0.172  Sum_probs=74.9

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEeeecCCCCCC--Ccee---eccCcccceee-cccHhhhc----c-
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVRYAKDDRYDT--EKVS---THDQQKLTAVS-AVELNKLI----P-  218 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k~~~D~R~~~--~~i~---s~~g~~~~a~~-~~~~~~~~----~-  218 (353)
                      .+.+++||-||||||-...-+..+... |++|+++.-  |++-..  +...   .+.|..+-... ..+..++.    . 
T Consensus       101 ~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~--D~~R~aa~eQL~~~a~~~gv~v~~~~~~~dp~~i~~~a~~~  178 (433)
T PRK10867        101 TVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAA--DVYRPAAIEQLKTLGEQIGVPVFPSGDGQDPVDIAKAALEE  178 (433)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEc--cccchHHHHHHHHHHhhcCCeEEecCCCCCHHHHHHHHHHH
Confidence            467889999999999999999999888 999998864  554221  1111   11221111110 11222222    2 


Q ss_pred             -cCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCC------CCCCccHHHHHHHHH
Q psy8456         219 -HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPP------PPEFPDVVSFAESMA  291 (353)
Q Consensus       219 -~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~------~~~f~~~~~~~~~~~  291 (353)
                       ...++|+|+||=+=.+                     +.....+.+|..+.+.+..++      +-.-.+.++.++...
T Consensus       179 a~~~~~DvVIIDTaGrl---------------------~~d~~lm~eL~~i~~~v~p~evllVlda~~gq~av~~a~~F~  237 (433)
T PRK10867        179 AKENGYDVVIVDTAGRL---------------------HIDEELMDELKAIKAAVNPDEILLVVDAMTGQDAVNTAKAFN  237 (433)
T ss_pred             HHhcCCCEEEEeCCCCc---------------------ccCHHHHHHHHHHHHhhCCCeEEEEEecccHHHHHHHHHHHH
Confidence             2467999999987653                     123445555555555332111      111135666665555


Q ss_pred             h-CCC-EEEEEecccccc
Q psy8456         292 N-AGK-IVVVAALDGTFQ  307 (353)
Q Consensus       292 ~-~g~-~Vi~~gLd~df~  307 (353)
                      + .++ -+|+--||+|-+
T Consensus       238 ~~~~i~giIlTKlD~~~r  255 (433)
T PRK10867        238 EALGLTGVILTKLDGDAR  255 (433)
T ss_pred             hhCCCCEEEEeCccCccc
Confidence            3 233 256666776644

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=85.13  E-value=1.1  Score=49.24  Aligned_cols=90  Identities=12%  Similarity=0.034  Sum_probs=52.7

Q ss_pred             CCchHHHHHHHHHHHHHcC--ceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhc---------ccCCCccEEEE
Q psy8456          10 INPYIVHFCRRIRRYQYAN--YRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLI---------PHTKDIDVIGI   78 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~ag--kkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~---------~~~~~~dvV~I   78 (353)
                      =+||||-+-..+.-+...|  .++++.-|.-  |.. ..+.--.|  .+|..+.++....         ......|+|+|
T Consensus       348 GTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg--~AA-~~L~e~~g--~~a~Tih~lL~~~~~~~~~~~~~~~~~~~llIv  422 (720)
T TIGR01448       348 GTGKTTITRAIIELAEELGGLLPVGLAAPTG--RAA-KRLGEVTG--LTASTIHRLLGYGPDTFRHNHLEDPIDCDLLIV  422 (720)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCceEEEEeCch--HHH-HHHHHhcC--CccccHHHHhhccCCccchhhhhccccCCEEEE
Confidence            4799998777777777777  8899988842  211 01110012  1232222221110         11235899999


Q ss_pred             ccccChH--HHHHHHHHHHhCCCEEEEEe
Q psy8456          79 DEGQFFP--DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        79 DEaQFF~--dIv~l~~~l~~~G~~VivaG  105 (353)
                      |||+.++  ....+.+.+ ..|..|++.|
T Consensus       423 DEaSMvd~~~~~~Ll~~~-~~~~rlilvG  450 (720)
T TIGR01448       423 DESSMMDTWLALSLLAAL-PDHARLLLVG  450 (720)
T ss_pred             eccccCCHHHHHHHHHhC-CCCCEEEEEC
Confidence            9999997  444554433 4688898887

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=85.06  E-value=1  Score=45.55  Aligned_cols=37  Identities=22%  Similarity=0.257  Sum_probs=28.9

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecC
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKD  189 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D  189 (353)
                      .+++|.+|||||+-+-.-+.....+|.+++|+-|.-|
T Consensus        18 ~li~G~~GsGKT~~i~~ll~~~~~~g~~~iI~D~kg~   54 (386)
T PF10412_consen   18 ILIIGATGSGKTQAIRHLLDQIRARGDRAIIYDPKGE   54 (386)
T ss_dssp             EEEEE-TTSSHHHHHHHHHHHHHHTT-EEEEEEETTH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCEEEEEECCch
Confidence            5789999999999777777777888999999988643

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>PLN02840 tRNA dimethylallyltransferase

Probab=84.98  E-value=2.1  Score=44.47  Aligned_cols=29  Identities=28%  Similarity=0.321  Sum_probs=22.0

Q ss_pred             cccccceeeeeccCCCCchhHHHHHHHHH
Q psy8456         146 KRIGQEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       146 ~Ri~geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ++..+.+.+|.||.+|||||-.++-+..+
T Consensus        17 ~~~~~~vi~I~GptgsGKTtla~~La~~~   45 (421)
T PLN02840         17 KTKKEKVIVISGPTGAGKSRLALELAKRL   45 (421)
T ss_pred             cccCCeEEEEECCCCCCHHHHHHHHHHHC
Confidence            33345578999999999999887766554

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=84.97  E-value=0.43  Score=40.67  Aligned_cols=21  Identities=29%  Similarity=0.115  Sum_probs=15.5

Q ss_pred             eeeeeccCCCCchhHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~  172 (353)
                      +.++.|+++|||||-.-....
T Consensus         1 li~l~G~~GsGKST~a~~l~~   21 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAE   21 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHh
Confidence            357899999999986544333

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK13938 phosphoheptose isomerase; Provisional

Probab=84.91  E-value=4.7  Score=37.38  Aligned_cols=43  Identities=7%  Similarity=0.140  Sum_probs=35.8

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCC
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR  191 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R  191 (353)
                      .....++++.-.||.|.++++.++..+..|-+++.+....++.
T Consensus       111 ~~~~DllI~iS~SG~t~~vi~a~~~Ak~~G~~vI~iT~~~~s~  153 (196)
T PRK13938        111 ARPGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQ  153 (196)
T ss_pred             CCCCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCCh
Confidence            3445678888899999999999999999999999888755443

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=84.85  E-value=1.6  Score=43.23  Aligned_cols=79  Identities=22%  Similarity=0.181  Sum_probs=45.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCC-CCC--ceeeccCcccceeecccHhhhccc--CCCccEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRY-DTE--KVSTHDQQKLTAVSAVELNKLIPH--TKDIDVI  226 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~-~~~--~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i  226 (353)
                      --+++|++.|||||-|...+.-.- ...|++.+.-+-.-+- ..+  .+.++.+..-  -...++.+++..  -.++|.|
T Consensus       145 siii~G~t~sGKTt~lnall~~Ip-~~~rivtIEdt~E~~~~~~n~~~l~~r~~~~~--~~~v~~~dll~aalR~rPd~I  221 (312)
T COG0630         145 SIIICGGTASGKTTLLNALLDFIP-PEERIVTIEDTPELKLPHENWVQLVTREGESG--SSEVSLEDLLRAALRQRPDYI  221 (312)
T ss_pred             cEEEECCCCCCHHHHHHHHHHhCC-chhcEEEEeccccccCCCCCEEEEEecCCCCC--ccccCHHHHHHHHHhcCCCeE
Confidence            457899999999998877665432 3344554442222221 122  2345544321  112345555432  4678999


Q ss_pred             EEecccc
Q psy8456         227 GIDEGQF  233 (353)
Q Consensus       227 ~IDE~QF  233 (353)
                      +++|.+=
T Consensus       222 ivgEvrg  228 (312)
T COG0630         222 IVGELRG  228 (312)
T ss_pred             EEeeeec
Confidence            9999985

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=84.84  E-value=3.2  Score=37.37  Aligned_cols=98  Identities=11%  Similarity=0.048  Sum_probs=51.7

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEE-eeccC---CCCCCCceee-ccCCceeeee-------------c--CChhhhc-
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIV-RYAKD---DRYDTEKVAT-HDQQKLTAVS-------------A--VELNKLI-   67 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~-Kp~iD---tRy~~~~I~S-r~G~~~~Ai~-------------i--~~l~ei~-   67 (353)
                      .-+||||-|.+.++.++..|.++--| +|..-   .|.|- .+++ ++|....--.             +  +...++. 
T Consensus         8 pG~GKTTll~k~i~~l~~~~~~v~Gf~t~evr~~g~r~GF-~iv~l~~g~~~~la~~~~~~~~~vgky~v~~e~fe~~~~   86 (168)
T PF03266_consen    8 PGVGKTTLLKKVIEELKKKGLPVGGFYTEEVRENGRRIGF-DIVDLNSGEEAILARVDFRSGPRVGKYFVDLESFEEIGL   86 (168)
T ss_dssp             TTSSHHHHHHHHHHHHHHTCGGEEEEEEEEEETTSSEEEE-EEEET-TS-EEEEEETTSS-SCECTTCEE-HHHHHCCCC
T ss_pred             CCCCHHHHHHHHHHHhhccCCccceEEeecccCCCceEEE-EEEECcCCCccccccccccccccCCCEEEcHHHHHHHHH
Confidence            45799999999999998888776444 33321   11111 1222 2332221110             1  1111111 


Q ss_pred             c----cCCCccEEEEccccChH----HHHHHHHHHHhCCCEEEEEeccc
Q psy8456          68 P----HTKDIDVIGIDEGQFFP----DVVSFAESMANAGKIVVVAALDG  108 (353)
Q Consensus        68 ~----~~~~~dvV~IDEaQFF~----dIv~l~~~l~~~G~~VivaGLd~  108 (353)
                      .    ...+.|+++|||+=++.    ...+.+..+.+.+++|+ +-+..
T Consensus        87 ~~L~~~~~~~~liviDEIG~mEl~~~~F~~~v~~~l~s~~~vi-~vv~~  134 (168)
T PF03266_consen   87 PALRNALSSSDLIVIDEIGKMELKSPGFREAVEKLLDSNKPVI-GVVHK  134 (168)
T ss_dssp             CCCHHHHHCCHEEEE---STTCCC-CHHHHHHHHHHCTTSEEE-EE--S
T ss_pred             HHHHhhcCCCCEEEEeccchhhhcCHHHHHHHHHHHcCCCcEE-EEEec
Confidence            1    12578999999999984    67777777778888854 44544

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=84.83  E-value=1.3  Score=42.05  Aligned_cols=22  Identities=32%  Similarity=0.377  Sum_probs=16.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++||-|+||||-+-..++..
T Consensus        41 ~ll~G~~G~GKt~~~~~l~~~l   62 (319)
T PRK00440         41 LLFAGPPGTGKTTAALALAREL   62 (319)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            3899999999998765554443

>KOG0924|consensus

Probab=84.81  E-value=0.84  Score=50.18  Aligned_cols=33  Identities=33%  Similarity=0.396  Sum_probs=26.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      ++..+|+|-.||||||+|-+-++.--++.+..+
T Consensus       371 n~vvvivgETGSGKTTQl~QyL~edGY~~~GmI  403 (1042)
T KOG0924|consen  371 NQVVVIVGETGSGKTTQLAQYLYEDGYADNGMI  403 (1042)
T ss_pred             CcEEEEEecCCCCchhhhHHHHHhcccccCCee
Confidence            356789999999999999998887766665544

>PRK04328 hypothetical protein; Provisional

Probab=84.79  E-value=1.4  Score=41.80  Aligned_cols=38  Identities=11%  Similarity=-0.056  Sum_probs=33.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +...++.|+.+||||+-.++-+.+....|.+++++.-.
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~e   60 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVALE   60 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEee
Confidence            56778999999999999999999988889999988753

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=84.74  E-value=1.7  Score=43.58  Aligned_cols=38  Identities=29%  Similarity=0.274  Sum_probs=32.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +.+.-|+||..|||||-++..+.+++..|..|+++.+.
T Consensus        53 G~ivEi~G~~ssGKttLaL~~ia~~q~~g~~~a~ID~e   90 (322)
T PF00154_consen   53 GRIVEIYGPESSGKTTLALHAIAEAQKQGGICAFIDAE   90 (322)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTT-EEEEEESS
T ss_pred             CceEEEeCCCCCchhhhHHHHHHhhhcccceeEEecCc
Confidence            34677899999999999999999999999999988763

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PRK13695 putative NTPase; Provisional

Probab=84.74  E-value=9.7  Score=33.49  Aligned_cols=37  Identities=27%  Similarity=0.256  Sum_probs=26.8

Q ss_pred             CCCccEEEEccccCh---H-HHHHHHHHHHhCCCEEEEEec
Q psy8456          70 TKDIDVIGIDEGQFF---P-DVVSFAESMANAGKIVVVAAL  106 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF---~-dIv~l~~~l~~~G~~VivaGL  106 (353)
                      ..+++++++||+..+   + +..+....+.+.|.++++.-=
T Consensus        94 l~~~~~lllDE~~~~e~~~~~~~~~l~~~~~~~~~~i~v~h  134 (174)
T PRK13695         94 LEEADVIIIDEIGKMELKSPKFVKAVEEVLDSEKPVIATLH  134 (174)
T ss_pred             cCCCCEEEEECCCcchhhhHHHHHHHHHHHhCCCeEEEEEC
Confidence            467999999996544   3 556667677788998877643

>PHA00729 NTP-binding motif containing protein

Probab=84.72  E-value=1.4  Score=42.12  Aligned_cols=22  Identities=41%  Similarity=0.430  Sum_probs=17.9

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+|+|+.|+||||-....+++.
T Consensus        20 IlItG~pGvGKT~LA~aLa~~l   41 (226)
T PHA00729         20 AVIFGKQGSGKTTYALKVARDV   41 (226)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            5899999999998777766653

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=84.50  E-value=1.9  Score=36.59  Aligned_cols=39  Identities=23%  Similarity=0.194  Sum_probs=30.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCC--EEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANY--RCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~--~~~~~k~~~  188 (353)
                      ++--++.||.|||||+-.+-.+-+.-.+++  +++++-|..
T Consensus        14 ~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~   54 (169)
T PF00270_consen   14 GKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTR   54 (169)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSH
T ss_pred             CCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecc
Confidence            344689999999999999877766555545  899999854

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=84.46  E-value=1.6  Score=40.10  Aligned_cols=39  Identities=18%  Similarity=0.169  Sum_probs=34.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +.+.++.|+.++|||+-.++-+.+...+|.+|+++....
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~e~   54 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLEE   54 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            567889999999999999999999888899999987654

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PRK14489 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional

Probab=84.34  E-value=1.3  Score=44.56  Aligned_cols=37  Identities=24%  Similarity=0.219  Sum_probs=32.7

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      .--++|+-+|||||-+-+.+..+...|++|-++|...
T Consensus       207 ~~~~~g~~~~GKtt~~~~l~~~l~~~g~~v~~iKh~~  243 (366)
T PRK14489        207 LLGVVGYSGTGKTTLLEKLIPELIARGYRIGLIKHSH  243 (366)
T ss_pred             EEEEecCCCCCHHHHHHHHHHHHHHcCCEEEEEEECC
Confidence            3457999999999999999999999999999999643

>PLN03025 replication factor C subunit; Provisional

Probab=84.26  E-value=1.9  Score=42.14  Aligned_cols=23  Identities=26%  Similarity=0.371  Sum_probs=18.0

Q ss_pred             eeeeccCCCCchhHHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQ  175 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~  175 (353)
                      -+++||.|+||||-+.-.++...
T Consensus        37 lll~Gp~G~GKTtla~~la~~l~   59 (319)
T PLN03025         37 LILSGPPGTGKTTSILALAHELL   59 (319)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            36899999999987776666653

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=84.16  E-value=1.2  Score=43.46  Aligned_cols=35  Identities=29%  Similarity=0.237  Sum_probs=30.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      --++|+-||||||-+.+-+..+..+| +|-++|..-
T Consensus         4 i~i~G~~gSGKTTLi~~Li~~L~~~G-~V~~IKhd~   38 (274)
T PRK14493          4 LSIVGYKATGKTTLVERLVDRLSGRG-RVGTVKHMD   38 (274)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCC-CEEEEEEcC
Confidence            35789999999999999999999999 799999854

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=84.12  E-value=1.8  Score=42.55  Aligned_cols=22  Identities=27%  Similarity=0.451  Sum_probs=17.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+|+||.+||||+-.++-+..+
T Consensus         2 i~i~G~t~~GKs~la~~l~~~~   23 (287)
T TIGR00174         2 IFIMGPTAVGKSQLAIQLAKKL   23 (287)
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            4799999999998777765543

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=84.00  E-value=1.5  Score=39.78  Aligned_cols=24  Identities=4%  Similarity=-0.349  Sum_probs=17.2

Q ss_pred             CCchHHHHHHH-HHHHHHcCceEEE
Q psy8456          10 INPYIVHFCRR-IRRYQYANYRCMI   33 (353)
Q Consensus        10 ~~GKSteLLrr-~~ry~~agkkvlv   33 (353)
                      =||||...+.. +..+..+|+.|+.
T Consensus        10 GsGKS~~av~~~i~~~l~~gr~V~t   34 (193)
T PF05707_consen   10 GSGKSYYAVSYVIIPALKKGRPVYT   34 (193)
T ss_dssp             TSSHHHHHHHHHHH-GGGS---EEE
T ss_pred             CCcHhHHHHHHHHHHHHhCCCEEEE
Confidence            48999999999 8887788888877

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.80  E-value=2.4  Score=44.72  Aligned_cols=15  Identities=27%  Similarity=0.344  Sum_probs=13.4

Q ss_pred             CCCccEEEEeccccc
Q psy8456         220 TKDIDVIGIDEGQFV  234 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~  234 (353)
                      ..++.|++|||+|++
T Consensus       114 ~~~~KVvIIDEah~L  128 (491)
T PRK14964        114 SSKFKVYIIDEVHML  128 (491)
T ss_pred             cCCceEEEEeChHhC
Confidence            468899999999997

>PRK06921 hypothetical protein; Provisional

Probab=83.79  E-value=1.4  Score=42.57  Aligned_cols=85  Identities=8%  Similarity=-0.012  Sum_probs=46.8

Q ss_pred             CCCchHHHHHHHHHHHHHc-CceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccC----
Q psy8456           9 RINPYIVHFCRRIRRYQYA-NYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQF----   83 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~a-gkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQF----   83 (353)
                      .-+|||.-+...++....+ |.+|+.+... |--   ..+..       +  .+...+......++|+++||+.|+    
T Consensus       126 ~G~GKThLa~aia~~l~~~~g~~v~y~~~~-~l~---~~l~~-------~--~~~~~~~~~~~~~~dlLiIDDl~~~~~g  192 (266)
T PRK06921        126 PGSGKTHLLTAAANELMRKKGVPVLYFPFV-EGF---GDLKD-------D--FDLLEAKLNRMKKVEVLFIDDLFKPVNG  192 (266)
T ss_pred             CCCcHHHHHHHHHHHHhhhcCceEEEEEHH-HHH---HHHHH-------H--HHHHHHHHHHhcCCCEEEEeccccccCC
Confidence            3467777666666666655 6666655531 100   00000       0  011122233456799999999976    


Q ss_pred             ---hH-----HHHHHHHHHHhCCCEEEEEec
Q psy8456          84 ---FP-----DVVSFAESMANAGKIVVVAAL  106 (353)
Q Consensus        84 ---F~-----dIv~l~~~l~~~G~~VivaGL  106 (353)
                         .+     .+.++++.--+.++++|+.+=
T Consensus       193 ~e~~t~~~~~~lf~iin~R~~~~k~tIitsn  223 (266)
T PRK06921        193 KPRATEWQIEQMYSVLNYRYLNHKPILISSE  223 (266)
T ss_pred             CccCCHHHHHHHHHHHHHHHHCCCCEEEECC
Confidence               22     355555555566888887764

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=83.77  E-value=3.2  Score=37.40  Aligned_cols=138  Identities=12%  Similarity=0.112  Sum_probs=74.7

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCC---CceeeccCc---ccceee-cccHhhhccc-CCCc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDT---EKVSTHDQQ---KLTAVS-AVELNKLIPH-TKDI  223 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~---~~i~s~~g~---~~~a~~-~~~~~~~~~~-~~~~  223 (353)
                      +.+|+|+.+||||+.-.+.+.++   +.+++.+....  -++.   ..|.-|...   ...-+. -.++.+++.. ..+.
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~---~~~~~~iat~~--~~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~~   77 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQS---GLQVLYIATAQ--PFDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAPG   77 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHc---CCCcEeCcCCC--CChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCCC
Confidence            46899999999999877765543   44554433322  1221   123333221   111111 1345555543 4557


Q ss_pred             cEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCC-ccHHHHHHHHHhCCCEEEEEec
Q psy8456         224 DVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEF-PDVVSFAESMANAGKIVVVAAL  302 (353)
Q Consensus       224 ~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f-~~~~~~~~~~~~~g~~Vi~~gL  302 (353)
                      ++|+||=...+.            +....+. +                    ...+ ..+.++++.|...|..+++-+-
T Consensus        78 ~~VlID~Lt~~~------------~n~l~~~-~--------------------~~~~~~~l~~li~~L~~~~~tvVlVs~  124 (170)
T PRK05800         78 RCVLVDCLTTWV------------TNLLFEE-G--------------------EEAIAAEIDALLAALQQLPAKIILVTN  124 (170)
T ss_pred             CEEEehhHHHHH------------HHHhccc-c--------------------hHHHHHHHHHHHHHHHcCCCCEEEEEc
Confidence            789999877641            0000000 0                    0011 3455677888888988888776


Q ss_pred             cccccCCCchhHHh------------hhhcccceEEe
Q psy8456         303 DGTFQRTGFNDILS------------LIPLAECVEKL  327 (353)
Q Consensus       303 d~df~~~~F~~~~~------------L~~~ad~v~kl  327 (353)
                      ...+-.-|.+...+            |-..||.|...
T Consensus       125 Evg~g~vp~~~~~r~~~d~lG~lnq~la~~ad~V~~v  161 (170)
T PRK05800        125 EVGMGIVPEYRLGRHFRDIAGRLNQQLAAAADEVYLV  161 (170)
T ss_pred             CCcccccCCCHHHHHHHHHHHHHHHHHHHHCCEEEEE
Confidence            66566666554433            44566766654

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.74  E-value=2.6  Score=47.68  Aligned_cols=23  Identities=17%  Similarity=0.010  Sum_probs=17.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      ...+++||.|+||||-...-++.
T Consensus        39 HAyLFtGPpGtGKTTLARiLAk~   61 (944)
T PRK14949         39 HAYLFTGTRGVGKTSLARLFAKG   61 (944)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            44589999999999865554444

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=83.72  E-value=0.84  Score=40.12  Aligned_cols=22  Identities=27%  Similarity=0.375  Sum_probs=17.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+++||++|||||.--+-+.+|
T Consensus         2 i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            4789999999999766655555

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=83.66  E-value=2.2  Score=51.27  Aligned_cols=38  Identities=18%  Similarity=0.086  Sum_probs=29.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH----HhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ----YANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~----~~~~~~~~~k~~  187 (353)
                      +.+.+|.|.-|+||||-|-..+.-++    ..|++|+.+-|+
T Consensus       984 dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~glAPT 1025 (1747)
T PRK13709        984 DRFTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGLGPT 1025 (1747)
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEECCc
Confidence            46889999999999998766555543    346788888774

>TIGR00767 rho transcription termination factor Rho

Probab=83.55  E-value=0.96  Score=46.79  Aligned_cols=42  Identities=19%  Similarity=0.256  Sum_probs=26.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR  191 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R  191 (353)
                      |+...|+||.++||||-+....+.+......+.++-..++.|
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER  209 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDER  209 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCCC
Confidence            566789999999999854444444433323334444556676

Members of this family differ in the specificity of RNA binding.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=83.45  E-value=1.6  Score=47.25  Aligned_cols=39  Identities=21%  Similarity=0.152  Sum_probs=29.8

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh----CCEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA----NYRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~----~~~~~~~k~~  187 (353)
                      .....+|.|+.|+||||-+.+.+..+...    +.++.+..|+
T Consensus       166 ~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APT  208 (615)
T PRK10875        166 TRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPT  208 (615)
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCc
Confidence            45789999999999999887777766432    2467777774

>PHA00350 putative assembly protein

Probab=83.43  E-value=2.4  Score=43.74  Aligned_cols=24  Identities=4%  Similarity=-0.241  Sum_probs=19.6

Q ss_pred             CCCchHHHHHH-HHHHHHHcCceEE
Q psy8456           9 RINPYIVHFCR-RIRRYQYANYRCM   32 (353)
Q Consensus         9 ~~~GKSteLLr-r~~ry~~agkkvl   32 (353)
                      .=||||.+.+. .+..+..+|++|+
T Consensus        10 pGSGKT~~aV~~~i~palk~GR~V~   34 (399)
T PHA00350         10 PGSYKSYEAVVYHIIPALKDGRKVI   34 (399)
T ss_pred             CCCchhHHHHHHHHHHHHHCCCEEE
Confidence            34899999998 6788888998764

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=83.30  E-value=1.2  Score=47.53  Aligned_cols=35  Identities=34%  Similarity=0.394  Sum_probs=28.1

Q ss_pred             CCCccEEEEccccChH-HHHHHHHHHHhCCCEEEEE
Q psy8456          70 TKDIDVIGIDEGQFFP-DVVSFAESMANAGKIVVVA  104 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF~-dIv~l~~~l~~~G~~Viva  104 (353)
                      .+-||+|+|||+|=|| ...++|..+..-.|+++.|
T Consensus       293 ~~~yD~ilIDE~QDFP~~F~~Lcf~~tkd~KrlvyA  328 (660)
T COG3972         293 KKAYDYILIDESQDFPQSFIDLCFMVTKDKKRLVYA  328 (660)
T ss_pred             cccccEEEecccccCCHHHHHHHHHHhcCcceEEEe
Confidence            3569999999999998 7999999998755554444

>PRK07413 hypothetical protein; Validated

Probab=83.16  E-value=4.2  Score=41.74  Aligned_cols=138  Identities=16%  Similarity=0.139  Sum_probs=84.0

Q ss_pred             cccccceeeeeccCCCCchhHHHHHHHHHHHhCC------EEEEEeeecC-C-CCCCCceee-------------ccCcc
Q psy8456         146 KRIGQEKEVILGPMFSGKTTELIRRIRRYQYANY------RCMIVRYAKD-D-RYDTEKVST-------------HDQQK  204 (353)
Q Consensus       146 ~Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~------~~~~~k~~~D-~-R~~~~~i~s-------------~~g~~  204 (353)
                      -|-.+-+++++|. +=||||..+-.+-|..-+|+      +|+++.--+. . .||+..+..             +-|..
T Consensus        16 ~~~~Gli~VytG~-GKGKTTAAlGlalRA~G~G~~~~~~~rV~ivQFlKg~~~~~GE~~~l~~l~~~~~~~i~~~~~g~~   94 (382)
T PRK07413         16 ERSKGQLHVYDGE-GKGKSQAALGVVLRTIGLGICEKRQTRVLLLRFLKGPGRAYDEDAAIEALQRGFPHLIDQVRTGRA   94 (382)
T ss_pred             cccCCeEEEEeCC-CCCHHHHHHHHHHHHhcCCCCcCCCCeEEEEEEEcCCCCCCcHHHHHHhccccCCCceEEEECCCC
Confidence            3444678889996 77999999999999999998      9999888887 3 455432211             11211


Q ss_pred             cceee----ccc---Hhhhc----c--cCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhc
Q psy8456         205 LTAVS----AVE---LNKLI----P--HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA  271 (353)
Q Consensus       205 ~~a~~----~~~---~~~~~----~--~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  271 (353)
                      ..-..    ...   ..+.+    .  ...++|+|+.||.-..-                 +.--++.            
T Consensus        95 ~~~~~~~~~~~~~~~a~~~~~~a~~~i~sg~ydlvILDEi~~Al-----------------~~gll~~------------  145 (382)
T PRK07413         95 EFFGADEITKFDRQEAQRGWDIAKGAIASGLYSVVVLDELNPVL-----------------DLGLLPV------------  145 (382)
T ss_pred             CeeeCCCCcHHHHHHHHHHHHHHHHHHhCCCCCEEEEehhHHHH-----------------HCCCccH------------
Confidence            11010    000   00111    1  14789999999987520                 0000111            


Q ss_pred             cCCCCCCCCccHHHHHHHHHhCCCEEEEEeccccccCCCchhHHhhhhcccceEEeeeecc
Q psy8456         272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM  332 (353)
Q Consensus       272 ~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~C~  332 (353)
                               .+|++++++ .-.+..||+-|=+         ....|+++||-|++++.+=+
T Consensus       146 ---------eevl~~L~~-rP~~~evVLTGR~---------ap~~Lie~ADlVTEm~~iKH  187 (382)
T PRK07413        146 ---------DEVVNTLKS-RPEGLEIIITGRA---------APQSLLDIADLHSEMRPHRR  187 (382)
T ss_pred             ---------HHHHHHHHh-CCCCCEEEEeCCC---------CCHHHHHhCCeeEEeceecC
Confidence                     234444432 2357789988743         35789999999999976643

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=83.04  E-value=1.4  Score=51.36  Aligned_cols=25  Identities=28%  Similarity=0.296  Sum_probs=19.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +...++.|+.||||||.|=+-+...
T Consensus        89 ~~VviI~GeTGSGKTTqlPq~lle~  113 (1294)
T PRK11131         89 HQVVIVAGETGSGKTTQLPKICLEL  113 (1294)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHc
Confidence            3466788999999999877665543

>PF02702 KdpD: Osmosensitive K+ channel His kinase sensor domain; InterPro: IPR003852 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []

Probab=82.91  E-value=7.6  Score=36.90  Aligned_cols=142  Identities=18%  Similarity=0.195  Sum_probs=74.6

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCC-------CCCcee----eccCCceeeeecCChhhhcccCCCccEEEE
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRY-------DTEKVA----THDQQKLTAVSAVELNKLIPHTKDIDVIGI   78 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy-------~~~~I~----Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~I   78 (353)
                      -.|||-.+|+.+++...+|..|++=--.--.|-       +-+.|.    .+.|..++-.   ++..+.  ..++++|+|
T Consensus        15 GVGKTy~ML~ea~~l~~~G~DVViG~vethgR~et~~l~~gLe~iP~~~i~y~g~~~~E~---DldaiL--~R~P~vvLV   89 (211)
T PF02702_consen   15 GVGKTYAMLQEAHRLKEQGVDVVIGYVETHGRPETEALLEGLEVIPRKKIEYRGRTLEEM---DLDAIL--ARRPQVVLV   89 (211)
T ss_dssp             TSSHHHHHHHHHHHHHHTT--EEEEE---TT-HHHHHHHCTS-B---EEEEETTEEEEE-----HHHHH--HH--SEEEE
T ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEEEecCCCcHHHHHHHcCCCcCCCeeEeeCCEecccC---CHHHHH--hcCCCEEEe
Confidence            369999999999999999999987443333331       111111    1112221111   233332  245899999


Q ss_pred             ccccCh--H-----HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceecccccccccccccccc
Q psy8456          79 DEGQFF--P-----DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQE  151 (353)
Q Consensus        79 DEaQFF--~-----dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~ge  151 (353)
                      ||-=.-  +     .=+|-++.+.+.||.|+.. |          .+..|=.+.|.|..++.+=...-=+..+ ++.-++
T Consensus        90 DELAHtN~pgsr~~kR~qDVeeLL~aGIdV~TT-l----------NvqHlESlnd~V~~iTgv~vrEtVPD~~-l~~Ade  157 (211)
T PF02702_consen   90 DELAHTNAPGSRHKKRYQDVEELLDAGIDVYTT-L----------NVQHLESLNDVVEQITGVRVRETVPDSV-LDRADE  157 (211)
T ss_dssp             S-TT-B--TT-SSSBHHHHHHHHHHTT-EEEEE-E----------EGGGBGGGHHHHHHHHS----S-B-HHH-HHT-SC
T ss_pred             CcccccCCCCCCCcccHHhHHHHHHCCCeEEEe-e----------eHHHhhhhHHHHHHHhCCeeeeeCCHHH-HhhcCe
Confidence            996554  1     3567788899999999853 3          3556667778888887776532223332 333467


Q ss_pred             eeeeeccCCCCchhHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +++|--+     -.+|++|++.
T Consensus       158 v~lVDi~-----Pe~L~~RL~~  174 (211)
T PF02702_consen  158 VELVDIT-----PEELLERLKE  174 (211)
T ss_dssp             EEEB--------HHHHHHHHHT
T ss_pred             EEEecCC-----HHHHHHHHHc
Confidence            7777554     3788887763

Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the N-terminal domain found in KdpD sensor kinase proteins, which regulate the kdpFABC operon responsible for potassium transport []. The N-terminal domain forms part of the cytoplasmic region of the protein, which may be the sensor domain responsible for sensing turgor pressure [].; GO: 0000155 two-component sensor activity, 0004673 protein histidine kinase activity, 0000160 two-component signal transduction system (phosphorelay), 0016020 membrane; PDB: 2R8R_B.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=82.90  E-value=0.73  Score=44.28  Aligned_cols=63  Identities=22%  Similarity=0.392  Sum_probs=41.4

Q ss_pred             CCCCCcchHHHHHHHhhccCCCC-------C-----CCC-ccHHHHHHHHHhCCCEEEEEeccccccCCCchhHHhhhhc
Q psy8456         254 KAPIKRSPFKTLANENAALNVPP-------P-----PEF-PDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPL  320 (353)
Q Consensus       254 ~~~~~~~~~~~l~~~~~~~~~~~-------~-----~~f-~~~~~~~~~~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~  320 (353)
                      +++++--| +|=..|+.+|+..|       |     |+. .++.++..+||+.|...+|.-=++.|-+          ..
T Consensus       134 P~qLSGGQ-qQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA~eGmTMivVTHEM~FAr----------~V  202 (240)
T COG1126         134 PAQLSGGQ-QQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLAEEGMTMIIVTHEMGFAR----------EV  202 (240)
T ss_pred             ccccCcHH-HHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHHHcCCeEEEEechhHHHH----------Hh
Confidence            44555555 33334666655543       2     333 4677888999999999999988888865          35


Q ss_pred             ccceEEe
Q psy8456         321 AECVEKL  327 (353)
Q Consensus       321 ad~v~kl  327 (353)
                      ||.|.-+
T Consensus       203 adrviFm  209 (240)
T COG1126         203 ADRVIFM  209 (240)
T ss_pred             hheEEEe
Confidence            6666554

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=82.86  E-value=3.5  Score=41.26  Aligned_cols=61  Identities=21%  Similarity=0.198  Sum_probs=36.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQ  232 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~Q  232 (353)
                      .+++||.|-||||-..=.++..   |-+                +.+-.|-.+  ....++..++...+.-||++|||+|
T Consensus        55 vLl~GPPGlGKTTLA~IIA~Em---gvn----------------~k~tsGp~l--eK~gDlaaiLt~Le~~DVLFIDEIH  113 (332)
T COG2255          55 VLLFGPPGLGKTTLAHIIANEL---GVN----------------LKITSGPAL--EKPGDLAAILTNLEEGDVLFIDEIH  113 (332)
T ss_pred             EEeeCCCCCcHHHHHHHHHHHh---cCC----------------eEecccccc--cChhhHHHHHhcCCcCCeEEEehhh
Confidence            4689999999998543322221   111                111122110  1134566666667889999999999


Q ss_pred             cc
Q psy8456         233 FV  234 (353)
Q Consensus       233 F~  234 (353)
                      .+
T Consensus       114 rl  115 (332)
T COG2255         114 RL  115 (332)
T ss_pred             hc
Confidence            96

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=82.82  E-value=2.7  Score=50.21  Aligned_cols=38  Identities=18%  Similarity=0.105  Sum_probs=27.8

Q ss_pred             cceeeeeccCCCCchhHHHHH---HHHH-HHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRR---IRRY-QYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~---~~~~-~~~~~~~~~~k~~  187 (353)
                      +...+|.|+-|+||||-|-..   +..+ +..|.+|+.+-|+
T Consensus       852 dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~glAPT  893 (1623)
T PRK14712        852 DRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPT  893 (1623)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEEech
Confidence            468899999999999986433   3333 2357888888874

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=82.67  E-value=1.7  Score=39.49  Aligned_cols=38  Identities=18%  Similarity=0.137  Sum_probs=32.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhC------CEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYAN------YRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~------~~~~~~k~~  187 (353)
                      +++..|.||.+||||+-+++.+.+....+      .+|+.+...
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e   62 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTE   62 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecC
Confidence            56889999999999999999998887776      788877653

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=82.67  E-value=1.4  Score=42.92  Aligned_cols=22  Identities=36%  Similarity=0.368  Sum_probs=16.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..++||.+|||||-|---+...
T Consensus       114 ~~i~g~~g~GKttl~~~l~~~~  135 (270)
T TIGR02858       114 TLIISPPQCGKTTLLRDLARIL  135 (270)
T ss_pred             EEEEcCCCCCHHHHHHHHhCcc
Confidence            4799999999998765554444

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.65  E-value=2.5  Score=42.28  Aligned_cols=23  Identities=22%  Similarity=0.037  Sum_probs=17.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..+++||-|+||||-....++..
T Consensus        40 ~~L~~Gp~G~GKTtla~~la~~l   62 (363)
T PRK14961         40 AWLLSGTRGVGKTTIARLLAKSL   62 (363)
T ss_pred             EEEEecCCCCCHHHHHHHHHHHh
Confidence            45899999999998665555543

>PRK13973 thymidylate kinase; Provisional

Probab=82.57  E-value=1.9  Score=39.62  Aligned_cols=43  Identities=19%  Similarity=0.147  Sum_probs=33.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRY  192 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~  192 (353)
                      |..-++-|+-||||||..-+-...+..+|++|..++-.-+++.
T Consensus         3 g~~IviEG~dGsGKtTq~~~l~~~l~~~g~~~~~~~~p~~~~~   45 (213)
T PRK13973          3 GRFITFEGGEGAGKSTQIRLLAERLRAAGYDVLVTREPGGSPG   45 (213)
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEECCCCCch
Confidence            4466789999999999988877888889999987753334443

>TIGR00750 lao LAO/AO transport system ATPase

Probab=82.57  E-value=2  Score=41.84  Aligned_cols=36  Identities=17%  Similarity=0.108  Sum_probs=31.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +....++||.+|||||-+..-...+...|.+|.++.
T Consensus        34 ~~~i~i~G~~G~GKttl~~~l~~~~~~~~~~v~~i~   69 (300)
T TIGR00750        34 AHRVGITGTPGAGKSTLLEALGMELRRRGLKVAVIA   69 (300)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            455678999999999999888888888899998876

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=82.56  E-value=1.5  Score=44.22  Aligned_cols=34  Identities=18%  Similarity=0.198  Sum_probs=26.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHHH-HhCCEEEEEee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQ-YANYRCMIVRY  186 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~-~~~~~~~~~k~  186 (353)
                      -++.|+|||||||-.-....... ..|.+|.++..
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l~~~~g~~v~~~~~   36 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATLRRERGWAVAVITY   36 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhccCCeEEEEcc
Confidence            47899999999997655555665 57898888765

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=82.33  E-value=0.69  Score=38.64  Aligned_cols=15  Identities=40%  Similarity=0.452  Sum_probs=12.8

Q ss_pred             eeeeccCCCCchhHH
Q psy8456         153 EVILGPMFSGKTTEL  167 (353)
Q Consensus       153 ~vi~G~M~sGKt~~L  167 (353)
                      .++.||.+|||||-.
T Consensus         2 ii~~G~pgsGKSt~a   16 (143)
T PF13671_consen    2 IILCGPPGSGKSTLA   16 (143)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999863

...

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=82.19  E-value=1.2  Score=36.12  Aligned_cols=20  Identities=40%  Similarity=0.144  Sum_probs=14.8

Q ss_pred             eeeccCCCCchhHHHHHHHH
Q psy8456         154 VILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +|.|+|+|||||-+-.-..+
T Consensus         2 ~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    2 GISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEESTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            68999999999855444444

...

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=82.18  E-value=0.85  Score=37.98  Aligned_cols=23  Identities=39%  Similarity=0.453  Sum_probs=18.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      .+++..|+|+.+|||||-| +.+.
T Consensus        10 ~g~~~~i~G~nGsGKStLl-~~l~   32 (137)
T PF00005_consen   10 PGEIVAIVGPNGSGKSTLL-KALA   32 (137)
T ss_dssp             TTSEEEEEESTTSSHHHHH-HHHT
T ss_pred             CCCEEEEEccCCCccccce-eeec
Confidence            4778899999999999765 4443

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>cd03279 ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends

Probab=82.17  E-value=0.81  Score=41.94  Aligned_cols=21  Identities=38%  Similarity=0.412  Sum_probs=17.1

Q ss_pred             cceeeeeccCCCCchhHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~  171 (353)
                      ++...++||++|||||-| +.+
T Consensus        28 ~~~~~i~G~NGsGKSTll-~~i   48 (213)
T cd03279          28 NGLFLICGPTGAGKSTIL-DAI   48 (213)
T ss_pred             cCEEEEECCCCCCHHHHH-HHh
Confidence            568899999999999865 444

They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.

>PRK14530 adenylate kinase; Provisional

Probab=82.09  E-value=1.2  Score=40.86  Aligned_cols=23  Identities=22%  Similarity=0.309  Sum_probs=18.9

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .-+++||++|||||-.-+-+++|
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            45889999999999877766666

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=82.05  E-value=1.5  Score=37.38  Aligned_cols=36  Identities=22%  Similarity=0.222  Sum_probs=27.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ...-++.+|+|||||--.+..+.++..   +++++-|..
T Consensus        25 ~~~~ll~~~tGsGKT~~~~~~~~~l~~---~~l~~~p~~   60 (184)
T PF04851_consen   25 ERRVLLNAPTGSGKTIIALALILELAR---KVLIVAPNI   60 (184)
T ss_dssp             CSEEEEEESTTSSHHHHHHHHHHHHHC---EEEEEESSH
T ss_pred             CCCEEEEECCCCCcChhhhhhhhcccc---ceeEecCHH
Confidence            345688999999999888876666554   888888763

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=82.00  E-value=0.76  Score=40.66  Aligned_cols=20  Identities=15%  Similarity=0.091  Sum_probs=16.0

Q ss_pred             cceeeeeccCCCCchhHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~  169 (353)
                      +.+.++.|+++|||||-.-.
T Consensus         2 ~~~i~l~G~~gsGKst~a~~   21 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARA   21 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            45788999999999985433

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.98  E-value=1  Score=47.52  Aligned_cols=22  Identities=32%  Similarity=0.301  Sum_probs=16.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      ..+++||.|+||||-..--++.
T Consensus        42 a~Lf~GP~GtGKTTlAriLAk~   63 (484)
T PRK14956         42 AYIFFGPRGVGKTTIARILAKR   63 (484)
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            4589999999999865554443

>PF05729 NACHT: NACHT domain

Probab=81.93  E-value=2.7  Score=35.28  Aligned_cols=27  Identities=26%  Similarity=0.111  Sum_probs=22.7

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhC
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYAN  178 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~  178 (353)
                      .-+|+|+.|+||||-+.+.+..+...+
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~   28 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEE   28 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcC
Confidence            347999999999999988888887665

>PRK06217 hypothetical protein; Validated

Probab=81.92  E-value=0.64  Score=41.55  Aligned_cols=21  Identities=33%  Similarity=0.093  Sum_probs=15.6

Q ss_pred             eeeeccCCCCchhHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      -+|+|+|+|||||---+-...
T Consensus         4 I~i~G~~GsGKSTla~~L~~~   24 (183)
T PRK06217          4 IHITGASGSGTTTLGAALAER   24 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            589999999999854444433

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=81.76  E-value=1.3  Score=38.84  Aligned_cols=23  Identities=30%  Similarity=0.345  Sum_probs=18.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +.++.||.||||||-+-+-+..|
T Consensus         5 ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         5 IIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            56789999999999776665554

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=81.62  E-value=2.1  Score=44.26  Aligned_cols=35  Identities=29%  Similarity=0.533  Sum_probs=25.9

Q ss_pred             CCccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEe
Q psy8456          71 KDIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        71 ~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaG  105 (353)
                      ..+|+++|||+||+.       .+..+.+.+.+.|+.+++.+
T Consensus       193 ~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIits  234 (440)
T PRK14088        193 KKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICS  234 (440)
T ss_pred             hcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEEC
Confidence            368999999999982       25555666777888777654

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=81.61  E-value=1.7  Score=44.16  Aligned_cols=38  Identities=21%  Similarity=0.219  Sum_probs=31.5

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD  190 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~  190 (353)
                      .+++|+++||||+-+-.-+.+....|.+++++-|.-+-
T Consensus        45 ~~i~g~tGsGKt~~i~~l~~~~~~~~~~~vi~D~kg~~   82 (410)
T cd01127          45 TMIIGTTGTGKTTQIRELLASIRARGDRAIIYDPNGGF   82 (410)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHhcCCCEEEEeCCcch
Confidence            47899999999998766677777788999999987663

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=81.45  E-value=6.1  Score=34.98  Aligned_cols=28  Identities=11%  Similarity=0.135  Sum_probs=24.9

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeec
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~   37 (353)
                      =|||||-+-+.+.++..+|.+|.++|+.
T Consensus         9 gsGKTtl~~~l~~~l~~~G~~V~viK~~   36 (155)
T TIGR00176         9 NSGKTTLIERLVKALKARGYRVATIKHD   36 (155)
T ss_pred             CCCHHHHHHHHHHHHHhcCCeEEEEecc
Confidence            4899998888888888899999999984

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PRK10744 pstB phosphate transporter ATP-binding protein; Provisional

Probab=81.40  E-value=1.6  Score=41.10  Aligned_cols=54  Identities=20%  Similarity=0.256  Sum_probs=35.5

Q ss_pred             HhhhhccccceEeccceecccccc-cc--ccccc-ccceeeeeccCCCCchhHHHHHHH
Q psy8456         118 ILSLIPLAECVEKLTAVCMSCFRD-AA--FTKRI-GQEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       118 ~~~Ll~lAD~I~kL~AvC~~CG~~-A~--f~~Ri-~geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      +..+++.+..+.+++.++...+.. ..  .|..+ .|++..|+||.||||||-| +.+-
T Consensus         3 ~~~~~~~~~~~l~~~~l~~~~~~~~il~~isl~i~~Ge~~~i~G~nGsGKSTLl-~~l~   60 (260)
T PRK10744          3 MMSMVATAPSKIQVRNLNFYYGKFHALKNINLDIAKNQVTAFIGPSGCGKSTLL-RTFN   60 (260)
T ss_pred             hhhHhcCCCceEEEEEEEEEeCCeEEeeceeEEEcCCCEEEEECCCCCCHHHHH-HHHh
Confidence            445677777777888777655532 11  12332 4678899999999999754 4443

>PRK14737 gmk guanylate kinase; Provisional

Probab=81.36  E-value=3.4  Score=37.65  Aligned_cols=21  Identities=24%  Similarity=0.191  Sum_probs=15.9

Q ss_pred             cceeeeeccCCCCchhHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~  171 (353)
                      +.+-+++||.||||||- ++++
T Consensus         4 ~~~ivl~GpsG~GK~tl-~~~l   24 (186)
T PRK14737          4 PKLFIISSVAGGGKSTI-IQAL   24 (186)
T ss_pred             CeEEEEECCCCCCHHHH-HHHH
Confidence            45678999999999864 4444

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=81.13  E-value=0.89  Score=44.19  Aligned_cols=48  Identities=19%  Similarity=0.236  Sum_probs=32.7

Q ss_pred             cCCCCCCCCc------cHHHHHHHHH-hCCCEEEEEeccccccCCCchhHHhhhhcccceEEeee
Q psy8456         272 LNVPPPPEFP------DVVSFAESMA-NAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTA  329 (353)
Q Consensus       272 ~~~~~~~~f~------~~~~~~~~~~-~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a  329 (353)
                      +-.|||--|=      ++.+.+.+++ ++|+.|++.==|-++          -..+||.+.-|+.
T Consensus       160 LLLDEPTs~LDi~~Q~evl~ll~~l~~~~~~tvv~vlHDlN~----------A~ryad~~i~lk~  214 (258)
T COG1120         160 LLLDEPTSHLDIAHQIEVLELLRDLNREKGLTVVMVLHDLNL----------AARYADHLILLKD  214 (258)
T ss_pred             EEeCCCccccCHHHHHHHHHHHHHHHHhcCCEEEEEecCHHH----------HHHhCCEEEEEEC
Confidence            4567776663      4778888888 568888776555432          3467888887764

>PRK00625 shikimate kinase; Provisional

Probab=81.08  E-value=0.71  Score=41.76  Aligned_cols=17  Identities=24%  Similarity=0.006  Sum_probs=13.4

Q ss_pred             eeeeccCCCCchhHHHH
Q psy8456         153 EVILGPMFSGKTTELIR  169 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~  169 (353)
                      -+++|.|+|||||---.
T Consensus         3 I~LiG~pGsGKTT~~k~   19 (173)
T PRK00625          3 IFLCGLPTVGKTSFGKA   19 (173)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            47899999999985433

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=81.05  E-value=0.98  Score=40.95  Aligned_cols=25  Identities=28%  Similarity=0.115  Sum_probs=19.5

Q ss_pred             cccc-ccceeeeeccCCCCchhHHHH
Q psy8456         145 TKRI-GQEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       145 ~~Ri-~geI~vi~G~M~sGKt~~Li~  169 (353)
                      ++++ .+++..++||.+|||||-|--
T Consensus        15 sl~i~~G~~~~l~G~nG~GKSTLl~~   40 (176)
T cd03238          15 DVSIPLNVLVVVTGVSGSGKSTLVNE   40 (176)
T ss_pred             EEEEcCCCEEEEECCCCCCHHHHHHH
Confidence            4444 467889999999999998743

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=81.04  E-value=4.7  Score=41.79  Aligned_cols=84  Identities=14%  Similarity=0.159  Sum_probs=47.3

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh--CCEEEEEeeecCCCCCC-Cce---eeccCcccceee-cccHhhhcccCC
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA--NYRCMIVRYAKDDRYDT-EKV---STHDQQKLTAVS-AVELNKLIPHTK  221 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~--~~~~~~~k~~~D~R~~~-~~i---~s~~g~~~~a~~-~~~~~~~~~~~~  221 (353)
                      .+++..++||.|+||||-|..-+.++...  +.++.++... ..|.+. +..   ...-|.....+. ..++...+....
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d-~~rigalEQL~~~a~ilGvp~~~v~~~~dl~~al~~l~  268 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTD-SYRIGGHEQLRIYGKLLGVSVRSIKDIADLQLMLHELR  268 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecC-CcchhHHHHHHHHHHHcCCceecCCCHHHHHHHHHHhc
Confidence            35678899999999999998888776432  3566555431 234431 111   111122211111 112222234467


Q ss_pred             CccEEEEecccc
Q psy8456         222 DIDVIGIDEGQF  233 (353)
Q Consensus       222 ~~~~i~IDE~QF  233 (353)
                      +.|+|+||.+=+
T Consensus       269 ~~d~VLIDTaGr  280 (420)
T PRK14721        269 GKHMVLIDTVGM  280 (420)
T ss_pred             CCCEEEecCCCC
Confidence            899999999755

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=81.03  E-value=5.8  Score=40.73  Aligned_cols=159  Identities=16%  Similarity=0.149  Sum_probs=89.9

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCC----------CCCCceee-c-cC-Cceee-eecCChhhhcccCCCccE
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDR----------YDTEKVAT-H-DQ-QKLTA-VSAVELNKLIPHTKDIDV   75 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtR----------y~~~~I~S-r-~G-~~~~A-i~i~~l~ei~~~~~~~dv   75 (353)
                      -||||+-+.+.+.....+|-+|.+..|.+|-=          ++.-.|.- | ++ -...| ..+.....++...+-+|+
T Consensus       126 GaGKTEMif~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~Lyg~S~~~fr~plvVaTtHQLlrFk~aFD~  205 (441)
T COG4098         126 GAGKTEMIFQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSNCDIDLLYGDSDSYFRAPLVVATTHQLLRFKQAFDL  205 (441)
T ss_pred             CCCchhhhHHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhhccCCeeeEecCCchhccccEEEEehHHHHHHHhhccE
Confidence            48999999999999999999999999998852          12112221 1 11 01112 112222333334567999


Q ss_pred             EEEccccChH----HHHHH-HHHHH-hCCCEEEEEeccccc-ccCCchhHhhhhccccceEeccc-----------eecc
Q psy8456          76 IGIDEGQFFP----DVVSF-AESMA-NAGKIVVVAALDGTF-QRTGFNDILSLIPLAECVEKLTA-----------VCMS  137 (353)
Q Consensus        76 V~IDEaQFF~----dIv~l-~~~l~-~~G~~VivaGLd~DF-r~~pF~~~~~Ll~lAD~I~kL~A-----------vC~~  137 (353)
                      ++|||+.=||    +-.++ ++... ..|-.+++.+-.++= .++.=.+-.       ...+|.+           .|+ 
T Consensus       206 liIDEVDAFP~~~d~~L~~Av~~ark~~g~~IylTATp~k~l~r~~~~g~~-------~~~klp~RfH~~pLpvPkf~w-  277 (441)
T COG4098         206 LIIDEVDAFPFSDDQSLQYAVKKARKKEGATIYLTATPTKKLERKILKGNL-------RILKLPARFHGKPLPVPKFVW-  277 (441)
T ss_pred             EEEeccccccccCCHHHHHHHHHhhcccCceEEEecCChHHHHHHhhhCCe-------eEeecchhhcCCCCCCCceEE-
Confidence            9999999997    33333 34444 457778777643310 011000000       1123322           232 


Q ss_pred             cccccccccccccceeeeeccCCCCc-hhHHHHHHHHHHHhCCEEEEEeeecCC
Q psy8456         138 CFRDAAFTKRIGQEKEVILGPMFSGK-TTELIRRIRRYQYANYRCMIVRYAKDD  190 (353)
Q Consensus       138 CG~~A~f~~Ri~geI~vi~G~M~sGK-t~~Li~~~~~~~~~~~~~~~~k~~~D~  190 (353)
                      ||.-   +..+.           -+| +..|.+.+......|+-+++|-|.+..
T Consensus       278 ~~~~---~k~l~-----------r~kl~~kl~~~lekq~~~~~P~liF~p~I~~  317 (441)
T COG4098         278 IGNW---NKKLQ-----------RNKLPLKLKRWLEKQRKTGRPVLIFFPEIET  317 (441)
T ss_pred             eccH---HHHhh-----------hccCCHHHHHHHHHHHhcCCcEEEEecchHH
Confidence            3321   11110           122 236888888888899999999998743

>PTZ00088 adenylate kinase 1; Provisional

Probab=80.96  E-value=1.2  Score=42.20  Aligned_cols=22  Identities=23%  Similarity=0.055  Sum_probs=18.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++|||+|||||.--+-+.+|
T Consensus         9 Ivl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999877776665

>PF02223 Thymidylate_kin: Thymidylate kinase; InterPro: IPR018094 Thymidylate kinase (2

Probab=80.93  E-value=2  Score=38.00  Aligned_cols=38  Identities=21%  Similarity=0.128  Sum_probs=30.7

Q ss_pred             eccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC
Q psy8456         156 LGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD  193 (353)
Q Consensus       156 ~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~  193 (353)
                      =|+=||||||..-...+.+...|.++++..|.-++..+
T Consensus         2 EGiDGsGKtT~~~~L~~~l~~~~~~~~~~~~~~~~~~g   39 (186)
T PF02223_consen    2 EGIDGSGKTTQIRLLAEALKEKGYKVIITFPPGSTPIG   39 (186)
T ss_dssp             EESTTSSHHHHHHHHHHHHHHTTEEEEEEESSTSSHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHcCCcccccCCCCCChHH
Confidence            37889999999888888889999998888886655543

7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages[]. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process; PDB: 2PLR_B 1NMX_A 1NN0_A 2XX3_A 1NN3_A 1E9F_A 1E2Q_A 1E2D_A 1E9A_A 1E99_A ....

>TIGR00347 bioD dethiobiotin synthase

Probab=80.90  E-value=2.1  Score=37.22  Aligned_cols=34  Identities=18%  Similarity=0.142  Sum_probs=29.6

Q ss_pred             eecc-CCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         155 ILGP-MFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       155 i~G~-M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      |+|. .++|||+-.+--++.++.+|++|.++||..
T Consensus         2 I~~t~~~~GKT~va~~L~~~l~~~g~~V~~~kP~~   36 (166)
T TIGR00347         2 VTGTDTGVGKTVASSALAAKLKKAGYSVGYYKPVQ   36 (166)
T ss_pred             eecCCCCccHHHHHHHHHHHHHHCCCcEEEEEeee
Confidence            3444 689999999999999999999999999876

Dethiobiotin synthase is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP (see motif in first 12 residues of the SEED alignment) and requires magnesium as a co-factor.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=80.85  E-value=1.4  Score=47.83  Aligned_cols=38  Identities=21%  Similarity=0.440  Sum_probs=29.7

Q ss_pred             ccCCCccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEe
Q psy8456          68 PHTKDIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        68 ~~~~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaG  105 (353)
                      ..+.++|+++||++||+.       .+..+.+.+.+.|+.|++.+
T Consensus       373 ~~y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITS  417 (617)
T PRK14086        373 RRYREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSS  417 (617)
T ss_pred             HHhhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEec
Confidence            345679999999999993       36677788888899888754

>PHA02653 RNA helicase NPH-II; Provisional

Probab=80.80  E-value=2.4  Score=46.35  Aligned_cols=29  Identities=34%  Similarity=0.362  Sum_probs=20.1

Q ss_pred             cCCCccEEEEecccccceecCCccchhhhhh
Q psy8456         219 HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRE  249 (353)
Q Consensus       219 ~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~  249 (353)
                      ..+++++|+|||+|-+...|  |.-..++++
T Consensus       288 ~L~~v~~VVIDEaHEr~~~~--DllL~llk~  316 (675)
T PHA02653        288 KLFDYGTVIIDEVHEHDQIG--DIIIAVARK  316 (675)
T ss_pred             ccccCCEEEccccccCccch--hHHHHHHHH
Confidence            35789999999999765443  544555553

>PRK14273 phosphate ABC transporter ATP-binding protein; Provisional

Probab=80.70  E-value=1.6  Score=40.83  Aligned_cols=48  Identities=21%  Similarity=0.323  Sum_probs=29.5

Q ss_pred             ccceEeccceecccccc-c--cccccc-ccceeeeeccCCCCchhHHHHHHHH
Q psy8456         125 AECVEKLTAVCMSCFRD-A--AFTKRI-GQEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       125 AD~I~kL~AvC~~CG~~-A--~f~~Ri-~geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      ++.+.+++.++...+.. .  ..|+.+ .|++..++||.|||||| |++.+..
T Consensus         4 ~~~~l~~~~l~~~~~~~~il~~vs~~i~~Ge~~~i~G~nGsGKST-Ll~~l~G   55 (254)
T PRK14273          4 NEAIIETENLNLFYTDFKALNNINIKILKNSITALIGPSGCGKST-FLRTLNR   55 (254)
T ss_pred             CCceEEEeeeEEEeCCceeecceeeEEcCCCEEEEECCCCCCHHH-HHHHHhc
Confidence            34455566666544432 1  123444 57788999999999998 4555443

>PRK08116 hypothetical protein; Validated

Probab=80.63  E-value=2.5  Score=40.74  Aligned_cols=88  Identities=11%  Similarity=0.056  Sum_probs=46.8

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCcee-eccCCceeeeecCChhhhcccCCCccEEEEccccCh--H
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVA-THDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFF--P   85 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~-Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF--~   85 (353)
                      .-+|||.-+-..++.+..+|.+|+++... |-   -..+. +..+.     .-.+..+++....++|+++||+.+.-  +
T Consensus       123 ~GtGKThLa~aia~~l~~~~~~v~~~~~~-~l---l~~i~~~~~~~-----~~~~~~~~~~~l~~~dlLviDDlg~e~~t  193 (268)
T PRK08116        123 VGTGKTYLAACIANELIEKGVPVIFVNFP-QL---LNRIKSTYKSS-----GKEDENEIIRSLVNADLLILDDLGAERDT  193 (268)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCeEEEEEHH-HH---HHHHHHHHhcc-----ccccHHHHHHHhcCCCEEEEecccCCCCC
Confidence            34788766666666666667776555421 10   00010 00000     00122234444567899999999653  2


Q ss_pred             -----HHHHHHHHHHhCCCEEEEEe
Q psy8456          86 -----DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        86 -----dIv~l~~~l~~~G~~VivaG  105 (353)
                           .+.++++...+.|+++|+.+
T Consensus       194 ~~~~~~l~~iin~r~~~~~~~IiTs  218 (268)
T PRK08116        194 EWAREKVYNIIDSRYRKGLPTIVTT  218 (268)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEC
Confidence                 34555555556788888776

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=80.55  E-value=3  Score=39.21  Aligned_cols=41  Identities=17%  Similarity=0.073  Sum_probs=35.3

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEeeecC
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVRYAKD  189 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k~~~D  189 (353)
                      .+++.+|-|..++|||+-+++.+.++... |.+|++|.....
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~SlEm~   59 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNGGYPVLYFSLEMS   59 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEESSS-
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcCCCC
Confidence            36789999999999999999999999887 699999998653

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK14494 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional

Probab=80.55  E-value=6.1  Score=37.70  Aligned_cols=28  Identities=7%  Similarity=0.074  Sum_probs=25.8

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeec
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~   37 (353)
                      =|||||-+-+.+.++..+|.+|.++||.
T Consensus        11 gsGKTtl~~~l~~~L~~~G~~V~viK~~   38 (229)
T PRK14494         11 DSGKTTLIEKILKNLKERGYRVATAKHT   38 (229)
T ss_pred             CChHHHHHHHHHHHHHhCCCeEEEEEec
Confidence            5899999999999999999999999974

>KOG0926|consensus

Probab=80.48  E-value=1.4  Score=49.20  Aligned_cols=28  Identities=29%  Similarity=0.268  Sum_probs=23.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCC
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANY  179 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~  179 (353)
                      ..+|.|..||||||++=+-++.+-++..
T Consensus       273 vvIIcGeTGsGKTTQvPQFLYEAGf~s~  300 (1172)
T KOG0926|consen  273 VVIICGETGSGKTTQVPQFLYEAGFASE  300 (1172)
T ss_pred             eEEEecCCCCCccccchHHHHHcccCCc
Confidence            5678999999999999999988755543

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=80.44  E-value=5.7  Score=37.30  Aligned_cols=30  Identities=7%  Similarity=-0.138  Sum_probs=22.1

Q ss_pred             CCchHHHHHHHHHHHHHcC--ceEEEEeeccC
Q psy8456          10 INPYIVHFCRRIRRYQYAN--YRCMIVRYAKD   39 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~ag--kkvlv~Kp~iD   39 (353)
                      =+|||.-.+..+...-..|  +++++.+|...
T Consensus        29 GTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~   60 (205)
T PF02562_consen   29 GTGKTFLALAAALELVKEGEYDKIIITRPPVE   60 (205)
T ss_dssp             TSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--
T ss_pred             CCcHHHHHHHHHHHHHHhCCCcEEEEEecCCC
Confidence            3799998888887776656  58999999885

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR03263 guanyl_kin guanylate kinase

Probab=80.35  E-value=1.2  Score=39.01  Aligned_cols=21  Identities=33%  Similarity=0.180  Sum_probs=16.1

Q ss_pred             cceeeeeccCCCCchhHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRR  170 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~  170 (353)
                      |.+.+++||.+|||||-+-.-
T Consensus         1 g~ii~l~G~~GsGKsTl~~~L   21 (180)
T TIGR03263         1 GLLIVISGPSGVGKSTLVKAL   21 (180)
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            356789999999999944333

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=80.32  E-value=1.9  Score=41.47  Aligned_cols=40  Identities=23%  Similarity=0.223  Sum_probs=30.1

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCC
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRY  192 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~  192 (353)
                      -+++|+-||||||-++.-++.....=..++++.|....-|
T Consensus        16 ~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~~~n~~~   55 (241)
T PF04665_consen   16 MVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITPEYNNEY   55 (241)
T ss_pred             EEEECCCCCCHHHHHHHHHHhhcccCCEEEEEecCCchhh
Confidence            4799999999999888888765544467778888555444

This is thought to be an ATPase involved in viral DNA packaging [].

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=80.32  E-value=2.5  Score=49.45  Aligned_cols=24  Identities=33%  Similarity=0.314  Sum_probs=19.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +...++.|+.||||||.|=+.+..
T Consensus        82 ~~vvii~g~TGSGKTTqlPq~lle  105 (1283)
T TIGR01967        82 NQVVIIAGETGSGKTTQLPKICLE  105 (1283)
T ss_pred             CceEEEeCCCCCCcHHHHHHHHHH
Confidence            356789999999999998766654

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=80.19  E-value=2  Score=40.16  Aligned_cols=35  Identities=17%  Similarity=0.068  Sum_probs=26.2

Q ss_pred             CCccEEEEccccChH-HHHHHHHHHHhCCCEEEEEe
Q psy8456          71 KDIDVIGIDEGQFFP-DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        71 ~~~dvV~IDEaQFF~-dIv~l~~~l~~~G~~VivaG  105 (353)
                      ..++.|+|||+|=++ -...+...+...+..+++.|
T Consensus       255 ~~~~~i~IDE~QD~s~~Q~~il~~l~~~~~~~~~vG  290 (315)
T PF00580_consen  255 QRYDHILIDEFQDTSPLQLRILKKLFKNPENLFIVG  290 (315)
T ss_dssp             HHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE
T ss_pred             hhCCeEEeEccccCCHHHHHHHHHHHHhhceeEEeC
Confidence            468999999999997 55678888887765566655

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=80.17  E-value=1  Score=42.99  Aligned_cols=65  Identities=18%  Similarity=0.257  Sum_probs=41.0

Q ss_pred             ccCCCCCcchHHHHHHHhhccCCCCCCCCc-------------cHHHHHHHHH-hCCCEEEEEeccccccCCCchhHHhh
Q psy8456         252 KQKAPIKRSPFKTLANENAALNVPPPPEFP-------------DVVSFAESMA-NAGKIVVVAALDGTFQRTGFNDILSL  317 (353)
Q Consensus       252 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~-------------~~~~~~~~~~-~~g~~Vi~~gLd~df~~~~F~~~~~L  317 (353)
                      +.+.+++--| +|=..++.++.-+|+-.+.             .+++...+++ +.|+.|+++-=|.           .|
T Consensus       138 ~~p~eLSGGq-qQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~-----------~l  205 (226)
T COG1136         138 KKPSELSGGQ-QQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVTHDP-----------EL  205 (226)
T ss_pred             CCchhcCHHH-HHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCH-----------HH
Confidence            3455556555 3444566666655555441             3778888887 4588988886553           46


Q ss_pred             hhcccceEEee
Q psy8456         318 IPLAECVEKLT  328 (353)
Q Consensus       318 ~~~ad~v~kl~  328 (353)
                      ..+||.+..+.
T Consensus       206 A~~~dr~i~l~  216 (226)
T COG1136         206 AKYADRVIELK  216 (226)
T ss_pred             HHhCCEEEEEe
Confidence            66778777664

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=80.16  E-value=1.6  Score=41.98  Aligned_cols=66  Identities=21%  Similarity=0.070  Sum_probs=35.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhc---ccCCCccEEE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLI---PHTKDIDVIG  227 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~---~~~~~~~~i~  227 (353)
                      ..-+++||-|+|||+-+-...+.   .+..+..+.+.. .+.  +.+  +          ..+.+..   +...+.++|+
T Consensus        44 ~~lll~G~~G~GKT~la~~l~~~---~~~~~~~i~~~~-~~~--~~i--~----------~~l~~~~~~~~~~~~~~vli  105 (316)
T PHA02544         44 NMLLHSPSPGTGKTTVAKALCNE---VGAEVLFVNGSD-CRI--DFV--R----------NRLTRFASTVSLTGGGKVII  105 (316)
T ss_pred             eEEEeeCcCCCCHHHHHHHHHHH---hCccceEeccCc-ccH--HHH--H----------HHHHHHHHhhcccCCCeEEE
Confidence            45667899999999754443332   245555555432 110  000  0          0111111   1224678999


Q ss_pred             Eeccccc
Q psy8456         228 IDEGQFV  234 (353)
Q Consensus       228 IDE~QF~  234 (353)
                      |||+|.+
T Consensus       106 iDe~d~l  112 (316)
T PHA02544        106 IDEFDRL  112 (316)
T ss_pred             EECcccc
Confidence            9999985

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=80.15  E-value=2.6  Score=42.17  Aligned_cols=81  Identities=25%  Similarity=0.197  Sum_probs=41.6

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CC--ceeeccCcccceeecccHhhhccc--CCCccE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TE--KVSTHDQQKLTAVSAVELNKLIPH--TKDIDV  225 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~--~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~  225 (353)
                      ...+++|+++|||||-| +.+-.+.....+.+.+.....-... .+  .+.++.... +......+.+++..  -.++|.
T Consensus       179 ~~ili~G~tGsGKTTll-~al~~~i~~~~riv~iEd~~El~~~~~~~~~l~~r~~~~-~g~~~~t~~~ll~~aLR~~PD~  256 (340)
T TIGR03819       179 LAFLISGGTGSGKTTLL-SALLALVAPDERIVLVEDAAELRPDHPHVVRLEARPANV-EGAGAVTLTDLVRQALRMRPDR  256 (340)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHccCCCCCcEEEECCcceecCCCCCeeeEEeccccc-cCcCccCHHHHHHHHhccCCCe
Confidence            35689999999998865 4444443344555544322211111 11  112222110 00112234455432  368999


Q ss_pred             EEEecccc
Q psy8456         226 IGIDEGQF  233 (353)
Q Consensus       226 i~IDE~QF  233 (353)
                      |+|.|+.=
T Consensus       257 IivGEiRg  264 (340)
T TIGR03819       257 IVVGEVRG  264 (340)
T ss_pred             EEEeCcCc
Confidence            99999874

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>TIGR00959 ffh signal recognition particle protein

Probab=80.10  E-value=2.3  Score=44.05  Aligned_cols=135  Identities=20%  Similarity=0.183  Sum_probs=73.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHH-HhCCEEEEEeeecCCCCCC--Cce---eeccCcccceee-cccHhhh----cc-
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQ-YANYRCMIVRYAKDDRYDT--EKV---STHDQQKLTAVS-AVELNKL----IP-  218 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~-~~~~~~~~~k~~~D~R~~~--~~i---~s~~g~~~~a~~-~~~~~~~----~~-  218 (353)
                      .+.+++|+-||||||-...-+..+. ..|++|+++.  .|++-..  +..   ..+.|...-... ..+..++    +. 
T Consensus       100 ~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~--~D~~R~~a~~QL~~~a~~~gvp~~~~~~~~~P~~i~~~al~~  177 (428)
T TIGR00959       100 TVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVA--CDLYRPAAIEQLKVLGQQVGVPVFALGKGQSPVEIARRALEY  177 (428)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEe--ccccchHHHHHHHHHHHhcCCceEecCCCCCHHHHHHHHHHH
Confidence            4678999999999999999988875 5799999884  4654321  111   111221111110 1122222    22 


Q ss_pred             -cCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCC------CCCCccHHHHHHHHH
Q psy8456         219 -HTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPP------PPEFPDVVSFAESMA  291 (353)
Q Consensus       219 -~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~------~~~f~~~~~~~~~~~  291 (353)
                       ..+++|+|+||=+=.+                     +.....+.+|..+.+.++.++      +..-.+.++.+....
T Consensus       178 ~~~~~~DvVIIDTaGr~---------------------~~d~~l~~eL~~i~~~~~p~e~lLVvda~tgq~~~~~a~~f~  236 (428)
T TIGR00959       178 AKENGFDVVIVDTAGRL---------------------QIDEELMEELAAIKEILNPDEILLVVDAMTGQDAVNTAKTFN  236 (428)
T ss_pred             HHhcCCCEEEEeCCCcc---------------------ccCHHHHHHHHHHHHhhCCceEEEEEeccchHHHHHHHHHHH
Confidence             1467999999987653                     123445555555555332211      111135666665554


Q ss_pred             h-CCC-EEEEEeccccccC
Q psy8456         292 N-AGK-IVVVAALDGTFQR  308 (353)
Q Consensus       292 ~-~g~-~Vi~~gLd~df~~  308 (353)
                      + .++ -||+--||+|-++
T Consensus       237 ~~v~i~giIlTKlD~~~~~  255 (428)
T TIGR00959       237 ERLGLTGVVLTKLDGDARG  255 (428)
T ss_pred             hhCCCCEEEEeCccCcccc
Confidence            2 233 3556666665443

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	353
2orv_A	234	Human Thymidine Kinase 1 In Complex With Tp4a Lengt		1e-45
1w4r_A	195	Structure Of A Type Ii Thymidine Kinase With Bound		1e-45
1xbt_A	193	Crystal Structure Of Human Thymidine Kinase 1 Lengt		2e-45
2wvj_A	193	Mutation Of Thr163 To Ser In Human Thymidine Kinase		4e-45
2j87_A	177	Structure Of Vaccinia Virus Thymidine Kinase In Com		2e-44
2j9r_A	214	Thymidine Kinase From B. Anthracis In Complex With		3e-19
2ja1_A	197	Thymidine Kinase From B. Cereus With Ttp Bound As P		7e-19
3e2i_A	219	Crystal Structure Of Thymidine Kinase From S. Aureu		5e-18
3e2i_A	219	Crystal Structure Of Thymidine Kinase From S. Aureu		2e-17
1xx6_A	191	X-Ray Structure Of Clostridium Acetobutylicum Thymi		1e-15
1xx6_A	191	X-Ray Structure Of Clostridium Acetobutylicum Thymi		2e-15
2b8t_A	223	Crystal Structure Of Thymidine Kinase From U.Urealy		1e-12
2uz3_A	243	Crystal Structure Of Thymidine Kinase With Dttp Fro		1e-12
2orw_A	184	Thermotoga Maritima Thymidine Kinase 1 Like Enzyme		3e-05

>pdb|2ORV|A Chain A, Human Thymidine Kinase 1 In Complex With Tp4a Length = 234

Iteration: 1
 Score =  180 bits (456), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 94/200 (47%), Positives = 119/200 (59%), Gaps = 47/200 (23%)
Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  
Sbjct: 22  QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACL 80
Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +      + VIGIDEGQF                                       
Sbjct: 81  LRDVAQEALGVAVIGIDEGQF--------------------------------------- 101
Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 102 -------FPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCM 154
Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            CFR+AA+TKR+G EKEV +
Sbjct: 155 ECFREAAYTKRLGTEKEVEV 174

>pdb|1W4R|A Chain A, Structure Of A Type Ii Thymidine Kinase With Bound Dttp Length = 195

Iteration: 1
 Score =  179 bits (455), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 94/200 (47%), Positives = 119/200 (59%), Gaps = 47/200 (23%)
Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  
Sbjct: 23  QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACL 81
Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +      + VIGIDEGQF                                       
Sbjct: 82  LRDVAQEALGVAVIGIDEGQF--------------------------------------- 102
Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 103 -------FPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCM 155
Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            CFR+AA+TKR+G EKEV +
Sbjct: 156 ECFREAAYTKRLGTEKEVEV 175

>pdb|1XBT|A Chain A, Crystal Structure Of Human Thymidine Kinase 1 Length = 193

Iteration: 1
 Score =  179 bits (455), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 94/200 (47%), Positives = 119/200 (59%), Gaps = 47/200 (23%)
Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  
Sbjct: 22  QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACL 80
Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +      + VIGIDEGQF                                       
Sbjct: 81  LRDVAQEALGVAVIGIDEGQF--------------------------------------- 101
Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 102 -------FPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCM 154
Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            CFR+AA+TKR+G EKEV +
Sbjct: 155 ECFREAAYTKRLGTEKEVEV 174

>pdb|2WVJ|A Chain A, Mutation Of Thr163 To Ser In Human Thymidine Kinase Shifts The Specificity From Thymidine Towards The Nucleoside Analogue Azidothymidine Length = 193

Iteration: 1
 Score =  178 bits (452), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 93/200 (46%), Positives = 119/200 (59%), Gaps = 47/200 (23%)
Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  
Sbjct: 22  QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACL 80
Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +      + VIGIDEGQF                                       
Sbjct: 81  LRDVAQEALGVAVIGIDEGQF--------------------------------------- 101
Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 102 -------FPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCM 154
Query: 333 SCFRDAAFTKRIGQEKEVRI 352
            CFR+AA++KR+G EKEV +
Sbjct: 155 ECFREAAYSKRLGTEKEVEV 174

>pdb|2J87|A Chain A, Structure Of Vaccinia Virus Thymidine Kinase In Complex With Dttp: Insights For Drug Design Length = 177

Iteration: 1
 Score =  176 bits (447), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 91/204 (44%), Positives = 121/204 (59%), Gaps = 47/204 (23%)
Query: 149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV 208
           G   ++I+GPMFSGK+TELIRR+RRYQ A Y+C+ ++Y+ D+RY T  + THD+    A+
Sbjct: 3   GGHIQLIIGPMFSGKSTELIRRVRRYQIAQYKCVTIKYSNDNRYGT-GLWTHDKNNFEAL 61
Query: 209 SAVELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANE 268
            A +L  ++    D  VIGIDEGQF                                   
Sbjct: 62  EATKLCDVLQSITDFSVIGIDEGQF----------------------------------- 86
Query: 269 NAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 328
                      FPD+V F E MAN GKIV+VAALDGTFQR  FN+IL+L+ L+E V KLT
Sbjct: 87  -----------FPDIVEFCERMANEGKIVIVAALDGTFQRKPFNNILNLLILSEMVVKLT 135
Query: 329 AVCMSCFRDAAFTKRIGQEKEVRI 352
           AVCM CF++A+F+KR+G+E E+ I
Sbjct: 136 AVCMKCFKEASFSKRLGEETEIEI 159

>pdb|2J9R|A Chain A, Thymidine Kinase From B. Anthracis In Complex With Dt Length = 214

Iteration: 1
 Score = 92.4 bits (228), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 62/193 (32%), Positives = 89/193 (46%), Gaps = 46/193 (23%)
Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           EVI G MFSGK+ ELIRR+RR Q+A    ++ +   D+RY  E V +H+  K+ AV    
Sbjct: 31  EVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSA 90
Query: 213 LNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
              +  H T+++DVI IDE QF +                                    
Sbjct: 91  SKDIFKHITEEMDVIAIDEVQFFD------------------------------------ 114
Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 331
                     D+V   + +AN G  V+VA LD  F+   F  +  L+ +AE V KL AVC
Sbjct: 115 ---------GDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVC 165
Query: 332 MSCFRDAAFTKRI 344
            +C   A+ T+R+
Sbjct: 166 SACGSPASRTQRL 178

>pdb|2JA1|A Chain A, Thymidine Kinase From B. Cereus With Ttp Bound As Phosphate Donor Length = 197

Iteration: 1
 Score = 91.3 bits (225), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 62/193 (32%), Positives = 88/193 (45%), Gaps = 46/193 (23%)
Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           EVI G MFSGK+ ELIRR+RR Q+A    ++ +   D+RY  E V +H+  K+ AV    
Sbjct: 13  EVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSA 72
Query: 213 LNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
              +  H T+++DVI IDE QF +                                    
Sbjct: 73  SKDIFEHITEELDVIAIDEVQFFD------------------------------------ 96
Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 331
                     D+V   + +AN G  V+VA LD  F+   F  +  L+ +AE V KL AVC
Sbjct: 97  ---------GDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVC 147
Query: 332 MSCFRDAAFTKRI 344
             C   A+ T+R+
Sbjct: 148 SVCGSPASRTQRL 160

>pdb|3E2I|A Chain A, Crystal Structure Of Thymidine Kinase From S. Aureus Length = 219

Iteration: 1
 Score = 88.6 bits (218), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 50/134 (37%), Positives = 77/134 (57%), Gaps = 2/134 (1%)
Query: 17  FCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH-TKDIDV 75
             RR+RR  YA  + ++ + A DDRY  EKV +H+   + A++  + +++  H   ++DV
Sbjct: 45  LIRRLRRGIYAKQKVVVFKPAIDDRYHKEKVVSHNGNAIEAINISKASEIXTHDLTNVDV 104
Query: 76  IGIDEGQFFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV 134
           IGIDE QFF D +VS  E ++  G  V+VA LD  F+   F     L  ++E V KL AV
Sbjct: 105 IGIDEVQFFDDEIVSIVEKLSADGHRVIVAGLDXDFRGEPFEPXPKLXAVSEQVTKLQAV 164
Query: 135 CMSCFRDAAFTKRI 148
           C  C   ++ T+R+
Sbjct: 165 CAVCGSSSSRTQRL 178

>pdb|3E2I|A Chain A, Crystal Structure Of Thymidine Kinase From S. Aureus Length = 219

Iteration: 1
 Score = 86.3 bits (212), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 60/202 (29%), Positives = 92/202 (45%), Gaps = 46/202 (22%)
Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           E I G  FSGK+ ELIRR+RR  YA  + ++ + A DDRY  EKV +H+   + A++  +
Sbjct: 31  ECITGSXFSGKSEELIRRLRRGIYAKQKVVVFKPAIDDRYHKEKVVSHNGNAIEAINISK 90
Query: 213 LNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
            +++  H   ++DVIGIDE QF +                                    
Sbjct: 91  ASEIXTHDLTNVDVIGIDEVQFFD------------------------------------ 114
Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 331
                     ++VS  E ++  G  V+VA LD  F+   F     L  ++E V KL AVC
Sbjct: 115 ---------DEIVSIVEKLSADGHRVIVAGLDXDFRGEPFEPXPKLXAVSEQVTKLQAVC 165
Query: 332 MSCFRDAAFTKRIGQEKEVRIE 353
             C   ++ T+R+   K  +I+
Sbjct: 166 AVCGSSSSRTQRLINGKPAKID 187

>pdb|1XX6|A Chain A, X-Ray Structure Of Clostridium Acetobutylicum Thymidine Kinase With Adp. Northeast Structural Genomics Target Car26. Length = 191

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/168 (32%), Positives = 84/168 (50%), Gaps = 7/168 (4%)
Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH-TKDIDVIG 77
           RRIRR + A  +  + +   D+RY  E V +H  +K  AV+     +++ +  +D +VI 
Sbjct: 27  RRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHXGEKEQAVAIKNSREILKYFEEDTEVIA 86
Query: 78  IDEGQFFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 136
           IDE QFF D +V     +A +G+ V+ A LD  F+   F  I  L  +AE V+K+ A+C+
Sbjct: 87  IDEVQFFDDEIVEIVNKIAESGRRVICAGLDXDFRGKPFGPIPELXAIAEFVDKIQAICV 146
Query: 137 SCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV 184
            C   A  T+R+   K     P F      LI     Y+    +C +V
Sbjct: 147 VCGNPATRTQRLINGK-----PAFYDDPVVLIGAXESYEARCRKCHVV 189

>pdb|1XX6|A Chain A, X-Ray Structure Of Clostridium Acetobutylicum Thymidine Kinase With Adp. Northeast Structural Genomics Target Car26. Length = 191

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 55/193 (28%), Positives = 87/193 (45%), Gaps = 46/193 (23%)
Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           EVI+GP +SGK+ ELIRRIRR + A  +  + +   D+RY  E V +H  +K  AV+   
Sbjct: 11  EVIVGPXYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHXGEKEQAVAIKN 70
Query: 213 LNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
             +++ +  +D +VI IDE QF +                                    
Sbjct: 71  SREILKYFEEDTEVIAIDEVQFFD------------------------------------ 94
Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 331
                     ++V     +A +G+ V+ A LD  F+   F  I  L  +AE V+K+ A+C
Sbjct: 95  ---------DEIVEIVNKIAESGRRVICAGLDXDFRGKPFGPIPELXAIAEFVDKIQAIC 145
Query: 332 MSCFRDAAFTKRI 344
           + C   A  T+R+
Sbjct: 146 VVCGNPATRTQRL 158

>pdb|2B8T|A Chain A, Crystal Structure Of Thymidine Kinase From U.Urealyticum In Complex With Thymidine Length = 223

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/211 (27%), Positives = 91/211 (43%), Gaps = 61/211 (28%)
Query: 143 AFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQ 202
           AF+K+IG   E I GPMF+GKT ELIRR+ R +YA+ + ++ +     + DT  +     
Sbjct: 6   AFSKKIGW-IEFITGPMFAGKTAELIRRLHRLEYADVKYLVFK----PKIDTRSIRNIQS 60
Query: 203 QKLTAVSAVE-------LNKLIPHT--KDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQ 253
           +  T++ +VE       LN ++ ++   +  VIGIDE QF                    
Sbjct: 61  RTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQF-------------------- 100
Query: 254 KAPIKRSPFKTLANENAALNVPPPPEFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFN 312
                                     F D +   A  +A  G +V+++ LD  F+   F 
Sbjct: 101 --------------------------FDDRICEVANILAENGFVVIISGLDKNFKGEPFG 134
Query: 313 DILSLIPLAECVEKLTAVCMSCFRDAAFTKR 343
            I  L   A+ + KLTA+C  C  +A  + R
Sbjct: 135 PIAKLFTYADKITKLTAICNECGAEATHSLR 165

>pdb|2UZ3|A Chain A, Crystal Structure Of Thymidine Kinase With Dttp From U. Urealyticum Length = 243

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/211 (27%), Positives = 91/211 (43%), Gaps = 61/211 (28%)
Query: 143 AFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQ 202
           AF+K+IG   E I GPMF+GKT ELIRR+ R +YA+ + ++ +     + DT  +     
Sbjct: 26  AFSKKIGW-IEFITGPMFAGKTAELIRRLHRLEYADVKYLVFK----PKIDTRSIRNIQS 80
Query: 203 QKLTAVSAVE-------LNKLIPHT--KDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQ 253
           +  T++ +VE       LN ++ ++   +  VIGIDE QF                    
Sbjct: 81  RTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQF-------------------- 120
Query: 254 KAPIKRSPFKTLANENAALNVPPPPEFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFN 312
                                     F D +   A  +A  G +V+++ LD  F+   F 
Sbjct: 121 --------------------------FDDRICEVANILAENGFVVIISGLDKNFKGEPFG 154
Query: 313 DILSLIPLAECVEKLTAVCMSCFRDAAFTKR 343
            I  L   A+ + KLTA+C  C  +A  + R
Sbjct: 155 PIAKLFTYADKITKLTAICNECGAEATHSLR 185

>pdb|2ORW|A Chain A, Thermotoga Maritima Thymidine Kinase 1 Like Enzyme In Complex With Tp4a Length = 184

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/204 (24%), Positives = 77/204 (37%), Gaps = 52/204 (25%)
Query: 154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA---VSA 210
           VI GPM+SGKTTEL+  +  Y+    +  + +   D RY +  + +H    + A      
Sbjct: 7   VITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERP 66
Query: 211 VELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENA 270
            E+ K I   +D   + IDE QF                                     
Sbjct: 67  EEMRKYIE--EDTRGVFIDEVQFFN----------------------------------- 89
Query: 271 ALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV 330
                     P +    + + + G  V  A LD T ++  F     L+ LA+ V K  AV
Sbjct: 90  ----------PSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAV 139
Query: 331 CMSCFR-DAAFTKRI-GQEKEVRI 352
           C  C   +A  T ++ G E+E+ +
Sbjct: 140 CHRCGEYNATLTLKVAGGEEEIDV 163

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	353
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	2e-58
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	3e-51
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	4e-04
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	2e-57
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	1e-52
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	3e-05
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	3e-57
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	1e-50
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	6e-04
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	2e-56
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	2e-49
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	2e-04
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	8e-55
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	4e-50
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	2e-54
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	3e-51
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	8e-05
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	4e-54
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	5e-48
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	3e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-09

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus} Length = 219

 Score =  187 bits (477), Expect = 2e-58
 Identities = 62/202 (30%), Positives = 96/202 (47%), Gaps = 46/202 (22%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           E I G MFSGK+ ELIRR+RR  YA  + ++ + A DDRY  EKV +H+   + A++  +
Sbjct: 31  ECITGSMFSGKSEELIRRLRRGIYAKQKVVVFKPAIDDRYHKEKVVSHNGNAIEAINISK 90

Query: 213 LNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
            ++++ H   ++DVIGIDE QF                            F         
Sbjct: 91  ASEIMTHDLTNVDVIGIDEVQF----------------------------FD-------- 114

Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 331
                     ++VS  E ++  G  V+VA LD  F+   F  +  L+ ++E V KL AVC
Sbjct: 115 ---------DEIVSIVEKLSADGHRVIVAGLDMDFRGEPFEPMPKLMAVSEQVTKLQAVC 165

Query: 332 MSCFRDAAFTKRIGQEKEVRIE 353
             C   ++ T+R+   K  +I+
Sbjct: 166 AVCGSSSSRTQRLINGKPAKID 187

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus} Length = 219

 Score =  169 bits (429), Expect = 3e-51
 Identities = 51/139 (36%), Positives = 81/139 (58%), Gaps = 2/139 (1%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH-TKDIDVIG 77
           RR+RR  YA  + ++ + A DDRY  EKV +H+   + A++  + ++++ H   ++DVIG
Sbjct: 47  RRLRRGIYAKQKVVVFKPAIDDRYHKEKVVSHNGNAIEAINISKASEIMTHDLTNVDVIG 106

Query: 78  IDEGQFFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 136
           IDE QFF D +VS  E ++  G  V+VA LD  F+   F  +  L+ ++E V KL AVC 
Sbjct: 107 IDEVQFFDDEIVSIVEKLSADGHRVIVAGLDMDFRGEPFEPMPKLMAVSEQVTKLQAVCA 166

Query: 137 SCFRDAAFTKRIGQEKEVI 155
            C   ++ T+R+   K   
Sbjct: 167 VCGSSSSRTQRLINGKPAK 185

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus} Length = 219

 Score = 40.0 bits (94), Expect = 4e-04
 Identities = 4/21 (19%), Positives = 10/21 (47%)

Query: 234 VEVIGGSDKYMAVCRECYKQK 254
           + ++G ++ Y   CR  +   
Sbjct: 190 IILVGANESYEPRCRAHHIVA 210

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A* Length = 195

 Score =  184 bits (468), Expect = 2e-57
 Identities = 94/198 (47%), Positives = 117/198 (59%), Gaps = 47/198 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY      THD+  + A+ A  
Sbjct: 23  QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACL 81

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +      + VIGIDEGQF                                       
Sbjct: 82  LRDVAQEALGVAVIGIDEGQF--------------------------------------- 102

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 103 -------FPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCM 155

Query: 333 SCFRDAAFTKRIGQEKEV 350
            CFR+AA+TKR+G EKEV
Sbjct: 156 ECFREAAYTKRLGTEKEV 173

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A* Length = 195

 Score =  171 bits (436), Expect = 1e-52
 Identities = 81/138 (58%), Positives = 102/138 (73%), Gaps = 1/138 (0%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
           RR+RR+Q A Y+C++++YAKD RY      THD+  + A+ A  L  +      + VIGI
Sbjct: 39  RRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLLRDVAQEALGVAVIGI 97

Query: 79  DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
           DEGQFFPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct: 98  DEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMEC 157

Query: 139 FRDAAFTKRIGQEKEVIL 156
           FR+AA+TKR+G EKEV +
Sbjct: 158 FREAAYTKRLGTEKEVEV 175

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A* Length = 195

 Score = 43.4 bits (103), Expect = 3e-05
 Identities = 16/28 (57%), Positives = 21/28 (75%)

Query: 228 IDEGQFVEVIGGSDKYMAVCRECYKQKA 255
           +   + VEVIGG+DKY +VCR CY +KA
Sbjct: 167 LGTEKEVEVIGGADKYHSVCRLCYFKKA 194

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14 Length = 191

 Score =  183 bits (467), Expect = 3e-57
 Identities = 59/203 (29%), Positives = 91/203 (44%), Gaps = 48/203 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           EVI+GPM+SGK+ ELIRRIRR + A  +  + +   D+RY  E V +H  +K  AV+   
Sbjct: 11  EVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKN 70

Query: 213 LNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
             +++ +  +D +VI IDE QF                                      
Sbjct: 71  SREILKYFEEDTEVIAIDEVQF-------------------------------------- 92

Query: 272 LNVPPPPEFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV 330
                   F D +V     +A +G+ V+ A LD  F+   F  I  L+ +AE V+K+ A+
Sbjct: 93  --------FDDEIVEIVNKIAESGRRVICAGLDMDFRGKPFGPIPELMAIAEFVDKIQAI 144

Query: 331 CMSCFRDAAFTKRIGQEKEVRIE 353
           C+ C   A  T+R+   K    +
Sbjct: 145 CVVCGNPATRTQRLINGKPAFYD 167

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14 Length = 191

 Score =  166 bits (422), Expect = 1e-50
 Identities = 47/139 (33%), Positives = 75/139 (53%), Gaps = 2/139 (1%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH-TKDIDVIG 77
           RRIRR + A  +  + +   D+RY  E V +H  +K  AV+     +++ +  +D +VI 
Sbjct: 27  RRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIA 86

Query: 78  IDEGQFFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 136
           IDE QFF D +V     +A +G+ V+ A LD  F+   F  I  L+ +AE V+K+ A+C+
Sbjct: 87  IDEVQFFDDEIVEIVNKIAESGRRVICAGLDMDFRGKPFGPIPELMAIAEFVDKIQAICV 146

Query: 137 SCFRDAAFTKRIGQEKEVI 155
            C   A  T+R+   K   
Sbjct: 147 VCGNPATRTQRLINGKPAF 165

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14 Length = 191

 Score = 39.5 bits (93), Expect = 6e-04
 Identities = 8/18 (44%), Positives = 12/18 (66%)

Query: 234 VEVIGGSDKYMAVCRECY 251
           V +IG  + Y A CR+C+
Sbjct: 170 VVLIGAMESYEARCRKCH 187

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A* Length = 214

 Score =  181 bits (462), Expect = 2e-56
 Identities = 63/202 (31%), Positives = 91/202 (45%), Gaps = 46/202 (22%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           EVI G MFSGK+ ELIRR+RR Q+A    ++ +   D+RY  E V +H+  K+ AV    
Sbjct: 31  EVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSA 90

Query: 213 LNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
              +  H T+++DVI IDE QF                            F         
Sbjct: 91  SKDIFKHITEEMDVIAIDEVQF----------------------------FD-------- 114

Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 331
                     D+V   + +AN G  V+VA LD  F+   F  +  L+ +AE V KL AVC
Sbjct: 115 ---------GDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVC 165

Query: 332 MSCFRDAAFTKRIGQEKEVRIE 353
            +C   A+ T+R+   +    +
Sbjct: 166 SACGSPASRTQRLIDGEPAAFD 187

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A* Length = 214

 Score =  163 bits (416), Expect = 2e-49
 Identities = 51/139 (36%), Positives = 77/139 (55%), Gaps = 2/139 (1%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH-TKDIDVIG 77
           RR+RR Q+A    ++ +   D+RY  E V +H+  K+ AV       +  H T+++DVI 
Sbjct: 47  RRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIA 106

Query: 78  IDEGQFFP-DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 136
           IDE QFF  D+V   + +AN G  V+VA LD  F+   F  +  L+ +AE V KL AVC 
Sbjct: 107 IDEVQFFDGDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVCS 166

Query: 137 SCFRDAAFTKRIGQEKEVI 155
           +C   A+ T+R+   +   
Sbjct: 167 ACGSPASRTQRLIDGEPAA 185

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A* Length = 214

 Score = 41.1 bits (97), Expect = 2e-04
 Identities = 6/21 (28%), Positives = 11/21 (52%)

Query: 234 VEVIGGSDKYMAVCRECYKQK 254
           + ++G S+ Y   CR C+   
Sbjct: 190 IILVGASESYEPRCRHCHAVP 210

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14 Length = 234

 Score =  178 bits (454), Expect = 8e-55
 Identities = 94/198 (47%), Positives = 117/198 (59%), Gaps = 47/198 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY      THD+  + A+ A  
Sbjct: 22  QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACL 80

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +      + VIGIDEGQF                                       
Sbjct: 81  LRDVAQEALGVAVIGIDEGQF--------------------------------------- 101

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM 332
                  FPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM
Sbjct: 102 -------FPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCM 154

Query: 333 SCFRDAAFTKRIGQEKEV 350
            CFR+AA+TKR+G EKEV
Sbjct: 155 ECFREAAYTKRLGTEKEV 172

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14 Length = 234

 Score =  166 bits (422), Expect = 4e-50
 Identities = 81/138 (58%), Positives = 102/138 (73%), Gaps = 1/138 (0%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
           RR+RR+Q A Y+C++++YAKD RY      THD+  + A+ A  L  +      + VIGI
Sbjct: 38  RRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLLRDVAQEALGVAVIGI 96

Query: 79  DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSC 138
           DEGQFFPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLTAVCM C
Sbjct: 97  DEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMEC 156

Query: 139 FRDAAFTKRIGQEKEVIL 156
           FR+AA+TKR+G EKEV +
Sbjct: 157 FREAAYTKRLGTEKEVEV 174

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A* Length = 184

 Score =  175 bits (447), Expect = 2e-54
 Identities = 45/200 (22%), Positives = 73/200 (36%), Gaps = 47/200 (23%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
            VI GPM+SGKTTEL+  +  Y+    +  + +   D RY +  + +H    + A     
Sbjct: 6   TVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIER 65

Query: 213 LNKLIPH-TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
             ++  +  +D   + IDE QF                            F         
Sbjct: 66  PEEMRKYIEEDTRGVFIDEVQF----------------------------FN-------- 89

Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 331
                    P +    + + + G  V  A LD T ++  F     L+ LA+ V K  AVC
Sbjct: 90  ---------PSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVC 140

Query: 332 MSCFR-DAAFTKRIGQEKEV 350
             C   +A  T ++   +E 
Sbjct: 141 HRCGEYNATLTLKVAGGEEE 160

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A* Length = 184

 Score =  168 bits (427), Expect = 3e-51
 Identities = 34/142 (23%), Positives = 60/142 (42%), Gaps = 3/142 (2%)

Query: 18  CRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH-TKDIDVI 76
              +  Y+    +  + +   D RY +  + +H    + A       ++  +  +D   +
Sbjct: 21  LSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGV 80

Query: 77  GIDEGQFF-PDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC 135
            IDE QFF P +    + + + G  V  A LD T ++  F     L+ LA+ V K  AVC
Sbjct: 81  FIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVC 140

Query: 136 MSCFR-DAAFTKRIGQEKEVIL 156
             C   +A  T ++   +E I 
Sbjct: 141 HRCGEYNATLTLKVAGGEEEID 162

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A* Length = 184

 Score = 41.8 bits (99), Expect = 8e-05
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 228 IDEGQFVEVIGGSDKYMAVCRECYKQK 254
           +  G+    +GG +KY+AVCR+CY   
Sbjct: 154 VAGGEEEIDVGGQEKYIAVCRDCYNTL 180

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A* Length = 223

 Score =  176 bits (449), Expect = 4e-54
 Identities = 51/208 (24%), Positives = 79/208 (37%), Gaps = 54/208 (25%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           E I GPMF+GKT ELIRR+ R +YA+ + ++ +   D R     + +     L +V    
Sbjct: 15  EFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSI-RNIQSRTGTSLPSVEVES 73

Query: 213 LNKLIPH------TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLA 266
             +++ +        +  VIGIDE QF                                 
Sbjct: 74  APEILNYIMSNSFNDETKVIGIDEVQF--------------------------------- 100

Query: 267 NENAALNVPPPPEFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVE 325
                        F D +   A  +A  G +V+++ LD  F+   F  I  L   A+ + 
Sbjct: 101 -------------FDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKIT 147

Query: 326 KLTAVCMSCFRDAAFTKRIGQEKEVRIE 353
           KLTA+C  C  +A  + R    K     
Sbjct: 148 KLTAICNECGAEATHSLRKIDGKHADYN 175

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A* Length = 223

 Score =  160 bits (408), Expect = 5e-48
 Identities = 39/144 (27%), Positives = 66/144 (45%), Gaps = 8/144 (5%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH------TKD 72
           RR+ R +YA+ + ++ +   D R     + +     L +V      +++ +        +
Sbjct: 31  RRLHRLEYADVKYLVFKPKIDTRSI-RNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDE 89

Query: 73  IDVIGIDEGQFFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL 131
             VIGIDE QFF D +   A  +A  G +V+++ LD  F+   F  I  L   A+ + KL
Sbjct: 90  TKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKL 149

Query: 132 TAVCMSCFRDAAFTKRIGQEKEVI 155
           TA+C  C  +A  + R    K   
Sbjct: 150 TAICNECGAEATHSLRKIDGKHAD 173

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A* Length = 223

 Score = 40.7 bits (96), Expect = 3e-04
 Identities = 8/21 (38%), Positives = 11/21 (52%)

Query: 234 VEVIGGSDKYMAVCRECYKQK 254
           +  IG  + Y AVCR  +K  
Sbjct: 178 IVKIGCQEFYSAVCRHHHKVP 198

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

 Score = 56.4 bits (135), Expect = 8e-09
 Identities = 55/375 (14%), Positives = 108/375 (28%), Gaps = 127/375 (33%)

Query: 28  NYRCMIVRYAKDDR--------YDTEKVATH-DQQKLTA--VSAVE--------LNKLIP 68
           NY+ ++     + R        Y  ++   + D Q      VS ++        L +L P
Sbjct: 90  NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRP 149

Query: 69  HTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVA--ALDGTFQRTGFNDILSLIPLAE 126
             K++ + G                +  +GK  V     L    Q    +  +  + L  
Sbjct: 150 A-KNVLIDG----------------VLGSGKTWVALDVCLSYKVQCK-MDFKIFWLNLKN 191

Query: 127 C------VEKLTAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRY-QYANY 179
           C      +E L  +      D  +T R      + L      +   +   +RR  +   Y
Sbjct: 192 CNSPETVLEMLQKLLYQI--DPNWTSRSDHSSNIKL------RIHSIQAELRRLLKSKPY 243

Query: 180 -RCMIVRYAKDDRYDTE---------K--VSTHDQQKLTAVSAVELNKLIPHTKDIDVIG 227
             C++V     +  + +         K  ++T  +Q    +SA         T  I +  
Sbjct: 244 ENCLLVL---LNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAA-------TTTHISLDH 293

Query: 228 IDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPP---PPE----F 280
                        D+  ++  +                      L+  P   P E     
Sbjct: 294 HSMT-LTP-----DEVKSLLLKY---------------------LDCRPQDLPREVLTTN 326

Query: 281 PDVVS-FAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM-SCFRD- 337
           P  +S  AES+ +      +A  D  ++    + + ++I     +  L        F   
Sbjct: 327 PRRLSIIAESIRDG-----LATWD-NWKHVNCDKLTTII--ESSLNVLEPAEYRKMFDRL 378

Query: 338 AAFTKRIGQEKEVRI 352
           + F           I
Sbjct: 379 SVF------PPSAHI 387

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	353
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	100.0
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	100.0
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	100.0
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	100.0
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	100.0
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	100.0
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	100.0
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	100.0
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	100.0
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	100.0
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	100.0
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	100.0
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	100.0
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	100.0
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.12
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	96.87
3bos_A	242	Putative DNA replication factor; P-loop containing	96.71
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.71
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.57
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	96.47
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.42
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.35
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.29
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.27
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.23
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.14
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.1
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	95.95
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	95.93
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.89
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	95.72
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	95.67
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	95.53
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	95.33
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.2
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	95.14
3h1t_A	590	Type I site-specific restriction-modification syst	95.02
3io5_A	333	Recombination and repair protein; storage dimer, i	94.83
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	94.83
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	94.8
1yks_A	440	Genome polyprotein [contains: flavivirin protease	94.63
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	94.61
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	94.56
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	94.55
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.53
1xp8_A	366	RECA protein, recombinase A; recombination, radior	94.49
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	94.46
1u94_A	356	RECA protein, recombinase A; homologous recombinat	94.43
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	94.34
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	94.14
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	94.0
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	93.95
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	93.93
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	93.87
2qgz_A	308	Helicase loader, putative primosome component; str	93.86
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	93.81
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.73
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	93.71
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	93.71
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	93.51
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	93.33
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	93.24
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	93.1
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	93.09
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	92.99
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	92.99
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	92.98
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	92.93
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	92.93
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	92.92
2chg_A	226	Replication factor C small subunit; DNA-binding pr	92.9
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	92.83
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	92.65
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	92.62
2ewv_A	372	Twitching motility protein PILT; pilus retraction	92.61
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.42
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	92.4
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	92.37
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	92.29
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	92.28
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	92.27
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	92.21
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	92.12
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	92.1
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	92.08
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	92.0
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	91.97
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	91.88
3bos_A	242	Putative DNA replication factor; P-loop containing	91.8
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	91.64
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	91.58
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	91.47
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	91.46
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	91.44
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	91.38
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	91.34
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	91.27
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	91.26
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	91.18
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	91.18
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	91.13
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	91.07
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.06
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	90.97
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	90.95
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	90.79
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	90.73
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	90.7
3bor_A	237	Human initiation factor 4A-II; translation initiat	90.7
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	90.58
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	90.48
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	90.47
4gl2_A	699	Interferon-induced helicase C domain-containing P;	90.36
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	90.36
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	90.32
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	90.32
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	90.3
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	90.27
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	90.23
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	90.04
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	90.0
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	89.96
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	89.71
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.55
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	89.52
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	89.5
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	89.49
3pvs_A	447	Replication-associated recombination protein A; ma	89.47
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	89.41
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	89.35
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	89.33
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	89.27
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	89.12
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	89.09
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	89.02
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	88.93
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	88.93
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	88.82
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	88.8
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	88.73
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	88.72
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	88.71
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	88.67
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	88.64
2cvh_A	220	DNA repair and recombination protein RADB; filamen	88.62
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	88.45
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	88.38
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	88.35
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	88.26
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	88.25
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	88.23
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	88.07
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	88.02
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	87.95
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	87.85
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	87.77
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	87.73
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	87.67
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	87.63
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	87.52
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	87.52
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	87.5
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	87.47
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	87.46
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	87.38
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	87.25
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	87.24
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	87.21
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	87.15
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	87.05
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	86.97
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	86.81
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	86.6
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	86.52
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	86.51
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	86.42
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	86.32
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	86.28
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	86.2
2chq_A	319	Replication factor C small subunit; DNA-binding pr	86.18
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	86.12
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	86.11
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	86.1
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	86.09
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	86.08
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	85.91
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	85.87
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	85.84
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	85.72
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	85.72
2eyu_A	261	Twitching motility protein PILT; pilus retraction	85.57
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	85.56
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	85.54
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	85.36
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	85.35
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	85.23
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	85.2
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	85.16
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	85.14
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	85.13
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	85.1
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	84.96
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	84.94
1yks_A	440	Genome polyprotein [contains: flavivirin protease	84.83
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	84.78
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	84.61
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	84.57
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	84.56
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	84.54
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	84.48
2og2_A	359	Putative signal recognition particle receptor; nuc	84.19
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	84.16
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	84.11
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	84.11
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	83.95
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	83.76
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	83.68
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	83.66
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	83.55
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	83.55
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	83.43
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	83.4
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	83.38
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	83.32
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	83.28
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	83.26
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	83.19
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	83.12
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	83.12
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	83.12
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	83.05
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	83.05
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	82.99
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	82.8
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	82.75
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	82.61
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	82.45
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	82.43
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	82.41
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	82.21
4a74_A	231	DNA repair and recombination protein RADA; hydrola	82.2
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	82.17
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	82.05
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	82.02
3kta_A	182	Chromosome segregation protein SMC; structural mai	81.86
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	81.86
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	81.85
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	81.74
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	81.71
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	81.64
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	81.57
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	81.33
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	81.24
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	81.1
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	81.07
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	81.01
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	80.97
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	80.93
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	80.93
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	80.93
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	80.7
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	80.64
2r6a_A	454	DNAB helicase, replicative helicase; replication,	80.63
1via_A	175	Shikimate kinase; structural genomics, transferase	80.61
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	80.47
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	80.4
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	80.39
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	80.33
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	80.3
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	80.19
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	80.12
2z43_A	324	DNA repair and recombination protein RADA; archaea	80.01
3h1t_A	590	Type I site-specific restriction-modification syst	80.01

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=100.00  E-value=7.9e-50  Score=370.45  Aligned_cols=142  Identities=35%  Similarity=0.570  Sum_probs=123.9

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhccc-CCCccEEEEccccChH-H
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH-TKDIDVIGIDEGQFFP-D   86 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~-~~~~dvV~IDEaQFF~-d   86 (353)
                      .-|||||+||++++||..+|++|++|||++|+||+.+.|+||+|++++|+.+.++.++... .+++|||+|||||||+ +
T Consensus        37 M~sGKTT~Llr~~~r~~~~g~kvli~kp~~D~R~~~~~I~Sr~G~~~~a~~v~~~~di~~~i~~~~dvV~IDEaQFf~~~  116 (219)
T 3e2i_A           37 MFSGKSEELIRRLRRGIYAKQKVVVFKPAIDDRYHKEKVVSHNGNAIEAINISKASEIMTHDLTNVDVIGIDEVQFFDDE  116 (219)
T ss_dssp             TTSCHHHHHHHHHHHHHHTTCCEEEEEEC-----------CBTTBCCEEEEESSGGGGGGSCCTTCSEEEECCGGGSCTH
T ss_pred             CCCCHHHHHHHHHHHHHHcCCceEEEEeccCCcchhhhHHHhcCCceeeEEeCCHHHHHHHHhcCCCEEEEechhcCCHH
Confidence            3689999999999999999999999999999999999999999999999999998888754 4789999999999998 7


Q ss_pred             HHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceeccccccccccccccc
Q psy8456          87 VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQ  150 (353)
Q Consensus        87 Iv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~g  150 (353)
                      ++++++.+++.|++|||||||+||+++||+++++||++||+|+||+|+|++||++|+||+|+++
T Consensus       117 ~v~~l~~la~~gi~Vi~~GLd~DF~~~~F~~~~~Ll~~Ad~v~kl~aiC~~CG~~A~~~~R~~~  180 (219)
T 3e2i_A          117 IVSIVEKLSADGHRVIVAGLDMDFRGEPFEPMPKLMAVSEQVTKLQAVCAVCGSSSSRTQRLIN  180 (219)
T ss_dssp             HHHHHHHHHHTTCEEEEEEESBCTTSCBCTTHHHHHHHCSEEEEECEECTTTCSEECEEEEEET
T ss_pred             HHHHHHHHHHCCCEEEEeecccccccCCCccHHHHHHhcceEEEeeeEccCCCCcceEEEEEEC
Confidence            9999998899999999999999999999999999999999999999999999999999999865

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=100.00  E-value=3.8e-49  Score=360.30  Aligned_cols=140  Identities=55%  Similarity=0.959  Sum_probs=132.4

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChHHHHH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVS   89 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~dIv~   89 (353)
                      -|||||+||++++||..+|++|+++||++|+||+ +.|+||+|...+|+.+++..++.....++|||+|||||||+++++
T Consensus        30 gsGKTt~Ll~~i~n~~~~~~kvl~~kp~~D~R~~-~~i~S~~g~~~~A~~~~~~~d~~~~~~~~DvIlIDEaQFfk~~ve  108 (195)
T 1w4r_A           30 FSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQFFPDIVE  108 (195)
T ss_dssp             TSCHHHHHHHHHHHHHHTTCCEEEEEETTCCCGG-GSCCHHHHHHSEEEEESSGGGGHHHHHTCSEEEESSGGGCTTHHH
T ss_pred             CCcHHHHHHHHHHHHHHcCCeEEEEccccCccch-hhhhhccCCcccceecCCHHHHHHhccCCCEEEEEchhhhHHHHH
Confidence            4899999999999999999999999999999999 459999999999999998888875556799999999999987899


Q ss_pred             HHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceeccccccccccccccc
Q psy8456          90 FAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQ  150 (353)
Q Consensus        90 l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~g  150 (353)
                      +++.+++.|++|||||||+||+++||+++++||++||+|+||+|+|+.||++|++|+|+++
T Consensus       109 ~~~~L~~~gk~VI~~GL~~DF~~~~F~~~~~Ll~~Ad~v~kl~aiC~~Cg~~A~~~~R~~~  169 (195)
T 1w4r_A          109 FCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGT  169 (195)
T ss_dssp             HHHHHHHTTCEEEEEEESBCTTSSBCTTGGGGGGGCSEEEECCEECTTTCSEECEEEESSC
T ss_pred             HHHHHHHCCCeEEEEecccccccccchhHHHHHHhcCeEEEeeeEecccCCeeeeEEEEcC
Confidence            9999999999999999999999999999999999999999999999999999999999854

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=100.00  E-value=3.6e-47  Score=352.60  Aligned_cols=157  Identities=38%  Similarity=0.612  Sum_probs=136.6

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc-CCCccEEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH-TKDIDVIG  227 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~-~~~~~~i~  227 (353)
                      .|++++|+|||||||||+|+++++||+.+|++|++++|++|+||+...|+||+|.+.+|+++.++.++... ..++|||+
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvli~kp~~D~R~~~~~I~Sr~G~~~~a~~v~~~~di~~~i~~~~dvV~  106 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRRLRRGIYAKQKVVVFKPAIDDRYHKEKVVSHNGNAIEAINISKASEIMTHDLTNVDVIG  106 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEEC-----------CBTTBCCEEEEESSGGGGGGSCCTTCSEEE
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHHHcCCceEEEEeccCCcchhhhHHHhcCCceeeEEeCCHHHHHHHHhcCCCEEE
Confidence            47899999999999999999999999999999999999999999999999999999999999888887654 47899999


Q ss_pred             EecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEecccccc
Q psy8456         228 IDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQ  307 (353)
Q Consensus       228 IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df~  307 (353)
                      |||||||+                                             +++|+++.+|++.|++|||||||+||+
T Consensus       107 IDEaQFf~---------------------------------------------~~~v~~l~~la~~gi~Vi~~GLd~DF~  141 (219)
T 3e2i_A          107 IDEVQFFD---------------------------------------------DEIVSIVEKLSADGHRVIVAGLDMDFR  141 (219)
T ss_dssp             ECCGGGSC---------------------------------------------THHHHHHHHHHHTTCEEEEEEESBCTT
T ss_pred             EechhcCC---------------------------------------------HHHHHHHHHHHHCCCEEEEeecccccc
Confidence            99999941                                             468888999999999999999999999


Q ss_pred             CCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCeeE
Q psy8456         308 RTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEV  350 (353)
Q Consensus       308 ~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~~  350 (353)
                      ++||+++++||++||+|+||+|+||.||++|+||+|+++|+++
T Consensus       142 ~~~F~~~~~Ll~~Ad~v~kl~aiC~~CG~~A~~~~R~~~g~~~  184 (219)
T 3e2i_A          142 GEPFEPMPKLMAVSEQVTKLQAVCAVCGSSSSRTQRLINGKPA  184 (219)
T ss_dssp             SCBCTTHHHHHHHCSEEEEECEECTTTCSEECEEEEEETTEEC
T ss_pred             cCCCccHHHHHHhcceEEEeeeEccCCCCcceEEEEEECCccc
Confidence            9999999999999999999999999999999999999998765

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=100.00  E-value=3.9e-47  Score=347.04  Aligned_cols=158  Identities=59%  Similarity=1.018  Sum_probs=145.7

Q ss_pred             cccccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccE
Q psy8456         146 KRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDV  225 (353)
Q Consensus       146 ~Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~  225 (353)
                      .+..+++++|+|||||||||+|+++++||..+|++|+++||++|+||+ +.|+||+|...+|+.+.+..++.....++||
T Consensus        16 ~~~~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~~D~R~~-~~i~S~~g~~~~A~~~~~~~d~~~~~~~~Dv   94 (195)
T 1w4r_A           16 SKTRGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLLRDVAQEALGVAV   94 (195)
T ss_dssp             ---CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEETTCCCGG-GSCCHHHHHHSEEEEESSGGGGHHHHHTCSE
T ss_pred             CCCceEEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccccCccch-hhhhhccCCcccceecCCHHHHHHhccCCCE
Confidence            344588999999999999999999999999999999999999999999 5599999999999998888887766667999


Q ss_pred             EEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEecccc
Q psy8456         226 IGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGT  305 (353)
Q Consensus       226 i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~d  305 (353)
                      |+|||+||                                              |++++++++.|++.|++|||+|||+|
T Consensus        95 IlIDEaQF----------------------------------------------fk~~ve~~~~L~~~gk~VI~~GL~~D  128 (195)
T 1w4r_A           95 IGIDEGQF----------------------------------------------FPDIVEFCEAMANAGKTVIVAALDGT  128 (195)
T ss_dssp             EEESSGGG----------------------------------------------CTTHHHHHHHHHHTTCEEEEEEESBC
T ss_pred             EEEEchhh----------------------------------------------hHHHHHHHHHHHHCCCeEEEEecccc
Confidence            99999999                                              67799999999999999999999999


Q ss_pred             ccCCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCeeE
Q psy8456         306 FQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEV  350 (353)
Q Consensus       306 f~~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~~  350 (353)
                      |+++||+++++|||+||+|+||+|+||.||++|+||+|+++++++
T Consensus       129 F~~~~F~~~~~Ll~~Ad~v~kl~aiC~~Cg~~A~~~~R~~~~~~~  173 (195)
T 1w4r_A          129 FQRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGTEKEV  173 (195)
T ss_dssp             TTSSBCTTGGGGGGGCSEEEECCEECTTTCSEECEEEESSCCCSS
T ss_pred             cccccchhHHHHHHhcCeEEEeeeEecccCCeeeeEEEEcCCCCE
Confidence            999999999999999999999999999999999999999876553

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=100.00  E-value=2.2e-46  Score=346.37  Aligned_cols=142  Identities=35%  Similarity=0.560  Sum_probs=116.3

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccC-CCccEEEEccccChH-HH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHT-KDIDVIGIDEGQFFP-DV   87 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~-~~~dvV~IDEaQFF~-dI   87 (353)
                      -|||||+||++++||..+|++|++|||.+|+||+.+.|+||+|++++|+.+++..++.... +++|+|+|||||||+ ++
T Consensus        38 gsGKTT~lL~~a~r~~~~g~kVli~k~~~d~R~ge~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~dvViIDEaQF~~~~~  117 (214)
T 2j9r_A           38 FSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAIDEVQFFDGDI  117 (214)
T ss_dssp             TSCHHHHHHHHHHHHHHTTCCEEEEECC-----------------CCEEECSSGGGGGGGCCSSCCEEEECCGGGSCTTH
T ss_pred             CCcHHHHHHHHHHHHHHCCCEEEEEEeccCCcchHHHHHhhcCCeeEEeecCCHHHHHHHHhcCCCEEEEECcccCCHHH
Confidence            5899999999999999999999999999999999999999999999999988887776544 369999999999996 67


Q ss_pred             HHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceecccccccccccccccc
Q psy8456          88 VSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQE  151 (353)
Q Consensus        88 v~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~ge  151 (353)
                      +++++.+++.|++|||+|||+||+++||+++++||++||+|+||+++|+.||++|++|+|++++
T Consensus       118 V~~l~~l~~~~~~Vi~~Gl~~DF~~~~F~~~~~Ll~~AD~Vtel~aiC~~Cg~~A~~~~R~~~g  181 (214)
T 2j9r_A          118 VEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVCSACGSPASRTQRLIDG  181 (214)
T ss_dssp             HHHHHHHHHTTCEEEEEECSBCTTSCBCTTHHHHHHHCSEEEECCCBCTTTSSBCCEEEEEETT
T ss_pred             HHHHHHHhhCCCEEEEEecccccccCccccHHHHHHhcccEEeeeeEecCcCCcceEEEEEeCC
Confidence            7999998989999999999999999999999999999999999999999999999999998654

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=100.00  E-value=9.1e-46  Score=346.27  Aligned_cols=140  Identities=55%  Similarity=0.959  Sum_probs=122.8

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChHHHHH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVS   89 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~dIv~   89 (353)
                      -|||||+||++++||..+|++|++|||.+|+||+ +.|+||+|.+++|+.+.+..++.....++|+|+|||||||+++++
T Consensus        29 gsGKTT~lL~~~~r~~~~g~kvli~kp~~D~Ryg-~~i~sr~G~~~~a~~i~~~~di~~~~~~~dvViIDEaQF~~~v~e  107 (234)
T 2orv_A           29 FSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQFFPDIVE  107 (234)
T ss_dssp             TSCHHHHHHHHHHHHHTTTCCEEEEEETTCCCC------------CEEEEESSGGGGHHHHTTCSEEEESSGGGCTTHHH
T ss_pred             CCcHHHHHHHHHHHHHHCCCeEEEEeecCCccch-HHHHhhcCCeeEEEecCCHHHHHHHhccCCEEEEEchhhhhhHHH
Confidence            5999999999999999999999999999999999 899999999999998888877765557899999999999988999


Q ss_pred             HHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceeccccccccccccccc
Q psy8456          90 FAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQ  150 (353)
Q Consensus        90 l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~g  150 (353)
                      +++.+++.|++|||+||++||+++||+++++||++||+|+||+++|+.||++|++|+|+++
T Consensus       108 l~~~l~~~gi~VI~~GL~~DF~~~~F~~~~~Ll~~AD~VtelkaIC~~Cg~~A~~t~R~~~  168 (234)
T 2orv_A          108 FCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGT  168 (234)
T ss_dssp             HHHHHHHTTCEEEEECCSBCTTSSBCTTGGGGGGGCSEEEECCEECTTTCSEECEEEESSC
T ss_pred             HHHHHHhCCCEEEEEecccccccCCcccHHHHHHhcccEEeeeeEecCcCCcceEEEEEcC
Confidence            9999999999999999999999999999999999999999999999999999999999854

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=100.00  E-value=2.9e-44  Score=325.02  Aligned_cols=142  Identities=32%  Similarity=0.492  Sum_probs=124.9

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccC-CCccEEEEccccChH-HH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHT-KDIDVIGIDEGQFFP-DV   87 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~-~~~dvV~IDEaQFF~-dI   87 (353)
                      -|||||+||++++||..+|++|+++||.+|+||+.+.|+||+|+..+|..+.+..++.... +++|+|+|||||||+ ++
T Consensus        18 gsGKTT~ll~~a~r~~~~g~kV~v~k~~~d~r~~~~~i~s~~g~~~~a~~~~~~~~i~~~~~~~~dvViIDEaqfl~~~~   97 (191)
T 1xx6_A           18 YSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDEVQFFDDEI   97 (191)
T ss_dssp             TSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEEECSGGGSCTHH
T ss_pred             CCcHHHHHHHHHHHHHHCCCEEEEEEeccCccchHHHHHhhcCCceeeEeeCCHHHHHHHHhccCCEEEEECCCCCCHHH
Confidence            5899999999999999999999999999999999889999999999998888877776433 459999999999995 77


Q ss_pred             HHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceecccccccccccccccc
Q psy8456          88 VSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQE  151 (353)
Q Consensus        88 v~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~ge  151 (353)
                      +++++.+++.|++||++||++||+++||+++++|+++||.|+|++++|+.||++|+||+|++++
T Consensus        98 v~~l~~l~~~~~~Vi~~Gl~~df~~~~F~~~~~L~~~AD~V~el~~iC~~Cg~~a~~~~r~~~g  161 (191)
T 1xx6_A           98 VEIVNKIAESGRRVICAGLDMDFRGKPFGPIPELMAIAEFVDKIQAICVVCGNPATRTQRLING  161 (191)
T ss_dssp             HHHHHHHHHTTCEEEEEECSBCTTSCBCTTHHHHHHHCSEEEECCEECTTTSSEECEEEEEETT
T ss_pred             HHHHHHHHhCCCEEEEEecccccccCcCccHHHHHHHcccEEeeeeEccccCCcceEEEEEcCC
Confidence            8889998888999999999999999999999999999999999999999999999999998653

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=100.00  E-value=1.3e-43  Score=327.84  Aligned_cols=157  Identities=39%  Similarity=0.595  Sum_probs=129.0

Q ss_pred             cccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCC-CccEE
Q psy8456         148 IGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTK-DIDVI  226 (353)
Q Consensus       148 i~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~-~~~~i  226 (353)
                      ..+++++++|||||||||+|+++++||..+|++|++++|.+|+||+...++||+|...++..+.+..++..... ++|+|
T Consensus        26 ~~G~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d~R~ge~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~dvV  105 (214)
T 2j9r_A           26 QNGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVI  105 (214)
T ss_dssp             CSCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC-----------------CCEEECSSGGGGGGGCCSSCCEE
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCCcchHHHHHhhcCCeeEEeecCCHHHHHHHHhcCCCEE
Confidence            35789999999999999999999999999999999999999999999999999999999999887777765543 69999


Q ss_pred             EEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEeccccc
Q psy8456         227 GIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTF  306 (353)
Q Consensus       227 ~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df  306 (353)
                      +|||+|||+                                             +++|++++.|++.|++|||+|||+||
T Consensus       106 iIDEaQF~~---------------------------------------------~~~V~~l~~l~~~~~~Vi~~Gl~~DF  140 (214)
T 2j9r_A          106 AIDEVQFFD---------------------------------------------GDIVEVVQVLANRGYRVIVAGLDQDF  140 (214)
T ss_dssp             EECCGGGSC---------------------------------------------TTHHHHHHHHHHTTCEEEEEECSBCT
T ss_pred             EEECcccCC---------------------------------------------HHHHHHHHHHhhCCCEEEEEeccccc
Confidence            999999941                                             56778888888889999999999999


Q ss_pred             cCCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCee
Q psy8456         307 QRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKE  349 (353)
Q Consensus       307 ~~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~  349 (353)
                      +++||+++.+||++||.|+||+++|+.||++|+||+|+++|++
T Consensus       141 ~~~~F~~~~~Ll~~AD~Vtel~aiC~~Cg~~A~~~~R~~~g~~  183 (214)
T 2j9r_A          141 RGLPFGQVPQLMAIAEHVTKLQAVCSACGSPASRTQRLIDGEP  183 (214)
T ss_dssp             TSCBCTTHHHHHHHCSEEEECCCBCTTTSSBCCEEEEEETTEE
T ss_pred             ccCccccHHHHHHhcccEEeeeeEecCcCCcceEEEEEeCCCc
Confidence            9999999999999999999999999999999999999999887

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=100.00  E-value=1.6e-43  Score=331.17  Aligned_cols=157  Identities=60%  Similarity=1.025  Sum_probs=133.5

Q ss_pred             ccccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEE
Q psy8456         147 RIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVI  226 (353)
Q Consensus       147 Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i  226 (353)
                      +..+.+++++|||||||||+||++++||..+|++|++++|.+|+||+ ..++||+|.+.+|+.+....++.....++|+|
T Consensus        16 ~~~g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D~Ryg-~~i~sr~G~~~~a~~i~~~~di~~~~~~~dvV   94 (234)
T 2orv_A           16 KTRGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLLRDVAQEALGVAVI   94 (234)
T ss_dssp             --CCEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCCC------------CEEEEESSGGGGHHHHTTCSEE
T ss_pred             CCceEEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCCccch-HHHHhhcCCeeEEEecCCHHHHHHHhccCCEE
Confidence            34588999999999999999999999999999999999999999999 99999999999998887766666555789999


Q ss_pred             EEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEeccccc
Q psy8456         227 GIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTF  306 (353)
Q Consensus       227 ~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df  306 (353)
                      +|||+||                                              |++++++++.+++.|++|||+||++||
T Consensus        95 iIDEaQF----------------------------------------------~~~v~el~~~l~~~gi~VI~~GL~~DF  128 (234)
T 2orv_A           95 GIDEGQF----------------------------------------------FPDIVEFCEAMANAGKTVIVAALDGTF  128 (234)
T ss_dssp             EESSGGG----------------------------------------------CTTHHHHHHHHHHTTCEEEEECCSBCT
T ss_pred             EEEchhh----------------------------------------------hhhHHHHHHHHHhCCCEEEEEeccccc
Confidence            9999999                                              455788888888999999999999999


Q ss_pred             cCCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCeeE
Q psy8456         307 QRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKEV  350 (353)
Q Consensus       307 ~~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~~  350 (353)
                      +++||+++.+||++||.|+||+++|+.||++|+||+|+++++++
T Consensus       129 ~~~~F~~~~~Ll~~AD~VtelkaIC~~Cg~~A~~t~R~~~~~~~  172 (234)
T 2orv_A          129 QRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGTEKEV  172 (234)
T ss_dssp             TSSBCTTGGGGGGGCSEEEECCEECTTTCSEECEEEESSCCCSS
T ss_pred             ccCCcccHHHHHHhcccEEeeeeEecCcCCcceEEEEEcCCCCE
Confidence            99999999999999999999999999999999999999877653

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=100.00  E-value=1.3e-41  Score=307.64  Aligned_cols=156  Identities=37%  Similarity=0.568  Sum_probs=136.5

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccC-CCccEEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHT-KDIDVIG  227 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~-~~~~~i~  227 (353)
                      .+++++++|||||||||+|+++++||..+|++|++++|.+|+||+...++||.|...++..+.+..+++... .++|+|+
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~d~r~~~~~i~s~~g~~~~a~~~~~~~~i~~~~~~~~dvVi   86 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIA   86 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEE
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCccchHHHHHhhcCCceeeEeeCCHHHHHHHHhccCCEEE
Confidence            478999999999999999999999999999999999999999999999999999988888877666665443 3599999


Q ss_pred             EecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEecccccc
Q psy8456         228 IDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQ  307 (353)
Q Consensus       228 IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df~  307 (353)
                      |||+||++                                             ++++++++.|++.|++|+++||++||+
T Consensus        87 IDEaqfl~---------------------------------------------~~~v~~l~~l~~~~~~Vi~~Gl~~df~  121 (191)
T 1xx6_A           87 IDEVQFFD---------------------------------------------DEIVEIVNKIAESGRRVICAGLDMDFR  121 (191)
T ss_dssp             ECSGGGSC---------------------------------------------THHHHHHHHHHHTTCEEEEEECSBCTT
T ss_pred             EECCCCCC---------------------------------------------HHHHHHHHHHHhCCCEEEEEecccccc
Confidence            99999941                                             677888888888899999999999999


Q ss_pred             CCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCee
Q psy8456         308 RTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKE  349 (353)
Q Consensus       308 ~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~  349 (353)
                      ++||+++.+|+++||.|+|++++|+.||++|+||+|+++|++
T Consensus       122 ~~~F~~~~~L~~~AD~V~el~~iC~~Cg~~a~~~~r~~~g~~  163 (191)
T 1xx6_A          122 GKPFGPIPELMAIAEFVDKIQAICVVCGNPATRTQRLINGKP  163 (191)
T ss_dssp             SCBCTTHHHHHHHCSEEEECCEECTTTSSEECEEEEEETTEE
T ss_pred             cCcCccHHHHHHHcccEEeeeeEccccCCcceEEEEEcCCCc
Confidence            999999999999999999999999999999999999999887

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=100.00  E-value=3.1e-38  Score=292.41  Aligned_cols=140  Identities=26%  Similarity=0.467  Sum_probs=128.5

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhccc------CCCccEEEEccccC
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPH------TKDIDVIGIDEGQF   83 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~------~~~~dvV~IDEaQF   83 (353)
                      -+||||+|++.++|+..+|++|++++|.+|+| +...|.||.|...++..+.+..++...      ..++|+|+|||+||
T Consensus        22 GsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvViIDEaQ~  100 (223)
T 2b8t_A           22 FAGKTAELIRRLHRLEYADVKYLVFKPKIDTR-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQF  100 (223)
T ss_dssp             TSCHHHHHHHHHHHHHHTTCCEEEEEECCCGG-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEEECSGGG
T ss_pred             CCcHHHHHHHHHHHHHhcCCEEEEEEeccCch-HHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEEEEecCcc
Confidence            58999999999999999999999999999999 888899999999888877776666421      24699999999999


Q ss_pred             hH-HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceeccccccccccccccc
Q psy8456          84 FP-DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQ  150 (353)
Q Consensus        84 F~-dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A~f~~Ri~g  150 (353)
                      |+ ++++++..+++.|++|+++||++||+++||++++.|+++||.|++|+++|+.||++|++|+|+.+
T Consensus       101 l~~~~ve~l~~L~~~gi~Vil~Gl~~df~~~~F~~~~~Ll~lAD~V~el~~ic~~Cg~~a~~~~r~~~  168 (223)
T 2b8t_A          101 FDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKID  168 (223)
T ss_dssp             SCTHHHHHHHHHHHTTCEEEEECCSBCTTSSBCTTHHHHHHHCSEEEECCEECTTTCSEECEEEEEET
T ss_pred             CcHHHHHHHHHHHhCCCeEEEEeccccccCCcCCCcHHHHHHhheEeecceeccccCCccceeEEecC
Confidence            96 88888899999999999999999999999999999999999999999999999999999999854

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=100.00  E-value=1.6e-37  Score=277.17  Aligned_cols=143  Identities=22%  Similarity=0.302  Sum_probs=122.6

Q ss_pred             CCCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccC-CCccEEEEccccChH-
Q psy8456           8 DRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHT-KDIDVIGIDEGQFFP-   85 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~-~~~dvV~IDEaQFF~-   85 (353)
                      .+-+||||.|++.++++..+|++|++++|.+|+||+.+.|.||+|...++..+.++.++.... +++|+|+|||+|||+ 
T Consensus        11 ~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~d~r~~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~dvviIDE~Q~~~~   90 (184)
T 2orw_A           11 PMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGVFIDEVQFFNP   90 (184)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTCEEEEEEEC-----CCCEECC----CEECEEESSGGGGGGGCCTTEEEEEECCGGGSCT
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCeEEEEeeccccccCcccEEecCCCceeeEEECCHHHHHHHhcCCCCEEEEECcccCCH
Confidence            356899999999999999999999999999999999999999999999988888887776443 479999999999994 


Q ss_pred             HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceecccc-ccccccccccc
Q psy8456          86 DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCF-RDAAFTKRIGQ  150 (353)
Q Consensus        86 dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG-~~A~f~~Ri~g  150 (353)
                      ++++++..+++.|++|+++||++||+++||++++.|+++||.|++|+++|+.|| ++|++|+|+++
T Consensus        91 ~~~~~l~~l~~~~~~Vi~~Gl~~~f~~~~f~~~~~ll~~ad~v~~l~~ic~~cg~~~a~~~~r~~~  156 (184)
T 2orw_A           91 SLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKVAG  156 (184)
T ss_dssp             THHHHHHHHHHTTCEEEEEEESBCTTSCBCHHHHHHHHHCSEEEECCBCCTTTCCSCBCEEEECSS
T ss_pred             HHHHHHHHHHHCCCCEEEEeeccccccCCccchHHHHHHhhheEEeeeecCCCCCeeceeEEEEcC
Confidence            778888878888999999999999999999999999999999999999999999 99999999864

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=100.00  E-value=5.4e-36  Score=267.26  Aligned_cols=156  Identities=28%  Similarity=0.406  Sum_probs=133.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccC-CCccEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHT-KDIDVIGI  228 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~-~~~~~i~I  228 (353)
                      +.+.+++|||||||||.|++.++++..+|++|++++|..|+||+.+.+.||+|....+....++.+++... +++|+|+|
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~d~r~~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~dvviI   82 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGVFI   82 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC-----CCCEECC----CEECEEESSGGGGGGGCCTTEEEEEE
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeeccccccCcccEEecCCCceeeEEECCHHHHHHHhcCCCCEEEE
Confidence            67899999999999999999999999999999999999999999999999999988888877777776554 47999999


Q ss_pred             ecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEeccccccC
Q psy8456         229 DEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQR  308 (353)
Q Consensus       229 DE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df~~  308 (353)
                      ||+||+                                             -+++++++..+++.|++|+++||++||++
T Consensus        83 DE~Q~~---------------------------------------------~~~~~~~l~~l~~~~~~Vi~~Gl~~~f~~  117 (184)
T 2orw_A           83 DEVQFF---------------------------------------------NPSLFEVVKDLLDRGIDVFCAGLDLTHKQ  117 (184)
T ss_dssp             CCGGGS---------------------------------------------CTTHHHHHHHHHHTTCEEEEEEESBCTTS
T ss_pred             ECcccC---------------------------------------------CHHHHHHHHHHHHCCCCEEEEeecccccc
Confidence            999994                                             16777788888888999999999999999


Q ss_pred             CCchhHHhhhhcccceEEeeeeccccc-cccceeEEeeCCeeE
Q psy8456         309 TGFNDILSLIPLAECVEKLTAVCMSCF-RDAAFTKRIGQEKEV  350 (353)
Q Consensus       309 ~~F~~~~~L~~~ad~v~kl~a~C~~Cg-~~A~~~~R~~~~~~~  350 (353)
                      ++|+.+..|+++||.|+||+++|+.|| ++|++|+|+++++++
T Consensus       118 ~~f~~~~~ll~~ad~v~~l~~ic~~cg~~~a~~~~r~~~~~~~  160 (184)
T 2orw_A          118 NPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKVAGGEEE  160 (184)
T ss_dssp             CBCHHHHHHHHHCSEEEECCBCCTTTCCSCBCEEEECSSCSCS
T ss_pred             CCccchHHHHHHhhheEEeeeecCCCCCeeceeEEEEcCCCCE
Confidence            999999999999999999999999999 999999999877654

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=100.00  E-value=6.8e-36  Score=276.68  Aligned_cols=158  Identities=31%  Similarity=0.499  Sum_probs=139.8

Q ss_pred             cccccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc------
Q psy8456         146 KRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH------  219 (353)
Q Consensus       146 ~Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~------  219 (353)
                      ....+.+.+++|||||||||+|++.++++..+|++|++++|.+|+| +...+.+|.|...++..+....++...      
T Consensus         8 ~~~~G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~   86 (223)
T 2b8t_A            8 SKKIGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTR-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSF   86 (223)
T ss_dssp             ---CCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGG-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTS
T ss_pred             ccCCcEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCch-HHHHHHHhcCCCccccccCCHHHHHHHHHHHhh
Confidence            3345789999999999999999999999999999999999999999 888999999988888776554444321      


Q ss_pred             CCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEE
Q psy8456         220 TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVV  299 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~  299 (353)
                      ..++|+|+|||+||+                                             -+++++++..|++.|++|++
T Consensus        87 ~~~~dvViIDEaQ~l---------------------------------------------~~~~ve~l~~L~~~gi~Vil  121 (223)
T 2b8t_A           87 NDETKVIGIDEVQFF---------------------------------------------DDRICEVANILAENGFVVII  121 (223)
T ss_dssp             CTTCCEEEECSGGGS---------------------------------------------CTHHHHHHHHHHHTTCEEEE
T ss_pred             CCCCCEEEEecCccC---------------------------------------------cHHHHHHHHHHHhCCCeEEE
Confidence            246999999999995                                             25677788888889999999


Q ss_pred             EeccccccCCCchhHHhhhhcccceEEeeeeccccccccceeEEeeCCee
Q psy8456         300 AALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDAAFTKRIGQEKE  349 (353)
Q Consensus       300 ~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~C~~Cg~~A~~~~R~~~~~~  349 (353)
                      +||++||+++||+.+..|+++||.|++|+++|+.||++|++|+|+.+|++
T Consensus       122 ~Gl~~df~~~~F~~~~~Ll~lAD~V~el~~ic~~Cg~~a~~~~r~~~g~~  171 (223)
T 2b8t_A          122 SGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKH  171 (223)
T ss_dssp             ECCSBCTTSSBCTTHHHHHHHCSEEEECCEECTTTCSEECEEEEEETTEE
T ss_pred             EeccccccCCcCCCcHHHHHHhheEeecceeccccCCccceeEEecCCCc
Confidence            99999999999999999999999999999999999999999999999876

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.12  E-value=0.0017  Score=55.28  Aligned_cols=61  Identities=11%  Similarity=0.054  Sum_probs=40.4

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGI  228 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~I  228 (353)
                      .++..+++||.||||||-+--....+...|++++.+... +-..       .              .+   ..++++++|
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~-~~~~-------~--------------~~---~~~~~lLil   89 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAA-SMPL-------T--------------DA---AFEAEYLAV   89 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETT-TSCC-------C--------------GG---GGGCSEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHH-HhhH-------H--------------HH---HhCCCEEEE
Confidence            356778999999999987666666666567666655321 1110       0              11   235799999


Q ss_pred             eccccc
Q psy8456         229 DEGQFV  234 (353)
Q Consensus       229 DE~QF~  234 (353)
                      ||.+.+
T Consensus        90 DE~~~~   95 (149)
T 2kjq_A           90 DQVEKL   95 (149)
T ss_dssp             ESTTCC
T ss_pred             eCcccc
Confidence            999985

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=96.87  E-value=0.0014  Score=58.89  Aligned_cols=23  Identities=26%  Similarity=0.238  Sum_probs=18.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +.+++|++|||||+.....+...
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~~   29 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMAND   29 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            67899999999999876655444

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.71  E-value=0.0053  Score=53.25  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=42.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGID  229 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~ID  229 (353)
                      +..-+++||.|+|||+-+-..++.....+.++..+....-.                    ..+.+.+....+.++++||
T Consensus        52 ~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~vliiD  111 (242)
T 3bos_A           52 VQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHA--------------------SISTALLEGLEQFDLICID  111 (242)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGGG--------------------GSCGGGGTTGGGSSEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHH--------------------HHHHHHHHhccCCCEEEEe
Confidence            34568999999999987766666666667777665432100                    0011122223557899999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |+|.+
T Consensus       112 e~~~~  116 (242)
T 3bos_A          112 DVDAV  116 (242)
T ss_dssp             TGGGG
T ss_pred             ccccc
Confidence            99986

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=96.71  E-value=0.0018  Score=66.96  Aligned_cols=38  Identities=13%  Similarity=-0.005  Sum_probs=33.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +...+|.||.|+||||-+...++.+...|++|++..|+
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT  241 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPT  241 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCc
Confidence            56789999999999999988888888999999998874

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.57  E-value=0.0016  Score=59.11  Aligned_cols=134  Identities=16%  Similarity=0.133  Sum_probs=76.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecC-CCCCCCceeeccCcccce-----------------eecc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKD-DRYDTEKVSTHDQQKLTA-----------------VSAV  211 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D-~R~~~~~i~s~~g~~~~a-----------------~~~~  211 (353)
                      +.+.++.| -|.||||..+-.+.|+--+|++|+++.-... ..+++..+..+-+..+..                 ....
T Consensus        29 g~i~v~tG-~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~  107 (196)
T 1g5t_A           29 GIIIVFTG-NGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMA  107 (196)
T ss_dssp             CCEEEEES-SSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHH
T ss_pred             ceEEEECC-CCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHH
Confidence            44555555 5699999999999999999999999954443 223322232222210000                 0001


Q ss_pred             cHhhhccc--CCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHH
Q psy8456         212 ELNKLIPH--TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAES  289 (353)
Q Consensus       212 ~~~~~~~~--~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~  289 (353)
                      .++.....  ..+||+|++||.=...-    =+|             ++                     .++++++..+
T Consensus       108 ~l~~a~~~l~~~~yDlvILDEi~~al~----~g~-------------l~---------------------~~ev~~~l~~  149 (196)
T 1g5t_A          108 VWQHGKRMLADPLLDMVVLDELTYMVA----YDY-------------LP---------------------LEEVISALNA  149 (196)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHHH----TTS-------------SC---------------------HHHHHHHHHT
T ss_pred             HHHHHHHHHhcCCCCEEEEeCCCcccc----CCC-------------CC---------------------HHHHHHHHHh
Confidence            12222222  37899999999843100    000             00                     1334443321


Q ss_pred             HHhCCCEEEEEeccccccCCCchhHHhhhhcccceEEeeeecc
Q psy8456         290 MANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCM  332 (353)
Q Consensus       290 ~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~C~  332 (353)
                       .-.+..||+-|=      .+   ...|+++||-|++++.+=+
T Consensus       150 -Rp~~~~vIlTGr------~a---p~~l~e~AD~VTem~~vkH  182 (196)
T 1g5t_A          150 -RPGHQTVIITGR------GC---HRDILDLADTVSELRPVKH  182 (196)
T ss_dssp             -SCTTCEEEEECS------SC---CHHHHHHCSEEEECCCSCC
T ss_pred             -CcCCCEEEEECC------CC---cHHHHHhCcceeeecceeC
Confidence             124788998874      33   3579999999999976643

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=96.47  E-value=0.011  Score=54.06  Aligned_cols=35  Identities=14%  Similarity=0.120  Sum_probs=28.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCC-EEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANY-RCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~-~~~~~k~~  187 (353)
                      -++.+|||||||...+..+..+...+. +++++-|.
T Consensus       131 ~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt  166 (282)
T 1rif_A          131 RILNLPTSAGRSLIQALLARYYLENYEGKILIIVPT  166 (282)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSS
T ss_pred             eEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECC
Confidence            478999999999998877777655554 99999885

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.42  E-value=0.0022  Score=58.27  Aligned_cols=115  Identities=10%  Similarity=0.075  Sum_probs=73.3

Q ss_pred             CchHHHHHHHHHHHHHcCceEEEEeeccC-CCCCCCceeeccCCceeeee----cCC-------------hhhhccc--C
Q psy8456          11 NPYIVHFCRRIRRYQYANYRCMIVRYAKD-DRYDTEKVATHDQQKLTAVS----AVE-------------LNKLIPH--T   70 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agkkvlv~Kp~iD-tRy~~~~I~Sr~G~~~~Ai~----i~~-------------l~ei~~~--~   70 (353)
                      .||||..+-.+.|.--+|++|+++.--.. ..+++..+..+.+..+....    .+.             +......  .
T Consensus        39 kGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~~l~~a~~~l~~  118 (196)
T 1g5t_A           39 KGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAVWQHGKRMLAD  118 (196)
T ss_dssp             SCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHHHHHHHHHHHhc
Confidence            69999999999999999999999943322 22333333344332222110    000             1111112  3


Q ss_pred             CCccEEEEcccc------ChHHHHHHHHHHHh--CCCEEEEEecccccccCCchhHhhhhccccceEecccee
Q psy8456          71 KDIDVIGIDEGQ------FFPDVVSFAESMAN--AGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVC  135 (353)
Q Consensus        71 ~~~dvV~IDEaQ------FF~dIv~l~~~l~~--~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC  135 (353)
                      ++||+|++||.=      ++ ++.++.+.+.+  .+..||+-|=      .+   .+.|+++||-|++++.+=
T Consensus       119 ~~yDlvILDEi~~al~~g~l-~~~ev~~~l~~Rp~~~~vIlTGr------~a---p~~l~e~AD~VTem~~vk  181 (196)
T 1g5t_A          119 PLLDMVVLDELTYMVAYDYL-PLEEVISALNARPGHQTVIITGR------GC---HRDILDLADTVSELRPVK  181 (196)
T ss_dssp             TTCSEEEEETHHHHHHTTSS-CHHHHHHHHHTSCTTCEEEEECS------SC---CHHHHHHCSEEEECCCSC
T ss_pred             CCCCEEEEeCCCccccCCCC-CHHHHHHHHHhCcCCCEEEEECC------CC---cHHHHHhCcceeeeccee
Confidence            679999999993      33 34455555664  4889999986      33   357999999999997654

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=96.35  E-value=0.0029  Score=59.08  Aligned_cols=73  Identities=19%  Similarity=0.241  Sum_probs=40.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDE  230 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE  230 (353)
                      ..-+++||.|+||||-+-..++.....+.+++.+....        ....   -..+........+.....+.++++|||
T Consensus        38 ~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~--------~~~~---~~~~~~~~~~~~~~~~~~~~~vL~iDE  106 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADD--------FAQA---MVEHLKKGTINEFRNMYKSVDLLLLDD  106 (324)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHH--------HHHH---HHHHHHHTCHHHHHHHHHTCSEEEEEC
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHH--------HHHH---HHHHHHcCcHHHHHHHhcCCCEEEEcC
Confidence            45689999999999765555555555567666554321        0000   000000011122222223578999999


Q ss_pred             cccc
Q psy8456         231 GQFV  234 (353)
Q Consensus       231 ~QF~  234 (353)
                      +|++
T Consensus       107 i~~l  110 (324)
T 1l8q_A          107 VQFL  110 (324)
T ss_dssp             GGGG
T ss_pred             cccc
Confidence            9996

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=96.29  E-value=0.0035  Score=62.16  Aligned_cols=36  Identities=19%  Similarity=0.071  Sum_probs=31.0

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCC-EEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANY-RCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~-~~~~~k~~  187 (353)
                      ..++.|+-|||||+-|...+..+...|. +++++.|+
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T   83 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEALISTGETGIILAAPT   83 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCc
Confidence            6789999999999988888888888887 78888775

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=96.27  E-value=0.0064  Score=51.77  Aligned_cols=35  Identities=14%  Similarity=0.108  Sum_probs=25.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH-HhCCEEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ-YANYRCMIV  184 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~-~~~~~~~~~  184 (353)
                      +...+++||.||||||-+-..+..+. ..|..++.+
T Consensus        38 g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~   73 (180)
T 3ec2_A           38 GKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFF   73 (180)
T ss_dssp             CCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            56678999999999987666666664 567665543

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.23  E-value=0.003  Score=54.70  Aligned_cols=37  Identities=19%  Similarity=0.059  Sum_probs=31.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +++.+++||.+|||||-+..-+......+.+|+++..
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~~   59 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVTT   59 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEES
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEEc
Confidence            5788999999999999988888787777888887764

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=96.14  E-value=0.016  Score=56.04  Aligned_cols=82  Identities=17%  Similarity=0.110  Sum_probs=52.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceee---cccHhh---hcc---cC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVS---AVELNK---LIP---HT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~---~~~~~~---~~~---~~  220 (353)
                      +++..|+||.+|||||-+++.+.+....|.+|+++......+   .....+.|....-+.   ..+..+   ++.   ..
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~---~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~~  137 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEHALD---PEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVRS  137 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCC---HHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcC---HHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHhc
Confidence            568899999999999999999999998999999887643111   011112222111111   112222   221   23


Q ss_pred             CCccEEEEeccccc
Q psy8456         221 KDIDVIGIDEGQFV  234 (353)
Q Consensus       221 ~~~~~i~IDE~QF~  234 (353)
                      .++++|+|||.+.+
T Consensus       138 ~~~~lIVIDsl~~l  151 (349)
T 2zr9_A          138 GALDIIVIDSVAAL  151 (349)
T ss_dssp             TCCSEEEEECGGGC
T ss_pred             CCCCEEEEcChHhh
Confidence            56999999999975

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=96.10  E-value=0.012  Score=53.27  Aligned_cols=32  Identities=28%  Similarity=0.239  Sum_probs=26.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      -++.||||+|||...+..+...   +.+++++-|.
T Consensus       111 ~ll~~~tG~GKT~~a~~~~~~~---~~~~liv~P~  142 (237)
T 2fz4_A          111 GCIVLPTGSGKTHVAMAAINEL---STPTLIVVPT  142 (237)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHS---CSCEEEEESS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHc---CCCEEEEeCC
Confidence            6889999999998887766553   7888888886

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=95.95  E-value=0.0068  Score=59.84  Aligned_cols=95  Identities=9%  Similarity=0.105  Sum_probs=56.9

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCC-EEEEEeeecC---------CCC---CCCceee-ccCccc-------ceeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANY-RCMIVRYAKD---------DRY---DTEKVST-HDQQKL-------TAVSA  210 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~-~~~~~k~~~D---------~R~---~~~~i~s-~~g~~~-------~a~~~  210 (353)
                      .-++.||||||||...+..+..+...++ +++++-|...         .++   ....+.. +.|...       .-+.+
T Consensus       130 ~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~I~i  209 (510)
T 2oca_A          130 RRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVV  209 (510)
T ss_dssp             EEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEECGGGCCTTGGGCTTCSEEE
T ss_pred             CcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHHHHHHhhcCCccceEEEecCCccccccccCCcEEE
Confidence            4589999999999999888887766666 9999999631         112   1112211 111111       12333


Q ss_pred             ccHhhhccc----CCCccEEEEecccccceecCCccchhhhhhh
Q psy8456         211 VELNKLIPH----TKDIDVIGIDEGQFVEVIGGSDKYMAVCREC  250 (353)
Q Consensus       211 ~~~~~~~~~----~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~  250 (353)
                      .....+...    .+++++|+|||+|.+.    .+.|..+.+..
T Consensus       210 ~T~~~l~~~~~~~~~~~~liIiDE~H~~~----~~~~~~il~~~  249 (510)
T 2oca_A          210 GTWQTVVKQPKEWFSQFGMMMNDECHLAT----GKSISSIISGL  249 (510)
T ss_dssp             EEHHHHTTSCGGGGGGEEEEEEETGGGCC----HHHHHHHGGGC
T ss_pred             EeHHHHhhchhhhhhcCCEEEEECCcCCC----cccHHHHHHhc
Confidence            333334332    4678999999999852    24455554444

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=95.93  E-value=0.045  Score=53.49  Aligned_cols=82  Identities=16%  Similarity=0.060  Sum_probs=51.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccce---eecccHhhhc---c---cC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA---VSAVELNKLI---P---HT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a---~~~~~~~~~~---~---~~  220 (353)
                      +.+..|+||.+|||||-+++.+..++..|.+|+++......+.   ....+.|.....   ....+..+++   .   ..
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~---~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~~  137 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDP---VYAKNLGVDLKSLLISQPDHGEQALEIVDELVRS  137 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCH---HHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccch---HHHHHcCCchhhhhhhhccCHHHHHHHHHHHhhh
Confidence            4678899999999999999999999989999988754321110   011122221111   1112222221   1   13


Q ss_pred             CCccEEEEeccccc
Q psy8456         221 KDIDVIGIDEGQFV  234 (353)
Q Consensus       221 ~~~~~i~IDE~QF~  234 (353)
                      ..+++|+||.++-+
T Consensus       138 ~~~dlvVIDSi~~l  151 (356)
T 3hr8_A          138 GVVDLIVVDSVAAL  151 (356)
T ss_dssp             SCCSEEEEECTTTC
T ss_pred             cCCCeEEehHhhhh
Confidence            57899999999964

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=95.89  E-value=0.0079  Score=59.70  Aligned_cols=72  Identities=25%  Similarity=0.381  Sum_probs=38.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH-HHh--CCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCC-CccEE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY-QYA--NYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTK-DIDVI  226 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~-~~~--~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~-~~~~i  226 (353)
                      +.-+++||.|+|||| |++.+.++ ...  +.+++.+....        ...   .-..++.......+..... +.+++
T Consensus       131 ~~lll~Gp~G~GKTt-La~aia~~l~~~~~~~~v~~v~~~~--------~~~---~~~~~~~~~~~~~~~~~~~~~~~vL  198 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTH-LLQSIGNYVVQNEPDLRVMYITSEK--------FLN---DLVDSMKEGKLNEFREKYRKKVDIL  198 (440)
T ss_dssp             CCEEEECSSSSSHHH-HHHHHHHHHHHHCCSSCEEEEEHHH--------HHH---HHHHHHHTTCHHHHHHHHTTTCSEE
T ss_pred             CeEEEECCCCCCHHH-HHHHHHHHHHHhCCCCeEEEeeHHH--------HHH---HHHHHHHcccHHHHHHHhcCCCCEE
Confidence            456899999999997 55555554 333  55555444321        000   0000000011122222234 78999


Q ss_pred             EEeccccc
Q psy8456         227 GIDEGQFV  234 (353)
Q Consensus       227 ~IDE~QF~  234 (353)
                      +|||+|++
T Consensus       199 ~IDEi~~l  206 (440)
T 2z4s_A          199 LIDDVQFL  206 (440)
T ss_dssp             EEECGGGG
T ss_pred             EEeCcccc
Confidence            99999996

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=95.72  E-value=0.012  Score=57.55  Aligned_cols=90  Identities=17%  Similarity=0.196  Sum_probs=52.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC---------CCCCCceee-ccCccc-ceeecccHhhhccc-
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD---------RYDTEKVST-HDQQKL-TAVSAVELNKLIPH-  219 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~---------R~~~~~i~s-~~g~~~-~a~~~~~~~~~~~~-  219 (353)
                      .-++.+|||||||...+..+...   +.+++++-|...-         +++...+.. +.+... ..+.+.....+... 
T Consensus       110 ~~ll~~~TGsGKT~~~l~~i~~~---~~~~Lvl~P~~~L~~Q~~~~~~~~~~~~v~~~~g~~~~~~~Ivv~T~~~l~~~~  186 (472)
T 2fwr_A          110 RGCIVLPTGSGKTHVAMAAINEL---STPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNA  186 (472)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH---CSCEEEEESSHHHHHHHHHHGGGGCGGGEEEBSSSCBCCCSEEEEEHHHHHHTH
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHc---CCCEEEEECCHHHHHHHHHHHHhCCCcceEEECCCcCCcCCEEEEEcHHHHHHH
Confidence            36889999999999888777654   8899999997321         122221222 222211 12223322222211 


Q ss_pred             ---CCCccEEEEecccccceecCCccchhhhh
Q psy8456         220 ---TKDIDVIGIDEGQFVEVIGGSDKYMAVCR  248 (353)
Q Consensus       220 ---~~~~~~i~IDE~QF~~~~~~~~~~~~~~~  248 (353)
                         .+++++|+|||+|.+    ....|..+.+
T Consensus       187 ~~~~~~~~liIvDEaH~~----~~~~~~~~~~  214 (472)
T 2fwr_A          187 EKLGNRFMLLIFDEVHHL----PAESYVQIAQ  214 (472)
T ss_dssp             HHHTTTCSEEEEETGGGT----TSTTTHHHHH
T ss_pred             HHhcCCCCEEEEECCcCC----CChHHHHHHH
Confidence               256999999999985    2345554433

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=95.67  E-value=0.0023  Score=64.77  Aligned_cols=37  Identities=19%  Similarity=0.210  Sum_probs=28.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR  191 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R  191 (353)
                      ..+.+|.|+-|||||+.+.+.+..     ++++++.|..-.+
T Consensus       161 ~~v~~I~G~aGsGKTt~I~~~~~~-----~~~lVlTpT~~aa  197 (446)
T 3vkw_A          161 AKVVLVDGVPGCGKTKEILSRVNF-----EEDLILVPGRQAA  197 (446)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHCCT-----TTCEEEESCHHHH
T ss_pred             ccEEEEEcCCCCCHHHHHHHHhcc-----CCeEEEeCCHHHH
Confidence            457899999999999999887642     5678888865333

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=95.53  E-value=0.077  Score=51.60  Aligned_cols=81  Identities=14%  Similarity=0.168  Sum_probs=43.5

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEeeecCCCCCC-CceeeccCcccceeecccHhhhccc--CCCcc
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVRYAKDDRYDT-EKVSTHDQQKLTAVSAVELNKLIPH--TKDID  224 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k~~~D~R~~~-~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~  224 (353)
                      .+++.+++||.||||||-|---+..+... +.+++.+.....-.... ....+.......   .....+.+..  ..++|
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~~~v~q~~~~~~---~~~~~~~La~aL~~~Pd  198 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRD---TLGFSEALRSALREDPD  198 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTT---BSCHHHHHHHHTTSCCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccccceeeeeeccc---cCCHHHHHHHHhhhCcC
Confidence            45688999999999999876655555544 66666554322211110 011111100000   0122222221  47899


Q ss_pred             EEEEeccc
Q psy8456         225 VIGIDEGQ  232 (353)
Q Consensus       225 ~i~IDE~Q  232 (353)
                      +|++||.-
T Consensus       199 villDEp~  206 (356)
T 3jvv_A          199 IILVGEMR  206 (356)
T ss_dssp             EEEESCCC
T ss_pred             EEecCCCC
Confidence            99999974

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=95.33  E-value=0.03  Score=55.31  Aligned_cols=37  Identities=19%  Similarity=0.121  Sum_probs=31.1

Q ss_pred             ceeeeeccCCCCchhH-HHHHHHHHHHhCCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTE-LIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~-Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +..++.+|.|||||+. ++..+......|.+++++.|.
T Consensus        20 ~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~lvl~Pt   57 (451)
T 2jlq_A           20 RLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPT   57 (451)
T ss_dssp             CEEEECCCTTSSCCTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CeEEEECCCCCCHhhHHHHHHHHHHHhcCCcEEEECCC
Confidence            4558899999999995 888777777788899999885

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.20  E-value=0.014  Score=50.25  Aligned_cols=35  Identities=23%  Similarity=0.148  Sum_probs=24.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      ..-+++||.|+|||+-+-..++.....+.+++.+.
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~   89 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVY   89 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            45689999999999855444444455567766554

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=95.14  E-value=0.07  Score=47.56  Aligned_cols=38  Identities=18%  Similarity=0.127  Sum_probs=27.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH-HHhCC----EEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY-QYANY----RCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~-~~~~~----~~~~~k~~  187 (353)
                      ++..++.||.||||||.+...+... ...+.    ++++..|.
T Consensus        76 g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~  118 (235)
T 3llm_A           76 NSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPR  118 (235)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESS
T ss_pred             CCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccc
Confidence            5667899999999999776665554 33333    77777764

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=95.02  E-value=0.047  Score=55.17  Aligned_cols=36  Identities=17%  Similarity=0.087  Sum_probs=29.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHh---------CCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYA---------NYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~---------~~~~~~~k~~  187 (353)
                      .-++.+|||||||...+..+.++..+         +.+++++-|.
T Consensus       200 ~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~  244 (590)
T 3h1t_A          200 RSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADR  244 (590)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-
T ss_pred             ceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCC
Confidence            35788999999999988888887654         5899999884

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=94.83  E-value=0.2  Score=48.98  Aligned_cols=80  Identities=15%  Similarity=0.057  Sum_probs=51.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHh--CCEEEEEeeecCCCCCCCceeeccCccccee---ecccHhhh----c-----
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYA--NYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV---SAVELNKL----I-----  217 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~--~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~---~~~~~~~~----~-----  217 (353)
                      +..|.||.+|||||-+++.+.+++..  |.+|+.+.....-+-   .-..+.|...+.+   ...+..++    +     
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~---~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l~~  106 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITP---AYLRSMGVDPERVIHTPVQSLEQLRIDMVNQLDA  106 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCH---HHHHHTTCCGGGEEEEECSBHHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhH---HHHHHhCCCHHHeEEEcCCCHHHHHHHHHHHHHH
Confidence            67899999999999999999999876  788988765432210   0112223222211   11222222    1     


Q ss_pred             ccCCCccEEEEeccccc
Q psy8456         218 PHTKDIDVIGIDEGQFV  234 (353)
Q Consensus       218 ~~~~~~~~i~IDE~QF~  234 (353)
                      -...++++|+||=+|-+
T Consensus       107 i~~~~~~lvVIDSI~aL  123 (333)
T 3io5_A          107 IERGEKVVVFIDSLGNL  123 (333)
T ss_dssp             CCTTCCEEEEEECSTTC
T ss_pred             hhccCceEEEEeccccc
Confidence            12357999999999975

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=94.83  E-value=0.041  Score=45.26  Aligned_cols=25  Identities=24%  Similarity=0.192  Sum_probs=18.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQY  176 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~  176 (353)
                      .-+++||.|+|||+-+-..++.+..
T Consensus        45 ~~ll~G~~G~GKT~l~~~~~~~~~~   69 (195)
T 1jbk_A           45 NPVLIGEPGVGKTAIVEGLAQRIIN   69 (195)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHh
Confidence            3589999999999866555555443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=94.80  E-value=0.018  Score=47.73  Aligned_cols=24  Identities=21%  Similarity=0.153  Sum_probs=17.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQ  175 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~  175 (353)
                      .-+++||.|+|||+-+-..++...
T Consensus        45 ~vll~G~~G~GKT~la~~~~~~~~   68 (187)
T 2p65_A           45 NPILLGDPGVGKTAIVEGLAIKIV   68 (187)
T ss_dssp             EEEEESCGGGCHHHHHHHHHHHHH
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHH
Confidence            348999999999976555544443

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=94.63  E-value=0.043  Score=54.19  Aligned_cols=39  Identities=15%  Similarity=0.094  Sum_probs=30.7

Q ss_pred             cceeeeeccCCCCchhH-HHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTE-LIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~-Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ++..++.||.|||||.. ++-.+......|.+++++-|..
T Consensus         8 g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~~~lil~Ptr   47 (440)
T 1yks_A            8 GMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTR   47 (440)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHHHHHhcCCeEEEEcchH
Confidence            55678999999999997 4556666666788999998853

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=94.61  E-value=0.028  Score=55.71  Aligned_cols=39  Identities=21%  Similarity=0.134  Sum_probs=32.4

Q ss_pred             cceeeeeccCCCCchhH-HHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTE-LIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~-Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ++..++.+|.|||||+. ++-.+..+...|.+++++-|..
T Consensus        21 ~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr   60 (459)
T 2z83_A           21 RQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTR   60 (459)
T ss_dssp             TCEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchH
Confidence            45668899999999997 7777777777889999999854

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=94.56  E-value=0.044  Score=50.35  Aligned_cols=37  Identities=16%  Similarity=0.116  Sum_probs=28.0

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHH--hCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQY--ANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~--~~~~~~~~k~~~  188 (353)
                      .-++.+|+|||||...+..+..+..  .+.+++++-|..
T Consensus        46 ~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~   84 (367)
T 1hv8_A           46 NIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTR   84 (367)
T ss_dssp             EEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCH
T ss_pred             CEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCH
Confidence            4578899999999887766655432  477899998863

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=94.55  E-value=0.03  Score=52.70  Aligned_cols=36  Identities=14%  Similarity=-0.003  Sum_probs=29.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHH-HhCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQ-YANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~-~~~~~~~~~k~~  187 (353)
                      .-++.+|||+|||...+..+..+. ..+.+++++-|.
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~   61 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPT   61 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSS
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECC
Confidence            457899999999999888876653 468899999996

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=94.53  E-value=0.085  Score=46.37  Aligned_cols=35  Identities=23%  Similarity=0.194  Sum_probs=30.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      ...+.|+.+|||||-+.+-+..+...|++|.+++.
T Consensus         6 ~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~ik~   40 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVKH   40 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEEEe
Confidence            45689999999999888888888888999999984

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=94.49  E-value=0.075  Score=51.95  Aligned_cols=82  Identities=17%  Similarity=0.159  Sum_probs=52.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCccccee---ecccHhh---hcc---cC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV---SAVELNK---LIP---HT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~---~~~~~~~---~~~---~~  220 (353)
                      +.+.+|.|+.+||||+-.++.+.+....|.+|+++.......   .....+.|....-+   ......+   ++.   ..
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~~---~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~~  150 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALD---PVYARALGVNTDELLVSQPDNGEQALEIMELLVRS  150 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCC---HHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTT
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCChh---HHHHHHcCCCHHHceeecCCcHHHHHHHHHHHHhc
Confidence            567889999999999999999999988899999887653211   00111222211111   1112222   221   13


Q ss_pred             CCccEEEEeccccc
Q psy8456         221 KDIDVIGIDEGQFV  234 (353)
Q Consensus       221 ~~~~~i~IDE~QF~  234 (353)
                      ..+++|+||..+.+
T Consensus       151 ~~~~lVVIDsl~~l  164 (366)
T 1xp8_A          151 GAIDVVVVDSVAAL  164 (366)
T ss_dssp             TCCSEEEEECTTTC
T ss_pred             CCCCEEEEeChHHh
Confidence            57999999999986

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=94.46  E-value=0.055  Score=53.18  Aligned_cols=39  Identities=23%  Similarity=0.171  Sum_probs=31.2

Q ss_pred             cceeeeeccCCCCchhH-HHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTE-LIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~-Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ++..++.||.|||||.- ++..++.....|.+++++-|..
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~   41 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTR   41 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHH
Confidence            34568999999999997 4666667777888999998854

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=94.43  E-value=0.098  Score=50.86  Aligned_cols=82  Identities=18%  Similarity=0.161  Sum_probs=52.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceee------cccHhhhcc---cC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVS------AVELNKLIP---HT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~------~~~~~~~~~---~~  220 (353)
                      +.+.++.|+.+|||||-.++.+.+....|.+|+++.....-.   .....+-|....-+.      ...+.+++.   ..
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~s~~---~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~~  139 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALD---PIYARKLGVDIDNLLCSQPDTGEQALEICDALARS  139 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCC---HHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCCcc---HHHHHHcCCChhheeeeCCCCHHHHHHHHHHHHhc
Confidence            568899999999999999999999998999999887643110   001112222111111      111222222   13


Q ss_pred             CCccEEEEeccccc
Q psy8456         221 KDIDVIGIDEGQFV  234 (353)
Q Consensus       221 ~~~~~i~IDE~QF~  234 (353)
                      .++++|+||..+.+
T Consensus       140 ~~~~lVVIDsl~~l  153 (356)
T 1u94_A          140 GAVDVIVVDSVAAL  153 (356)
T ss_dssp             TCCSEEEEECGGGC
T ss_pred             cCCCEEEEcCHHHh
Confidence            57999999999975

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=94.34  E-value=0.07  Score=50.96  Aligned_cols=36  Identities=17%  Similarity=0.028  Sum_probs=28.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      ..++.+|.|||||...+-.+......|.+++++-|.
T Consensus        38 ~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt   73 (414)
T 3oiy_A           38 SFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPT   73 (414)
T ss_dssp             CEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECC
Confidence            458899999999996655555555678899999886

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=94.14  E-value=0.034  Score=57.49  Aligned_cols=39  Identities=21%  Similarity=0.163  Sum_probs=31.1

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHH----hCCEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQY----ANYRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~----~~~~~~~~k~~  187 (353)
                      .+...++.|+.|+||||-+...+..+..    .+.++++..|+
T Consensus       163 ~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APT  205 (608)
T 1w36_D          163 TRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPT  205 (608)
T ss_dssp             TBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSS
T ss_pred             cCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCC
Confidence            4678899999999999888777776653    46689988885

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=94.00  E-value=0.12  Score=43.69  Aligned_cols=71  Identities=8%  Similarity=0.019  Sum_probs=43.6

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChH----
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFP----   85 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~----   85 (353)
                      -+|||+-+-..+..+...|.+++.+.. -+...  .                   ++   ..++++++|||.+.++    
T Consensus        46 G~GKTtL~~~i~~~~~~~g~~~~~~~~-~~~~~--~-------------------~~---~~~~~lLilDE~~~~~~~~~  100 (149)
T 2kjq_A           46 GAGKSHLLQAWVAQALEAGKNAAYIDA-ASMPL--T-------------------DA---AFEAEYLAVDQVEKLGNEEQ  100 (149)
T ss_dssp             TTTTCHHHHHHHHHHHTTTCCEEEEET-TTSCC--C-------------------GG---GGGCSEEEEESTTCCCSHHH
T ss_pred             CCCHHHHHHHHHHHHHhcCCcEEEEcH-HHhhH--H-------------------HH---HhCCCEEEEeCccccChHHH
Confidence            468887666665555555655544432 11110  0                   11   2358999999999984    


Q ss_pred             -HHHHHHHHHHhCCCE-EEEEe
Q psy8456          86 -DVVSFAESMANAGKI-VVVAA  105 (353)
Q Consensus        86 -dIv~l~~~l~~~G~~-VivaG  105 (353)
                       .+.++.+.+.+.|++ +++.+
T Consensus       101 ~~l~~li~~~~~~g~~~iiits  122 (149)
T 2kjq_A          101 ALLFSIFNRFRNSGKGFLLLGS  122 (149)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEEE
T ss_pred             HHHHHHHHHHHHcCCcEEEEEC
Confidence             356777777778887 66655

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=93.95  E-value=0.021  Score=58.98  Aligned_cols=90  Identities=10%  Similarity=0.011  Sum_probs=53.8

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhh-----hc---ccCCCccEEEEccc
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNK-----LI---PHTKDIDVIGIDEG   81 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~e-----i~---~~~~~~dvV~IDEa   81 (353)
                      =+|||+-+...+..+...|.+|++..|.-  |.. ..+....|  .++..+.++..     ..   ....++|+|+|||+
T Consensus       214 GTGKTt~i~~l~~~l~~~g~~Vl~~ApT~--~Aa-~~L~e~~~--~~a~Tih~ll~~~~~~~~~~~~~~~~~dvlIIDEa  288 (574)
T 3e1s_A          214 GTGKSTTTKAVADLAESLGLEVGLCAPTG--KAA-RRLGEVTG--RTASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEV  288 (574)
T ss_dssp             TSCHHHHHHHHHHHHHHTTCCEEEEESSH--HHH-HHHHHHHT--SCEEEHHHHTTEETTEESCSSSSCCSCSEEEECCG
T ss_pred             CCCHHHHHHHHHHHHHhcCCeEEEecCcH--HHH-HHhHhhhc--ccHHHHHHHHcCCcchhhhhhcccccCCEEEEcCc
Confidence            47999999888888899999999998842  211 11111111  11221111110     10   11236899999999


Q ss_pred             cChH--HHHHHHHHHHhCCCEEEEEe
Q psy8456          82 QFFP--DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        82 QFF~--dIv~l~~~l~~~G~~VivaG  105 (353)
                      |.++  .+..+.+.+ ..|..|++.|
T Consensus       289 sml~~~~~~~Ll~~~-~~~~~lilvG  313 (574)
T 3e1s_A          289 SMMGDALMLSLLAAV-PPGARVLLVG  313 (574)
T ss_dssp             GGCCHHHHHHHHTTS-CTTCEEEEEE
T ss_pred             cCCCHHHHHHHHHhC-cCCCEEEEEe
Confidence            9996  344443322 3688888877

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=93.93  E-value=0.067  Score=55.60  Aligned_cols=39  Identities=18%  Similarity=0.100  Sum_probs=32.4

Q ss_pred             ccceeeeeccCCCCchhH-HHHHHHHHHHhCCEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTE-LIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~-Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      .++..++.+|.|||||+. ++..+.+....+.+++++.|.
T Consensus       185 ~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~Pt  224 (618)
T 2whx_A          185 KKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPT  224 (618)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cCCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcCh
Confidence            355678999999999998 677887777788899999885

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=93.87  E-value=0.063  Score=53.10  Aligned_cols=96  Identities=13%  Similarity=0.018  Sum_probs=54.3

Q ss_pred             CCCchHHHHHHHHHHHHHcCc-eEEEEeeccCC------CCCCCceee-ccCCceeeeecCChhhh----cccCCCccEE
Q psy8456           9 RINPYIVHFCRRIRRYQYANY-RCMIVRYAKDD------RYDTEKVAT-HDQQKLTAVSAVELNKL----IPHTKDIDVI   76 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agk-kvlv~Kp~iDt------Ry~~~~I~S-r~G~~~~Ai~i~~l~ei----~~~~~~~dvV   76 (353)
                      .-+|||+-|...+..+...|. ++++..|.--.      |-+.. ..| |.-.............+    ......+++|
T Consensus        54 aGTGKT~ll~~~~~~l~~~~~~~il~~a~T~~Aa~~l~~~~~~~-~~T~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  132 (459)
T 3upu_A           54 AGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLSGKE-ASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVL  132 (459)
T ss_dssp             TTSCHHHHHHHHHHHHHHTTCCCEEEEESSHHHHHHHHHHHSSC-EEEHHHHHTEEEEECSSCEEEEECSCCCCSSCSEE
T ss_pred             CCCCHHHHHHHHHHHHHhcCCceEEEecCcHHHHHHHHhhhccc-hhhHHHHhccCcccccccchhcccccccccCCCEE
Confidence            358999988888888888887 78998884210      11111 111 21111111000000001    0123468999


Q ss_pred             EEccccChH-HHHHHHHHHHhCCCEEEEEe
Q psy8456          77 GIDEGQFFP-DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        77 ~IDEaQFF~-dIv~l~~~l~~~G~~VivaG  105 (353)
                      +|||+|.++ .+......+...+..|++.|
T Consensus       133 iiDE~~~~~~~~~~~l~~~~~~~~~~~~vG  162 (459)
T 3upu_A          133 ICDEVSMYDRKLFKILLSTIPPWCTIIGIG  162 (459)
T ss_dssp             EESCGGGCCHHHHHHHHHHSCTTCEEEEEE
T ss_pred             EEECchhCCHHHHHHHHHhccCCCEEEEEC
Confidence            999999996 44443333444788899888

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=93.86  E-value=0.041  Score=52.02  Aligned_cols=36  Identities=14%  Similarity=0.149  Sum_probs=26.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHH-HhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQ-YANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~-~~~~~~~~~k~  186 (353)
                      ..-+++||.|+|||+-+...++... ..|.+|+.+..
T Consensus       153 ~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~  189 (308)
T 2qgz_A          153 KGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHF  189 (308)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEH
Confidence            4558999999999976666666666 77888876653

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=93.81  E-value=0.075  Score=48.28  Aligned_cols=34  Identities=21%  Similarity=0.199  Sum_probs=26.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +.-++.+|+|||||...+..+..   .+.+++++-|.
T Consensus        32 ~~~lv~~~TGsGKT~~~~~~~~~---~~~~~liv~P~   65 (337)
T 2z0m_A           32 KNVVVRAKTGSGKTAAYAIPILE---LGMKSLVVTPT   65 (337)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH---HTCCEEEECSS
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHh---hcCCEEEEeCC
Confidence            44688999999999876655433   48889999886

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=93.73  E-value=0.046  Score=54.88  Aligned_cols=37  Identities=24%  Similarity=0.175  Sum_probs=33.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+.+++||-||||||-+..-+..+...|++|+++.-
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~  133 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAA  133 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEec
Confidence            5677889999999999999999999999999998764

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=93.71  E-value=0.22  Score=42.54  Aligned_cols=38  Identities=11%  Similarity=0.109  Sum_probs=25.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH-H--HhCCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY-Q--YANYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~-~--~~~~~~~~~k~~~  188 (353)
                      ..-++.+|+|||||...+-.+-.. .  ..+.+++++-|..
T Consensus        41 ~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~   81 (206)
T 1vec_A           41 RDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTR   81 (206)
T ss_dssp             CCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCH
T ss_pred             CCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcH
Confidence            346889999999997554433332 1  2355788888853

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=93.71  E-value=0.15  Score=44.53  Aligned_cols=38  Identities=18%  Similarity=0.060  Sum_probs=31.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH-HHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY-QYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~-~~~~~~~~~~k~~  187 (353)
                      +.+.++.|+.++|||+-.++-+.+. ...|.+|+++...
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E   68 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLE   68 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeeccc
Confidence            5688999999999999999988775 5568889888654

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=93.51  E-value=0.2  Score=48.12  Aligned_cols=134  Identities=19%  Similarity=0.169  Sum_probs=78.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCC-Cce---eeccCccc-----ceeecccHhhhc-
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDT-EKV---STHDQQKL-----TAVSAVELNKLI-  217 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~-~~i---~s~~g~~~-----~a~~~~~~~~~~-  217 (353)
                      .+.+..++||.||||||-+-.-+..+...+.+|++..-  |. |.+. +..   ..+.|..+     ...+.....+-+ 
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l~~~~g~V~l~g~--D~~r~~a~eql~~~~~~~gv~~v~q~~~~~p~~~v~e~l~  205 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWLKNHGFSVVIAAS--DTFRAGAIEQLEEHAKRIGVKVIKHSYGADPAAVAYDAIQ  205 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE--CCSSTTHHHHHHHHHHHTTCEEECCCTTCCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEee--cccccchHHHHHHHHHHcCceEEeccccCCHHHHHHHHHH
Confidence            36788899999999999888878778888888887643  32 2110 000   01112100     000100111111 


Q ss_pred             -ccCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCC-------ccHHHHHHH
Q psy8456         218 -PHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEF-------PDVVSFAES  289 (353)
Q Consensus       218 -~~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f-------~~~~~~~~~  289 (353)
                       ....++|+++||.+-..                     +.......+|..+...+..++| .+       .++++.+..
T Consensus       206 ~~~~~~~d~vliDtaG~~---------------------~~~~~l~~eL~~i~ral~~de~-llvLDa~t~~~~~~~~~~  263 (328)
T 3e70_C          206 HAKARGIDVVLIDTAGRS---------------------ETNRNLMDEMKKIARVTKPNLV-IFVGDALAGNAIVEQARQ  263 (328)
T ss_dssp             HHHHHTCSEEEEEECCSC---------------------CTTTCHHHHHHHHHHHHCCSEE-EEEEEGGGTTHHHHHHHH
T ss_pred             HHHhccchhhHHhhccch---------------------hHHHHHHHHHHHHHHHhcCCCC-EEEEecHHHHHHHHHHHH
Confidence             11256889999987653                     2245567777777665554443 22       468888887


Q ss_pred             HH-hCCC-EEEEEeccccc
Q psy8456         290 MA-NAGK-IVVVAALDGTF  306 (353)
Q Consensus       290 ~~-~~g~-~Vi~~gLd~df  306 (353)
                      +. ..|+ .|++-=||++-
T Consensus       264 ~~~~~~it~iilTKlD~~a  282 (328)
T 3e70_C          264 FNEAVKIDGIILTKLDADA  282 (328)
T ss_dssp             HHHHSCCCEEEEECGGGCS
T ss_pred             HHHhcCCCEEEEeCcCCcc
Confidence            77 4577 46667777754

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=93.33  E-value=0.17  Score=44.54  Aligned_cols=37  Identities=14%  Similarity=0.075  Sum_probs=25.6

Q ss_pred             ceeeeeccCCCCchhHHHHHHH-HHH------HhCCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIR-RYQ------YANYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~-~~~------~~~~~~~~~k~~  187 (353)
                      +.-++.+|+|||||...+--+- ...      ..+.+++++-|.
T Consensus        63 ~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt  106 (236)
T 2pl3_A           63 KDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPT  106 (236)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSS
T ss_pred             CCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCC
Confidence            3468899999999987443332 221      347789999886

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=93.24  E-value=0.52  Score=43.54  Aligned_cols=34  Identities=15%  Similarity=0.009  Sum_probs=30.1

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      -++.|+-|+||||-.+..++....+|++|+++.-
T Consensus         9 I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~   42 (228)
T 2r8r_A            9 VFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVV   42 (228)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEe
Confidence            5678999999999999999999999999986654

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=93.10  E-value=0.093  Score=45.95  Aligned_cols=37  Identities=11%  Similarity=0.152  Sum_probs=24.5

Q ss_pred             eeeeeccCCCCchhHHH-HHHHHH--------HHhCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELI-RRIRRY--------QYANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li-~~~~~~--------~~~~~~~~~~k~~~  188 (353)
                      .-++.+|.|||||...+ -.+...        ...+.+++++-|..
T Consensus        59 ~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~  104 (228)
T 3iuy_A           59 DLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTR  104 (228)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSH
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCH
Confidence            45889999999997533 223322        23677889888864

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=93.09  E-value=0.12  Score=54.27  Aligned_cols=40  Identities=18%  Similarity=0.099  Sum_probs=32.4

Q ss_pred             ccceeeeeccCCCCchhH-HHHHHHHHHHhCCEEEEEeeec
Q psy8456         149 GQEKEVILGPMFSGKTTE-LIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~-Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      .++..++.+|.|||||+. ++..+......+.+++++-|..
T Consensus       240 ~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr  280 (673)
T 2wv9_A          240 KRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTR  280 (673)
T ss_dssp             TTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHH
Confidence            356678999999999997 6767767677888999999853

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=92.99  E-value=0.098  Score=44.54  Aligned_cols=36  Identities=28%  Similarity=0.151  Sum_probs=29.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +.+.++.|+|+|||||-.-.-...+...|.++.++.
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~   48 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLD   48 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEee
Confidence            557789999999999987777777777788887664

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=92.99  E-value=0.12  Score=48.55  Aligned_cols=35  Identities=11%  Similarity=0.025  Sum_probs=25.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHH---hCCEEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQY---ANYRCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~---~~~~~~~~k~~  187 (353)
                      -++.+|+|||||...+-.+.....   .+.+++++-|.
T Consensus        61 ~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~   98 (400)
T 1s2m_A           61 ILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPT   98 (400)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             EEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCC
Confidence            588999999999865554443321   45688988886

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=92.98  E-value=0.12  Score=51.45  Aligned_cols=82  Identities=20%  Similarity=0.143  Sum_probs=50.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCC--Cceee---ccCccc------ceeecccHhhhccc
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDT--EKVST---HDQQKL------TAVSAVELNKLIPH  219 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~--~~i~s---~~g~~~------~a~~~~~~~~~~~~  219 (353)
                      ....++|+.|+||||-...-+..+...|++|+++..  |.+...  +...+   +.|...      +..+..-+.+.+..
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~--D~~r~~a~~qL~~~~~~~gv~v~~~~~~~~dp~~i~~~~l~~  177 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAA--DTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEK  177 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECC--SCCCTTGGGSSHHHHHHSSCCEECCSSSCCSSSTTHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEec--cccCchHHHHHHHhhhccCcceEecCCCCCCHHHHHHHHHHH
Confidence            356789999999999999999999889999998865  433211  00000   001000      00001112233333


Q ss_pred             CCCccEEEEeccccc
Q psy8456         220 TKDIDVIGIDEGQFV  234 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~  234 (353)
                      ..++|+|+||.+-.+
T Consensus       178 ~~~~D~vIIDT~G~~  192 (432)
T 2v3c_C          178 FKKADVLIIDTAGRH  192 (432)
T ss_dssp             TSSCSEEEEECCCSC
T ss_pred             hhCCCEEEEcCCCCc
Confidence            478999999999874

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=92.93  E-value=0.17  Score=49.40  Aligned_cols=24  Identities=21%  Similarity=0.231  Sum_probs=19.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +.+-+|+|||+|||||-.++-+.+
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            347799999999999877766544

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=92.93  E-value=0.087  Score=48.84  Aligned_cols=38  Identities=11%  Similarity=0.048  Sum_probs=27.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHH---HhCCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQ---YANYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~---~~~~~~~~~k~~~  188 (353)
                      ..-++.+|+|||||...+..+...-   ..+.+++++-|..
T Consensus        45 ~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~   85 (395)
T 3pey_A           45 RNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSR   85 (395)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCH
Confidence            4568899999999987655544431   2467899998854

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=92.92  E-value=0.051  Score=50.41  Aligned_cols=36  Identities=14%  Similarity=0.224  Sum_probs=25.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh---CCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA---NYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~---~~~~~~~k  185 (353)
                      +..-+++||-|+||||-+-..++.....   +..++.+.
T Consensus        45 ~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~   83 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYIN   83 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEE
Confidence            3466899999999998766655555544   66666655

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=92.90  E-value=0.094  Score=44.13  Aligned_cols=25  Identities=28%  Similarity=0.212  Sum_probs=17.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHh
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYA  177 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~  177 (353)
                      .+++||-|+|||+-+-..++.+...
T Consensus        41 ~ll~G~~G~GKT~l~~~l~~~~~~~   65 (226)
T 2chg_A           41 LLFSGPPGTGKTATAIALARDLFGE   65 (226)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHGG
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhcc
Confidence            6899999999997555444444333

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=92.83  E-value=0.13  Score=53.34  Aligned_cols=39  Identities=18%  Similarity=0.128  Sum_probs=31.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH-HHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY-QYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~-~~~~~~~~~~k~~~  188 (353)
                      ++.-++.||.|||||+.....+.+. ...|.+++++-|..
T Consensus        46 ~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r   85 (715)
T 2va8_A           46 GNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLR   85 (715)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCH
T ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcH
Confidence            4567899999999999987776554 33688999999865

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=92.65  E-value=0.082  Score=43.16  Aligned_cols=27  Identities=19%  Similarity=0.129  Sum_probs=19.0

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      +-++.||+||||||- .+.+   +.-|..++
T Consensus         3 ~I~l~G~~GsGKsT~-a~~L---~~~g~~~i   29 (179)
T 3lw7_A            3 VILITGMPGSGKSEF-AKLL---KERGAKVI   29 (179)
T ss_dssp             EEEEECCTTSCHHHH-HHHH---HHTTCEEE
T ss_pred             EEEEECCCCCCHHHH-HHHH---HHCCCcEE
Confidence            357899999999984 4555   44466554

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=92.62  E-value=0.3  Score=44.54  Aligned_cols=27  Identities=19%  Similarity=0.089  Sum_probs=18.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhC
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYAN  178 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~  178 (353)
                      --+++||.|+|||+-.-..++.+...+
T Consensus        69 ~vll~G~~GtGKT~la~~la~~l~~~~   95 (309)
T 3syl_A           69 HMSFTGNPGTGKTTVALKMAGLLHRLG   95 (309)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            458999999999965554444444433

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=92.61  E-value=0.78  Score=44.48  Aligned_cols=37  Identities=22%  Similarity=0.314  Sum_probs=27.7

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEe
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVR  185 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k  185 (353)
                      .+++..++||.||||||-|-.-+..+... ..+++++.
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~~e  172 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIE  172 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEEec
Confidence            46678999999999999877776666655 45665554

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.42  E-value=0.13  Score=45.02  Aligned_cols=38  Identities=13%  Similarity=-0.043  Sum_probs=33.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +++.+++||.+|||||-+++-+......|.+|+++...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e   60 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALE   60 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            56889999999999999999998888888899988654

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=92.37  E-value=0.16  Score=47.34  Aligned_cols=34  Identities=24%  Similarity=0.319  Sum_probs=23.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVR  185 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k  185 (353)
                      .-+++||.|+||||-+-..++..... +..++.+.
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWELYKDKTTARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEe
Confidence            57899999999998775555544443 45555444

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=92.29  E-value=0.21  Score=51.97  Aligned_cols=38  Identities=18%  Similarity=0.060  Sum_probs=29.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHH-HHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIR-RYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~-~~~~~~~~~~~~k~~  187 (353)
                      ++.-++.||.|||||+.....+- .....|.+++++-|.
T Consensus        39 ~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~   77 (720)
T 2zj8_A           39 GKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPL   77 (720)
T ss_dssp             TCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSS
T ss_pred             CCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCc
Confidence            45578999999999988744443 334468999999996

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=92.28  E-value=0.14  Score=50.19  Aligned_cols=38  Identities=18%  Similarity=0.094  Sum_probs=28.9

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh-----CCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA-----NYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~-----~~~~~~~k~~~  188 (353)
                      ...++.+|||||||...+--+......     +.+++++-|..
T Consensus        23 ~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~   65 (556)
T 4a2p_A           23 KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKV   65 (556)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSH
T ss_pred             CCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCH
Confidence            346889999999998876666555444     77899998863

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=92.27  E-value=0.22  Score=50.04  Aligned_cols=33  Identities=21%  Similarity=0.202  Sum_probs=22.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      ..-+++||.|+|||+-+-..++.   .|..++-+..
T Consensus        78 ~~lLL~GppGtGKTtla~~la~~---l~~~~i~in~  110 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVAQE---LGYDILEQNA  110 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH---TTCEEEEECT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH---cCCCEEEEeC
Confidence            35689999999999755444333   3777665543

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=92.21  E-value=0.11  Score=48.72  Aligned_cols=37  Identities=11%  Similarity=0.145  Sum_probs=26.7

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH-HH--hCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY-QY--ANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~-~~--~~~~~~~~k~~~  188 (353)
                      .-++.+|+|||||...+..+... ..  .+.+++++-|..
T Consensus        79 ~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~  118 (414)
T 3eiq_A           79 DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTR  118 (414)
T ss_dssp             CEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             CEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChH
Confidence            35889999999998855544433 22  567899998863

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=92.12  E-value=0.068  Score=53.87  Aligned_cols=40  Identities=28%  Similarity=0.311  Sum_probs=34.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR  191 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R  191 (353)
                      ..+.+++|+-||||||-+..-++.+...|++|+++.-  |++
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~--D~~  139 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCS--DTW  139 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEC--CCS
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeC--CCc
Confidence            4567889999999999999999999999999999863  554

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=92.10  E-value=0.11  Score=43.50  Aligned_cols=33  Identities=18%  Similarity=0.126  Sum_probs=26.0

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      +-++.|+++|||||-.-.-..++...|..+..+
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~   35 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKII   35 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCceEEEE
Confidence            357899999999997766666676677777766

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=92.08  E-value=0.39  Score=47.06  Aligned_cols=35  Identities=17%  Similarity=0.092  Sum_probs=27.9

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhC--CEEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYAN--YRCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~--~~~~~~k~~  187 (353)
                      -++..+||+|||-..+..+..+...+  .+++|+-|.
T Consensus        59 ~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P~   95 (500)
T 1z63_A           59 ICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPL   95 (500)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECS
T ss_pred             EEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEccH
Confidence            35667999999999888888776554  789999884

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=92.00  E-value=0.14  Score=49.91  Aligned_cols=37  Identities=14%  Similarity=0.072  Sum_probs=29.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh-----CCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA-----NYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~-----~~~~~~~k~~  187 (353)
                      ..-++.+|||||||...+--+......     +.+++++-|.
T Consensus        20 ~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~   61 (555)
T 3tbk_A           20 KNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQ   61 (555)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSS
T ss_pred             CCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCC
Confidence            446889999999998876666555444     7889999986

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=91.97  E-value=0.13  Score=45.74  Aligned_cols=19  Identities=37%  Similarity=0.581  Sum_probs=14.6

Q ss_pred             eeeeeccCCCCchhHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~  171 (353)
                      .-+++||.||||||- ++++
T Consensus         3 pIVi~GPSG~GK~Tl-~~~L   21 (186)
T 1ex7_A            3 PIVISGPSGTGKSTL-LKKL   21 (186)
T ss_dssp             CEEEECCTTSSHHHH-HHHH
T ss_pred             EEEEECCCCCCHHHH-HHHH
Confidence            458999999999984 4443

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=91.88  E-value=0.11  Score=45.23  Aligned_cols=36  Identities=14%  Similarity=0.144  Sum_probs=25.5

Q ss_pred             eeeeeccCCCCchhH-HHHHHHHHH--HhCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTE-LIRRIRRYQ--YANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~-Li~~~~~~~--~~~~~~~~~k~~  187 (353)
                      .-++.+|+|||||.. ++-.+.+..  ..+.+++++-|.
T Consensus        53 ~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (224)
T 1qde_A           53 DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPT   91 (224)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSS
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECC
Confidence            358899999999977 444444432  245688888886

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=91.80  E-value=0.59  Score=40.11  Aligned_cols=36  Identities=19%  Similarity=0.321  Sum_probs=23.5

Q ss_pred             CCCccEEEEccccChH--H-----HHHHHHHHHhCCCE-EEEEe
Q psy8456          70 TKDIDVIGIDEGQFFP--D-----VVSFAESMANAGKI-VVVAA  105 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF~--d-----Iv~l~~~l~~~G~~-VivaG  105 (353)
                      ..+..+|+|||+|.++  .     +.++.+...+.+.. +++.+
T Consensus       102 ~~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~  145 (242)
T 3bos_A          102 LEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSA  145 (242)
T ss_dssp             GGGSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEE
T ss_pred             ccCCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEc
Confidence            3557899999999984  2     34444445556655 55554

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=91.64  E-value=0.31  Score=42.21  Aligned_cols=36  Identities=8%  Similarity=-0.005  Sum_probs=25.7

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHH---hCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQY---ANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~---~~~~~~~~k~~  187 (353)
                      .-++.+|+|||||...+-.+.....   .+.+++++-|.
T Consensus        53 ~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt   91 (220)
T 1t6n_A           53 DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHT   91 (220)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSC
T ss_pred             CEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCC
Confidence            3688999999999876655544421   24489999886

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=91.58  E-value=0.17  Score=43.82  Aligned_cols=33  Identities=18%  Similarity=-0.026  Sum_probs=24.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      +.+.+++|||||||||-+-.-...+...|..+.
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~   57 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQMLYQKGKLCY   57 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCceEE
Confidence            567889999999999876665566666676543

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=91.47  E-value=0.15  Score=49.81  Aligned_cols=33  Identities=15%  Similarity=-0.043  Sum_probs=26.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      ...+++||.++|||+-.++.+..   .|.+|+.+.-
T Consensus       124 sviLI~GpPGsGKTtLAlqlA~~---~G~~VlyIs~  156 (331)
T 2vhj_A          124 GMVIVTGKGNSGKTPLVHALGEA---LGGKDKYATV  156 (331)
T ss_dssp             EEEEEECSCSSSHHHHHHHHHHH---HHTTSCCEEE
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHh---CCCCEEEEEe
Confidence            34589999999999998888776   6677766655

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=91.46  E-value=0.32  Score=45.05  Aligned_cols=27  Identities=22%  Similarity=0.247  Sum_probs=19.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA  177 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~  177 (353)
                      ..-+++||.|+|||+-+-..++.....
T Consensus        45 ~~vll~G~~G~GKT~l~~~~~~~~~~~   71 (387)
T 2v1u_A           45 SNALLYGLTGTGKTAVARLVLRRLEAR   71 (387)
T ss_dssp             CCEEECBCTTSSHHHHHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            456899999999998665555555443

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=91.44  E-value=0.16  Score=51.93  Aligned_cols=38  Identities=13%  Similarity=0.028  Sum_probs=28.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhC-----CEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYAN-----YRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~-----~~~~~~k~~  187 (353)
                      +...++.+|||||||...+--+......+     .+++++-|.
T Consensus        28 g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt   70 (696)
T 2ykg_A           28 GKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQ   70 (696)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSS
T ss_pred             CCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECC
Confidence            34568999999999998777666553332     678888885

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=91.38  E-value=0.26  Score=45.53  Aligned_cols=65  Identities=20%  Similarity=0.037  Sum_probs=35.9

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecc-cHhhhc---ccCCCccEE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAV-ELNKLI---PHTKDIDVI  226 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~-~~~~~~---~~~~~~~~i  226 (353)
                      ...++.||.|+|||+-.-..++.   .+..++-+..+.            .+  ..  .+. .+.+..   +...+..++
T Consensus        49 ~~~L~~G~~G~GKT~la~~la~~---l~~~~~~i~~~~------------~~--~~--~i~~~~~~~~~~~~~~~~~~vl  109 (324)
T 3u61_B           49 HIILHSPSPGTGKTTVAKALCHD---VNADMMFVNGSD------------CK--ID--FVRGPLTNFASAASFDGRQKVI  109 (324)
T ss_dssp             SEEEECSSTTSSHHHHHHHHHHH---TTEEEEEEETTT------------CC--HH--HHHTHHHHHHHBCCCSSCEEEE
T ss_pred             eEEEeeCcCCCCHHHHHHHHHHH---hCCCEEEEcccc------------cC--HH--HHHHHHHHHHhhcccCCCCeEE
Confidence            45678888999999655443332   255555554321            01  00  000 111111   223478999


Q ss_pred             EEeccccc
Q psy8456         227 GIDEGQFV  234 (353)
Q Consensus       227 ~IDE~QF~  234 (353)
                      +|||+|++
T Consensus       110 iiDEi~~l  117 (324)
T 3u61_B          110 VIDEFDRS  117 (324)
T ss_dssp             EEESCCCG
T ss_pred             EEECCccc
Confidence            99999997

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=91.34  E-value=0.14  Score=53.18  Aligned_cols=39  Identities=15%  Similarity=0.072  Sum_probs=31.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ++.-++.+|.|||||+.....+.+.-..|.+++++-|..
T Consensus        40 ~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~P~r   78 (702)
T 2p6r_A           40 GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLR   78 (702)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             CCcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEeCcH
Confidence            455689999999999988777666555688999999865

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=91.27  E-value=0.39  Score=42.71  Aligned_cols=36  Identities=22%  Similarity=0.213  Sum_probs=24.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHH------------hCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQY------------ANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~------------~~~~~~~~k~~  187 (353)
                      .-++.+|+|||||...+--+-..-.            .+.+++++-|.
T Consensus        62 ~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt  109 (253)
T 1wrb_A           62 DIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPT  109 (253)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSS
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECC
Confidence            4578899999999864443333221            23578888886

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=91.26  E-value=0.33  Score=52.93  Aligned_cols=35  Identities=17%  Similarity=0.110  Sum_probs=30.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCC--EEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANY--RCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~--~~~~~k~~  187 (353)
                      -++.++||+|||-..+..+..+...|+  +++++-|.
T Consensus       173 ~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~  209 (968)
T 3dmq_A          173 VLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPE  209 (968)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCH
Confidence            477889999999999999999888876  99999985

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=91.18  E-value=0.11  Score=45.24  Aligned_cols=24  Identities=33%  Similarity=0.419  Sum_probs=18.3

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .+.+.+++||+|||||| |.+.+..
T Consensus        11 ~~~~i~l~G~sGsGKsT-l~~~L~~   34 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGT-LIKKVLS   34 (204)
T ss_dssp             CCCCEEEECCTTSCHHH-HHHHHHH
T ss_pred             cCCEEEEECCCCCCHHH-HHHHHHH
Confidence            45678899999999999 5555543

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=91.13  E-value=0.39  Score=44.63  Aligned_cols=37  Identities=8%  Similarity=-0.015  Sum_probs=26.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHH---HhCCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQ---YANYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~---~~~~~~~~~k~~  187 (353)
                      ..-++.+|+|||||...+-.+...-   ..+.+++++-|.
T Consensus        46 ~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~   85 (391)
T 1xti_A           46 MDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHT   85 (391)
T ss_dssp             CCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSC
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCC
Confidence            3468899999999987655554431   235689999886

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=91.07  E-value=0.52  Score=54.71  Aligned_cols=81  Identities=19%  Similarity=0.135  Sum_probs=52.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccce---eecccHhhhccc------CC
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA---VSAVELNKLIPH------TK  221 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a---~~~~~~~~~~~~------~~  221 (353)
                      ++.++.||.++||||-+++.+.+....|.+|+++.-....+-   ....+.|....-   .....+.++...      ..
T Consensus       733 ~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS~Ees~~q---l~A~~lGvd~~~L~i~~~~~leei~~~l~~lv~~~  809 (1706)
T 3cmw_A          733 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDP---IYARKLGVDIDNLLCSQPDTGEQALEICDALARSG  809 (1706)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCH---HHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEeccchHHH---HHHHHcCCChhheEEecCCcHHHHHHHHHHHHHcc
Confidence            478899999999999999999999989999998865432210   011222321111   111233333211      35


Q ss_pred             CccEEEEeccccc
Q psy8456         222 DIDVIGIDEGQFV  234 (353)
Q Consensus       222 ~~~~i~IDE~QF~  234 (353)
                      ++++|+||+.|.+
T Consensus       810 ~~~lVVIDsLq~l  822 (1706)
T 3cmw_A          810 AVDVIVVDSVAAL  822 (1706)
T ss_dssp             CCSEEEESCSTTC
T ss_pred             CCCEEEEechhhh
Confidence            7999999999985

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=91.06  E-value=0.23  Score=41.95  Aligned_cols=36  Identities=17%  Similarity=0.062  Sum_probs=24.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +...++.|+|+|||||-+-.-...+...|..++.+.
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d   40 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   40 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEEC
Confidence            456678999999999965544444455677666443

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=90.97  E-value=0.23  Score=42.54  Aligned_cols=36  Identities=22%  Similarity=0.189  Sum_probs=28.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +.+.++.|+|+|||||-.-.-..++...+..+..+.
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~~~~v~~~~   44 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   44 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEee
Confidence            456789999999999987777777777888876553

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=90.95  E-value=0.076  Score=44.49  Aligned_cols=17  Identities=18%  Similarity=0.206  Sum_probs=14.2

Q ss_pred             ceeeeeccCCCCchhHH
Q psy8456         151 EKEVILGPMFSGKTTEL  167 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~L  167 (353)
                      .+.+++|+|+|||||-.
T Consensus         4 ~~i~l~G~~GsGKST~a   20 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45689999999999854

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=90.79  E-value=0.18  Score=46.98  Aligned_cols=35  Identities=11%  Similarity=0.110  Sum_probs=24.5

Q ss_pred             eeeeccCCCCchhHHHH-HHHHHH--HhCCEEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIR-RIRRYQ--YANYRCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~-~~~~~~--~~~~~~~~~k~~  187 (353)
                      -++.+|+|||||...+- .+....  ..+.+++++-|.
T Consensus        61 ~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~   98 (394)
T 1fuu_A           61 VLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPT   98 (394)
T ss_dssp             EEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSS
T ss_pred             EEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCC
Confidence            57899999999977433 333322  246689999886

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=90.73  E-value=0.25  Score=41.48  Aligned_cols=32  Identities=22%  Similarity=0.105  Sum_probs=24.9

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      -++.|+++|||||-.-.-..++...|..++-.
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~   34 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLY   34 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            47899999999997766666666678877654

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=90.70  E-value=0.22  Score=42.08  Aligned_cols=23  Identities=17%  Similarity=0.008  Sum_probs=17.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..+++||.|+||||-+-..++..
T Consensus        47 ~~ll~G~~G~GKT~l~~~~~~~~   69 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIARLLAKGL   69 (250)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            56899999999998665544444

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=90.70  E-value=0.19  Score=44.66  Aligned_cols=35  Identities=11%  Similarity=0.183  Sum_probs=24.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHH-H--HhCCEEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY-Q--YANYRCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~-~--~~~~~~~~~k~~  187 (353)
                      -++.+|+|||||...+-.+... .  ..+.+++++-|.
T Consensus        70 ~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt  107 (237)
T 3bor_A           70 VIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPT  107 (237)
T ss_dssp             EEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECc
Confidence            5889999999997744443332 1  246688988886

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=90.58  E-value=0.83  Score=42.27  Aligned_cols=61  Identities=20%  Similarity=0.131  Sum_probs=35.1

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQ  232 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~Q  232 (353)
                      -+++||.|+|||+- ++.+.+  ..+.....+....-.                  ....+..++....+..+++|||+|
T Consensus        58 vll~G~~GtGKT~l-a~~ia~--~~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~~~~vl~lDEi~  116 (338)
T 3pfi_A           58 ILFSGPAGLGKTTL-ANIISY--EMSANIKTTAAPMIE------------------KSGDLAAILTNLSEGDILFIDEIH  116 (338)
T ss_dssp             EEEECSTTSSHHHH-HHHHHH--HTTCCEEEEEGGGCC------------------SHHHHHHHHHTCCTTCEEEEETGG
T ss_pred             EEEECcCCCCHHHH-HHHHHH--HhCCCeEEecchhcc------------------chhHHHHHHHhccCCCEEEEechh
Confidence            58999999999965 444422  234444333221100                  111233333334567899999999


Q ss_pred             cc
Q psy8456         233 FV  234 (353)
Q Consensus       233 F~  234 (353)
                      .+
T Consensus       117 ~l  118 (338)
T 3pfi_A          117 RL  118 (338)
T ss_dssp             GC
T ss_pred             hc
Confidence            86

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=90.48  E-value=0.27  Score=42.10  Aligned_cols=36  Identities=19%  Similarity=0.039  Sum_probs=27.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +.+-++.|+|+|||||-.-.-...+...+..+.+++
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~~~~~~~~~~   45 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLY   45 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            456789999999999976666666777788776544

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=90.47  E-value=0.28  Score=45.93  Aligned_cols=84  Identities=13%  Similarity=-0.004  Sum_probs=47.8

Q ss_pred             ChHHHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEeccceeccccccc------ccccccccceeeee
Q psy8456          83 FFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAVCMSCFRDA------AFTKRIGQEKEVIL  156 (353)
Q Consensus        83 FF~dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~AvC~~CG~~A------~f~~Ri~geI~vi~  156 (353)
                      +|..+..+...+...++++++.|=..|-..+.  .+..+..+++...++ .-+..|..+.      .|+. +.+.+..++
T Consensus       100 s~~~l~~~l~~~~~~~~piilv~NK~DL~~~~--~v~~~~~~~~~~~~~-~~~~~~SAktg~gv~~lf~~-l~geiv~l~  175 (301)
T 1u0l_A          100 STYIIDKFLVLAEKNELETVMVINKMDLYDED--DLRKVRELEEIYSGL-YPIVKTSAKTGMGIEELKEY-LKGKISTMA  175 (301)
T ss_dssp             CHHHHHHHHHHHHHTTCEEEEEECCGGGCCHH--HHHHHHHHHHHHTTT-SCEEECCTTTCTTHHHHHHH-HSSSEEEEE
T ss_pred             CHHHHHHHHHHHHHCCCCEEEEEeHHHcCCch--hHHHHHHHHHHHhhh-CcEEEEECCCCcCHHHHHHH-hcCCeEEEE
Confidence            45566666666667899999999988874321  112223333332221 1111233221      2222 246788999


Q ss_pred             ccCCCCchhHHHHHH
Q psy8456         157 GPMFSGKTTELIRRI  171 (353)
Q Consensus       157 G~M~sGKt~~Li~~~  171 (353)
                      ||.||||||-| +.+
T Consensus       176 G~sG~GKSTll-~~l  189 (301)
T 1u0l_A          176 GLSGVGKSSLL-NAI  189 (301)
T ss_dssp             CSTTSSHHHHH-HHH
T ss_pred             CCCCCcHHHHH-HHh
Confidence            99999999754 444

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=90.36  E-value=0.073  Score=54.47  Aligned_cols=38  Identities=13%  Similarity=0.058  Sum_probs=28.7

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhC------CEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYAN------YRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~------~~~~~~k~~~  188 (353)
                      ...++.+|||||||...+--+..+...+      .+++++-|..
T Consensus        23 ~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~   66 (699)
T 4gl2_A           23 KNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKV   66 (699)
T ss_dssp             CCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCS
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCH
Confidence            4568999999999988777766553322      7889999864

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=90.36  E-value=0.097  Score=44.33  Aligned_cols=22  Identities=27%  Similarity=0.255  Sum_probs=17.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~  171 (353)
                      .+.+.+++|||||||||-+ +.+
T Consensus         8 ~g~~i~l~G~~GsGKSTl~-~~L   29 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIA-EAL   29 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHH-HHH
T ss_pred             CCeEEEEECCCCCCHHHHH-HHH
Confidence            3667889999999999854 444

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=90.32  E-value=0.19  Score=50.30  Aligned_cols=23  Identities=26%  Similarity=0.290  Sum_probs=19.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +.+|+||.+|||||-.++.+.++
T Consensus         4 ~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHH
T ss_pred             EEEEECcchhhHHHHHHHHHHHC
Confidence            56899999999998877776665

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=90.32  E-value=0.46  Score=44.69  Aligned_cols=37  Identities=14%  Similarity=0.089  Sum_probs=24.7

Q ss_pred             ceeeeeccCCCCchhH-HHHHHHHHHHhC--------------------CEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTE-LIRRIRRYQYAN--------------------YRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~-Li~~~~~~~~~~--------------------~~~~~~k~~  187 (353)
                      +.-++.+|+|||||.. ++-.+......+                    .+++++-|.
T Consensus        53 ~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  110 (417)
T 2i4i_A           53 RDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPT  110 (417)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSS
T ss_pred             CCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCc
Confidence            4458899999999974 444444433222                    468888886

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=90.30  E-value=0.22  Score=51.44  Aligned_cols=38  Identities=24%  Similarity=0.294  Sum_probs=34.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      ..+.+|.||.|+|||+-+...+...-..|.++++..|+
T Consensus       205 ~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~T  242 (646)
T 4b3f_X          205 KELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPS  242 (646)
T ss_dssp             SSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCc
Confidence            35889999999999999999999998999999999985

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=90.27  E-value=0.28  Score=46.31  Aligned_cols=36  Identities=14%  Similarity=0.134  Sum_probs=26.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH---HHhCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY---QYANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~---~~~~~~~~~~k~~  187 (353)
                      .-++.+|+|||||...+-.+...   ...+.+++++-|.
T Consensus        76 ~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt  114 (410)
T 2j0s_A           76 DVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPT  114 (410)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSS
T ss_pred             CEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCc
Confidence            35889999999997655544433   2356789999985

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=90.23  E-value=0.67  Score=42.12  Aligned_cols=105  Identities=10%  Similarity=0.053  Sum_probs=56.7

Q ss_pred             ccCCCCchHHHHHHHHHHHHHcCc-eEEEEeeccCC---------CCCC---Cceee-ccCCc------e-eeeecCChh
Q psy8456           6 RDDRINPYIVHFCRRIRRYQYANY-RCMIVRYAKDD---------RYDT---EKVAT-HDQQK------L-TAVSAVELN   64 (353)
Q Consensus         6 ~~~~~~GKSteLLrr~~ry~~agk-kvlv~Kp~iDt---------Ry~~---~~I~S-r~G~~------~-~Ai~i~~l~   64 (353)
                      .+..-+|||.-.+..+..+...+. +++++-|...-         +++.   ..+.. ..|..      . .-+.+.+..
T Consensus       134 ~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~T~~  213 (282)
T 1rif_A          134 NLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQ  213 (282)
T ss_dssp             CCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECSTTCSSTTCCCTTCSEEEECHH
T ss_pred             EcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHHHHhcccccceEEEEeCCCcchhhhccCCcEEEEchH
Confidence            355678999998888777665554 99999984210         0111   01111 11111      1 112333333


Q ss_pred             hhcc----cCCCccEEEEccccChH-HHHHHHHHHHhCCCEEEEEeccccccc
Q psy8456          65 KLIP----HTKDIDVIGIDEGQFFP-DVVSFAESMANAGKIVVVAALDGTFQR  112 (353)
Q Consensus        65 ei~~----~~~~~dvV~IDEaQFF~-dIv~l~~~l~~~G~~VivaGLd~DFr~  112 (353)
                      -+..    ...++++|+|||||-+. .  .+...+........+.||..+..+
T Consensus       214 ~l~~~~~~~~~~~~~vIiDEaH~~~~~--~~~~il~~~~~~~~~l~lSATp~~  264 (282)
T 1rif_A          214 TVVKQPKEWFSQFGMMMNDECHLATGK--SISSIISGLNNCMFKFGLSGSLRD  264 (282)
T ss_dssp             HHTTSCGGGGGGEEEEEEETGGGCCHH--HHHHHTTTCTTCCEEEEECSSCCT
T ss_pred             HHHhhHHHHHhhCCEEEEECCccCCcc--cHHHHHHHhhcCCeEEEEeCCCCC
Confidence            3321    23568999999999996 2  222233333234566677766543

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=90.04  E-value=0.18  Score=49.32  Aligned_cols=37  Identities=11%  Similarity=0.143  Sum_probs=25.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhC---CEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYAN---YRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~---~~~~~~k~~  187 (353)
                      ...++.+|+|||||...+-.+-..-..+   .+++++-|.
T Consensus       132 ~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  171 (479)
T 3fmp_B          132 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT  171 (479)
T ss_dssp             CEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSS
T ss_pred             CcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeCh
Confidence            5568899999999988544443332222   278888885

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=90.00  E-value=0.17  Score=56.18  Aligned_cols=39  Identities=18%  Similarity=0.075  Sum_probs=33.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +...++.+|.|||||.-....+......|.+++++.|..
T Consensus       199 g~dvLV~ApTGSGKTlva~l~i~~~l~~g~rvlvl~Ptr  237 (1108)
T 3l9o_A          199 GESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIK  237 (1108)
T ss_dssp             TCCEEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEESSH
T ss_pred             CCCEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEcCcH
Confidence            345689999999999988888888878899999999963

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=89.96  E-value=0.29  Score=42.73  Aligned_cols=36  Identities=14%  Similarity=0.003  Sum_probs=27.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH-HhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ-YANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~-~~~~~~~~~k  185 (353)
                      +...++.|+|+|||||-.-.-...+. ..|.++..+.
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~   61 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   61 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEEC
Confidence            45678899999999997666556665 6787776664

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=89.71  E-value=0.72  Score=41.54  Aligned_cols=33  Identities=27%  Similarity=0.445  Sum_probs=21.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      .--+++||.|+|||+ |.+.+.+..  +..++.+..
T Consensus        51 ~~vll~G~~GtGKT~-la~~la~~l--~~~~~~i~~   83 (310)
T 1ofh_A           51 KNILMIGPTGVGKTE-IARRLAKLA--NAPFIKVEA   83 (310)
T ss_dssp             CCEEEECCTTSSHHH-HHHHHHHHH--TCCEEEEEG
T ss_pred             ceEEEECCCCCCHHH-HHHHHHHHh--CCCEEEEcc
Confidence            345899999999995 555554433  555554443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.55  E-value=1.4  Score=52.00  Aligned_cols=132  Identities=13%  Similarity=0.034  Sum_probs=75.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcc---cceeecccHhhhc---cc---CC
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQK---LTAVSAVELNKLI---PH---TK  221 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~---~~a~~~~~~~~~~---~~---~~  221 (353)
                      ++.++.|+.++|||+-+++.+.+.+..|.+|+++.-....+--   ...+.|..   +--.+..++.++.   ..   ..
T Consensus       733 ~lilIaG~PG~GKTtLalqlA~~~a~~g~~VlyiS~Ees~~ql---~A~rlG~~~~~l~i~~~~~i~~i~~~~r~l~~~~  809 (2050)
T 3cmu_A          733 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPI---YARKLGVDIDNLLCSQPDTGEQALEICDALARSG  809 (2050)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHH---HHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHT
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECCCcHHHH---HHHHcCCCccceEEecCCCHHHHHHHHHHHhhcc
Confidence            5678999999999999999999998888889988765433210   11122211   1111112233332   11   25


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcch---HHHHHHHhhccCCCCCCCCccHHHHHHHHH-hCCCEE
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSP---FKTLANENAALNVPPPPEFPDVVSFAESMA-NAGKIV  297 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~-~~g~~V  297 (353)
                      .+++|+||..|-+..            ......++-++.|   +.+++.+..               -...|| +.|++|
T Consensus       810 ~~~LVIIDsLq~i~~------------~~~~~~~~Gs~~q~La~Reis~ilr---------------~Lk~lAke~~v~V  862 (2050)
T 3cmu_A          810 AVDVIVVDSVAALTP------------KAEIEGEIGDSHMGLAARMMSQAMR---------------KLAGNLKQSNTLL  862 (2050)
T ss_dssp             CCSEEEESCGGGCCC------------HHHHHSCTTCCCTTHHHHHHHHHHH---------------HHHHHHHTTTCEE
T ss_pred             CCCEEEEcchhhhcc------------cccccCCCCchhhHHHHHHHHHHHH---------------HHHHHHHHhCCEE
Confidence            789999999997510            0111123344555   444444332               234455 489999


Q ss_pred             EEEeccccccCCCch
Q psy8456         298 VVAALDGTFQRTGFN  312 (353)
Q Consensus       298 i~~gLd~df~~~~F~  312 (353)
                      ++.+=-..=-...|+
T Consensus       863 I~l~Qv~r~~e~~fg  877 (2050)
T 3cmu_A          863 IFINQIRMKIGVMFG  877 (2050)
T ss_dssp             EEEECCEECTTCCSS
T ss_pred             EEeccccccchhhcC
Confidence            887754443334564

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=89.52  E-value=0.56  Score=50.24  Aligned_cols=36  Identities=19%  Similarity=0.143  Sum_probs=31.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      .-++.||+|||||.-.+..+...-..|.+++++-|.
T Consensus       391 ~~Ll~a~TGSGKTlvall~il~~l~~g~qvlvlaPt  426 (780)
T 1gm5_A          391 NRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPT  426 (780)
T ss_dssp             CCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSC
T ss_pred             cEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEeCc
Confidence            357899999999999888887777789999999986

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=89.50  E-value=0.49  Score=51.90  Aligned_cols=39  Identities=13%  Similarity=0.008  Sum_probs=31.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +...++.+|.|||||+-.+-.+......|.+++++.|..
T Consensus        54 g~~vlv~apTGsGKTlv~~~~i~~~~~~g~~vlvl~Ptr   92 (997)
T 4a4z_A           54 GDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIK   92 (997)
T ss_dssp             TCEEEEECCTTSCSHHHHHHHHHHHHHTTCEEEEEESCG
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHHHHhcCCeEEEEeCCH
Confidence            345789999999999865556666667789999999964

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=89.47  E-value=0.51  Score=47.00  Aligned_cols=21  Identities=48%  Similarity=0.692  Sum_probs=15.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++||.|+|||| |.+.+.+.
T Consensus        53 vLL~GppGtGKTt-lAr~ia~~   73 (447)
T 3pvs_A           53 MILWGPPGTGKTT-LAEVIARY   73 (447)
T ss_dssp             EEEECSTTSSHHH-HHHHHHHH
T ss_pred             EEEECCCCCcHHH-HHHHHHHH
Confidence            5889999999986 45555543

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=89.41  E-value=0.25  Score=42.10  Aligned_cols=32  Identities=13%  Similarity=-0.028  Sum_probs=23.9

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMI  183 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~  183 (353)
                      .+.++.|+++|||||-.-.-...+...| .++.
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g-~~~~   36 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELKR-DVYL   36 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTTS-CEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhcC-CEEE
Confidence            4568999999999997766666666566 5543

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=89.35  E-value=0.27  Score=51.94  Aligned_cols=38  Identities=18%  Similarity=0.094  Sum_probs=29.6

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh-----CCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA-----NYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~-----~~~~~~~k~~~  188 (353)
                      ...++.+|||||||...+--+......     +.+++++-|..
T Consensus       264 ~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~  306 (797)
T 4a2q_A          264 KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKV  306 (797)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSH
T ss_pred             CCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCH
Confidence            346889999999998877776665444     78899998854

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=89.33  E-value=0.3  Score=40.90  Aligned_cols=28  Identities=18%  Similarity=0.078  Sum_probs=20.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhC
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYAN  178 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~  178 (353)
                      .+-++.|+++|||||-.-.-..++...|
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g   31 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRKEG   31 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            3568999999999996555555555455

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=89.27  E-value=0.33  Score=44.48  Aligned_cols=39  Identities=15%  Similarity=0.106  Sum_probs=32.3

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k~~  187 (353)
                      .|++.+++||.+|||||-+...+...... |.+|+++...
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~e   73 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLE   73 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeCc
Confidence            46789999999999999999888887765 7788877643

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=89.12  E-value=0.28  Score=47.38  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=17.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +.+|+|||+|||||--.+-+.+
T Consensus         7 ~i~i~GptGsGKTtla~~La~~   28 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALADA   28 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5689999999999866655544

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=89.09  E-value=0.39  Score=52.77  Aligned_cols=37  Identities=16%  Similarity=0.059  Sum_probs=30.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      ..-++.+|.|||||....-.+......|.+++++.|.
T Consensus       102 ~~vLV~apTGSGKTlva~lai~~~l~~g~rvL~l~Pt  138 (1010)
T 2xgj_A          102 ESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPI  138 (1010)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             CCEEEECCCCCChHHHHHHHHHHHhccCCeEEEECCh
Confidence            4468899999999998766666666788999999996

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=89.02  E-value=0.81  Score=41.79  Aligned_cols=63  Identities=21%  Similarity=0.223  Sum_probs=35.7

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc-CCCccEEEEe
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH-TKDIDVIGID  229 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~-~~~~~~i~ID  229 (353)
                      ..-+++||-|+|||+- ++.+.+..  +..+..+....        +.          ...++...+.. ..+..+++||
T Consensus        39 ~~vll~G~~GtGKT~l-a~~i~~~~--~~~~~~~~~~~--------~~----------~~~~l~~~l~~~~~~~~~l~lD   97 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTL-AHVIAHEL--GVNLRVTSGPA--------IE----------KPGDLAAILANSLEEGDILFID   97 (324)
T ss_dssp             CCCEEECCTTCCCHHH-HHHHHHHH--TCCEEEECTTT--------CC----------SHHHHHHHHTTTCCTTCEEEET
T ss_pred             CcEEEECCCCCCHHHH-HHHHHHHh--CCCEEEEeccc--------cC----------ChHHHHHHHHHhccCCCEEEEE
Confidence            3468999999999964 44444322  44433322110        00          01223333333 4567899999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |+|.+
T Consensus        98 Ei~~l  102 (324)
T 1hqc_A           98 EIHRL  102 (324)
T ss_dssp             TTTSC
T ss_pred             CCccc
Confidence            99986

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=88.93  E-value=0.86  Score=48.15  Aligned_cols=36  Identities=17%  Similarity=0.255  Sum_probs=28.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      .++.-++.+|.|||||+.+...+.   ..|.+++++.|.
T Consensus       231 ~~~~vlv~ApTGSGKT~a~~l~ll---~~g~~vLVl~PT  266 (666)
T 3o8b_A          231 SFQVAHLHAPTGSGKSTKVPAAYA---AQGYKVLVLNPS  266 (666)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHH---HTTCCEEEEESC
T ss_pred             cCCeEEEEeCCchhHHHHHHHHHH---HCCCeEEEEcch
Confidence            345567899999999998876544   367899999995

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=88.93  E-value=1.9  Score=40.37  Aligned_cols=31  Identities=0%  Similarity=-0.332  Sum_probs=24.8

Q ss_pred             cCCCCchHHHHHHHHHHHH-HcCceEEEEeec
Q psy8456           7 DDRINPYIVHFCRRIRRYQ-YANYRCMIVRYA   37 (353)
Q Consensus         7 ~~~~~GKSteLLrr~~ry~-~agkkvlv~Kp~   37 (353)
                      +..-+|||...+.-+..+. ..+.+++++-|.
T Consensus        30 ~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~   61 (494)
T 1wp9_A           30 LPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPT   61 (494)
T ss_dssp             CCTTSCHHHHHHHHHHHHHHHSCSCEEEECSS
T ss_pred             cCCCCCHHHHHHHHHHHHHhcCCCeEEEEECC
Confidence            5667999999888876554 468899999995

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=88.82  E-value=0.18  Score=49.03  Aligned_cols=24  Identities=29%  Similarity=0.409  Sum_probs=19.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+.+|+||.+|||||-.++.+.++
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTT
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhC
Confidence            356899999999998877766553

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=88.80  E-value=0.82  Score=53.13  Aligned_cols=81  Identities=19%  Similarity=0.129  Sum_probs=52.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccce---eecccHhhh---cc---cCC
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA---VSAVELNKL---IP---HTK  221 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a---~~~~~~~~~---~~---~~~  221 (353)
                      .+.+|.||.++||||-.++.+.+....|.+|+++........   ....+.|....-   ...++..++   +.   ...
T Consensus       384 ~lilI~G~pGsGKTtLaLq~a~~~~~~G~~vlyis~E~s~~~---~~a~~lGvd~~~L~i~~~~~~e~~l~~l~~lv~~~  460 (1706)
T 3cmw_A          384 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDP---IYARKLGVDIDNLLCSQPDTGEQALEICDALARSG  460 (1706)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCH---HHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEccCchHH---HHHHHcCCCHHHeEEcCCCCHHHHHHHHHHHHHhc
Confidence            468899999999999999999999999999998876542210   011222222111   111222222   21   135


Q ss_pred             CccEEEEeccccc
Q psy8456         222 DIDVIGIDEGQFV  234 (353)
Q Consensus       222 ~~~~i~IDE~QF~  234 (353)
                      ++++|+||..|-+
T Consensus       461 ~~~lVVIDSL~al  473 (1706)
T 3cmw_A          461 AVDVIVVDSVAAL  473 (1706)
T ss_dssp             CCSEEEESCSTTC
T ss_pred             CCCEEEECCHHHh
Confidence            7999999999975

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=88.73  E-value=0.3  Score=43.92  Aligned_cols=35  Identities=26%  Similarity=0.241  Sum_probs=27.8

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      .+...++.||.+|||||.+-+-...+.. |..++..
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~-~~~~~~~   59 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK-DYDVIMT   59 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT-TSCEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc-CCCceee
Confidence            4567789999999999988777777766 7777654

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=88.72  E-value=0.14  Score=44.07  Aligned_cols=34  Identities=18%  Similarity=0.049  Sum_probs=26.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +.++.|+.||||||-+-.-...+...|..|.+++
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~~g~~v~~~~   35 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA   35 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHEEEEEEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEe
Confidence            3578999999999977666666666777777664

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=88.71  E-value=0.37  Score=45.33  Aligned_cols=38  Identities=18%  Similarity=0.169  Sum_probs=32.7

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHH-hCCEEEEEee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQY-ANYRCMIVRY  186 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~-~~~~~~~~k~  186 (353)
                      .+.+..++||.||||||-+..-+..+.. +|++|+++.-
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~  142 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITT  142 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEEC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEec
Confidence            3567889999999999999998888875 8999998874

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=88.67  E-value=0.46  Score=40.40  Aligned_cols=78  Identities=19%  Similarity=0.120  Sum_probs=46.6

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecc--cHhhhccc-CCCccEEEEec
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAV--ELNKLIPH-TKDIDVIGIDE  230 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~--~~~~~~~~-~~~~~~i~IDE  230 (353)
                      |..+--|+||||-...-+..+...|++|+++..  |...+...........++.++..  .+.+++.. ..+||+|+||=
T Consensus         6 v~s~kgG~GKTt~a~~la~~la~~g~~vlliD~--D~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~yD~viiD~   83 (206)
T 4dzz_A            6 FLNPKGGSGKTTAVINIATALSRSGYNIAVVDT--DPQMSLTNWSKAGKAAFDVFTAASEKDVYGIRKDLADYDFAIVDG   83 (206)
T ss_dssp             ECCSSTTSSHHHHHHHHHHHHHHTTCCEEEEEC--CTTCHHHHHHTTSCCSSEEEECCSHHHHHTHHHHTTTSSEEEEEC
T ss_pred             EEeCCCCccHHHHHHHHHHHHHHCCCeEEEEEC--CCCCCHHHHHhcCCCCCcEEecCcHHHHHHHHHhcCCCCEEEEEC
Confidence            334557899999999999999889999999975  32222111111111123333322  23333332 46799999996


Q ss_pred             ccc
Q psy8456         231 GQF  233 (353)
Q Consensus       231 ~QF  233 (353)
                      .-.
T Consensus        84 ~~~   86 (206)
T 4dzz_A           84 AGS   86 (206)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=88.64  E-value=0.21  Score=42.55  Aligned_cols=33  Identities=21%  Similarity=0.107  Sum_probs=22.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      +.+-++.|+|+|||||-.-.-..++  .|..++.+
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l--~g~~~~~~   36 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESI--PANTIKYL   36 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTS--CGGGEEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH--CCCceEEE
Confidence            3456899999999999765544444  35666644

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=88.62  E-value=0.44  Score=40.85  Aligned_cols=34  Identities=24%  Similarity=0.203  Sum_probs=28.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +++.+++||.+|||||-+..-+.   ..|.+|+++..
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~---~~~~~v~~i~~   53 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL---LSGKKVAYVDT   53 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH---HHCSEEEEEES
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH---HcCCcEEEEEC
Confidence            56889999999999998888777   56888888764

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=88.45  E-value=0.14  Score=49.63  Aligned_cols=24  Identities=29%  Similarity=0.364  Sum_probs=19.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      ..+.+|+||.+|||||-.++.+..
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~   33 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKI   33 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CcEEEEECCCccCHHHHHHHHHHh
Confidence            346789999999999887776655

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=88.38  E-value=0.17  Score=45.77  Aligned_cols=36  Identities=25%  Similarity=0.124  Sum_probs=17.2

Q ss_pred             eecccccccccccccccceeeeeccCCCCchhHHHH
Q psy8456         134 VCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       134 vC~~CG~~A~f~~Ri~geI~vi~G~M~sGKt~~Li~  169 (353)
                      -|..|-..+.-++...+...++.|+++|||||.+-.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~I~ieG~~GsGKST~~~~   43 (263)
T 1p5z_B            8 PKRSCPSFSASSEGTRIKKISIEGNIAAGKSTFVNI   43 (263)
T ss_dssp             ---------------CCEEEEEECSTTSSHHHHHTT
T ss_pred             hhccCCCCcccccccCceEEEEECCCCCCHHHHHHH
Confidence            355566665555554556778999999999997643

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=88.35  E-value=0.42  Score=46.94  Aligned_cols=103  Identities=11%  Similarity=0.059  Sum_probs=57.5

Q ss_pred             cCCCCchHHHHHHHHHHHHHcCc-eEEEEeeccC---------CCC---CCCceee-ccCCce------ee-eecCChhh
Q psy8456           7 DDRINPYIVHFCRRIRRYQYANY-RCMIVRYAKD---------DRY---DTEKVAT-HDQQKL------TA-VSAVELNK   65 (353)
Q Consensus         7 ~~~~~GKSteLLrr~~ry~~agk-kvlv~Kp~iD---------tRy---~~~~I~S-r~G~~~------~A-i~i~~l~e   65 (353)
                      ++.-+|||.-.+.-+..+...++ +++++-|...         .++   ....+.. +.|...      .+ +.+.+...
T Consensus       135 ~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~I~i~T~~~  214 (510)
T 2oca_A          135 LPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQT  214 (510)
T ss_dssp             CCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEECGGGCCTTGGGCTTCSEEEEEHHH
T ss_pred             eCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHHHHHHhhcCCccceEEEecCCccccccccCCcEEEEeHHH
Confidence            45669999999888877766666 9999999521         112   1112221 112111      11 22333332


Q ss_pred             hcc----cCCCccEEEEccccChHHHHHHHHHHHhCCCEEEEEeccccc
Q psy8456          66 LIP----HTKDIDVIGIDEGQFFPDVVSFAESMANAGKIVVVAALDGTF  110 (353)
Q Consensus        66 i~~----~~~~~dvV~IDEaQFF~dIv~l~~~l~~~G~~VivaGLd~DF  110 (353)
                      +..    ...++++|+|||+|.+.. .++...+......+.+.||..+-
T Consensus       215 l~~~~~~~~~~~~liIiDE~H~~~~-~~~~~il~~~~~~~~~l~lSATp  262 (510)
T 2oca_A          215 VVKQPKEWFSQFGMMMNDECHLATG-KSISSIISGLNNCMFKFGLSGSL  262 (510)
T ss_dssp             HTTSCGGGGGGEEEEEEETGGGCCH-HHHHHHGGGCTTCCEEEEEESCG
T ss_pred             HhhchhhhhhcCCEEEEECCcCCCc-ccHHHHHHhcccCcEEEEEEeCC
Confidence            321    245689999999999962 12223334444445566776655

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=88.26  E-value=0.55  Score=41.82  Aligned_cols=36  Identities=17%  Similarity=0.165  Sum_probs=24.7

Q ss_pred             CccEEEEccccCh--H--------HHHHHHHHHHhCCCEEEEEecc
Q psy8456          72 DIDVIGIDEGQFF--P--------DVVSFAESMANAGKIVVVAALD  107 (353)
Q Consensus        72 ~~dvV~IDEaQFF--~--------dIv~l~~~l~~~G~~VivaGLd  107 (353)
                      ...+|+|||||.+  +        .+....+.-...|..|++.|-.
T Consensus        87 ~~~vliIDEAq~l~~~~~~~~e~~rll~~l~~~r~~~~~iil~tq~  132 (199)
T 2r2a_A           87 IGSIVIVDEAQDVWPARSAGSKIPENVQWLNTHRHQGIDIFVLTQG  132 (199)
T ss_dssp             TTCEEEETTGGGTSBCCCTTCCCCHHHHGGGGTTTTTCEEEEEESC
T ss_pred             CceEEEEEChhhhccCccccchhHHHHHHHHhcCcCCeEEEEECCC
Confidence            3679999999998  2        2223333333568899999876

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=88.25  E-value=0.17  Score=43.09  Aligned_cols=21  Identities=33%  Similarity=0.537  Sum_probs=16.0

Q ss_pred             cceeeeeccCCCCchhHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~  171 (353)
                      +.+.+++||++|||||- ++.+
T Consensus         2 g~ii~l~G~~GaGKSTl-~~~L   22 (189)
T 2bdt_A            2 KKLYIITGPAGVGKSTT-CKRL   22 (189)
T ss_dssp             EEEEEEECSTTSSHHHH-HHHH
T ss_pred             CeEEEEECCCCCcHHHH-HHHH
Confidence            34678999999999984 4444

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=88.23  E-value=0.41  Score=45.51  Aligned_cols=37  Identities=14%  Similarity=0.067  Sum_probs=32.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+..++||.||||||-+..-+..+...|.+|+++.-
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~  140 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA  140 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEcc
Confidence            4577899999999999999999999888999998753

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=88.07  E-value=0.85  Score=44.84  Aligned_cols=29  Identities=10%  Similarity=-0.009  Sum_probs=24.0

Q ss_pred             CCCchHHH-HHHHHHHHHHcCceEEEEeec
Q psy8456           9 RINPYIVH-FCRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus         9 ~~~GKSte-LLrr~~ry~~agkkvlv~Kp~   37 (353)
                      .-||||+. ++..+.+....|.+++++-|.
T Consensus        28 TGsGKT~~~~~~~l~~~~~~~~~~lvl~Pt   57 (451)
T 2jlq_A           28 PGAGKTKRILPSIVREALLRRLRTLILAPT   57 (451)
T ss_dssp             TTSSCCTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCHhhHHHHHHHHHHHhcCCcEEEECCC
Confidence            45899995 777777777788999999993

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=88.02  E-value=0.81  Score=48.24  Aligned_cols=35  Identities=23%  Similarity=0.152  Sum_probs=24.3

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      .++..++.||.|||||+-+++++..   ++ +.+++-|.
T Consensus       154 ~rk~vlv~apTGSGKT~~al~~l~~---~~-~gl~l~Pt  188 (677)
T 3rc3_A          154 QRKIIFHSGPTNSGKTYHAIQKYFS---AK-SGVYCGPL  188 (677)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH---SS-SEEEEESS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHh---cC-CeEEEeCH
Confidence            4567789999999999977766543   23 33555553

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=87.95  E-value=0.076  Score=53.67  Aligned_cols=87  Identities=15%  Similarity=0.116  Sum_probs=46.5

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeecc---CCce-eeeecCChhhh-ccc-C---CCccEEEEcc
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHD---QQKL-TAVSAVELNKL-IPH-T---KDIDVIGIDE   80 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~---G~~~-~Ai~i~~l~ei-~~~-~---~~~dvV~IDE   80 (353)
                      -+|||+.+.+.+.     .++++++.|..-.+   ..+..+.   |... ....+...... ++. .   -.+|+|+|||
T Consensus       171 GsGKTt~I~~~~~-----~~~~lVlTpT~~aa---~~l~~kl~~~~~~~~~~~~V~T~dsfL~~~~~~~~~~~d~liiDE  242 (446)
T 3vkw_A          171 GCGKTKEILSRVN-----FEEDLILVPGRQAA---EMIRRRANASGIIVATKDNVRTVDSFLMNYGKGARCQFKRLFIDE  242 (446)
T ss_dssp             TSCHHHHHHHHCC-----TTTCEEEESCHHHH---HHHHHHHTTTSCCCCCTTTEEEHHHHHHTTTSSCCCCCSEEEEET
T ss_pred             CCCHHHHHHHHhc-----cCCeEEEeCCHHHH---HHHHHHhhhcCccccccceEEEeHHhhcCCCCCCCCcCCEEEEeC
Confidence            4899999988764     26789999953332   2222221   1100 00111111111 111 1   1389999999


Q ss_pred             ccChH-HHHHHHHHHHhCCCEEEEEe
Q psy8456          81 GQFFP-DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        81 aQFF~-dIv~l~~~l~~~G~~VivaG  105 (353)
                      ++-++ .....+-.+. ....|++.|
T Consensus       243 ~sm~~~~~l~~l~~~~-~~~~vilvG  267 (446)
T 3vkw_A          243 GLMLHTGCVNFLVEMS-LCDIAYVYG  267 (446)
T ss_dssp             GGGSCHHHHHHHHHHT-TCSEEEEEE
T ss_pred             cccCCHHHHHHHHHhC-CCCEEEEec
Confidence            99987 4333332222 338888887

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=87.85  E-value=0.5  Score=41.91  Aligned_cols=35  Identities=31%  Similarity=0.221  Sum_probs=31.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      .+.++.|..|+||||-+.+-+..+. .|++|+++..
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~-~g~~v~vvd~   49 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLE-DNYKVAYVNL   49 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHT-TTSCEEEEEC
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHH-CCCeEEEEeC
Confidence            5678999999999999999888888 9999998863

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=87.77  E-value=1.6  Score=41.34  Aligned_cols=32  Identities=22%  Similarity=0.347  Sum_probs=20.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      .--+++||+|+|||+ |.+.+.+..  +..++.+.
T Consensus        73 ~~ill~Gp~GtGKT~-la~~la~~l--~~~~~~~~  104 (376)
T 1um8_A           73 SNILLIGPTGSGKTL-MAQTLAKHL--DIPIAISD  104 (376)
T ss_dssp             CCEEEECCTTSSHHH-HHHHHHHHT--TCCEEEEE
T ss_pred             CCEEEECCCCCCHHH-HHHHHHHHh--CCCEEEec
Confidence            346899999999995 555554432  55555443

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=87.73  E-value=0.53  Score=41.03  Aligned_cols=35  Identities=20%  Similarity=0.015  Sum_probs=29.2

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      ...++|+.||||||-+-+-+..+...|.++-.++.
T Consensus         8 ~i~i~G~sGsGKTTl~~~l~~~l~~~g~~v~~i~~   42 (174)
T 1np6_A            8 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIKH   42 (174)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHhccccCCceeEEee
Confidence            56789999999999877777777778888887775

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=87.67  E-value=0.43  Score=44.22  Aligned_cols=35  Identities=20%  Similarity=0.410  Sum_probs=25.8

Q ss_pred             CCccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEe
Q psy8456          71 KDIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        71 ~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaG  105 (353)
                      .+.++++|||+|+++       .+..+.+.+.+.|+.+++.+
T Consensus        97 ~~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~  138 (324)
T 1l8q_A           97 KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILAS  138 (324)
T ss_dssp             HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             cCCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEe
Confidence            347899999999985       13345555667888888877

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=87.63  E-value=0.45  Score=41.12  Aligned_cols=25  Identities=28%  Similarity=0.161  Sum_probs=18.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +.+.+++||+||||||-+-.-...+
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhh
Confidence            5678899999999998654444443

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=87.52  E-value=0.48  Score=42.91  Aligned_cols=22  Identities=27%  Similarity=0.126  Sum_probs=16.5

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+++||-|+|||+-+-..++..
T Consensus        45 ~ll~G~~G~GKt~la~~l~~~l   66 (323)
T 1sxj_B           45 MIISGMPGIGKTTSVHCLAHEL   66 (323)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHh
Confidence            6899999999997555444443

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=87.52  E-value=0.21  Score=42.51  Aligned_cols=21  Identities=29%  Similarity=0.235  Sum_probs=17.7

Q ss_pred             ccceeeeeccCCCCchhHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~  169 (353)
                      .+++..++||.||||||-+-.
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            467889999999999997653

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=87.50  E-value=0.33  Score=39.85  Aligned_cols=22  Identities=18%  Similarity=0.134  Sum_probs=16.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +-++.||+||||||-.-.-..+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~   24 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKE   24 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999965444333

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=87.47  E-value=0.67  Score=54.68  Aligned_cols=81  Identities=19%  Similarity=0.129  Sum_probs=51.9

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccce---eecccHhhh---cc---cCC
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTA---VSAVELNKL---IP---HTK  221 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a---~~~~~~~~~---~~---~~~  221 (353)
                      .+.+|.||.++||||-+++.+.+....|.+|+++........   ....+.|....-   ....++.++   +.   ...
T Consensus       384 ~lilI~G~pGsGKTtLaLqia~~~a~~G~~vlyis~E~s~~~---~~a~~lGvd~~~L~I~~~~~~e~il~~~~~lv~~~  460 (2050)
T 3cmu_A          384 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDP---IYARKLGVDIDNLLCSQPDTGEQALEICDALARSG  460 (2050)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCH---HHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEcCCCHHH---HHHHHcCCCHHHeEEeCCCCHHHHHHHHHHHHHhc
Confidence            478899999999999999999999988899998876542210   001112221111   111222222   22   135


Q ss_pred             CccEEEEeccccc
Q psy8456         222 DIDVIGIDEGQFV  234 (353)
Q Consensus       222 ~~~~i~IDE~QF~  234 (353)
                      .+++|+||..|-+
T Consensus       461 ~~~lIVIDSL~al  473 (2050)
T 3cmu_A          461 AVDVIVVDSVAAL  473 (2050)
T ss_dssp             CCSEEEESCGGGC
T ss_pred             CCcEEEECCHHHh
Confidence            7999999999975

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=87.46  E-value=0.21  Score=41.49  Aligned_cols=19  Identities=32%  Similarity=0.412  Sum_probs=15.0

Q ss_pred             ceeeeeccCCCCchhHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~  169 (353)
                      ...+++|||+|||||-+-.
T Consensus         5 ~~i~l~G~~GsGKSTl~~~   23 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQ   23 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            4568999999999985433

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=87.38  E-value=1.4  Score=43.18  Aligned_cols=30  Identities=10%  Similarity=-0.041  Sum_probs=23.6

Q ss_pred             CCCCchHHHH-HHHHHHHHHcCceEEEEeec
Q psy8456           8 DRINPYIVHF-CRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus         8 ~~~~GKSteL-Lrr~~ry~~agkkvlv~Kp~   37 (353)
                      +.-||||.-. +..++.....|.+++++-|.
T Consensus        10 ~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt   40 (431)
T 2v6i_A           10 HPGAGKTRRVLPQLVREAVKKRLRTVILAPT   40 (431)
T ss_dssp             CTTSCTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCCHHHHHHHHHHHHHHhCCCCEEEECcH
Confidence            3459999984 66666777788999999994

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=87.25  E-value=0.2  Score=46.97  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=16.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+++||.|+||||-+...++..
T Consensus        49 ~ll~Gp~G~GKTtla~~la~~l   70 (340)
T 1sxj_C           49 LLFYGPPGTGKTSTIVALAREI   70 (340)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999998665554443

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=87.24  E-value=0.84  Score=43.11  Aligned_cols=22  Identities=14%  Similarity=-0.078  Sum_probs=16.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      ...+++||-++||||-...-++
T Consensus        19 ~~~Lf~Gp~G~GKtt~a~~la~   40 (305)
T 2gno_A           19 ISILINGEDLSYPREVSLELPE   40 (305)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            3578899999999875554444

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=87.21  E-value=0.53  Score=42.77  Aligned_cols=33  Identities=15%  Similarity=0.071  Sum_probs=24.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      +.++.|++||||||-.-.-...+...|..++++
T Consensus         6 lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~   38 (260)
T 3a4m_A            6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVL   38 (260)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEE
Confidence            568999999999997655555556678777654

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=87.15  E-value=1.6  Score=42.09  Aligned_cols=97  Identities=9%  Similarity=0.004  Sum_probs=58.4

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeee---cCChhhhc---c---cCCCccEEEEc
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVS---AVELNKLI---P---HTKDIDVIGID   79 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~---i~~l~ei~---~---~~~~~dvV~ID   79 (353)
                      .=+||||-+++.+.+....|.+|+++.-....+   .....+.|...+.+.   ..+..++.   .   ...++++|+||
T Consensus        70 pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~---~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~~~~~~lIVID  146 (349)
T 2zr9_A           70 ESSGKTTVALHAVANAQAAGGIAAFIDAEHALD---PEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVRSGALDIIVID  146 (349)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCC---HHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCSEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcC---HHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCCEEEEc
Confidence            348999999999999998999999887642111   112233443322211   12233322   1   13569999999


Q ss_pred             cccChH---H----------------HHHHHHH----HHhCCCEEEEEeccc
Q psy8456          80 EGQFFP---D----------------VVSFAES----MANAGKIVVVAALDG  108 (353)
Q Consensus        80 EaQFF~---d----------------Iv~l~~~----l~~~G~~VivaGLd~  108 (353)
                      |.+.+-   +                +.+....    +.+.|++|++..-..
T Consensus       147 sl~~l~~~~e~~~~~gd~~~~~q~r~~~~~l~~L~~~a~~~~~tVI~inh~~  198 (349)
T 2zr9_A          147 SVAALVPRAEIEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFINELR  198 (349)
T ss_dssp             CGGGCCCHHHHTTC----CCCHHHHHHHHHHHHHHHHHHHHTCEEEEEEECC
T ss_pred             ChHhhcchhhhccccccchhhHHHHHHHHHHHHHHHHHHHhCCEEEEEeccc
Confidence            999862   1                1222333    357799998876543

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=87.05  E-value=0.67  Score=51.41  Aligned_cols=38  Identities=16%  Similarity=0.023  Sum_probs=30.7

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ...++.+|.|||||+-.+-.+......|.+++++-|..
T Consensus        94 ~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~Ptr  131 (1104)
T 4ddu_A           94 KSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTV  131 (1104)
T ss_dssp             CCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSH
T ss_pred             CCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechH
Confidence            45688999999999977776666667789999999863

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=86.97  E-value=0.54  Score=44.44  Aligned_cols=37  Identities=22%  Similarity=0.228  Sum_probs=31.1

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      .+++..++||.||||||-+-.-+..+...+.+|++..
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~~g~V~l~g  135 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLMAA  135 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            3678889999999999998888888887788888764

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=86.81  E-value=0.58  Score=41.93  Aligned_cols=38  Identities=18%  Similarity=0.094  Sum_probs=31.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +..-++.|+.+|||||.+-.-...+...|..|..++..
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~~~p   43 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTREP   43 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEESS
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHcCCCcccccCC
Confidence            45678899999999999988888888889999876543

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=86.60  E-value=1.3  Score=43.00  Aligned_cols=37  Identities=16%  Similarity=0.130  Sum_probs=25.7

Q ss_pred             ceeeeeccCCCCchhHH-HHHHHHHHHh-------CCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTEL-IRRIRRYQYA-------NYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~L-i~~~~~~~~~-------~~~~~~~k~~  187 (353)
                      ..-++.+|+|||||... +-.+.+....       +.+++++-|.
T Consensus        94 ~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~Pt  138 (434)
T 2db3_A           94 RDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPT  138 (434)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSS
T ss_pred             CCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecC
Confidence            45688999999999853 3344444332       4589999885

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=86.52  E-value=0.86  Score=50.17  Aligned_cols=38  Identities=18%  Similarity=0.109  Sum_probs=31.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +..++.+|.|||||+-++-.+.+....|.+++++-|..
T Consensus        72 ~dvlv~apTGSGKTl~~lp~l~~~~~~~~~~lil~Ptr  109 (1054)
T 1gku_B           72 ESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTS  109 (1054)
T ss_dssp             CCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHHhhcCCeEEEEeccH
Confidence            44688999999999877777777777788999999864

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=86.51  E-value=1.4  Score=45.57  Aligned_cols=29  Identities=10%  Similarity=-0.033  Sum_probs=23.9

Q ss_pred             CCCchHHH-HHHHHHHHHHcCceEEEEeec
Q psy8456           9 RINPYIVH-FCRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus         9 ~~~GKSte-LLrr~~ry~~agkkvlv~Kp~   37 (353)
                      .=||||+. ++..++++...+.+++++-|.
T Consensus       195 TGSGKT~~~~lpil~~l~~~~~~vLvl~Pt  224 (618)
T 2whx_A          195 PGAGKTKRILPSIVREALKRRLRTLILAPT  224 (618)
T ss_dssp             TTSSTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCeEEEEcCh
Confidence            34899998 677887777788899999993

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=86.42  E-value=0.62  Score=41.02  Aligned_cols=34  Identities=18%  Similarity=0.130  Sum_probs=28.5

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      ++=|+-||||||.+-.-...++..|.+|++.+.-
T Consensus         4 ~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~treP   37 (197)
T 3hjn_A            4 TFEGIDGSGKSTQIQLLAQYLEKRGKKVILKREP   37 (197)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCcEEEEECC
Confidence            4569999999999888778888999999877643

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=86.32  E-value=0.69  Score=43.58  Aligned_cols=69  Identities=16%  Similarity=0.171  Sum_probs=36.9

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee-cCCCCCCCceeeccCcccceeecccHhhhcc--cCCCccEEE
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA-KDDRYDTEKVSTHDQQKLTAVSAVELNKLIP--HTKDIDVIG  227 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~-~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~--~~~~~~~i~  227 (353)
                      .--+++||.|+|||+-. +.+.+.. .+..++.+... +-..|        .|.     ....+..+..  ......+|+
T Consensus        46 ~~iLL~GppGtGKT~la-~ala~~~-~~~~~~~i~~~~l~~~~--------~g~-----~~~~~~~lf~~a~~~~~~vl~  110 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLA-KAVATEA-NNSTFFSISSSDLVSKW--------LGE-----SEKLVKNLFQLARENKPSIIF  110 (322)
T ss_dssp             SEEEEESSSSSCHHHHH-HHHHHHT-TSCEEEEEECCSSCCSS--------CCS-----CHHHHHHHHHHHHHTSSEEEE
T ss_pred             ceEEEECCCCccHHHHH-HHHHHHc-CCCcEEEEEhHHHHhhh--------hhH-----HHHHHHHHHHHHHhcCCcEEE
Confidence            45689999999999644 4443321 25555544432 11111        111     1112222321  134578999


Q ss_pred             Eeccccc
Q psy8456         228 IDEGQFV  234 (353)
Q Consensus       228 IDE~QF~  234 (353)
                      |||++.+
T Consensus       111 iDEid~l  117 (322)
T 1xwi_A          111 IDEIDSL  117 (322)
T ss_dssp             EETTTGG
T ss_pred             eecHHHh
Confidence            9999975

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=86.28  E-value=0.56  Score=45.51  Aligned_cols=39  Identities=21%  Similarity=0.078  Sum_probs=32.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD  190 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~  190 (353)
                      =.+++|+++||||+-+-..+.+....|..++++-|.-|.
T Consensus        55 h~~i~G~tGsGKs~~~~~li~~~~~~g~~viv~Dpkge~   93 (437)
T 1e9r_A           55 HLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDM   93 (437)
T ss_dssp             CEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCCch
Confidence            357999999999998766777777889999999997654

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=86.20  E-value=0.6  Score=38.94  Aligned_cols=20  Identities=25%  Similarity=0.228  Sum_probs=16.1

Q ss_pred             cceeeeeccCCCCchhHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~  169 (353)
                      +.+.+++||++|||||-+-.
T Consensus         8 g~~i~l~G~~GsGKSTl~~~   27 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASE   27 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHH
Confidence            56778999999999985433

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=86.18  E-value=0.48  Score=42.84  Aligned_cols=21  Identities=33%  Similarity=0.357  Sum_probs=15.9

Q ss_pred             eeeeccCCCCchhHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .+++||-|+|||+-+-..++.
T Consensus        41 ~ll~G~~G~GKt~la~~l~~~   61 (319)
T 2chq_A           41 LLFSGPPGTGKTATAIALARD   61 (319)
T ss_dssp             EEEESSSSSSHHHHHHHHHHH
T ss_pred             EEEECcCCcCHHHHHHHHHHH
Confidence            689999999999755444444

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=86.12  E-value=0.51  Score=44.08  Aligned_cols=24  Identities=21%  Similarity=0.216  Sum_probs=17.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +..-+++||.|+|||+ |.+.+.+.
T Consensus        70 ~~~vLl~GppGtGKT~-la~~la~~   93 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTA-IAMGMAQA   93 (368)
T ss_dssp             TCEEEEEESTTSSHHH-HHHHHHHH
T ss_pred             CCEEEEECCCCCCHHH-HHHHHHHH
Confidence            3467899999999997 45555444

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=86.11  E-value=0.63  Score=44.63  Aligned_cols=39  Identities=18%  Similarity=0.115  Sum_probs=32.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +.-.+|+||++|||||-+-..+..+...|.+++++-|.-
T Consensus        35 ~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D~~~   73 (392)
T 4ag6_A           35 NSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIIDPER   73 (392)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEESSC
T ss_pred             cCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEeCCc
Confidence            444689999999999988887777777899999988753

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=86.10  E-value=0.43  Score=41.16  Aligned_cols=25  Identities=28%  Similarity=0.145  Sum_probs=19.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +...+++|||+|||||-.-.-...+
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            4567899999999998765555444

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=86.09  E-value=0.66  Score=44.52  Aligned_cols=33  Identities=21%  Similarity=0.288  Sum_probs=22.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      .--+++||.|+|||+ |.+.+.  ...+..++.+..
T Consensus       149 ~~vLL~GppGtGKT~-la~aia--~~~~~~~~~v~~  181 (389)
T 3vfd_A          149 RGLLLFGPPGNGKTM-LAKAVA--AESNATFFNISA  181 (389)
T ss_dssp             SEEEEESSTTSCHHH-HHHHHH--HHTTCEEEEECS
T ss_pred             ceEEEECCCCCCHHH-HHHHHH--HhhcCcEEEeeH
Confidence            446899999999996 445542  345666665543

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=86.08  E-value=0.3  Score=52.91  Aligned_cols=38  Identities=18%  Similarity=0.094  Sum_probs=28.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh-----CCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA-----NYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~-----~~~~~~~k~~~  188 (353)
                      ...++.+|||||||...+--+......     +.+++++-|..
T Consensus       264 ~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~  306 (936)
T 4a2w_A          264 KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKV  306 (936)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSH
T ss_pred             CCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCH
Confidence            446899999999998876666554333     77899998854

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=85.91  E-value=0.43  Score=43.01  Aligned_cols=68  Identities=21%  Similarity=0.164  Sum_probs=35.7

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcc--cCCCccEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIP--HTKDIDVIGID  229 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~--~~~~~~~i~ID  229 (353)
                      --+++||.|+|||+-+ +.+.+  ..+..++.+....-       .....|.     ....+..++.  ......+++||
T Consensus        53 ~~ll~G~~GtGKT~la-~~la~--~~~~~~~~v~~~~~-------~~~~~~~-----~~~~~~~~~~~~~~~~~~vl~iD  117 (285)
T 3h4m_A           53 GILLYGPPGTGKTLLA-KAVAT--ETNATFIRVVGSEL-------VKKFIGE-----GASLVKDIFKLAKEKAPSIIFID  117 (285)
T ss_dssp             EEEEESSSSSSHHHHH-HHHHH--HTTCEEEEEEGGGG-------CCCSTTH-----HHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             eEEEECCCCCcHHHHH-HHHHH--HhCCCEEEEehHHH-------HHhccch-----HHHHHHHHHHHHHHcCCeEEEEE
Confidence            4689999999999654 44432  34555554433110       0000111     0111222221  13456899999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |++.+
T Consensus       118 Eid~l  122 (285)
T 3h4m_A          118 EIDAI  122 (285)
T ss_dssp             TTHHH
T ss_pred             CHHHh
Confidence            99985

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=85.87  E-value=0.54  Score=41.50  Aligned_cols=67  Identities=21%  Similarity=0.202  Sum_probs=33.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec-CCCCCCCceeeccCcccceeecccHhhhccc--CCCccEEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK-DDRYDTEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVIGI  228 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~-D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i~I  228 (353)
                      --+++||.|+|||+- .+.+.+  ..+..++.+.... ...+        .|.     ....+..++..  .....+++|
T Consensus        41 ~vll~G~~GtGKT~l-a~~la~--~~~~~~~~~~~~~~~~~~--------~~~-----~~~~~~~~~~~a~~~~~~vl~i  104 (262)
T 2qz4_A           41 GALLLGPPGCGKTLL-AKAVAT--EAQVPFLAMAGAEFVEVI--------GGL-----GAARVRSLFKEARARAPCIVYI  104 (262)
T ss_dssp             EEEEESCTTSSHHHH-HHHHHH--HHTCCEEEEETTTTSSSS--------TTH-----HHHHHHHHHHHHHHTCSEEEEE
T ss_pred             eEEEECCCCCCHHHH-HHHHHH--HhCCCEEEechHHHHhhc--------cCh-----hHHHHHHHHHHHHhcCCeEEEE
Confidence            358999999999964 444443  2355555444321 0001        010     11122222221  235689999


Q ss_pred             eccccc
Q psy8456         229 DEGQFV  234 (353)
Q Consensus       229 DE~QF~  234 (353)
                      ||+|.+
T Consensus       105 Deid~l  110 (262)
T 2qz4_A          105 DEIDAV  110 (262)
T ss_dssp             ECC---
T ss_pred             eCcchh
Confidence            999985

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=85.84  E-value=0.25  Score=42.58  Aligned_cols=16  Identities=38%  Similarity=0.202  Sum_probs=13.1

Q ss_pred             eeeeeccCCCCchhHH
Q psy8456         152 KEVILGPMFSGKTTEL  167 (353)
Q Consensus       152 I~vi~G~M~sGKt~~L  167 (353)
                      +..++|||+|||||-.
T Consensus         4 ~i~l~G~~GsGKST~~   19 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIA   19 (206)
T ss_dssp             EEEEECSTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3568999999999854

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=85.72  E-value=1.1  Score=42.21  Aligned_cols=22  Identities=32%  Similarity=0.333  Sum_probs=16.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +..+++||.|+||||- ++.+-+
T Consensus        52 ~~~ll~Gp~G~GKTTL-a~~ia~   73 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTL-AHIIAS   73 (334)
T ss_dssp             CCEEEESSTTSSHHHH-HHHHHH
T ss_pred             CeEEEECCCCCcHHHH-HHHHHH
Confidence            4568999999999975 444443

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=85.72  E-value=0.31  Score=41.53  Aligned_cols=22  Identities=36%  Similarity=0.265  Sum_probs=17.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      +.+.+++||+||||||-+ +.+.
T Consensus         6 g~~i~l~G~~GsGKSTl~-~~L~   27 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVR-KRIF   27 (207)
T ss_dssp             CCEEEEECSTTSCHHHHH-HHHH
T ss_pred             CCEEEEECCCCCCHHHHH-HHHH
Confidence            557789999999999854 4443

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=85.57  E-value=0.83  Score=42.09  Aligned_cols=37  Identities=22%  Similarity=0.314  Sum_probs=26.3

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHh-CCEEEEEe
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYA-NYRCMIVR  185 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~-~~~~~~~k  185 (353)
                      .+++..++||.||||||-|---+.-+... ..++.+..
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~~g   61 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIE   61 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEEEE
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEEcC
Confidence            46788999999999999776655555544 44555443

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=85.56  E-value=0.28  Score=41.93  Aligned_cols=19  Identities=26%  Similarity=0.132  Sum_probs=15.1

Q ss_pred             cceeeeeccCCCCchhHHH
Q psy8456         150 QEKEVILGPMFSGKTTELI  168 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li  168 (353)
                      +..-+++|+|+|||||-.-
T Consensus        10 ~~~I~l~G~~GsGKSTv~~   28 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAE   28 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            3456899999999998643

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=85.54  E-value=0.32  Score=41.49  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=18.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .|.+..++||.||||||- ++.+..
T Consensus         6 ~g~ii~l~Gp~GsGKSTl-~~~L~~   29 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSL-VRALVK   29 (205)
T ss_dssp             CCCEEEEECCTTSCHHHH-HHHHHH
T ss_pred             CCcEEEEECcCCCCHHHH-HHHHHh
Confidence            366788999999999985 444443

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=85.36  E-value=0.4  Score=44.31  Aligned_cols=54  Identities=20%  Similarity=0.242  Sum_probs=29.0

Q ss_pred             HhhhhccccceEeccceecccccc-cc--ccccc-ccceeeeeccCCCCchhHHHHHHH
Q psy8456         118 ILSLIPLAECVEKLTAVCMSCFRD-AA--FTKRI-GQEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       118 ~~~Ll~lAD~I~kL~AvC~~CG~~-A~--f~~Ri-~geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      +.-|.|..+.+.+++.++..-|.. +-  .|+.+ .|++..++||.||||||- ++.+.
T Consensus        10 ~~~~~~~~~~~l~~~~l~~~y~~~~vl~~vsl~i~~Ge~~~l~G~NGsGKSTL-lk~l~   67 (267)
T 2zu0_C           10 SSGLVPRGSHMLSIKDLHVSVEDKAILRGLSLDVHPGEVHAIMGPNGSGKSTL-SATLA   67 (267)
T ss_dssp             ----------CEEEEEEEEEETTEEEEEEEEEEECTTCEEEEECCTTSSHHHH-HHHHH
T ss_pred             cCCCcCCCCceEEEEeEEEEECCEEEEEeeEEEEcCCCEEEEECCCCCCHHHH-HHHHh
Confidence            455777777777777777544432 21  23444 467889999999999985 44443

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=85.35  E-value=0.59  Score=40.63  Aligned_cols=27  Identities=19%  Similarity=0.178  Sum_probs=18.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      +..+.|+++|||||- .+.+..   .|..++
T Consensus         6 ~I~i~G~~GSGKST~-~~~L~~---lg~~~i   32 (218)
T 1vht_A            6 IVALTGGIGSGKSTV-ANAFAD---LGINVI   32 (218)
T ss_dssp             EEEEECCTTSCHHHH-HHHHHH---TTCEEE
T ss_pred             EEEEECCCCCCHHHH-HHHHHH---cCCEEE
Confidence            567999999999984 344433   465443

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=85.23  E-value=0.65  Score=43.95  Aligned_cols=38  Identities=24%  Similarity=0.204  Sum_probs=31.1

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      .++...++||.||||||-+-.-+..+...+.+|++..-
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~~~g~V~l~g~  138 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAG  138 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEee
Confidence            35678899999999999888888888777888887643

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=85.20  E-value=0.5  Score=39.70  Aligned_cols=22  Identities=23%  Similarity=0.102  Sum_probs=16.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      .+.++.|+|+|||||-.-.-..
T Consensus         6 ~~I~l~G~~GsGKST~~~~L~~   27 (193)
T 2rhm_A            6 ALIIVTGHPATGKTTLSQALAT   27 (193)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3568999999999996544333

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=85.16  E-value=0.48  Score=39.79  Aligned_cols=24  Identities=29%  Similarity=0.400  Sum_probs=17.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ...++.|+|+|||||-.-.-..++
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            456899999999999655444433

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=85.14  E-value=0.75  Score=43.83  Aligned_cols=36  Identities=25%  Similarity=0.337  Sum_probs=31.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +....++||.||||||-+..-+..+...|++|+++.
T Consensus       105 ~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid  140 (320)
T 1zu4_A          105 LNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAA  140 (320)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            456778999999999999999888888899999875

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=85.13  E-value=0.81  Score=43.01  Aligned_cols=40  Identities=10%  Similarity=0.020  Sum_probs=35.1

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      .+++.+|.|+.++||||-+++.+.+....|.+|++|....
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~slE~  106 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLEM  106 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEESSS
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEECCC
Confidence            3678999999999999999999988888889999998653

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=85.10  E-value=1.7  Score=42.89  Aligned_cols=29  Identities=7%  Similarity=-0.069  Sum_probs=24.1

Q ss_pred             CCCchHHH-HHHHHHHHHHcCceEEEEeec
Q psy8456           9 RINPYIVH-FCRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus         9 ~~~GKSte-LLrr~~ry~~agkkvlv~Kp~   37 (353)
                      .-||||+. ++-.++.+...|.+++++-|.
T Consensus        30 TGsGKT~~~~l~il~~~~~~~~~~lvl~Pt   59 (459)
T 2z83_A           30 PGSGKTRKILPQIIKDAIQQRLRTAVLAPT   59 (459)
T ss_dssp             TTSCTTTTHHHHHHHHHHHTTCCEEEEECS
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCcEEEECch
Confidence            35899998 777777777788999999994

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=84.96  E-value=0.51  Score=39.84  Aligned_cols=22  Identities=23%  Similarity=0.265  Sum_probs=16.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .++.|+|+|||||-.-.-...+
T Consensus         3 I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            3 IAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCccCHHHHHHHHHHhc
Confidence            4789999999999665544444

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=84.94  E-value=0.55  Score=39.45  Aligned_cols=24  Identities=21%  Similarity=0.138  Sum_probs=17.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..-+++|||+|||||-.-.-..++
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            346789999999998655544443

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=84.83  E-value=2  Score=42.21  Aligned_cols=29  Identities=3%  Similarity=-0.053  Sum_probs=22.4

Q ss_pred             CCCchHHH-HHHHHHHHHHcCceEEEEeec
Q psy8456           9 RINPYIVH-FCRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus         9 ~~~GKSte-LLrr~~ry~~agkkvlv~Kp~   37 (353)
                      .-||||.- ++..+......|.+++++-|.
T Consensus        17 TGSGKT~~~l~~~l~~~~~~~~~~lil~Pt   46 (440)
T 1yks_A           17 PGAGKTRRFLPQILAECARRRLRTLVLAPT   46 (440)
T ss_dssp             TTSSTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCeEEEEcch
Confidence            45999998 466666666778899999993

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=84.78  E-value=0.46  Score=41.57  Aligned_cols=23  Identities=35%  Similarity=0.313  Sum_probs=17.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .-++.|||||||||..-.-..++
T Consensus         7 ~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            7 KVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            45889999999999655444443

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=84.61  E-value=1.1  Score=45.10  Aligned_cols=38  Identities=13%  Similarity=0.106  Sum_probs=24.7

Q ss_pred             cceeeeeccCCCCchhHHHH-HHHHHHHh------CCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIR-RIRRYQYA------NYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~-~~~~~~~~------~~~~~~~k~~  187 (353)
                      +...++.+|+|||||...+- .+......      +.+++++-|.
T Consensus        60 ~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Pt  104 (579)
T 3sqw_A           60 DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPT  104 (579)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSS
T ss_pred             CCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcch
Confidence            34567889999999986333 33333222      3488999886

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=84.57  E-value=0.92  Score=41.28  Aligned_cols=37  Identities=24%  Similarity=0.096  Sum_probs=27.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh----CCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA----NYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~----~~~~~~~k~  186 (353)
                      +..-++.||.+|||||..-+-...+...    |..|.+++.
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~~~re   65 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVVVTRE   65 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHHHHHHGGGTCCEEEEES
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhccccceeeeeecC
Confidence            5677889999999999988888888777    999876653

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=84.56  E-value=1.3  Score=37.20  Aligned_cols=36  Identities=11%  Similarity=-0.021  Sum_probs=25.7

Q ss_pred             CCCccEEEEccccCh--H-----HHHHHHHHHHhCCCEEEEEe
Q psy8456          70 TKDIDVIGIDEGQFF--P-----DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF--~-----dIv~l~~~l~~~G~~VivaG  105 (353)
                      ..+++++++||.+..  +     .+.++.+...+.|+++++..
T Consensus        98 ~~~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~ts  140 (180)
T 3ec2_A           98 VLNSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITT  140 (180)
T ss_dssp             HHTCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEEC
T ss_pred             hcCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEc
Confidence            346899999999843  2     24455666667899988865

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=84.54  E-value=1.9  Score=37.44  Aligned_cols=15  Identities=27%  Similarity=0.364  Sum_probs=12.6

Q ss_pred             CCCccEEEEccccCh
Q psy8456          70 TKDIDVIGIDEGQFF   84 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF   84 (353)
                      ..++++|+|||||-+
T Consensus       165 ~~~~~~lViDEah~~  179 (228)
T 3iuy_A          165 LRSITYLVIDEADKM  179 (228)
T ss_dssp             CTTCCEEEECCHHHH
T ss_pred             cccceEEEEECHHHH
Confidence            467899999999964

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=84.48  E-value=1.7  Score=40.32  Aligned_cols=22  Identities=18%  Similarity=0.009  Sum_probs=16.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      ..+++||-|+||||-+-..++.
T Consensus        40 ~~ll~G~~G~GKT~la~~la~~   61 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIARLLAKG   61 (373)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999766444433

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=84.19  E-value=0.85  Score=44.44  Aligned_cols=37  Identities=22%  Similarity=0.228  Sum_probs=31.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      .+++..++||.||||||-+-.-+..+...+.+|++..
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~~G~V~l~g  192 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLMAA  192 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhccccCCEEEEec
Confidence            3678889999999999998888888877788888764

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=84.16  E-value=0.98  Score=39.11  Aligned_cols=35  Identities=20%  Similarity=0.003  Sum_probs=25.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      +.+..++|+.+|||||-+-.-...+...|..+.+.
T Consensus        22 ~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~   56 (201)
T 1rz3_A           22 RLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVF   56 (201)
T ss_dssp             SEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEe
Confidence            45678999999999997665555555567666655

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=84.11  E-value=1.1  Score=43.40  Aligned_cols=76  Identities=12%  Similarity=0.015  Sum_probs=44.6

Q ss_pred             cCCCCchHHHHHHHHHHHHHcCceEEEEeeccCCC---------CCCCceee-ccCCceee-eecCChhhhc----ccCC
Q psy8456           7 DDRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDR---------YDTEKVAT-HDQQKLTA-VSAVELNKLI----PHTK   71 (353)
Q Consensus         7 ~~~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtR---------y~~~~I~S-r~G~~~~A-i~i~~l~ei~----~~~~   71 (353)
                      ++.-+|||...+..+...   +++++++-|...--         ++...+.. +.+....+ +.+.+..-+.    ...+
T Consensus       115 ~~TGsGKT~~~l~~i~~~---~~~~Lvl~P~~~L~~Q~~~~~~~~~~~~v~~~~g~~~~~~~Ivv~T~~~l~~~~~~~~~  191 (472)
T 2fwr_A          115 LPTGSGKTHVAMAAINEL---STPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGN  191 (472)
T ss_dssp             CCTTSCHHHHHHHHHHHH---CSCEEEEESSHHHHHHHHHHGGGGCGGGEEEBSSSCBCCCSEEEEEHHHHHHTHHHHTT
T ss_pred             eCCCCCHHHHHHHHHHHc---CCCEEEEECCHHHHHHHHHHHHhCCCcceEEECCCcCCcCCEEEEEcHHHHHHHHHhcC
Confidence            456699999988887765   88999999962211         22221222 22222222 2233322221    1125


Q ss_pred             CccEEEEccccChH
Q psy8456          72 DIDVIGIDEGQFFP   85 (353)
Q Consensus        72 ~~dvV~IDEaQFF~   85 (353)
                      ++++|+|||+|-+.
T Consensus       192 ~~~liIvDEaH~~~  205 (472)
T 2fwr_A          192 RFMLLIFDEVHHLP  205 (472)
T ss_dssp             TCSEEEEETGGGTT
T ss_pred             CCCEEEEECCcCCC
Confidence            69999999999985

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=84.11  E-value=1.6  Score=37.47  Aligned_cols=34  Identities=26%  Similarity=0.198  Sum_probs=24.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      ..+++|+.||||||-+-+-+..... .+++.++..
T Consensus        32 ~i~i~G~~g~GKTTl~~~l~~~~~~-~~~~~~i~~   65 (221)
T 2wsm_A           32 AVNIMGAIGSGKTLLIERTIERIGN-EVKIGAMLG   65 (221)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHTT-TSCEEEEEC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhcc-CCeEEEEec
Confidence            4578999999999977666665533 366766653

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=83.95  E-value=0.68  Score=40.28  Aligned_cols=37  Identities=16%  Similarity=0.123  Sum_probs=28.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHH------hCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQY------ANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~------~~~~~~~~k~  186 (353)
                      +++..++||.+|||||-+...+..+..      .+.+++.+..
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEEC
Confidence            568899999999999998888776433      2567776654

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=83.76  E-value=0.87  Score=37.44  Aligned_cols=22  Identities=14%  Similarity=0.229  Sum_probs=17.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      --+++||.|+||| .|.+.++++
T Consensus        26 ~vll~G~~GtGKt-~lA~~i~~~   47 (145)
T 3n70_A           26 AVWLYGAPGTGRM-TGARYLHQF   47 (145)
T ss_dssp             CEEEESSTTSSHH-HHHHHHHHS
T ss_pred             CEEEECCCCCCHH-HHHHHHHHh
Confidence            3589999999998 567777765

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=83.68  E-value=0.59  Score=42.48  Aligned_cols=22  Identities=36%  Similarity=0.492  Sum_probs=16.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +.+|+|||+|||||-..+-+.+
T Consensus         3 li~I~G~~GSGKSTla~~La~~   24 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQE   24 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHhc
Confidence            5689999999999965554444

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=83.66  E-value=2.1  Score=38.60  Aligned_cols=116  Identities=16%  Similarity=0.145  Sum_probs=69.6

Q ss_pred             cceeeeeccCCCCchhHHHHH-HHHHHHhCCEEEEEeeecCCCCC-------CCceeeccCcccceeecccHhhhcccCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRR-IRRYQYANYRCMIVRYAKDDRYD-------TEKVSTHDQQKLTAVSAVELNKLIPHTK  221 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~-~~~~~~~~~~~~~~k~~~D~R~~-------~~~i~s~~g~~~~a~~~~~~~~~~~~~~  221 (353)
                      ....++.|+-+|+|+++.+.. +.-.+..|++|.++.|.--.+-.       .+.+.|+....-+..          ...
T Consensus        51 ~~~~iv~g~ggs~~~~~~~a~L~~~a~~~Gr~V~vLAp~~~s~~~l~~~~~l~~~t~t~~~ll~~~~----------~~t  120 (189)
T 2l8b_A           51 PSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGRRQLLEGM----------AFT  120 (189)
T ss_dssp             CCEECCBCSSCSHHHHHHHHHHHHHHHHTTCCEEEECSTTHHHHHHSCTTTCSSCSSSTTTTTTTSC----------CCC
T ss_pred             CceEEEecccchHHHHHHHHHHHHHHHhcCeEEEEEcCchHHHHHHHhhcCcCcceeehhhhhcCCC----------CCC
Confidence            457788999999999995544 45568899999999985422210       011111111000000          013


Q ss_pred             CccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEe
Q psy8456         222 DIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAA  301 (353)
Q Consensus       222 ~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~g  301 (353)
                      .-++++||||..+                       +-++...|                     .+.....|-.|+..+
T Consensus       121 p~s~lIVD~AekL-----------------------S~kE~~~L---------------------ld~A~~~naqvvll~  156 (189)
T 2l8b_A          121 PGSTVIVDQGEKL-----------------------SLKETLTL---------------------LDGAARHNVQVLITD  156 (189)
T ss_dssp             CCCEEEEEESSSH-----------------------HHHHHHHH---------------------HHHHHHTTCCEEEEE
T ss_pred             CCCEEEEechhhc-----------------------CHHHHHHH---------------------HHHHHhcCCEEEEeC
Confidence            4568999999997                       22333333                     333336666776643


Q ss_pred             ccccccCCCchhHHhhhhccc
Q psy8456         302 LDGTFQRTGFNDILSLIPLAE  322 (353)
Q Consensus       302 Ld~df~~~~F~~~~~L~~~ad  322 (353)
                        .. +|.+++...+++.-|-
T Consensus       157 --~~-~RqG~GnAl~vl~~ag  174 (189)
T 2l8b_A          157 --SG-QRTGTGSALMAMKDAG  174 (189)
T ss_dssp             --SS-TTTCSHHHHHHHHHTT
T ss_pred             --Cc-ccccCCCHHHHHHhCC
Confidence              33 8888888888887553

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=83.55  E-value=0.77  Score=45.33  Aligned_cols=34  Identities=24%  Similarity=0.515  Sum_probs=25.3

Q ss_pred             CccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEe
Q psy8456          72 DIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        72 ~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaG  105 (353)
                      ++++++|||+|++.       .+..+.+.+.+.|+.+++.+
T Consensus       194 ~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt  234 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICS  234 (440)
T ss_dssp             TCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             CCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEE
Confidence            78999999999994       14444555567788888764

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=83.55  E-value=1.3  Score=41.66  Aligned_cols=23  Identities=13%  Similarity=-0.063  Sum_probs=17.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..+++||-|+|||+-...-++..
T Consensus        26 a~L~~G~~G~GKt~~a~~la~~l   48 (334)
T 1a5t_A           26 ALLIQALPGMGDDALIYALSRYL   48 (334)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCchHHHHHHHHHHHH
Confidence            46899999999997665555443

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=83.43  E-value=1.2  Score=40.72  Aligned_cols=37  Identities=22%  Similarity=0.091  Sum_probs=30.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCE-EEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYR-CMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~-~~~~k~  186 (353)
                      +..-++.|+.+|||||.+-.-...+...|.. +.+++.
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~~~~~~~~~~re   64 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTRE   64 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHHTTCCCEEEEES
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCCeeeeecC
Confidence            4567889999999999988888888889988 666653

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=83.40  E-value=0.82  Score=41.61  Aligned_cols=38  Identities=21%  Similarity=0.006  Sum_probs=31.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHH-hCCEEEE-Eee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQY-ANYRCMI-VRY  186 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~-~~~~~~~-~k~  186 (353)
                      .+...++.|+++|||||..-.-...+.. .|.+|.+ .+.
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~~tre   59 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTRE   59 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHHHCGGGEEEEES
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhccCceeeEeeeC
Confidence            3567788999999999998887788888 8988887 543

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=83.38  E-value=1.1  Score=47.99  Aligned_cols=21  Identities=24%  Similarity=0.415  Sum_probs=15.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++||.|+|||+ |++.+.+.
T Consensus       194 vlL~G~pG~GKT~-la~~la~~  214 (854)
T 1qvr_A          194 PVLIGEPGVGKTA-IVEGLAQR  214 (854)
T ss_dssp             CEEEECTTSCHHH-HHHHHHHH
T ss_pred             eEEEcCCCCCHHH-HHHHHHHH
Confidence            5899999999997 45555444

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=83.32  E-value=1.6  Score=46.21  Aligned_cols=34  Identities=24%  Similarity=0.131  Sum_probs=25.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHHH---HhCCEEEEEee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQ---YANYRCMIVRY  186 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~---~~~~~~~~~k~  186 (353)
                      -++.-+||+|||-..+..+..+.   ..+..++|+-|
T Consensus       258 ~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P  294 (800)
T 3mwy_W          258 GILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP  294 (800)
T ss_dssp             EEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC
T ss_pred             EEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC
Confidence            46788899999988877776542   33567888888

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=83.28  E-value=1.3  Score=39.79  Aligned_cols=37  Identities=22%  Similarity=0.096  Sum_probs=29.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCC-EEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANY-RCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~-~~~~~k~  186 (353)
                      +..-++.|+.+|||||.+-.-...+...|. .|.+.+.
T Consensus         3 g~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~~v~~~re   40 (213)
T 4tmk_A            3 SKYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTRE   40 (213)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEES
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCCcceeeeC
Confidence            445678999999999998888888888897 6665554

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=83.26  E-value=0.39  Score=39.77  Aligned_cols=16  Identities=31%  Similarity=0.119  Sum_probs=13.5

Q ss_pred             eeeeeccCCCCchhHH
Q psy8456         152 KEVILGPMFSGKTTEL  167 (353)
Q Consensus       152 I~vi~G~M~sGKt~~L  167 (353)
                      +.++.|+++|||||-.
T Consensus         4 ~I~i~G~~GsGKST~a   19 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWA   19 (181)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEecCCCCCHHHHH
Confidence            4578999999999854

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=83.19  E-value=0.58  Score=39.86  Aligned_cols=22  Identities=18%  Similarity=0.076  Sum_probs=17.1

Q ss_pred             ccceeeeeccCCCCchhHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRR  170 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~  170 (353)
                      .+.+.+++||.||||||-+-.-
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~L   25 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNTL   25 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            3567899999999999854443

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=83.12  E-value=2.4  Score=41.24  Aligned_cols=121  Identities=11%  Similarity=-0.011  Sum_probs=67.4

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeee---cCChhhhc---c---cCCCccEEEEc
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVS---AVELNKLI---P---HTKDIDVIGID   79 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~---i~~l~ei~---~---~~~~~dvV~ID   79 (353)
                      .=+||||-+++.+..+...|.+|+.+...-..+   .....|.|...+...   ..+..++.   .   ....+++|+||
T Consensus        70 pGsGKSTLal~la~~~~~~gg~VlyId~E~s~~---~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~~~~~dlvVID  146 (356)
T 3hr8_A           70 ESSGKTTLALHAIAEAQKMGGVAAFIDAEHALD---PVYAKNLGVDLKSLLISQPDHGEQALEIVDELVRSGVVDLIVVD  146 (356)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCC---HHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTSCCSEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEEEecccccc---hHHHHHcCCchhhhhhhhccCHHHHHHHHHHHhhhcCCCeEEeh
Confidence            458999999999999998999998875532111   112233443322211   22333332   1   13578999999


Q ss_pred             cccCh-H--HH----------------HHH----HHHHHhCCCEEEEEecccccccCCch-----hHhhhh-ccccceEe
Q psy8456          80 EGQFF-P--DV----------------VSF----AESMANAGKIVVVAALDGTFQRTGFN-----DILSLI-PLAECVEK  130 (353)
Q Consensus        80 EaQFF-~--dI----------------v~l----~~~l~~~G~~VivaGLd~DFr~~pF~-----~~~~Ll-~lAD~I~k  130 (353)
                      .+|-+ +  ++                .++    ...+.+.|++|++.+--.+=-+..|+     .-++.+ -+++-+..
T Consensus       147 Si~~l~~~~el~g~~G~~q~~~qar~la~~L~~L~~lak~~~~tVI~inqv~~k~g~~fg~p~~~~GG~~l~h~~~~rl~  226 (356)
T 3hr8_A          147 SVAALVPRAEIEGAMGDMQVGLQARLMSQALRKIAGSVNKSKAVVIFTNQIRMKIGVMFGSPETTTGGLALKFYATMRME  226 (356)
T ss_dssp             CTTTCCCHHHHTTCCCSSCSSHHHHHHHHHHHHHHHHHHTSSCEEEEEEESSSCSSSSSCSCSSCTHHHHHHHHCSEEEE
T ss_pred             HhhhhcChhhhcccchhhHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEeeeeeccccccCCcccCCCcchhhhhCcEEEE
Confidence            99865 2  11                122    22333679999998765332233342     123334 35555555


Q ss_pred             cc
Q psy8456         131 LT  132 (353)
Q Consensus       131 L~  132 (353)
                      |.
T Consensus       227 l~  228 (356)
T 3hr8_A          227 VR  228 (356)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=83.12  E-value=0.62  Score=39.14  Aligned_cols=24  Identities=21%  Similarity=0.037  Sum_probs=17.5

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..-+++|+|+|||||-.-.-...+
T Consensus        12 ~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHh
Confidence            356899999999998655544443

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=83.12  E-value=0.58  Score=44.06  Aligned_cols=36  Identities=19%  Similarity=0.221  Sum_probs=26.7

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      .+.+++|+.||||||-|-.-+ .. ..|+++.++.|..
T Consensus         5 ~v~~i~G~~GaGKTTll~~l~-~~-~~~~~~aVi~~d~   40 (318)
T 1nij_A            5 AVTLLTGFLGAGKTTLLRHIL-NE-QHGYKIAVIENEF   40 (318)
T ss_dssp             EEEEEEESSSSSCHHHHHHHH-HS-CCCCCEEEECSSC
T ss_pred             cEEEEEecCCCCHHHHHHHHH-hh-cCCCcEEEEEecC
Confidence            356899999999999764443 33 2688899888853

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=83.05  E-value=0.78  Score=42.54  Aligned_cols=20  Identities=25%  Similarity=0.406  Sum_probs=15.5

Q ss_pred             eeeeccCCCCchhHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~  172 (353)
                      .+++||.|+||||-+-.-++
T Consensus        39 ~ll~Gp~G~GKTtl~~~la~   58 (354)
T 1sxj_E           39 LLLYGPNGTGKKTRCMALLE   58 (354)
T ss_dssp             EEEECSTTSSHHHHHHTHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999986544444

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=83.05  E-value=0.61  Score=40.69  Aligned_cols=24  Identities=29%  Similarity=0.421  Sum_probs=17.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -..++.|+|+|||||..-.-..++
T Consensus         5 ~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            5 IRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            346889999999999755444443

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=82.99  E-value=1.2  Score=41.90  Aligned_cols=37  Identities=19%  Similarity=0.157  Sum_probs=32.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+..++|+.|+||||-+..-+..+...|++|+++..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~  134 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGA  134 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEec
Confidence            5667789999999999999999999889999998864

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=82.80  E-value=0.43  Score=43.31  Aligned_cols=22  Identities=32%  Similarity=0.339  Sum_probs=16.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+++||-|+|||+-+-..++..
T Consensus        49 ~ll~G~~G~GKT~la~~l~~~l   70 (327)
T 1iqp_A           49 LLFAGPPGVGKTTAALALAREL   70 (327)
T ss_dssp             EEEESCTTSSHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHh
Confidence            6899999999997655444443

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=82.75  E-value=1  Score=46.20  Aligned_cols=36  Identities=19%  Similarity=0.220  Sum_probs=30.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      .+.+..++|+.||||||-|-.-+..+...+.+|++.
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~~~G~V~l~  327 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLA  327 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhhcCCeEEEe
Confidence            366888999999999998887777777778888876

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=82.61  E-value=1.4  Score=39.61  Aligned_cols=75  Identities=12%  Similarity=0.027  Sum_probs=40.9

Q ss_pred             CCCCchHHHHHHHHHHHHHcCceEEEEeeccCCC---------CCCCceeeccC-Ccee-eeecCChhhhc----ccCCC
Q psy8456           8 DRINPYIVHFCRRIRRYQYANYRCMIVRYAKDDR---------YDTEKVATHDQ-QKLT-AVSAVELNKLI----PHTKD   72 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtR---------y~~~~I~Sr~G-~~~~-Ai~i~~l~ei~----~~~~~   72 (353)
                      ..-+|||...+..+...   +.+++++-|...--         ++...+..-.| .... -+.+.+..-+.    .....
T Consensus       116 ~tG~GKT~~a~~~~~~~---~~~~liv~P~~~L~~q~~~~~~~~~~~~v~~~~g~~~~~~~i~v~T~~~l~~~~~~~~~~  192 (237)
T 2fz4_A          116 PTGSGKTHVAMAAINEL---STPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNR  192 (237)
T ss_dssp             SSSTTHHHHHHHHHHHS---CSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSCBCCCSEEEEEHHHHHHTHHHHTTT
T ss_pred             CCCCCHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHhCCCCeEEEEeCCCCCcCCEEEEeHHHHHhhHHHhccc
Confidence            44589999988877653   78899999963211         11110211111 1111 12222222221    11246


Q ss_pred             ccEEEEccccChH
Q psy8456          73 IDVIGIDEGQFFP   85 (353)
Q Consensus        73 ~dvV~IDEaQFF~   85 (353)
                      +++|+|||+|.+.
T Consensus       193 ~~llIiDEaH~l~  205 (237)
T 2fz4_A          193 FMLLIFDEVHHLP  205 (237)
T ss_dssp             CSEEEEECSSCCC
T ss_pred             CCEEEEECCccCC
Confidence            8999999999996

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=82.45  E-value=0.98  Score=45.72  Aligned_cols=38  Identities=29%  Similarity=0.398  Sum_probs=31.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhC----CEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYAN----YRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~----~~~~~~k~~  187 (353)
                      ++..+|.|+.|||||+-|+.++......+    .+++++.++
T Consensus        22 ~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft   63 (647)
T 3lfu_A           22 RSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFT   63 (647)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESS
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEecc
Confidence            45568999999999999999998886653    688888764

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=82.43  E-value=0.72  Score=39.58  Aligned_cols=24  Identities=21%  Similarity=0.080  Sum_probs=17.4

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+.++.|++||||||-.-.-...+
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            467899999999999654433433

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=82.41  E-value=0.42  Score=40.94  Aligned_cols=15  Identities=27%  Similarity=0.208  Sum_probs=12.8

Q ss_pred             eeeeccCCCCchhHH
Q psy8456         153 EVILGPMFSGKTTEL  167 (353)
Q Consensus       153 ~vi~G~M~sGKt~~L  167 (353)
                      -.|+|+|+|||||-+
T Consensus         4 i~i~G~~GsGKSTl~   18 (204)
T 2if2_A            4 IGLTGNIGCGKSTVA   18 (204)
T ss_dssp             EEEEECTTSSHHHHH
T ss_pred             EEEECCCCcCHHHHH
Confidence            478999999999854

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=82.21  E-value=1.4  Score=42.55  Aligned_cols=40  Identities=10%  Similarity=0.004  Sum_probs=36.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      .+++.++.|+.++||||-+++.+.+....|.+|++|....
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSlEm   84 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSLEM   84 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEESSS
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCC
Confidence            3678999999999999999999999988999999998754

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=82.20  E-value=0.84  Score=39.26  Aligned_cols=37  Identities=22%  Similarity=0.085  Sum_probs=26.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHH------hCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQY------ANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~------~~~~~~~~k~  186 (353)
                      +++..++||.+|||||-+..-+..+..      .+..++.+..
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~   67 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDT   67 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEES
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEEC
Confidence            678899999999999988777665543      2445655543

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=82.17  E-value=0.52  Score=41.20  Aligned_cols=24  Identities=25%  Similarity=0.094  Sum_probs=18.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      .+.+.+++||+||||||-+-.-+.
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~   30 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFK   30 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHh
Confidence            366788999999999986544433

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=82.05  E-value=3.2  Score=43.60  Aligned_cols=29  Identities=7%  Similarity=-0.085  Sum_probs=23.4

Q ss_pred             CCCchHHH-HHHHHHHHHHcCceEEEEeec
Q psy8456           9 RINPYIVH-FCRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus         9 ~~~GKSte-LLrr~~ry~~agkkvlv~Kp~   37 (353)
                      .=||||+. ++..++.....|.+++++-|.
T Consensus       250 TGSGKTl~~ll~il~~l~~~~~~~lilaPT  279 (673)
T 2wv9_A          250 PGAGKTRRILPQIIKDAIQKRLRTAVLAPT  279 (673)
T ss_dssp             TTTTTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCcEEEEccH
Confidence            45999998 677777767788899999994

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=82.02  E-value=0.55  Score=40.18  Aligned_cols=24  Identities=25%  Similarity=0.181  Sum_probs=17.7

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .+++..++||++|||||- ++.+..
T Consensus        32 ~Ge~v~L~G~nGaGKTTL-lr~l~g   55 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTL-TRGMLQ   55 (158)
T ss_dssp             SCEEEEEECSTTSSHHHH-HHHHHH
T ss_pred             CCCEEEEECCCCCCHHHH-HHHHHH
Confidence            356778999999999975 444444

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=81.86  E-value=1  Score=37.82  Aligned_cols=28  Identities=21%  Similarity=0.069  Sum_probs=19.9

Q ss_pred             ccccccceeeeeccCCCCchhHHHHHHHH
Q psy8456         145 TKRIGQEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       145 ~~Ri~geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +..+..++.+|+||.+|||||- ++.+.-
T Consensus        21 ~~~~~~g~~~i~G~NGsGKStl-l~ai~~   48 (182)
T 3kta_A           21 VIPFSKGFTAIVGANGSGKSNI-GDAILF   48 (182)
T ss_dssp             EEECCSSEEEEEECTTSSHHHH-HHHHHH
T ss_pred             EEecCCCcEEEECCCCCCHHHH-HHHHHH
Confidence            3444456899999999999975 444443

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=81.86  E-value=0.24  Score=46.63  Aligned_cols=35  Identities=23%  Similarity=0.183  Sum_probs=23.5

Q ss_pred             ceeee--eccCCCCchhHHHHHHHHHHHh------CCEEEEEe
Q psy8456         151 EKEVI--LGPMFSGKTTELIRRIRRYQYA------NYRCMIVR  185 (353)
Q Consensus       151 eI~vi--~G~M~sGKt~~Li~~~~~~~~~------~~~~~~~k  185 (353)
                      ..-++  +||.|+|||+-+-..++.....      +..++.+.
T Consensus        51 ~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~   93 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN   93 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE
T ss_pred             CEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEE
Confidence            35577  9999999998766666555443      44555444

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=81.85  E-value=1.1  Score=40.65  Aligned_cols=27  Identities=11%  Similarity=0.126  Sum_probs=23.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQ  175 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~  175 (353)
                      .+++..|+||.+|||||-++.-+....
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            467889999999999999988887554

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=81.74  E-value=0.87  Score=38.29  Aligned_cols=23  Identities=22%  Similarity=0.248  Sum_probs=16.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .+-++.|+++|||||-.-.-..+
T Consensus        10 ~~I~l~G~~GsGKsT~~~~La~~   32 (196)
T 2c95_A           10 NIIFVVGGPGSGKGTQCEKIVQK   32 (196)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            46789999999999954443333

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=81.71  E-value=0.56  Score=40.77  Aligned_cols=24  Identities=33%  Similarity=0.421  Sum_probs=18.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .|++..++||.||||||-+ +.+..
T Consensus        19 ~Gei~~l~GpnGsGKSTLl-~~l~g   42 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVV-RCLRE   42 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHH-HHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHh
Confidence            3668889999999999854 44443

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=81.64  E-value=1.4  Score=43.72  Aligned_cols=40  Identities=10%  Similarity=0.020  Sum_probs=35.8

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      .+++.+|.|+.++||||-+++.+.+....|.+|++|....
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSlEm  235 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLEM  235 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECSSS
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEECCC
Confidence            3678999999999999999999999988899999998764

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=81.57  E-value=0.64  Score=39.79  Aligned_cols=120  Identities=8%  Similarity=0.079  Sum_probs=61.9

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceee---ccCCc--------eeeee-----------cC--Chh
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVAT---HDQQK--------LTAVS-----------AV--ELN   64 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~S---r~G~~--------~~Ai~-----------i~--~l~   64 (353)
                      .=+||||-+...+......+.+|+++.......    .+..   +.|..        +..+.           ..  +..
T Consensus        32 ~GsGKTtl~~~l~~~~~~~~~~v~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  107 (235)
T 2w0m_A           32 PGTGKTIFSLHFIAKGLRDGDPCIYVTTEESRD----SIIRQAKQFNWDFEEYIEKKLIIIDALMKEKEDQWSLVNLTPE  107 (235)
T ss_dssp             TTSSHHHHHHHHHHHHHHHTCCEEEEESSSCHH----HHHHHHHHTTCCCGGGBTTTEEEEECCC----CTTBCSSCCHH
T ss_pred             CCCCHHHHHHHHHHHHHHCCCeEEEEEcccCHH----HHHHHHHHhcchHHHHhhCCEEEEeccccccCceeeecCCCHH
Confidence            458999999888878777788888876433210    0000   01100        00000           00  222


Q ss_pred             hhc----c--cCCCcc--EEEEccccCh---H-----HHHHHHHHH-HhCCCEEEEEecccccccCCchhHhhhhccccc
Q psy8456          65 KLI----P--HTKDID--VIGIDEGQFF---P-----DVVSFAESM-ANAGKIVVVAALDGTFQRTGFNDILSLIPLAEC  127 (353)
Q Consensus        65 ei~----~--~~~~~d--vV~IDEaQFF---~-----dIv~l~~~l-~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~  127 (353)
                      ++.    .  ...+++  +|++||.+.+   +     ++.+....+ .+.|+.|++..=+.+.......  ..+..+||.
T Consensus       108 ~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~~vi~~~h~~~~~~~~~~--~~~~~~~d~  185 (235)
T 2w0m_A          108 ELVNKVIEAKQKLGYGKARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNFTIYATSQYAITTSQAFG--FGVEHVADG  185 (235)
T ss_dssp             HHHHHHHHHHHHHCSSCEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTEEEEEEEC-------------CHHHHCSE
T ss_pred             HHHHHHHHHHHhhCCCceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCCeEEEEeccCcccccccc--cchheeeeE
Confidence            221    1  124688  9999999954   2     344444444 3579999988766533222222  345567788


Q ss_pred             eEeccce
Q psy8456         128 VEKLTAV  134 (353)
Q Consensus       128 I~kL~Av  134 (353)
                      |..|...
T Consensus       186 vi~l~~~  192 (235)
T 2w0m_A          186 IIRFRRM  192 (235)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEEE
Confidence            8777543

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=81.33  E-value=1.7  Score=37.64  Aligned_cols=30  Identities=17%  Similarity=0.010  Sum_probs=20.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANY  179 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~  179 (353)
                      +.+..|+||.+|||||-+-.-...+...|.
T Consensus        22 g~~v~I~G~sGsGKSTl~~~l~~~~~~~g~   51 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLSNPLAAALSAQGL   51 (208)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHHHHTTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCC
Confidence            567789999999999965444444444343

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=81.24  E-value=0.9  Score=40.48  Aligned_cols=25  Identities=40%  Similarity=0.438  Sum_probs=18.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..+.+++||+||||||-+-.-..++
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4577899999999999765544443

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=81.10  E-value=5.5  Score=37.69  Aligned_cols=30  Identities=3%  Similarity=-0.287  Sum_probs=22.9

Q ss_pred             CCCCchHHHHHHHHHHHHHcCceEEEEeec
Q psy8456           8 DRINPYIVHFCRRIRRYQYANYRCMIVRYA   37 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry~~agkkvlv~Kp~   37 (353)
                      ..-+|||.-.+-.+......|.+++++-|.
T Consensus        44 pTGsGKT~~~l~~~~~~~~~~~~~lil~Pt   73 (414)
T 3oiy_A           44 PTGVGKTTFGMMTALWLARKGKKSALVFPT   73 (414)
T ss_dssp             CSSSSHHHHHHHHHHHHHTTTCCEEEEESS
T ss_pred             CCCCCHHHHHHHHHHHHhcCCCEEEEEECC
Confidence            345899996666655555678999999995

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=81.07  E-value=0.78  Score=39.89  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=16.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -++.|+++|||||..-.-...+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            3 IILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            3789999999999765554444

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=81.01  E-value=1.1  Score=39.54  Aligned_cols=22  Identities=36%  Similarity=0.360  Sum_probs=16.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -++.|+++|||||..-.-..++
T Consensus         3 I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            3 ILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4789999999999655544444

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=80.97  E-value=0.54  Score=42.59  Aligned_cols=22  Identities=23%  Similarity=0.061  Sum_probs=16.7

Q ss_pred             cceeeeeccCCCCchhHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~  171 (353)
                      +.+..|+|||||||||-+-.-.
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La   48 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALA   48 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4567899999999998654433

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=80.93  E-value=0.82  Score=39.47  Aligned_cols=22  Identities=32%  Similarity=0.412  Sum_probs=16.0

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++||++|||||-.-.-..++
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999998654443443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=80.93  E-value=1.4  Score=39.94  Aligned_cols=33  Identities=18%  Similarity=0.234  Sum_probs=20.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      ..--+++||.|+|||+-+ +.+.+  ..+...+-+.
T Consensus        54 ~~~vll~Gp~GtGKT~la-~~la~--~~~~~~~~i~   86 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLA-RAVAT--ECSATFLNIS   86 (297)
T ss_dssp             CSEEEEESSSSSCHHHHH-HHHHH--HTTCEEEEEE
T ss_pred             CCeEEEECcCCCCHHHHH-HHHHH--HhCCCeEEee
Confidence            445689999999999654 44433  2344444333

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=80.93  E-value=1.1  Score=39.18  Aligned_cols=23  Identities=26%  Similarity=0.293  Sum_probs=17.0

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .-++.|+|+|||||..-.-..++
T Consensus         7 ~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            7 NLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999755444444

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=80.70  E-value=1.8  Score=47.93  Aligned_cols=38  Identities=24%  Similarity=0.077  Sum_probs=27.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHh--CCEEEEEeeecC
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYA--NYRCMIVRYAKD  189 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~--~~~~~~~k~~~D  189 (353)
                      .-++..++|||||.-.+..++.....  ..+|+++.|..+
T Consensus       302 ~gli~~~TGSGKT~t~~~l~~ll~~~~~~~rvLvlvpr~e  341 (1038)
T 2w00_A          302 GGYIWHTTGSGKTLTSFKAARLATELDFIDKVFFVVDRKD  341 (1038)
T ss_dssp             SEEEEECTTSSHHHHHHHHHHHHTTCTTCCEEEEEECGGG
T ss_pred             CEEEEecCCCCHHHHHHHHHHHHHhcCCCceEEEEeCcHH
Confidence            34889999999999877666444322  368999998644

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=80.63  E-value=1.5  Score=43.32  Aligned_cols=40  Identities=13%  Similarity=0.049  Sum_probs=34.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHH-hCCEEEEEeeec
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQY-ANYRCMIVRYAK  188 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~-~~~~~~~~k~~~  188 (353)
                      .+++.++.|+.++||||-+++.+.+... .|.+|+++....
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E~  242 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEM  242 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECCC
Confidence            3678899999999999999999998876 588999987654

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=80.61  E-value=0.86  Score=38.15  Aligned_cols=22  Identities=32%  Similarity=0.238  Sum_probs=15.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      ..++.|+|+|||||-.-.-..+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            3578999999999854443333

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=80.47  E-value=1  Score=40.69  Aligned_cols=25  Identities=24%  Similarity=0.335  Sum_probs=20.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..+-+++||.+|||||.--+-+.+|
T Consensus        29 ~kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           29 AKVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             CEEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4567889999999999876666665

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=80.40  E-value=0.55  Score=39.80  Aligned_cols=16  Identities=38%  Similarity=0.221  Sum_probs=13.3

Q ss_pred             eeeeeccCCCCchhHH
Q psy8456         152 KEVILGPMFSGKTTEL  167 (353)
Q Consensus       152 I~vi~G~M~sGKt~~L  167 (353)
                      +..|+|+|+|||||-.
T Consensus        10 ~I~i~G~~GsGKST~~   25 (203)
T 1uf9_A           10 IIGITGNIGSGKSTVA   25 (203)
T ss_dssp             EEEEEECTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4578999999999853

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=80.39  E-value=1.5  Score=44.17  Aligned_cols=66  Identities=20%  Similarity=0.219  Sum_probs=36.3

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee-cCCCCCCCceeeccCcccceeecccHhhhcc--cCCCccEEEEe
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA-KDDRYDTEKVSTHDQQKLTAVSAVELNKLIP--HTKDIDVIGID  229 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~-~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~--~~~~~~~i~ID  229 (353)
                      -+++||.|+|||+ |.+.+.+  ..+..++.+... +-..+.        |.     ....+..++.  ......+++||
T Consensus       241 vLL~GppGtGKT~-lAraia~--~~~~~fv~vn~~~l~~~~~--------g~-----~~~~~~~~f~~A~~~~p~iLfLD  304 (489)
T 3hu3_A          241 ILLYGPPGTGKTL-IARAVAN--ETGAFFFLINGPEIMSKLA--------GE-----SESNLRKAFEEAEKNAPAIIFID  304 (489)
T ss_dssp             EEEECSTTSSHHH-HHHHHHH--HCSSEEEEEEHHHHHTSCT--------TH-----HHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             EEEECcCCCCHHH-HHHHHHH--HhCCCEEEEEchHhhhhhc--------ch-----hHHHHHHHHHHHHhcCCcEEEec
Confidence            5899999999986 5566643  346665554421 111110        11     0111222221  12446799999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |++.+
T Consensus       305 EId~l  309 (489)
T 3hu3_A          305 ELDAI  309 (489)
T ss_dssp             SHHHH
T ss_pred             chhhh
Confidence            99985

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=80.33  E-value=1.2  Score=45.17  Aligned_cols=34  Identities=24%  Similarity=0.355  Sum_probs=21.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      +....++||.||||||-| +.+-.+.....+++.+
T Consensus       260 g~~i~I~GptGSGKTTlL-~aL~~~i~~~~giiti  293 (511)
T 2oap_1          260 KFSAIVVGETASGKTTTL-NAIMMFIPPDAKVVSI  293 (511)
T ss_dssp             TCCEEEEESTTSSHHHHH-HHHGGGSCTTCCEEEE
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHhhCCCCCCEEEE
Confidence            445789999999999876 4444443334444433

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=80.30  E-value=0.91  Score=38.77  Aligned_cols=20  Identities=25%  Similarity=0.180  Sum_probs=15.5

Q ss_pred             ceeeeeccCCCCchhHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRR  170 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~  170 (353)
                      .+-++.|+++|||||-.-+-
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L   35 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKL   35 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            35688999999999865433

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=80.19  E-value=1  Score=38.02  Aligned_cols=23  Identities=26%  Similarity=0.267  Sum_probs=16.8

Q ss_pred             ceeeeeccCCCCchhHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      .+.++.|+++|||||-.-.-..+
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~   35 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEK   35 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            46789999999999864443333

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=80.12  E-value=0.67  Score=41.93  Aligned_cols=23  Identities=39%  Similarity=0.403  Sum_probs=18.1

Q ss_pred             ccceeeeeccCCCCchhHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      .|++..|+||.||||||- ++.+.
T Consensus        30 ~Ge~~~iiG~nGsGKSTL-l~~l~   52 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTM-LNIIG   52 (235)
T ss_dssp             TTCEEEEECSTTSSHHHH-HHHHT
T ss_pred             CCCEEEEECCCCCcHHHH-HHHHh
Confidence            467888999999999984 55544

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=80.01  E-value=1  Score=42.28  Aligned_cols=39  Identities=15%  Similarity=0.088  Sum_probs=31.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh------CCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA------NYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~------~~~~~~~k~~~  188 (353)
                      +.+.+|+||.+||||+-+++.+.+.+..      +.+|+++....
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            5688999999999999999988876554      77888876543

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=80.01  E-value=3.4  Score=41.48  Aligned_cols=31  Identities=6%  Similarity=-0.184  Sum_probs=24.8

Q ss_pred             cCCCCchHHHHHHHHHHHHH---------cCceEEEEeec
Q psy8456           7 DDRINPYIVHFCRRIRRYQY---------ANYRCMIVRYA   37 (353)
Q Consensus         7 ~~~~~GKSteLLrr~~ry~~---------agkkvlv~Kp~   37 (353)
                      +..-+|||...+..+.++..         .+++++++-|.
T Consensus       205 ~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~  244 (590)
T 3h1t_A          205 MATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADR  244 (590)
T ss_dssp             ECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-
T ss_pred             ecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCC
Confidence            34569999999998888876         45899999994

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	353
d1xx6a1	141	c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-termi	3e-26
d1xx6a1	141	c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-termi	3e-19
d1xbta1	133	c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-term	3e-26
d1xbta1	133	c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-term	3e-21
d2b8ta1	139	c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-term	2e-25
d2b8ta1	139	c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-term	4e-19
d1xbta2	41	g.39.1.14 (A:151-191) Thymidine kinase, TK1, C-ter	5e-04
d1xbta2	41	g.39.1.14 (A:151-191) Thymidine kinase, TK1, C-ter	6e-04
d1xx6a2	49	g.39.1.14 (A:143-191) Thymidine kinase, TK1, C-ter	6e-04
d2b8ta2	67	g.39.1.14 (A:150-216) Thymidine kinase, TK1, C-ter	0.001
d2b8ta2	67	g.39.1.14 (A:150-216) Thymidine kinase, TK1, C-ter	0.002

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]} Length = 141

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

 Score = 99.8 bits (248), Expect = 3e-26
 Identities = 48/176 (27%), Positives = 79/176 (44%), Gaps = 46/176 (26%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           EVI+GPM+SGK+ ELIRRIRR + A  +  + +   D+RY  E V +H  +K  AV+   
Sbjct: 10  EVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKN 69

Query: 213 LNKLIPHTKD-IDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAA 271
             +++ + ++  +VI IDE QF +     D+ + +  +  +                   
Sbjct: 70  SREILKYFEEDTEVIAIDEVQFFD-----DEIVEIVNKIAES------------------ 106

Query: 272 LNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL 327
                                 G+ V+ A LD  F+   F  I  L+ +AE V+K+
Sbjct: 107 ----------------------GRRVICAGLDMDFRGKPFGPIPELMAIAEFVDKI 140

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]} Length = 141

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

 Score = 80.9 bits (199), Expect = 3e-19
 Identities = 38/115 (33%), Positives = 63/115 (54%), Gaps = 2/115 (1%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKD-IDVIG 77
           RRIRR + A  +  + +   D+RY  E V +H  +K  AV+     +++ + ++  +VI 
Sbjct: 26  RRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIA 85

Query: 78  IDEGQFFPDVVS-FAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL 131
           IDE QFF D +      +A +G+ V+ A LD  F+   F  I  L+ +AE V+K+
Sbjct: 86  IDEVQFFDDEIVEIVNKIAESGRRVICAGLDMDFRGKPFGPIPELMAIAEFVDKI 140

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 133

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 99.8 bits (248), Expect = 3e-26
 Identities = 77/176 (43%), Positives = 98/176 (55%), Gaps = 47/176 (26%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVE 212
           +VILGPMFSGK+TEL+RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  
Sbjct: 5   QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSS-SFCTHDRNTMEALPACL 63

Query: 213 LNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAAL 272
           L  +      + VIGIDEGQF                                       
Sbjct: 64  LRDVAQEALGVAVIGIDEGQF--------------------------------------- 84

Query: 273 NVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 328
                  FPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLT
Sbjct: 85  -------FPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLT 133

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 133

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.3 bits (213), Expect = 3e-21
 Identities = 64/114 (56%), Positives = 82/114 (71%), Gaps = 1/114 (0%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGI 78
           RR+RR+Q A Y+C++++YAKD RY +    THD+  + A+ A  L  +      + VIGI
Sbjct: 21  RRVRRFQIAQYKCLVIKYAKDTRYSS-SFCTHDRNTMEALPACLLRDVAQEALGVAVIGI 79

Query: 79  DEGQFFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT 132
           DEGQFFPD+V F E+MANAGK V+VAALDGTFQR  F  IL+L+PLAE V KLT
Sbjct: 80  DEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLT 133

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]} Length = 139

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

 Score = 97.5 bits (242), Expect = 2e-25
 Identities = 42/181 (23%), Positives = 65/181 (35%), Gaps = 52/181 (28%)

Query: 153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSA-- 210
           E I GPMF+GKT ELIRR+ R +YA+ + ++ +   D R     + +     L +V    
Sbjct: 5   EFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSI-RNIQSRTGTSLPSVEVES 63

Query: 211 ----VELNKLIPHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLA 266
               +          +  VIGIDE QF +                               
Sbjct: 64  APEILNYIMSNSFNDETKVIGIDEVQFFD------------------------------- 92

Query: 267 NENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEK 326
                           +   A  +A  G +V+++ LD  F+   F  I  L   A+ + K
Sbjct: 93  --------------DRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITK 138

Query: 327 L 327
           L
Sbjct: 139 L 139

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]} Length = 139

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

 Score = 80.5 bits (198), Expect = 4e-19
 Identities = 32/120 (26%), Positives = 53/120 (44%), Gaps = 8/120 (6%)

Query: 19  RRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSA------VELNKLIPHTKD 72
           RR+ R +YA+ + ++ +   D R     + +     L +V        +          +
Sbjct: 21  RRLHRLEYADVKYLVFKPKIDTRSI-RNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDE 79

Query: 73  IDVIGIDEGQFFPD-VVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL 131
             VIGIDE QFF D +   A  +A  G +V+++ LD  F+   F  I  L   A+ + KL
Sbjct: 80  TKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKL 139

>d1xbta2 g.39.1.14 (A:151-191) Thymidine kinase, TK1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 41

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (81), Expect = 5e-04
 Identities = 15/26 (57%), Positives = 19/26 (73%), Gaps = 1/26 (3%)

Query: 228 IDEGQFVEVIGGSDKYMAVCRECYKQ 253
             E + VEVIGG+DKY +VCR CY +
Sbjct: 17  GTEKE-VEVIGGADKYHSVCRLCYFK 41

>d1xbta2 g.39.1.14 (A:151-191) Thymidine kinase, TK1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 41

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (81), Expect = 6e-04
 Identities = 17/24 (70%), Positives = 21/24 (87%)

Query: 133 AVCMSCFRDAAFTKRIGQEKEVIL 156
           AVCM CFR+AA+TKR+G EKEV +
Sbjct: 1   AVCMECFREAAYTKRLGTEKEVEV 24

>d1xx6a2 g.39.1.14 (A:143-191) Thymidine kinase, TK1, C-terminal domain {Clostridium acetobutylicum [TaxId: 1488]} Length = 49

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

 Score = 35.2 bits (81), Expect = 6e-04
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 234 VEVIGGSDKYMAVCRECYK 252
           V +IG  + Y A CR+C+ 
Sbjct: 28  VVLIGAMESYEARCRKCHV 46

>d2b8ta2 g.39.1.14 (A:150-216) Thymidine kinase, TK1, C-terminal domain {Ureaplasma urealyticum [TaxId: 2130]} Length = 67

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 11/66 (16%), Positives = 17/66 (25%), Gaps = 5/66 (7%)

Query: 132 TAVCMSCFRDAAFTKRIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDR 191
           TA+C  C  +A  + R    K               I     Y         V       
Sbjct: 1   TAICNECGAEATHSLRKIDGKHAD-----YNDDIVKIGCQEFYSAVCRHHHKVPNRPYLN 55

Query: 192 YDTEKV 197
            ++E+ 
Sbjct: 56  SNSEEF 61

>d2b8ta2 g.39.1.14 (A:150-216) Thymidine kinase, TK1, C-terminal domain {Ureaplasma urealyticum [TaxId: 2130]} Length = 67

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

 Score = 34.1 bits (78), Expect = 0.002
 Identities = 7/26 (26%), Positives = 10/26 (38%)

Query: 328 TAVCMSCFRDAAFTKRIGQEKEVRIE 353
           TA+C  C  +A  + R    K     
Sbjct: 1   TAICNECGAEATHSLRKIDGKHADYN 26

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	353
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	100.0
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	100.0
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	100.0
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	100.0
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	100.0
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	100.0
d1xbta2	41	Thymidine kinase, TK1, C-terminal domain {Human (H	98.94
d2b8ta2	67	Thymidine kinase, TK1, C-terminal domain {Ureaplas	98.9
d1xx6a2	49	Thymidine kinase, TK1, C-terminal domain {Clostrid	98.85
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.62
d2b8ta2	67	Thymidine kinase, TK1, C-terminal domain {Ureaplas	97.4
d1xx6a2	49	Thymidine kinase, TK1, C-terminal domain {Clostrid	97.39
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.25
d1xbta2	41	Thymidine kinase, TK1, C-terminal domain {Human (H	97.18
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.6
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	96.58
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	96.49
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	95.82
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.76
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	95.73
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	95.56
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	95.4
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.29
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	95.28
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	95.22
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	95.12
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.07
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.8
d1vmaa2	213	GTPase domain of the signal recognition particle r	94.8
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	94.72
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	94.68
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	94.65
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.55
d1okkd2	207	GTPase domain of the signal recognition particle r	94.45
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	94.28
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	94.23
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	94.13
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.05
d2qy9a2	211	GTPase domain of the signal recognition particle r	93.79
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	93.23
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	92.8
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	92.75
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	92.7
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	92.54
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	92.13
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	91.56
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	91.51
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	91.48
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	91.4
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	91.15
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	91.12
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	91.12
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	91.04
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.99
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	90.45
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	90.38
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	90.36
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.36
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	90.13
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	89.96
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	89.96
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	89.92
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	89.52
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	89.44
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	89.44
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	89.42
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	89.37
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	89.31
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	89.28
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	89.28
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	89.05
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	88.93
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	88.85
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	88.59
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	88.46
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	88.44
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	88.41
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	88.3
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	88.29
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	88.1
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	87.92
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	87.85
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	87.74
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	87.43
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	87.2
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	86.96
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	86.83
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	86.79
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	86.75
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	86.53
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	86.47
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	86.46
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	86.37
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	86.21
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	85.81
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	85.72
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	85.61
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	85.57
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	85.39
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	85.17
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	85.0
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	84.73
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.51
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	84.34
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	84.07
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	83.98
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	83.76
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	83.28
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	83.22
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	83.2
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	83.19
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	82.83
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	82.71
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	82.33
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	82.19
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	82.18
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	81.91
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	81.74
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	81.72
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	81.58
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	81.11
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	80.38
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	80.36
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	80.26
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	80.09
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	80.04

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=100.00  E-value=5.4e-43  Score=302.49  Aligned_cols=134  Identities=39%  Similarity=0.600  Sum_probs=119.1

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc-CCCccEEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH-TKDIDVIG  227 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~-~~~~~~i~  227 (353)
                      .|++++|+|||||||||||||+++||+.+|++|++++|+.|+||+.+.++||+|.+.+|+.+.++.++... .+++|||+
T Consensus         6 ~G~l~lI~GpMfSGKTteLi~~~~~~~~~g~~vl~i~~~~D~Ry~~~~i~sh~g~~~~a~~~~~~~~~~~~~~~~~dvI~   85 (141)
T d1xx6a1           6 HGWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIA   85 (141)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEE
T ss_pred             ceeEEEEEeccccHHHHHHHHHHHHhhhcCCcEEEEEeccccccccceeeecccceEEEEEecchhhhhhhhcccccEEE
Confidence            48899999999999999999999999999999999999999999999999999999999999888777643 57899999


Q ss_pred             EecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCcc-HHHHHHHHHhCCCEEEEEeccccc
Q psy8456         228 IDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPD-VVSFAESMANAGKIVVVAALDGTF  306 (353)
Q Consensus       228 IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~-~~~~~~~~~~~g~~Vi~~gLd~df  306 (353)
                      |||+||                                              |++ +++++..+++.|++|+|||||+||
T Consensus        86 IDE~QF----------------------------------------------f~d~~~~~~~~l~~~g~~Viv~GLd~Df  119 (141)
T d1xx6a1          86 IDEVQF----------------------------------------------FDDEIVEIVNKIAESGRRVICAGLDMDF  119 (141)
T ss_dssp             ECSGGG----------------------------------------------SCTHHHHHHHHHHHTTCEEEEEECSBCT
T ss_pred             Eeehhh----------------------------------------------ccccHHHHHHhheeCCcEEEEEEecccc
Confidence            999999                                              654 788899999999999999999999


Q ss_pred             cCCCchhHHhhhhcccceEEee
Q psy8456         307 QRTGFNDILSLIPLAECVEKLT  328 (353)
Q Consensus       307 ~~~~F~~~~~L~~~ad~v~kl~  328 (353)
                      +|+||+++++|||+||+|+||+
T Consensus       120 ~~~~F~~~~~Ll~~Ad~v~kLk  141 (141)
T d1xx6a1         120 RGKPFGPIPELMAIAEFVDKIQ  141 (141)
T ss_dssp             TSCBCTTHHHHHHHCSEEEECC
T ss_pred             ccCccchHHHHHhhcCeeEECC
Confidence            9999999999999999999985

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=100.00  E-value=7.3e-41  Score=287.93  Aligned_cols=131  Identities=34%  Similarity=0.566  Sum_probs=119.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcc------cCCCc
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIP------HTKDI  223 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~------~~~~~  223 (353)
                      |.+++|+|||||||||||||+++||+.+|++|++++|+.|+||+. .++||+|...+|+.+.+..++..      ...++
T Consensus         2 G~L~~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~D~R~~~-~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (139)
T d2b8ta1           2 GWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIR-NIQSRTGTSLPSVEVESAPEILNYIMSNSFNDET   80 (139)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCS-SCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTC
T ss_pred             cEEEEEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEcccccccc-eEEcccCceeeeEEeccchhhHHHHHhhccccCc
Confidence            679999999999999999999999999999999999999999874 68999999999999876555432      24689


Q ss_pred             cEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCcc-HHHHHHHHHhCCCEEEEEec
Q psy8456         224 DVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPD-VVSFAESMANAGKIVVVAAL  302 (353)
Q Consensus       224 ~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~-~~~~~~~~~~~g~~Vi~~gL  302 (353)
                      |+|+|||+||                                              |+| ++++++.+++.|++|+||||
T Consensus        81 dvI~IDE~QF----------------------------------------------f~d~i~~~~~~~~~~g~~Viv~GL  114 (139)
T d2b8ta1          81 KVIGIDEVQF----------------------------------------------FDDRICEVANILAENGFVVIISGL  114 (139)
T ss_dssp             CEEEECSGGG----------------------------------------------SCTHHHHHHHHHHHTTCEEEEECC
T ss_pred             CEEEechhhh----------------------------------------------cchhHHHHHHHHHhcCceEEEEEe
Confidence            9999999999                                              665 67777888899999999999


Q ss_pred             cccccCCCchhHHhhhhcccceEEe
Q psy8456         303 DGTFQRTGFNDILSLIPLAECVEKL  327 (353)
Q Consensus       303 d~df~~~~F~~~~~L~~~ad~v~kl  327 (353)
                      |+||+|+||+++.+|+|+||+|+||
T Consensus       115 d~Df~~~~F~~~~~Li~~Ad~V~kL  139 (139)
T d2b8ta1         115 DKNFKGEPFGPIAKLFTYADKITKL  139 (139)
T ss_dssp             SBCTTSSBCTTHHHHHHHCSEEEEC
T ss_pred             ccccccCcCccHHHHHHhhCeEEeC
Confidence            9999999999999999999999997

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=6.2e-41  Score=286.24  Aligned_cols=132  Identities=58%  Similarity=0.990  Sum_probs=111.7

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGID  229 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~ID  229 (353)
                      |.+++|+|||||||||+||+++++|+.+|++|++++|+.|+||+.+ ++||++...+++.+.+..++..+..++|+|+||
T Consensus         2 G~L~li~GpMfsGKTt~Li~~~~~~~~~g~~v~~ikp~~D~R~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~d~I~ID   80 (133)
T d1xbta1           2 GQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACLLRDVAQEALGVAVIGID   80 (133)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCC---------------CEEESSGGGGHHHHHTCSEEEES
T ss_pred             cEEEEEEecccCHHHHHHHHHHHHHHHcCCcEEEEecccccCCcce-eeecCCCcceeeeeechhhhhhhhcccceEEee
Confidence            7899999999999999999999999999999999999999999855 567777788888887777666666789999999


Q ss_pred             cccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEeccccccCC
Q psy8456         230 EGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTFQRT  309 (353)
Q Consensus       230 E~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df~~~  309 (353)
                      |+||                                              |+||+++++.+++.|++|+|||||+||+|+
T Consensus        81 EaQF----------------------------------------------f~dl~~~~~~~~~~~~~Viv~GLd~Df~~~  114 (133)
T d1xbta1          81 EGQF----------------------------------------------FPDIVEFCEAMANAGKTVIVAALDGTFQRK  114 (133)
T ss_dssp             SGGG----------------------------------------------CTTHHHHHHHHHHTTCEEEEECCSBCTTSS
T ss_pred             hhHH----------------------------------------------HHHHHHHHHHHHhcCCcEEEEEeccccccC
Confidence            9999                                              789999999999999999999999999999


Q ss_pred             CchhHHhhhhcccceEEee
Q psy8456         310 GFNDILSLIPLAECVEKLT  328 (353)
Q Consensus       310 ~F~~~~~L~~~ad~v~kl~  328 (353)
                      ||+++.+|+|+||+|+||+
T Consensus       115 ~F~~~~~Ll~~Ad~I~kLt  133 (133)
T d1xbta1         115 PFGAILNLVPLAESVVKLT  133 (133)
T ss_dssp             BCTTGGGGGGGCSEEEECC
T ss_pred             cchhHHHHHHhcCEEEecC
Confidence            9999999999999999996

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=100.00  E-value=4e-39  Score=278.10  Aligned_cols=123  Identities=32%  Similarity=0.498  Sum_probs=109.5

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcc-cCCCccEEEEccccChH-HH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIP-HTKDIDVIGIDEGQFFP-DV   87 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~-~~~~~dvV~IDEaQFF~-dI   87 (353)
                      .||||||||++++||+.+|++|++|||++||||+.+.|+||+|.+++|+.+.++.++.. ..+++|+|+|||||||+ .+
T Consensus        17 fSGKTteLi~~~~~~~~~g~~vl~i~~~~D~Ry~~~~i~sh~g~~~~a~~~~~~~~~~~~~~~~~dvI~IDE~QFf~d~~   96 (141)
T d1xx6a1          17 YSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDEVQFFDDEI   96 (141)
T ss_dssp             TSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEEECSGGGSCTHH
T ss_pred             ccHHHHHHHHHHHHhhhcCCcEEEEEeccccccccceeeecccceEEEEEecchhhhhhhhcccccEEEEeehhhccccH
Confidence            59999999999999999999999999999999999999999999999999999888763 45689999999999997 57


Q ss_pred             HHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEecc
Q psy8456          88 VSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT  132 (353)
Q Consensus        88 v~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~  132 (353)
                      ++++..+++.|++|+|||||+||+++||+++.+|||+||+|+||+
T Consensus        97 ~~~~~~l~~~g~~Viv~GLd~Df~~~~F~~~~~Ll~~Ad~v~kLk  141 (141)
T d1xx6a1          97 VEIVNKIAESGRRVICAGLDMDFRGKPFGPIPELMAIAEFVDKIQ  141 (141)
T ss_dssp             HHHHHHHHHTTCEEEEEECSBCTTSCBCTTHHHHHHHCSEEEECC
T ss_pred             HHHHHhheeCCcEEEEEEeccccccCccchHHHHHhhcCeeEECC
Confidence            888999999999999999999999999999999999999999996

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.7e-37  Score=264.86  Aligned_cols=122  Identities=52%  Similarity=0.893  Sum_probs=102.4

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcccCCCccEEEEccccChHHHHH
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQFFPDVVS   89 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~~~~~~dvV~IDEaQFF~dIv~   89 (353)
                      -|||||+||++++||+.+|++|+++||+.|+||+.+ ++||++...+|+.+.+..++.....++|+|+|||||||+++++
T Consensus        12 fsGKTt~Li~~~~~~~~~g~~v~~ikp~~D~R~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~d~I~IDEaQFf~dl~~   90 (133)
T d1xbta1          12 FSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSS-FCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQFFPDIVE   90 (133)
T ss_dssp             TSCHHHHHHHHHHHHHTTTCCEEEEEETTCCC---------------CEEESSGGGGHHHHHTCSEEEESSGGGCTTHHH
T ss_pred             cCHHHHHHHHHHHHHHHcCCcEEEEecccccCCcce-eeecCCCcceeeeeechhhhhhhhcccceEEeehhHHHHHHHH
Confidence            599999999999999999999999999999999854 6788888889988888777665567899999999999999999


Q ss_pred             HHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEecc
Q psy8456          90 FAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT  132 (353)
Q Consensus        90 l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~  132 (353)
                      +++.+++.|++|+|||||+||+++||+++.+|+|+||+|+||+
T Consensus        91 ~~~~~~~~~~~Viv~GLd~Df~~~~F~~~~~Ll~~Ad~I~kLt  133 (133)
T d1xbta1          91 FCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLT  133 (133)
T ss_dssp             HHHHHHHTTCEEEEECCSBCTTSSBCTTGGGGGGGCSEEEECC
T ss_pred             HHHHHHhcCCcEEEEEeccccccCcchhHHHHHHhcCEEEecC
Confidence            9999999999999999999999999999999999999999996

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=100.00  E-value=3.1e-37  Score=265.18  Aligned_cols=121  Identities=26%  Similarity=0.454  Sum_probs=112.0

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceeeeecCChhhhcc------cCCCccEEEEccccC
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTAVSAVELNKLIP------HTKDIDVIGIDEGQF   83 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~Ai~i~~l~ei~~------~~~~~dvV~IDEaQF   83 (353)
                      -||||||||++++||+.+|++|+++||++|+||+. .|+||+|...+|+.+.+..++..      ...++|+|+||||||
T Consensus        12 fsGKTteLi~~~~~~~~~~~kv~~ikp~~D~R~~~-~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dvI~IDE~QF   90 (139)
T d2b8ta1          12 FAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIR-NIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQF   90 (139)
T ss_dssp             TSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCS-SCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEEECSGGG
T ss_pred             cCHHHHHHHHHHHHHHHCCCcEEEEEEcccccccc-eEEcccCceeeeEEeccchhhHHHHHhhccccCcCEEEechhhh
Confidence            59999999999999999999999999999999974 59999999999999887766542      246899999999999


Q ss_pred             hH-HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEec
Q psy8456          84 FP-DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKL  131 (353)
Q Consensus        84 F~-dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL  131 (353)
                      |+ ++.++++.+++.|++|+|||||+||+++||+++.+|+|+||+|+||
T Consensus        91 f~d~i~~~~~~~~~~g~~Viv~GLd~Df~~~~F~~~~~Li~~Ad~V~kL  139 (139)
T d2b8ta1          91 FDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKL  139 (139)
T ss_dssp             SCTHHHHHHHHHHHTTCEEEEECCSBCTTSSBCTTHHHHHHHCSEEEEC
T ss_pred             cchhHHHHHHHHHhcCceEEEEEeccccccCcCccHHHHHHhhCeEEeC
Confidence            97 6899999999999999999999999999999999999999999997

>d1xbta2 g.39.1.14 (A:151-191) Thymidine kinase, TK1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=7.8e-11  Score=80.82  Aligned_cols=18  Identities=67%  Similarity=1.322  Sum_probs=16.5

Q ss_pred             eecCCccchhhhhhhhcc
Q psy8456         236 VIGGSDKYMAVCRECYKQ  253 (353)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~  253 (353)
                      +|||.|.|+|+||.||.+
T Consensus        24 ~IGg~d~Y~~~CR~cy~K   41 (41)
T d1xbta2          24 VIGGADKYHSVCRLCYFK   41 (41)
T ss_dssp             CCCSTTTEEEECHHHHTC
T ss_pred             EECCCCcEEehhhhhhcC
Confidence            489999999999999974

>d2b8ta2 g.39.1.14 (A:150-216) Thymidine kinase, TK1, C-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=98.90  E-value=2.2e-10  Score=86.26  Aligned_cols=20  Identities=30%  Similarity=0.441  Sum_probs=18.2

Q ss_pred             cceecccccccccccccccc
Q psy8456         132 TAVCMSCFRDAAFTKRIGQE  151 (353)
Q Consensus       132 ~AvC~~CG~~A~f~~Ri~ge  151 (353)
                      +|||+.||++|+||+|++++
T Consensus         1 TAIC~~CG~~A~~t~R~~~~   20 (67)
T d2b8ta2           1 TAICNECGAEATHSLRKIDG   20 (67)
T ss_dssp             CEECTTTCSEECEEEEEETT
T ss_pred             CcCcccCCCcceeEEEEeCC
Confidence            69999999999999999765

>d1xx6a2 g.39.1.14 (A:143-191) Thymidine kinase, TK1, C-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=98.85  E-value=1.8e-10  Score=81.82  Aligned_cols=19  Identities=37%  Similarity=0.761  Sum_probs=13.1

Q ss_pred             eecCCccchhhhhhhhccC
Q psy8456         236 VIGGSDKYMAVCRECYKQK  254 (353)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~  254 (353)
                      +|||.|.|+|+||.||+.+
T Consensus        30 ~IGg~e~Y~~~CR~~~~~p   48 (49)
T d1xx6a2          30 LIGAMESYEARCRKCHVVP   48 (49)
T ss_dssp             -----EEEEEECTTTCCCC
T ss_pred             EECCCccEEeechhcccCC
Confidence            5899999999999999865

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=97.62  E-value=2.2e-05  Score=61.13  Aligned_cols=38  Identities=16%  Similarity=0.126  Sum_probs=29.5

Q ss_pred             cceeeeeccCCCCchhHHHHHH-HHHHHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRI-RRYQYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~-~~~~~~~~~~~~~k~~  187 (353)
                      +...++.+|||||||...+..+ +.....+.+++++-|.
T Consensus         7 ~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~   45 (140)
T d1yksa1           7 GMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPT   45 (140)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecc
Confidence            4566889999999998877665 4556778888888775

>d2b8ta2 g.39.1.14 (A:150-216) Thymidine kinase, TK1, C-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=97.40  E-value=2.6e-05  Score=57.97  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=20.7

Q ss_pred             eeeccccccccceeEEeeCCeeE
Q psy8456         328 TAVCMSCFRDAAFTKRIGQEKEV  350 (353)
Q Consensus       328 ~a~C~~Cg~~A~~~~R~~~~~~~  350 (353)
                      +|+|+.||++|+||+|+++|+++
T Consensus         1 TAIC~~CG~~A~~t~R~~~~~~~   23 (67)
T d2b8ta2           1 TAICNECGAEATHSLRKIDGKHA   23 (67)
T ss_dssp             CEECTTTCSEECEEEEEETTEEC
T ss_pred             CcCcccCCCcceeEEEEeCCCCc
Confidence            69999999999999999987754

>d1xx6a2 g.39.1.14 (A:143-191) Thymidine kinase, TK1, C-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=97.39  E-value=3.3e-05  Score=54.07  Aligned_cols=21  Identities=33%  Similarity=0.523  Sum_probs=19.0

Q ss_pred             eeccccccccceeEEeeCCee
Q psy8456         329 AVCMSCFRDAAFTKRIGQEKE  349 (353)
Q Consensus       329 a~C~~Cg~~A~~~~R~~~~~~  349 (353)
                      |+|+.||++|+||+|++++++
T Consensus         1 AvC~~CG~~A~~t~R~~~~~~   21 (49)
T d1xx6a2           1 AICVVCGNPATRTQRLINGKP   21 (49)
T ss_dssp             EECTTTSSEECEEEEEETTEE
T ss_pred             CCCCcCCCcceeEEEEcCCCC
Confidence            799999999999999998653

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=97.25  E-value=0.00019  Score=57.11  Aligned_cols=34  Identities=18%  Similarity=0.296  Sum_probs=27.2

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~  187 (353)
                      +..++.+|.|||||+-++..+   ...|++++++-|.
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~---~~~~~~vli~~P~   42 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAY---AAQGYKVLVLNPS   42 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHH---HTTTCCEEEEESC
T ss_pred             CEEEEEeCCCCCHHHHHHHHH---HHcCCcEEEEcCh
Confidence            356899999999998776544   4568899999886

>d1xbta2 g.39.1.14 (A:151-191) Thymidine kinase, TK1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Type II thymidine kinase zinc finger
domain: Thymidine kinase, TK1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.18  E-value=3.4e-05  Score=52.14  Aligned_cols=23  Identities=74%  Similarity=1.326  Sum_probs=20.2

Q ss_pred             eeccccccccceeEEeeCCeeEE
Q psy8456         329 AVCMSCFRDAAFTKRIGQEKEVR  351 (353)
Q Consensus       329 a~C~~Cg~~A~~~~R~~~~~~~~  351 (353)
                      |+|+.||++|+||+|+++++++.
T Consensus         1 AvC~~Cg~~A~ft~R~~~~~~~v   23 (41)
T d1xbta2           1 AVCMECFREAAYTKRLGTEKEVE   23 (41)
T ss_dssp             EECTTTCSEECEEEECSCCCSSC
T ss_pred             CCCCCCCCcceEEEEEcCCCCEE
Confidence            79999999999999999877643

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.60  E-value=0.0012  Score=57.34  Aligned_cols=71  Identities=20%  Similarity=0.217  Sum_probs=40.5

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQ  232 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~Q  232 (353)
                      -+|+||.|||||.-|--..+.+...++.++.+.... .       ..+.   ..+.......++.......|+++||++|
T Consensus        39 l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~-~-------~~~~---~~~~~~~~~~~~~~~~~~~dll~iDDi~  107 (213)
T d1l8qa2          39 IFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADD-F-------AQAM---VEHLKKGTINEFRNMYKSVDLLLLDDVQ  107 (213)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHH-H-------HHHH---HHHHHHTCHHHHHHHHHTCSEEEEECGG
T ss_pred             EEEECCCCCcHHHHHHHHHHHhccCccceEEechHH-H-------HHHH---HHHHHccchhhHHHHHhhccchhhhhhh
Confidence            589999999998554444555566677766554321 0       0000   0001111222333334578999999999


Q ss_pred             cc
Q psy8456         233 FV  234 (353)
Q Consensus       233 F~  234 (353)
                      ++
T Consensus       108 ~i  109 (213)
T d1l8qa2         108 FL  109 (213)
T ss_dssp             GG
T ss_pred             hh
Confidence            96

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.58  E-value=0.0015  Score=55.91  Aligned_cols=80  Identities=18%  Similarity=0.132  Sum_probs=45.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC---------CCCCCceeeccCcc--cceeecccHhhhcc--
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD---------RYDTEKVSTHDQQK--LTAVSAVELNKLIP--  218 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~---------R~~~~~i~s~~g~~--~~a~~~~~~~~~~~--  218 (353)
                      .-++.+|||||||.-.+..+.   ..+.+++++-|...-         +++...+....|..  ...+.+.....+..  
T Consensus        87 ~~ll~~~tG~GKT~~a~~~~~---~~~~~~Liv~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~  163 (206)
T d2fz4a1          87 RGCIVLPTGSGKTHVAMAAIN---ELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNA  163 (206)
T ss_dssp             EEEEEESSSTTHHHHHHHHHH---HSCSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSCBCCCSEEEEEHHHHHHTH
T ss_pred             CcEEEeCCCCCceehHHhHHH---HhcCceeEEEcccchHHHHHHHHHhhcccchhhcccccccccccccceehhhhhhh
Confidence            347899999999976665554   347889988885321         12222222222211  11122222222221  


Q ss_pred             --cCCCccEEEEeccccc
Q psy8456         219 --HTKDIDVIGIDEGQFV  234 (353)
Q Consensus       219 --~~~~~~~i~IDE~QF~  234 (353)
                        ..+++++|+|||+|.+
T Consensus       164 ~~~~~~~~lvIiDEaH~~  181 (206)
T d2fz4a1         164 EKLGNRFMLLIFDEVHHL  181 (206)
T ss_dssp             HHHTTTCSEEEEECSSCC
T ss_pred             HhhCCcCCEEEEECCeeC
Confidence              1468999999999985

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=96.49  E-value=0.0013  Score=57.73  Aligned_cols=39  Identities=18%  Similarity=0.128  Sum_probs=31.3

Q ss_pred             cceeeeeccCCCCchhH-HHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTE-LIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~-Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ++..++.+|.|||||+. |+..++.....|.+++++-|..
T Consensus         9 ~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr   48 (305)
T d2bmfa2           9 KRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTR   48 (305)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSH
T ss_pred             CCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHH
Confidence            45678999999999974 5566666777899999998853

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.82  E-value=0.0044  Score=52.69  Aligned_cols=37  Identities=19%  Similarity=0.190  Sum_probs=33.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+.+|+|+.+||||+-+++-+.+....|.+|+.+..
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~   62 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACANKERAILFAY   62 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeec
Confidence            4578999999999999999999999999999998864

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=95.76  E-value=0.02  Score=53.55  Aligned_cols=39  Identities=21%  Similarity=0.143  Sum_probs=30.3

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHH----HhCCEEEEEeee
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQ----YANYRCMIVRYA  187 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~----~~~~~~~~~k~~  187 (353)
                      .+.+.+|.||.|+||||-+.+.+....    ..|.++++..|+
T Consensus       162 ~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApT  204 (359)
T d1w36d1         162 TRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPT  204 (359)
T ss_dssp             TBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSS
T ss_pred             cCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCc
Confidence            467899999999999998766554442    356789988886

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=95.73  E-value=0.0064  Score=57.61  Aligned_cols=133  Identities=17%  Similarity=0.209  Sum_probs=77.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc--CCCccEE
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVI  226 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i  226 (353)
                      ..++-++.||+||||||-|--.++.....+++++-+---.--... +....+..    ...-.+..+.+..  -.|+|+|
T Consensus       157 ~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~~~-~~~q~~v~----~~~~~~~~~~l~~~lR~dPDvi  231 (401)
T d1p9ra_         157 PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDID-GIGQTQVN----PRVDMTFARGLRAILRQDPDVV  231 (401)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSCCS-SSEEEECB----GGGTBCHHHHHHHHGGGCCSEE
T ss_pred             hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcccccC-CCCeeeec----CCcCCCHHHHHHHHHhhcCCEE
Confidence            457889999999999999988887654445676644432222111 11111000    0001122222222  3789999


Q ss_pred             EEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHHHHhCCCEEEEEeccccc
Q psy8456         227 GIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAESMANAGKIVVVAALDGTF  306 (353)
Q Consensus       227 ~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~g~~Vi~~gLd~df  306 (353)
                      .|.|.-=                                               +.-+..+-++|..|..|+. .|   .
T Consensus       232 ~igEiRd-----------------------------------------------~~ta~~a~~aa~tGhlV~t-Tl---H  260 (401)
T d1p9ra_         232 MVGEIRD-----------------------------------------------LETAQIAVQASLTGHLVMS-TL---H  260 (401)
T ss_dssp             EESCCCS-----------------------------------------------HHHHHHHHHHHHTTCEEEE-EE---C
T ss_pred             EecCcCC-----------------------------------------------hHHHHHHHHHHhcCCeEEE-Ee---c
Confidence            9999986                                               2334456677788888764 33   4


Q ss_pred             cCCCchhHHhhhhccc-------ce------EEeeeeccccccc
Q psy8456         307 QRTGFNDILSLIPLAE-------CV------EKLTAVCMSCFRD  337 (353)
Q Consensus       307 ~~~~F~~~~~L~~~ad-------~v------~kl~a~C~~Cg~~  337 (353)
                      -+..++.+.+|+.+.-       .+      .-+...|..|..+
T Consensus       261 a~~a~~~~~Rl~~~~~~~~~l~~~l~~vv~QrLv~~lCp~Ck~~  304 (401)
T d1p9ra_         261 TNTAVGAVTRLRDMGIEPFLISSSLLGVLAQRLVRTLCPDCKEP  304 (401)
T ss_dssp             CSSSHHHHHHHHHHTCCHHHHHHHEEEEEEEEEEEEECTTTCEE
T ss_pred             cCchHhhhhhhhhcccchhhHHHHHHHHHhccchhhhCCCcCcC
Confidence            4567777777765432       11      1236678888643

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=95.56  E-value=0.012  Score=44.86  Aligned_cols=29  Identities=10%  Similarity=0.054  Sum_probs=22.2

Q ss_pred             CCCchHHHHHHHH-HHHHHcCceEEEEeec
Q psy8456           9 RINPYIVHFCRRI-RRYQYANYRCMIVRYA   37 (353)
Q Consensus         9 ~~~GKSteLLrr~-~ry~~agkkvlv~Kp~   37 (353)
                      .-||||...+..+ +.+...+++++++-|.
T Consensus        16 tGsGKT~~~~~~~~~~~~~~~~~vli~~p~   45 (140)
T d1yksa1          16 PGAGKTRRFLPQILAECARRRLRTLVLAPT   45 (140)
T ss_dssp             TTSSTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCChhHHHHHHHHHHhhhcCceeeeeecc
Confidence            4589998887664 5555788899999984

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=95.40  E-value=0.0074  Score=47.79  Aligned_cols=37  Identities=19%  Similarity=0.025  Sum_probs=32.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +..|+|+-||||||-+-+-++++..+|.++.+++...
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~~~d~   40 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIKHTH   40 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEecccc
Confidence            3468999999999999999999999999999888754

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.29  E-value=0.0056  Score=48.79  Aligned_cols=36  Identities=17%  Similarity=0.136  Sum_probs=30.3

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      .+-+|.|++||||||-+-+-..++...+.++.++..
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~~   37 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSF   37 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTCCCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEec
Confidence            467899999999999988888888888888877643

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=95.28  E-value=0.0083  Score=47.08  Aligned_cols=15  Identities=33%  Similarity=0.153  Sum_probs=12.9

Q ss_pred             eeeeeccCCCCchhH
Q psy8456         152 KEVILGPMFSGKTTE  166 (353)
Q Consensus       152 I~vi~G~M~sGKt~~  166 (353)
                      +-++.||++|||||-
T Consensus         4 lIii~G~pGsGKTTl   18 (152)
T d1ly1a_           4 IILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            457899999999994

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=95.22  E-value=0.012  Score=46.00  Aligned_cols=74  Identities=9%  Similarity=-0.007  Sum_probs=40.0

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCC----------CCCCCceeeccCCceee---eecCChhh----hcccCC
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDD----------RYDTEKVATHDQQKLTA---VSAVELNK----LIPHTK   71 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDt----------Ry~~~~I~Sr~G~~~~A---i~i~~l~e----i~~~~~   71 (353)
                      --||||+-+...+   ...|++++++-|...-          .++......+.|.....   +.+.....    ......
T Consensus        17 TGsGKT~~~~~~~---~~~~~~vli~~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (136)
T d1a1va1          17 TGSGKSTKVPAAY---AAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGGCSGG   93 (136)
T ss_dssp             TTSCTTTHHHHHH---HTTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCEECCCCSEEEEEHHHHHHTTGGGGC
T ss_pred             CCCCHHHHHHHHH---HHcCCcEEEEcChHHHHHHHHHHHHHHhhccccccccccccccccceEEEeeeeeccccchhhh
Confidence            4589998765543   4678999999994211          01212222222221111   11111111    112346


Q ss_pred             CccEEEEccccChH
Q psy8456          72 DIDVIGIDEGQFFP   85 (353)
Q Consensus        72 ~~dvV~IDEaQFF~   85 (353)
                      ++|+|+|||+|.++
T Consensus        94 ~~~~vIiDE~H~~~  107 (136)
T d1a1va1          94 AYDIIICDECHSTD  107 (136)
T ss_dssp             CCSEEEEETTTCCS
T ss_pred             cCCEEEEecccccC
Confidence            89999999999996

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.12  E-value=0.022  Score=47.88  Aligned_cols=115  Identities=10%  Similarity=0.107  Sum_probs=75.6

Q ss_pred             CchHHHHHHHHHHHHHcCceEEEEeeccCCCCCC-CceeeccCCceeee----e--cCChhhh-------c------ccC
Q psy8456          11 NPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDT-EKVATHDQQKLTAV----S--AVELNKL-------I------PHT   70 (353)
Q Consensus        11 ~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~-~~I~Sr~G~~~~Ai----~--i~~l~ei-------~------~~~   70 (353)
                      -||||..|..+-|.-=.|++|+++.--....++. .......+......    .  -.+..+.       .      -..
T Consensus        13 KGKTTAAlG~alRA~G~G~rV~ivQFlKg~~~~ge~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~a~~~~~~   92 (157)
T d1g5ta_          13 KGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAVWQHGKRMLAD   92 (157)
T ss_dssp             SCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCcHHHHHHHHHHHhcCCCEEEEEEEecCCcccchhhhhcccCcEEEEecCCCcccCCChHHHHHHHHHHHHHHHHHhhc
Confidence            4999999999999999999999998877655432 22222333332221    0  0111100       0      024


Q ss_pred             CCccEEEEccccCh-H----HHHHHHHHHHh--CCCEEEEEecccccccCCchhHhhhhccccceEeccce
Q psy8456          71 KDIDVIGIDEGQFF-P----DVVSFAESMAN--AGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  134 (353)
Q Consensus        71 ~~~dvV~IDEaQFF-~----dIv~l~~~l~~--~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~Av  134 (353)
                      ..||+|+.||+--- .    +..++.+.+.+  .+..||+-|=+.         ...|+++||-|++++.+
T Consensus        93 ~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~---------p~~L~e~ADlVTEm~~v  154 (157)
T d1g5ta_          93 PLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC---------HRDILDLADTVSELRPV  154 (157)
T ss_dssp             TTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC---------CHHHHHHCSEEEECCCS
T ss_pred             CccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCC---------CHHHHHhcceeeeeeee
Confidence            67999999998653 1    34455555554  588999999633         35699999999998653

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.07  E-value=0.01  Score=48.07  Aligned_cols=37  Identities=22%  Similarity=0.167  Sum_probs=32.8

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      +.-|+|+-||||||-+-+-+.++..+|.+|-+++...
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik~d~   39 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVKHHG   39 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEECCC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEEecc
Confidence            3458999999999999999999999999999998654

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=94.80  E-value=0.015  Score=50.70  Aligned_cols=143  Identities=20%  Similarity=0.187  Sum_probs=84.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCC-CceeeccCc-ccceeec---ccHhhh------c
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDT-EKVSTHDQQ-KLTAVSA---VELNKL------I  217 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~-~~i~s~~g~-~~~a~~~---~~~~~~------~  217 (353)
                      .++.+++||.|+||||-+.+-++++...|++|.++..  |+ |.+. +...+.... ..+...+   .++.++      +
T Consensus        10 ~~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~--Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~   87 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA--DTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEK   87 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEEC--CSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEec--ccccchHHHHHHHHHHhcCCccccccccchhhHHHHHHHHH
Confidence            3456779999999999999999999999999998775  43 4331 222222110 1122222   233332      1


Q ss_pred             ccCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCC------CCCCccHHHHHHHHH
Q psy8456         218 PHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPP------PPEFPDVVSFAESMA  291 (353)
Q Consensus       218 ~~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~------~~~f~~~~~~~~~~~  291 (353)
                      ....++|+|+||=+=.                     .|....++++|.++.+.++.++      +..-.+-++.+..-.
T Consensus        88 ~~~~~~d~vlIDTaGr---------------------~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~~~~f~  146 (207)
T d1ls1a2          88 ARLEARDLILVDTAGR---------------------LQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFD  146 (207)
T ss_dssp             HHHHTCCEEEEECCCC---------------------SSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHHHHHHH
T ss_pred             HhhccCcceeeccccc---------------------chhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHHHHHHH
Confidence            2347889999998765                     2446677788877766433211      111123445554443


Q ss_pred             h-CCCE-EEEEeccccccCCCchhHHhhh
Q psy8456         292 N-AGKI-VVVAALDGTFQRTGFNDILSLI  318 (353)
Q Consensus       292 ~-~g~~-Vi~~gLd~df~~~~F~~~~~L~  318 (353)
                      + .|+. +|+-=||.+-+   ++.+..+.
T Consensus       147 ~~~~~~~~I~TKlDe~~~---~G~~l~~~  172 (207)
T d1ls1a2         147 EKVGVTGLVLTKLDGDAR---GGAALSAR  172 (207)
T ss_dssp             HHTCCCEEEEECGGGCSS---CHHHHHHH
T ss_pred             hhCCCCeeEEeecCcccc---chHHHHHH
Confidence            3 4543 77777887543   56655543

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=94.80  E-value=0.012  Score=51.71  Aligned_cols=140  Identities=17%  Similarity=0.216  Sum_probs=81.0

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCC-CCceeeccC-cccceeec---ccHhhhc------cc
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYD-TEKVSTHDQ-QKLTAVSA---VELNKLI------PH  219 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~-~~~i~s~~g-~~~~a~~~---~~~~~~~------~~  219 (353)
                      +.+.+||.|+||||-+.+-+.++..+|++|.++.-  |+ |-+ .++..++-. ...+....   .++..+.      ..
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~--Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~~~~   90 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA--DTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAVAHAL   90 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE--CTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEee--cccccchhHHHHHHhhhcCccccccCCCCcHHHHHHHHHHHHH
Confidence            44569999999999999999999999999998875  43 433 122222210 01111111   1232221      22


Q ss_pred             CCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccC--CCCCCC---C--------ccHHHH
Q psy8456         220 TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALN--VPPPPE---F--------PDVVSF  286 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~~~---f--------~~~~~~  286 (353)
                      .+++|+|+||=+=.                     .|....++++|..+....+  .+..|.   +        .++.+.
T Consensus        91 ~~~~d~ilIDTaGr---------------------~~~d~~~~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~  149 (213)
T d1vmaa2          91 ARNKDVVIIDTAGR---------------------LHTKKNLMEELRKVHRVVKKKIPDAPHETLLVIDATTGQNGLVQA  149 (213)
T ss_dssp             HTTCSEEEEEECCC---------------------CSCHHHHHHHHHHHHHHGGGTCTTCCSEEEEEEEGGGHHHHHHHH
T ss_pred             HcCCCEEEEecccc---------------------ccchHHHHHHHHHHHhhhhhccccccceeEEeeccccCcchhhhh
Confidence            46899999998854                     1235566666666654322  222111   1        234444


Q ss_pred             HHHHHhCCCE-EEEEeccccccCCCchhHHhh
Q psy8456         287 AESMANAGKI-VVVAALDGTFQRTGFNDILSL  317 (353)
Q Consensus       287 ~~~~~~~g~~-Vi~~gLd~df~~~~F~~~~~L  317 (353)
                      .......|+. +|+-=||.+   ..++.+..+
T Consensus       150 ~~~~~~~~~~~lI~TKlDe~---~~~G~~l~~  178 (213)
T d1vmaa2         150 KIFKEAVNVTGIILTKLDGT---AKGGITLAI  178 (213)
T ss_dssp             HHHHHHSCCCEEEEECGGGC---SCTTHHHHH
T ss_pred             hhhccccCCceEEEecccCC---CcccHHHHH
Confidence            4444555665 788888886   334555554

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.72  E-value=0.022  Score=46.86  Aligned_cols=35  Identities=17%  Similarity=0.083  Sum_probs=25.2

Q ss_pred             eeeeccCCCCchhHHHHHHH-HHHHhCCEEEEEeee
Q psy8456         153 EVILGPMFSGKTTELIRRIR-RYQYANYRCMIVRYA  187 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~-~~~~~~~~~~~~k~~  187 (353)
                      .++.+|+|||||.-.+..+. .....+.+++++-|.
T Consensus        26 ~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~   61 (200)
T d1wp9a1          26 CLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPT   61 (200)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSS
T ss_pred             eEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCc
Confidence            57889999999975443333 345567889988885

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.68  E-value=0.04  Score=43.99  Aligned_cols=23  Identities=30%  Similarity=0.288  Sum_probs=16.5

Q ss_pred             eeeeccCCCCchhHHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQ  175 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~  175 (353)
                      -+|+||.||||||-|-..+..+.
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~   25 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCC
Confidence            37899999999995444444443

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.65  E-value=0.016  Score=48.53  Aligned_cols=36  Identities=17%  Similarity=0.069  Sum_probs=26.9

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      -++.+|.|||||+-.+-.+-+....+.+++++-|..
T Consensus        43 ~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~~   78 (202)
T d2p6ra3          43 LLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLR   78 (202)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             EEEEcCCCCchhHHHHHHHHHHhhccCcceeecccH
Confidence            478999999999875444444555677889888864

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=94.55  E-value=0.014  Score=51.07  Aligned_cols=35  Identities=17%  Similarity=0.175  Sum_probs=27.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+++||.|+||||-+.+-+++|..+|++|.++.-
T Consensus        14 vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~   48 (211)
T d1j8yf2          14 VIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGA   48 (211)
T ss_dssp             EEEEECSCCC----HHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEe
Confidence            45668999999999999999999999999998864

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=94.45  E-value=0.013  Score=51.08  Aligned_cols=81  Identities=19%  Similarity=0.184  Sum_probs=51.9

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCCC-Cceeecc---Ccccce-eecccHhhhcc------
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYDT-EKVSTHD---QQKLTA-VSAVELNKLIP------  218 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~~-~~i~s~~---g~~~~a-~~~~~~~~~~~------  218 (353)
                      .+.+++||.||||||-+.+-++++...|++|.++.-  |+ |-+. +...+..   |..+.. ....++.++..      
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~--Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~~~   84 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAG--DTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAM   84 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECC--CCSSTTHHHHHHHHHHHHTCCEECCCTTCCHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEe--ccccccchhhHhhcccccCceEEeccCCccHHHHHHHHHHHH
Confidence            455679999999999999999999999999998864  54 6542 2222221   221111 11122333321      


Q ss_pred             cCCCccEEEEecccc
Q psy8456         219 HTKDIDVIGIDEGQF  233 (353)
Q Consensus       219 ~~~~~~~i~IDE~QF  233 (353)
                      ...++|+|+||=+=.
T Consensus        85 ~~~~~d~ilIDTaGr   99 (207)
T d1okkd2          85 KARGYDLLFVDTAGR   99 (207)
T ss_dssp             HHHTCSEEEECCCCC
T ss_pred             HHCCCCEEEcCcccc
Confidence            236789999997765

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.28  E-value=0.11  Score=44.14  Aligned_cols=36  Identities=22%  Similarity=0.189  Sum_probs=28.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      |.+-+|-|+.||||||..-.-...+...|.+|++++
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            445567799999999987776777788999998764

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=94.23  E-value=0.015  Score=46.40  Aligned_cols=35  Identities=20%  Similarity=0.196  Sum_probs=30.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +-+|.|++||||||-.-.-..++...|..+..+++
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~~~   37 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINY   37 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEC
Confidence            45789999999999988888888888999887775

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=94.13  E-value=0.027  Score=50.60  Aligned_cols=36  Identities=14%  Similarity=0.145  Sum_probs=26.6

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHH-HhCCEEEEEeee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQ-YANYRCMIVRYA  187 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~-~~~~~~~~~k~~  187 (353)
                      .-++..|++||||.-....++.+. ..+.+++++-|.
T Consensus       130 ~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~  166 (282)
T d1rifa_         130 RRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPT  166 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSS
T ss_pred             CceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcC
Confidence            347788999999976555555553 346789999886

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.05  E-value=0.017  Score=45.54  Aligned_cols=32  Identities=19%  Similarity=0.089  Sum_probs=27.2

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEE
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIV  184 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~  184 (353)
                      -+|+||.|+||||-+-..++.++..|.++.++
T Consensus         4 v~ItG~~GtGKTtl~~~i~~~l~~~~~~v~~~   35 (189)
T d2i3ba1           4 VFLTGPPGVGKTTLIHKASEVLKSSGVPVDGF   35 (189)
T ss_dssp             EEEESCCSSCHHHHHHHHHHHHHHTTCCCEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            57999999999998888888888888877644

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=93.79  E-value=0.02  Score=50.16  Aligned_cols=140  Identities=21%  Similarity=0.239  Sum_probs=79.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCC-CCC-CCceeec---cCcccceee-cccHhhhcc------c
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDD-RYD-TEKVSTH---DQQKLTAVS-AVELNKLIP------H  219 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~-R~~-~~~i~s~---~g~~~~a~~-~~~~~~~~~------~  219 (353)
                      +.+++||.||||||-+.+-++++...|++|.++.-  |+ |-+ .+...+.   .|..+.... ..++..++.      .
T Consensus        11 vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~--Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~a~   88 (211)
T d2qy9a2          11 VILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAG--DTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAAK   88 (211)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECC--CTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEec--ccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHHHHHHH
Confidence            44569999999999999999999999999998875  54 433 1222221   122211111 123333321      1


Q ss_pred             CCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHH---hhccCCCCCCC--C--------ccHHHH
Q psy8456         220 TKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANE---NAALNVPPPPE--F--------PDVVSF  286 (353)
Q Consensus       220 ~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~~~~--f--------~~~~~~  286 (353)
                      .+++|+|+||=+=..                     +.....+++|.++   ..++++..|.+  +        .++.+.
T Consensus        89 ~~~~d~ilIDTaGr~---------------------~~d~~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~  147 (211)
T d2qy9a2          89 ARNIDVLIADTAGRL---------------------QNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQA  147 (211)
T ss_dssp             HTTCSEEEECCCCCG---------------------GGHHHHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHHHH
T ss_pred             HcCCCEEEeccCCCc---------------------cccHHHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHHHH
Confidence            468999999987542                     1134444555444   44333333322  1        123343


Q ss_pred             HHHHHhCCCE-EEEEeccccccCCCchhHHhh
Q psy8456         287 AESMANAGKI-VVVAALDGTFQRTGFNDILSL  317 (353)
Q Consensus       287 ~~~~~~~g~~-Vi~~gLd~df~~~~F~~~~~L  317 (353)
                      .......|+. +|+--||.+-+   ++.+..+
T Consensus       148 ~~~~~~~~~~~lIlTKlDe~~~---~G~~l~~  176 (211)
T d2qy9a2         148 KLFHEAVGLTGITLTKLDGTAK---GGVIFSV  176 (211)
T ss_dssp             HHHHHHSCCCEEEEECCTTCTT---TTHHHHH
T ss_pred             hhhhhccCCceEEEeecCCCCC---ccHHHHH
Confidence            4444445555 77788888654   4555554

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.23  E-value=0.013  Score=46.53  Aligned_cols=18  Identities=33%  Similarity=0.285  Sum_probs=15.6

Q ss_pred             ccceeeeeccCCCCchhH
Q psy8456         149 GQEKEVILGPMFSGKTTE  166 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~  166 (353)
                      .|.+-++.|||+|||||-
T Consensus         3 ~g~iI~l~G~~GsGKSTi   20 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTI   20 (176)
T ss_dssp             TTEEEEEEECTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            467788999999999993

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.80  E-value=0.16  Score=42.35  Aligned_cols=132  Identities=16%  Similarity=0.128  Sum_probs=80.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCC-ceeeccCcccce-------eecc------cHhh
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTE-KVSTHDQQKLTA-------VSAV------ELNK  215 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~-~i~s~~g~~~~a-------~~~~------~~~~  215 (353)
                      |-+++++|+ +=||||..+-.+-|..-.|++|+++.--+...++.+ ......+..+..       ....      ...+
T Consensus         3 G~i~vytG~-GKGKTTAAlG~alRA~G~G~rV~ivQFlKg~~~~ge~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~   81 (157)
T d1g5ta_           3 GIIIVFTGN-GKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMA   81 (157)
T ss_dssp             CCEEEEESS-SSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHH
T ss_pred             cEEEEEeCC-CCCcHHHHHHHHHHHhcCCCEEEEEEEecCCcccchhhhhcccCcEEEEecCCCcccCCChHHHHHHHHH
Confidence            457788886 779999999999999999999999999887765432 111112211110       0000      0011


Q ss_pred             hc------ccCCCccEEEEecccccceecCCccchhhhhhhhccCCCCCcchHHHHHHHhhccCCCCCCCCccHHHHHHH
Q psy8456         216 LI------PHTKDIDVIGIDEGQFVEVIGGSDKYMAVCRECYKQKAPIKRSPFKTLANENAALNVPPPPEFPDVVSFAES  289 (353)
Q Consensus       216 ~~------~~~~~~~~i~IDE~QF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~  289 (353)
                      ..      -...++|+|+.||+-..-                 ..--++.                     .++++++++
T Consensus        82 ~~~~a~~~~~~~~~dllILDEi~~Ai-----------------~~gli~~---------------------~~v~~ll~~  123 (157)
T d1g5ta_          82 VWQHGKRMLADPLLDMVVLDELTYMV-----------------AYDYLPL---------------------EEVISALNA  123 (157)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHH-----------------HTTSSCH---------------------HHHHHHHHT
T ss_pred             HHHHHHHHhhcCccCEEeHHHHHHHH-----------------HcCCCCH---------------------HHHHHHHHh
Confidence            11      124779999999987510                 0000111                     245554432


Q ss_pred             HHhCCCEEEEEeccccccCCCchhHHhhhhcccceEEeeee
Q psy8456         290 MANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLTAV  330 (353)
Q Consensus       290 ~~~~g~~Vi~~gLd~df~~~~F~~~~~L~~~ad~v~kl~a~  330 (353)
                       ...+..||+-|=+         ....|+++||-|++++.+
T Consensus       124 -rp~~~evVlTGr~---------~p~~L~e~ADlVTEm~~v  154 (157)
T d1g5ta_         124 -RPGHQTVIITGRG---------CHRDILDLADTVSELRPV  154 (157)
T ss_dssp             -SCTTCEEEEECSS---------CCHHHHHHCSEEEECCCS
T ss_pred             -CCCCCEEEEECCC---------CCHHHHHhcceeeeeeee
Confidence             2467889988732         235699999999998653

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.75  E-value=0.074  Score=44.43  Aligned_cols=21  Identities=24%  Similarity=0.444  Sum_probs=15.8

Q ss_pred             eeeeccCCCCchhHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~  173 (353)
                      -+++||.|+||||-+-..++.
T Consensus        36 lll~Gp~G~GKTtl~~~i~~~   56 (237)
T d1sxjd2          36 MLFYGPPGTGKTSTILALTKE   56 (237)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHH
Confidence            489999999999855444444

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=92.70  E-value=0.14  Score=44.13  Aligned_cols=106  Identities=9%  Similarity=0.047  Sum_probs=53.6

Q ss_pred             CCchHHH-HHHHHHHHHHcCceEEEEeeccCC------CC---CCCc-eee-ccCCceee-eecCChhhh---c---ccC
Q psy8456          10 INPYIVH-FCRRIRRYQYANYRCMIVRYAKDD------RY---DTEK-VAT-HDQQKLTA-VSAVELNKL---I---PHT   70 (353)
Q Consensus        10 ~~GKSte-LLrr~~ry~~agkkvlv~Kp~iDt------Ry---~~~~-I~S-r~G~~~~A-i~i~~l~ei---~---~~~   70 (353)
                      =||||+. |+..++.....|.+++++-|...=      |.   +... ... +....-.+ +.+....-+   .   ...
T Consensus        19 GsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~t~~~l~~~~~~~~~~   98 (305)
T d2bmfa2          19 GAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRV   98 (305)
T ss_dssp             TSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHTTTSCCBCCC--------CCCSEEEEEHHHHHHHHTSSSCC
T ss_pred             CCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEeecccCccccccCCcHHHHHHHhcCccc
Confidence            4899975 446666666778999999993211      01   1110 011 11111111 111111111   1   124


Q ss_pred             CCccEEEEccccChH----HHHHHHHHHH-hCCCEEEEEecccccccCCc
Q psy8456          71 KDIDVIGIDEGQFFP----DVVSFAESMA-NAGKIVVVAALDGTFQRTGF  115 (353)
Q Consensus        71 ~~~dvV~IDEaQFF~----dIv~l~~~l~-~~G~~VivaGLd~DFr~~pF  115 (353)
                      .+++.|+|||+|.++    .+..+...+. ..+..+++..-..+....+|
T Consensus        99 ~~~~~vViDE~H~~~~~~~~~~~~l~~~~~~~~~~~v~~SAT~~~~~~~~  148 (305)
T d2bmfa2          99 PNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPF  148 (305)
T ss_dssp             CCCSEEEEESTTCCSHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSS
T ss_pred             cceeEEEeeeeeecchhhHHHHHHHHHhhccccceEEEeecCCCcceeee
Confidence            679999999999995    2334444443 45667776655444333333

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=92.54  E-value=0.016  Score=44.67  Aligned_cols=18  Identities=33%  Similarity=0.372  Sum_probs=13.5

Q ss_pred             eeeeccCCCCchhHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRR  170 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~  170 (353)
                      -+++|||||||||---.-
T Consensus         5 I~l~G~~GsGKSTvak~L   22 (169)
T d1kaga_           5 IFLVGPMGAGKSTIGRQL   22 (169)
T ss_dssp             EEEECCTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            467899999999754333

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=92.13  E-value=0.024  Score=44.66  Aligned_cols=19  Identities=16%  Similarity=0.104  Sum_probs=14.8

Q ss_pred             ceeeeeccCCCCchhHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~  169 (353)
                      .+-++.|||+|||||-.-.
T Consensus         4 kiI~l~G~~GsGKsTva~~   22 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRC   22 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4567899999999975433

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=91.56  E-value=0.14  Score=44.57  Aligned_cols=83  Identities=18%  Similarity=0.127  Sum_probs=47.2

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCcccce---ee-----cccHhhhccc
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTA---VS-----AVELNKLIPH  219 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a---~~-----~~~~~~~~~~  219 (353)
                      .+++.+|+||..|||||-|=...-..-.|+--+  +-|+...+.+ -+.|-||.|..-..   .+     ...+..++..
T Consensus        34 ~~~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~--~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~  111 (224)
T d1ewqa2          34 AHELVLITGPNMAGKSTFLRQTALIALLAQVGS--FVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKE  111 (224)
T ss_dssp             SSCEEEEESCSSSSHHHHHHHHHHHHHHHTTTC--CBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCccccchhhhhhHHHHHHHhccc--eeecCceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhcc
Confidence            445789999999999996665555554554322  2233222222 23566666543221   11     2345555555


Q ss_pred             CCCccEEEEecccc
Q psy8456         220 TKDIDVIGIDEGQF  233 (353)
Q Consensus       220 ~~~~~~i~IDE~QF  233 (353)
                      ..+-..|+|||.=-
T Consensus       112 ~~~~sLvliDE~~~  125 (224)
T d1ewqa2         112 ATENSLVLLDEVGR  125 (224)
T ss_dssp             CCTTEEEEEESTTT
T ss_pred             CCCCcEEeeccccc
Confidence            55567999999765

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=91.51  E-value=0.069  Score=46.78  Aligned_cols=38  Identities=21%  Similarity=0.286  Sum_probs=30.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHhC----CEEEEEeeec
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYAN----YRCMIVRYAK  188 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~~----~~~~~~k~~~  188 (353)
                      +.-+|.|+-||||||-|+.++..+...+    .+++++.+..
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~   66 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTN   66 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSH
T ss_pred             CCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccH
Confidence            4468899999999999999987775544    4788887653

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=91.48  E-value=0.087  Score=43.25  Aligned_cols=33  Identities=18%  Similarity=0.072  Sum_probs=28.0

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      -+|-|+-||||||.+-.-..++...|.+|.+++
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~   35 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA   35 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEe
Confidence            467899999999988777778888999988765

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=91.40  E-value=0.046  Score=42.91  Aligned_cols=27  Identities=19%  Similarity=0.092  Sum_probs=18.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      -+++||+||||||-.-+-..++   |..++
T Consensus         7 I~i~G~pGsGKTTia~~La~~l---~~~~i   33 (173)
T d1rkba_           7 ILLTGTPGVGKTTLGKELASKS---GLKYI   33 (173)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH---CCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHH---CCcEE
Confidence            3689999999998655544544   55443

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=91.15  E-value=0.077  Score=41.47  Aligned_cols=30  Identities=17%  Similarity=-0.071  Sum_probs=20.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANY  179 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~  179 (353)
                      |-.-+++|+|||||||---.-.+++...+.
T Consensus         6 g~~I~l~G~~GsGKTTia~~La~~L~~~~~   35 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIARALQVTLNQQGG   35 (183)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCC
Confidence            445678999999999954444444444443

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.12  E-value=0.51  Score=41.00  Aligned_cols=82  Identities=16%  Similarity=0.146  Sum_probs=48.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCcccc---eee-----cccHhhhcccC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLT---AVS-----AVELNKLIPHT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~---a~~-----~~~~~~~~~~~  220 (353)
                      .+..+|+||..|||||-|-...-..-.|+--+.+  |+...+.+ -+.|-||.|..-.   ..+     ...+..++...
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~V--pA~~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~  118 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMAYIGSYV--PAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNA  118 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCB--SSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHC
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeE--ecCceecccchhheeEEccCcccccchhHHHHHHHHHHHHHHhc
Confidence            3567999999999999988877777666543322  22222222 2456666543221   111     23455556555


Q ss_pred             CCccEEEEecccc
Q psy8456         221 KDIDVIGIDEGQF  233 (353)
Q Consensus       221 ~~~~~i~IDE~QF  233 (353)
                      .+-..|+|||.=-
T Consensus       119 ~~~sLvliDE~~~  131 (234)
T d1wb9a2         119 TEYSLVLMDEIGR  131 (234)
T ss_dssp             CTTEEEEEESCCC
T ss_pred             ccccEEeeccccc
Confidence            5567999999765

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=91.12  E-value=0.054  Score=46.82  Aligned_cols=37  Identities=19%  Similarity=0.188  Sum_probs=29.0

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHHHHh----CCEEEEEeee
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRYQYA----NYRCMIVRYA  187 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~~~~----~~~~~~~k~~  187 (353)
                      +.-+|.|+-||||||-|+.++...-..    ..+++++.++
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~t   55 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFT   55 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESS
T ss_pred             CCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCc
Confidence            345789999999999999988766433    2589988886

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=91.04  E-value=0.095  Score=44.15  Aligned_cols=61  Identities=21%  Similarity=0.115  Sum_probs=34.8

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEEEEeccc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVIGIDEGQ  232 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i~IDE~Q  232 (353)
                      -+++||.|+|||| |.+.+-+  ..+.....+.. .+.+.                 ..++..++...+.-.+++|||++
T Consensus        38 ~L~~GPpGtGKT~-lA~~la~--~~~~~~~~~~~-~~~~~-----------------~~~~~~~~~~~~~~~~~~ide~~   96 (238)
T d1in4a2          38 VLLAGPPGLGKTT-LAHIIAS--ELQTNIHVTSG-PVLVK-----------------QGDMAAILTSLERGDVLFIDEIH   96 (238)
T ss_dssp             EEEESSTTSSHHH-HHHHHHH--HHTCCEEEEET-TTCCS-----------------HHHHHHHHHHCCTTCEEEEETGG
T ss_pred             EEEECCCCCcHHH-HHHHHHh--ccCCCcccccC-ccccc-----------------HHHHHHHHHhhccCCchHHHHHH
Confidence            4789999999998 4444433  34554444332 11110                 11233333334455788999999


Q ss_pred             cc
Q psy8456         233 FV  234 (353)
Q Consensus       233 F~  234 (353)
                      .+
T Consensus        97 ~~   98 (238)
T d1in4a2          97 RL   98 (238)
T ss_dssp             GC
T ss_pred             Hh
Confidence            86

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.45  E-value=0.063  Score=46.30  Aligned_cols=32  Identities=22%  Similarity=0.297  Sum_probs=23.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      +.+|.|..||||||-|-+.++ . ..|+|+.++-
T Consensus         5 v~iitGFLGaGKTTll~~lL~-~-~~~~riaVI~   36 (222)
T d1nija1           5 VTLLTGFLGAGKTTLLRHILN-E-QHGYKIAVIE   36 (222)
T ss_dssp             EEEEEESSSSSCHHHHHHHHH-S-CCCCCEEEEC
T ss_pred             EEEEeeCCCCCHHHHHHHHHh-c-CCCCcEEEEE
Confidence            578999999999995444443 3 4578887775

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=90.36  E-value=0.083  Score=48.46  Aligned_cols=75  Identities=15%  Similarity=0.098  Sum_probs=43.2

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCC-CCceeeccCcccceeecccHhhhccc--CCCccEEEEe
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYD-TEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVIGID  229 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~-~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i~ID  229 (353)
                      -+|+||++|||||-| +.+-.+...+.+++.+-....-... ...+..-.+     .....+.+++..  -.++|.|++.
T Consensus       169 ili~G~tgSGKTT~l-~al~~~i~~~~rivtiEd~~El~l~~~~~~~~~~~-----~~~~~~~~ll~~~lR~~pd~iivg  242 (323)
T d1g6oa_         169 VIVCGGTGSGKTTYI-KSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFF-----GGNITSADCLKSCLRMRPDRIILG  242 (323)
T ss_dssp             EEEEESTTSSHHHHH-HHHGGGSCTTCCEEEEESSCCCCCSSCSSEEEEEC-----BTTBCHHHHHHHHTTSCCSEEEES
T ss_pred             EEEEeeccccchHHH-HHHhhhcccccceeeccchhhhhcccccccceecc-----ccchhHHHHHHHHhccCCCcccCC
Confidence            489999999999876 6666666667777766332211111 111111111     011234444432  3689999999


Q ss_pred             cccc
Q psy8456         230 EGQF  233 (353)
Q Consensus       230 E~QF  233 (353)
                      |..=
T Consensus       243 EiR~  246 (323)
T d1g6oa_         243 ELRS  246 (323)
T ss_dssp             CCCS
T ss_pred             ccCc
Confidence            9874

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=90.13  E-value=0.28  Score=43.87  Aligned_cols=37  Identities=27%  Similarity=0.205  Sum_probs=33.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +.+..++||.+||||+-+++.+.+++.+|..|+.+..
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDt   96 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDA   96 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEEC
Confidence            5678999999999999999999999999999887764

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=89.96  E-value=0.088  Score=41.45  Aligned_cols=25  Identities=20%  Similarity=0.174  Sum_probs=19.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..+.++.||+||||||-.-.-..++
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3577899999999999766655544

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=89.96  E-value=0.21  Score=42.23  Aligned_cols=65  Identities=6%  Similarity=0.007  Sum_probs=39.4

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhC---CEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhc------ccCCCc
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYAN---YRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLI------PHTKDI  223 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~---~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~------~~~~~~  223 (353)
                      -+++||-++|||+-.+.-.+......   -.++.+.|.              |..   +.++.+.+++      +...+.
T Consensus        18 ~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~--------------~~~---I~Id~IR~i~~~~~~~~~~~~~   80 (198)
T d2gnoa2          18 ILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPE--------------GEN---IGIDDIRTIKDFLNYSPELYTR   80 (198)
T ss_dssp             EEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCS--------------SSC---BCHHHHHHHHHHHTSCCSSSSS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCC--------------cCC---CCHHHHHHHHHHHhhCcccCCC
Confidence            47899999999988776664332111   135555542              211   2333333332      224677


Q ss_pred             cEEEEeccccc
Q psy8456         224 DVIGIDEGQFV  234 (353)
Q Consensus       224 ~~i~IDE~QF~  234 (353)
                      .|++|||+|.+
T Consensus        81 KviIId~ad~l   91 (198)
T d2gnoa2          81 KYVIVHDCERM   91 (198)
T ss_dssp             EEEEETTGGGB
T ss_pred             EEEEEeCcccc
Confidence            89999999998

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=89.92  E-value=0.1  Score=44.50  Aligned_cols=20  Identities=15%  Similarity=0.187  Sum_probs=15.9

Q ss_pred             cceeeeeccCCCCchhHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~  169 (353)
                      |.+-+++||.+|||||-.=+
T Consensus         2 G~livi~GPSG~GK~tl~~~   21 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQA   21 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            56789999999999974433

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.52  E-value=0.13  Score=42.72  Aligned_cols=18  Identities=39%  Similarity=0.735  Sum_probs=14.2

Q ss_pred             eeeeccCCCCchhHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~  171 (353)
                      -+++||.+||||| |.+++
T Consensus         3 Ivl~GPsGsGK~t-l~~~L   20 (190)
T d1lvga_           3 VVLSGPSGAGKST-LLKKL   20 (190)
T ss_dssp             EEEECCTTSSHHH-HHHHH
T ss_pred             EEEECCCCCCHHH-HHHHH
Confidence            4799999999998 44444

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.44  E-value=0.086  Score=42.30  Aligned_cols=33  Identities=18%  Similarity=0.059  Sum_probs=21.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      |-+-+++|+|||||||---.-..++...+..+.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l~~~~~~~~   51 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCY   51 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHHHHTTCCEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCCcc
Confidence            446678999999999844333344555555444

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=89.44  E-value=0.13  Score=42.71  Aligned_cols=33  Identities=36%  Similarity=0.389  Sum_probs=25.1

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      .+++|+-+|||||-+-+ +.++..+++++.+++.
T Consensus         3 i~v~G~~GsGKTTLl~~-ll~~~~~~~~~~ivn~   35 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGE-FGRYLEDNYKVAYVNL   35 (244)
T ss_dssp             EEEECSTTSSHHHHHHH-HHHHHTTTSCEEEEEC
T ss_pred             EEEEcCCCCcHHHHHHH-HHHHHhhCCeEEEEec
Confidence            57899999999986544 4555567888888863

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=89.42  E-value=0.14  Score=44.06  Aligned_cols=39  Identities=10%  Similarity=0.031  Sum_probs=34.0

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHH-HhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQ-YANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~-~~~~~~~~~k~~~  188 (353)
                      |++.++.|+.++|||+-+++.+.++. ..|.+|+++....
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E~   74 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEE   74 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESSS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeecc
Confidence            67999999999999999999998874 5699999997653

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.37  E-value=0.12  Score=43.82  Aligned_cols=39  Identities=18%  Similarity=0.119  Sum_probs=31.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      |+-.++.+|.|||||+-.+-.+..+...|++++++-|..
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt~   96 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTS   96 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCH
T ss_pred             CCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEeccH
Confidence            445678999999999877666666667789999999953

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=89.31  E-value=0.16  Score=45.24  Aligned_cols=82  Identities=20%  Similarity=0.192  Sum_probs=51.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceee------cccHhhhcc---cC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVS------AVELNKLIP---HT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~------~~~~~~~~~---~~  220 (353)
                      +.+..++||.+||||+-.++.+.+++..|..|+.+....  .++.+. ..+.|....-+.      ..+..+++.   ..
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~--~~~~~~-a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~~  130 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH--ALDPIY-ARKLGVDIDNLLCSQPDTGEQALEICDALARS  130 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSC--CCCHHH-HHHTTCCGGGCEEECCSSHHHHHHHHHHHHHH
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEcccc--ccCHHH-HHHhCCCHHHEEEecCCCHHHHHHHHHHHHhc
Confidence            458899999999999999999999999999998776543  111110 111232211111      111222221   23


Q ss_pred             CCccEEEEeccccc
Q psy8456         221 KDIDVIGIDEGQFV  234 (353)
Q Consensus       221 ~~~~~i~IDE~QF~  234 (353)
                      .++++|+||=+.-+
T Consensus       131 ~~~~liViDSi~al  144 (263)
T d1u94a1         131 GAVDVIVVDSVAAL  144 (263)
T ss_dssp             TCCSEEEEECGGGC
T ss_pred             CCCCEEEEECcccc
Confidence            67899999988864

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=89.28  E-value=0.16  Score=41.23  Aligned_cols=36  Identities=19%  Similarity=0.160  Sum_probs=32.6

Q ss_pred             ceeeeeccC-CCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         151 EKEVILGPM-FSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       151 eI~vi~G~M-~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      ...+|+|-. |.||||--+--++-...+|++|+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id~   38 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKP   38 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEECS
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEECc
Confidence            356899997 999999999999999999999999997

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=89.28  E-value=0.078  Score=41.18  Aligned_cols=18  Identities=39%  Similarity=0.429  Sum_probs=14.5

Q ss_pred             eeeeeccCCCCchhHHHH
Q psy8456         152 KEVILGPMFSGKTTELIR  169 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~  169 (353)
                      +-++.||+||||||-.-+
T Consensus         4 lI~i~G~~GsGKTTva~~   21 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKR   21 (176)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            568899999999996433

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=89.05  E-value=0.16  Score=42.15  Aligned_cols=34  Identities=26%  Similarity=0.158  Sum_probs=26.5

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMI  183 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~  183 (353)
                      |..-++-|+.||||||..=+-...+...|.++.+
T Consensus         2 gkfIviEG~dGsGKsT~~~~L~~~L~~~g~~~~~   35 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNVVVETLEQLGIRDMV   35 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhCCCCeEE
Confidence            3455778999999999987777778888876443

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=88.93  E-value=0.094  Score=42.88  Aligned_cols=22  Identities=32%  Similarity=0.279  Sum_probs=16.2

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -++.||+||||||..-.-..+|
T Consensus         6 I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           6 VMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            4789999999999654444444

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.85  E-value=0.056  Score=43.52  Aligned_cols=15  Identities=40%  Similarity=0.250  Sum_probs=12.0

Q ss_pred             eeeccCCCCchhHHH
Q psy8456         154 VILGPMFSGKTTELI  168 (353)
Q Consensus       154 vi~G~M~sGKt~~Li  168 (353)
                      +++|+|||||||---
T Consensus         5 vliG~~G~GKSTig~   19 (165)
T d2iyva1           5 VLVGLPGSGKSTIGR   19 (165)
T ss_dssp             EEECSTTSSHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            567999999998533

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.59  E-value=0.1  Score=42.18  Aligned_cols=22  Identities=27%  Similarity=0.486  Sum_probs=16.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -++.||+||||||.--+-...|
T Consensus         3 I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            3789999999999655555555

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=88.46  E-value=0.085  Score=41.54  Aligned_cols=16  Identities=31%  Similarity=0.289  Sum_probs=13.3

Q ss_pred             eeeeeccCCCCchhHH
Q psy8456         152 KEVILGPMFSGKTTEL  167 (353)
Q Consensus       152 I~vi~G~M~sGKt~~L  167 (353)
                      .-+++|||||||||-.
T Consensus         7 ~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           7 NILITGTPGTGKTSMA   22 (174)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEEeCCCCCHHHHH
Confidence            3578999999999954

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=88.44  E-value=0.11  Score=42.21  Aligned_cols=22  Identities=32%  Similarity=0.430  Sum_probs=17.3

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++||++|||||..-.-+.+|
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            3789999999999766555555

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.41  E-value=0.22  Score=40.21  Aligned_cols=35  Identities=17%  Similarity=0.063  Sum_probs=27.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      +-+++|.++|||||-.-+-.+.+...+.++.++..
T Consensus         4 li~l~GlpgsGKSTla~~L~~~l~~~~~~~~~~~~   38 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKKLTRYLNFIGVPTREFNV   38 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCCCeEEcc
Confidence            45789999999999766666666777888887765

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=88.30  E-value=0.11  Score=41.96  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=16.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++||+||||||..-+-+.+|
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999765544444

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.29  E-value=0.3  Score=41.01  Aligned_cols=32  Identities=22%  Similarity=0.172  Sum_probs=21.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      .-+++||.|+||||-+-.-++   .-+..+..+..
T Consensus        54 ~lll~GPpG~GKTt~a~~la~---~~~~~~~~~~~   85 (253)
T d1sxja2          54 AAMLYGPPGIGKTTAAHLVAQ---ELGYDILEQNA   85 (253)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH---HTTCEEEEECT
T ss_pred             eEEEECCCCCCHHHHHHHHHH---HHHhhhhcccc
Confidence            458999999999976554443   33555554443

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=88.10  E-value=0.12  Score=41.38  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=16.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++||+||||||..-.-+.+|
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            3789999999999765544554

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.92  E-value=0.12  Score=41.99  Aligned_cols=21  Identities=33%  Similarity=0.512  Sum_probs=16.9

Q ss_pred             eeeccCCCCchhHHHHHHHHH
Q psy8456         154 VILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +++||+||||||..-.-+.+|
T Consensus         6 vl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           6 VLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEECCTTSSHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHh
Confidence            678999999999876665554

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=87.85  E-value=0.19  Score=45.87  Aligned_cols=37  Identities=22%  Similarity=0.104  Sum_probs=32.0

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecC
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKD  189 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D  189 (353)
                      .+|+|+.|||||+-|..-+.+....|..++++-|.-|
T Consensus        53 ~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~kge   89 (433)
T d1e9ra_          53 LLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGD   89 (433)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTH
T ss_pred             EEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCChh
Confidence            4799999999999877778888888999999998755

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=87.74  E-value=0.48  Score=38.93  Aligned_cols=29  Identities=7%  Similarity=-0.121  Sum_probs=20.4

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeecc
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAK   38 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~i   38 (353)
                      -+|||+-.+-.+-+....+.+++++-|..
T Consensus        50 GsGKT~~a~l~i~~~~~~~~~vl~l~P~~   78 (202)
T d2p6ra3          50 AAGKTLLAEMAMVREAIKGGKSLYVVPLR   78 (202)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             CCchhHHHHHHHHHHhhccCcceeecccH
Confidence            38999875444444555678899999943

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=87.43  E-value=0.26  Score=39.19  Aligned_cols=32  Identities=22%  Similarity=0.069  Sum_probs=23.9

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEe
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVR  185 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k  185 (353)
                      -|.||.+|||||-.-+-...+...+..+..+.
T Consensus        26 gI~G~~GSGKSTla~~L~~~l~~~~~~~~~~~   57 (198)
T d1rz3a_          26 GIDGLSRSGKTTLANQLSQTLREQGISVCVFH   57 (198)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEECCCCCCHHHHHHHHHHHhccccccceecc
Confidence            38999999999866666666677777666553

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.20  E-value=0.16  Score=41.32  Aligned_cols=27  Identities=30%  Similarity=0.497  Sum_probs=20.7

Q ss_pred             eeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         153 EVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      -+|+||.||||||..-+-+..|   |...+
T Consensus         4 I~i~GppGSGKsT~a~~La~~~---g~~~i   30 (194)
T d1teva_           4 VFVLGGPGAGKGTQCARIVEKY---GYTHL   30 (194)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH---CCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHh---CCceE
Confidence            4799999999999877666655   55444

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.96  E-value=0.13  Score=42.15  Aligned_cols=23  Identities=26%  Similarity=0.346  Sum_probs=18.3

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +-+++||+||||||..-.-...|
T Consensus        10 iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            46789999999999876666655

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.83  E-value=0.32  Score=39.89  Aligned_cols=18  Identities=44%  Similarity=0.750  Sum_probs=14.3

Q ss_pred             eeeeccCCCCchhHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~  171 (353)
                      -+++||.|||||| |++++
T Consensus         4 Ivl~GpsG~GK~t-l~~~L   21 (186)
T d1gkya_           4 IVISGPSGTGKST-LLKKL   21 (186)
T ss_dssp             EEEECCTTSSHHH-HHHHH
T ss_pred             EEEECCCCCCHHH-HHHHH
Confidence            4899999999998 44444

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=86.79  E-value=0.17  Score=41.23  Aligned_cols=24  Identities=29%  Similarity=0.351  Sum_probs=17.1

Q ss_pred             ceeeeeccCCCCchhHHHHHHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .+-+++||+||||||---+-+..|
T Consensus         7 ~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           7 NVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            356899999999999644433433

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=86.75  E-value=0.26  Score=42.03  Aligned_cols=38  Identities=18%  Similarity=0.323  Sum_probs=31.3

Q ss_pred             CCCccEEEEccccChH-------HHHHHHHHHHhCCCEEEEEecc
Q psy8456          70 TKDIDVIGIDEGQFFP-------DVVSFAESMANAGKIVVVAALD  107 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF~-------dIv~l~~~l~~~G~~VivaGLd  107 (353)
                      ....|+++||++|++.       .+..+.+.+.+.|+++++.+-.
T Consensus        95 ~~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~  139 (213)
T d1l8qa2          95 YKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDR  139 (213)
T ss_dssp             HHTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             HhhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCC
Confidence            4568999999999993       2667888888999999998763

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=86.53  E-value=0.14  Score=39.77  Aligned_cols=23  Identities=26%  Similarity=0.268  Sum_probs=17.4

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      .-+|+||++|||||-.-+-...|
T Consensus         9 ~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           9 TVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             EEEEECCTTSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            45899999999998765555544

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=86.47  E-value=0.24  Score=41.54  Aligned_cols=75  Identities=11%  Similarity=0.014  Sum_probs=41.0

Q ss_pred             CCCCchHHHHHHHHHHHHHcCceEEEEeeccCC---------CCCCCceeeccCCcee--eeecCChhhhc----ccCCC
Q psy8456           8 DRINPYIVHFCRRIRRYQYANYRCMIVRYAKDD---------RYDTEKVATHDQQKLT--AVSAVELNKLI----PHTKD   72 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDt---------Ry~~~~I~Sr~G~~~~--Ai~i~~l~ei~----~~~~~   72 (353)
                      ..-+|||.-.+..+.+   .++++|++-|...=         +++...+....|...+  -+.+.....+.    ...++
T Consensus        93 ~tG~GKT~~a~~~~~~---~~~~~Liv~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~  169 (206)
T d2fz4a1          93 PTGSGKTHVAMAAINE---LSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNR  169 (206)
T ss_dssp             SSSTTHHHHHHHHHHH---SCSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSCBCCCSEEEEEHHHHHHTHHHHTTT
T ss_pred             CCCCCceehHHhHHHH---hcCceeEEEcccchHHHHHHHHHhhcccchhhcccccccccccccceehhhhhhhHhhCCc
Confidence            3468999877766654   47889999994211         1222222222222111  12222222111    12467


Q ss_pred             ccEEEEccccChH
Q psy8456          73 IDVIGIDEGQFFP   85 (353)
Q Consensus        73 ~dvV~IDEaQFF~   85 (353)
                      +++|+|||+|.+.
T Consensus       170 ~~lvIiDEaH~~~  182 (206)
T d2fz4a1         170 FMLLIFDEVHHLP  182 (206)
T ss_dssp             CSEEEEECSSCCC
T ss_pred             CCEEEEECCeeCC
Confidence            9999999999985

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=86.46  E-value=0.1  Score=46.94  Aligned_cols=32  Identities=34%  Similarity=0.512  Sum_probs=22.1

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      --+++||.|+||| +|.+.+.+.  .+...+.+..
T Consensus        51 ~iLl~GPpG~GKT-~lAkalA~~--~~~~~~~i~~   82 (309)
T d1ofha_          51 NILMIGPTGVGKT-EIARRLAKL--ANAPFIKVEA   82 (309)
T ss_dssp             CEEEECCTTSSHH-HHHHHHHHH--HTCCEEEEEG
T ss_pred             eEEEECCCCCCHH-HHHHHHhhc--cccchhcccc
Confidence            3478999999997 666776654  4555555554

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.37  E-value=0.16  Score=41.32  Aligned_cols=18  Identities=33%  Similarity=0.429  Sum_probs=15.5

Q ss_pred             cceeeeeccCCCCchhHH
Q psy8456         150 QEKEVILGPMFSGKTTEL  167 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~L  167 (353)
                      |.+-+++||+||||||-.
T Consensus         2 G~iivl~GpsG~GK~tl~   19 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVV   19 (182)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            677899999999999853

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=86.21  E-value=0.65  Score=39.35  Aligned_cols=27  Identities=11%  Similarity=0.126  Sum_probs=23.0

Q ss_pred             ccceeeeeccCCCCchhHHHHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIRRYQ  175 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~~~~  175 (353)
                      .+.+.+++|+-++|||+-+++.+....
T Consensus        28 pg~~~~i~G~~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          28 AGTVGALVSPGGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            367899999999999999999887643

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.81  E-value=0.13  Score=40.55  Aligned_cols=29  Identities=17%  Similarity=0.069  Sum_probs=24.9

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYAN  178 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~  178 (353)
                      |.+.+|.||.+||||+-+++.+.++...+
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~~~~~~   51 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVTCQLPI   51 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCG
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHHHHhh
Confidence            56889999999999999999998875443

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=85.72  E-value=0.38  Score=39.03  Aligned_cols=38  Identities=16%  Similarity=0.081  Sum_probs=30.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH-HHhCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY-QYANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~-~~~~~~~~~~k~~  187 (353)
                      +.+.+|.|+.+||||+-.++.+.+. ...+.+++.+...
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e   64 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   64 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccccc
Confidence            5688999999999999999977765 5556788877653

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=85.61  E-value=0.71  Score=38.25  Aligned_cols=123  Identities=9%  Similarity=0.012  Sum_probs=73.9

Q ss_pred             CCCchHHHHHHHHHHHHHcCceEEEEeeccCCCCCCCceeeccCCceee------ee-------cCChhhhc----c--c
Q psy8456           9 RINPYIVHFCRRIRRYQYANYRCMIVRYAKDDRYDTEKVATHDQQKLTA------VS-------AVELNKLI----P--H   69 (353)
Q Consensus         9 ~~~GKSteLLrr~~ry~~agkkvlv~Kp~iDtRy~~~~I~Sr~G~~~~A------i~-------i~~l~ei~----~--~   69 (353)
                      .-+|||+-+++-+.+....|.+|+.+......+.-. .-..+.|.....      ..       ...+.++.    .  .
T Consensus        35 pGsGKT~l~~qia~~~~~~~~~~~~is~e~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~  113 (242)
T d1tf7a2          35 TGTGKTLLVSRFVENACANKERAILFAYEESRAQLL-RNAYSWGMDFEEMERQNLLKIVCAYPESAGLEDHLQIIKSEIN  113 (242)
T ss_dssp             TTSSHHHHHHHHHHHHHTTTCCEEEEESSSCHHHHH-HHHHTTSCCHHHHHHTTSEEECCCCGGGSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhccccceeeccCCHHHHH-HHHHHcCCChHHHhhcCceEEEEeecchhhHHHHHHHHHHHHH
Confidence            458999999999999999999999987532111000 000111211110      00       11122211    1  2


Q ss_pred             CCCccEEEEccccChH----------HHHHHHHHHHhCCCEEEEEecccccccCCchhHhhhhccccceEecc
Q psy8456          70 TKDIDVIGIDEGQFFP----------DVVSFAESMANAGKIVVVAALDGTFQRTGFNDILSLIPLAECVEKLT  132 (353)
Q Consensus        70 ~~~~dvV~IDEaQFF~----------dIv~l~~~l~~~G~~VivaGLd~DFr~~pF~~~~~Ll~lAD~I~kL~  132 (353)
                      ..+++.|+||-.+.+-          .+..+...+.+.|+.+++...-.........+...+..+||.|..|.
T Consensus       114 ~~~~~~vviDs~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~ad~vi~l~  186 (242)
T d1tf7a2         114 DFKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFMGAHSITDSHISTITDTIILLQ  186 (242)
T ss_dssp             TTCCSEEEEECHHHHTSSSCHHHHHHHHHHHHHHHHHTTCEEEEEEECSSSSCCCSSCSSCCTTTCSEEEEEE
T ss_pred             hcCCceeeeecchhhhcCCCHHHHHHHHHHHHHHHHHcCCeEEEEEeeEeeccccccCCcceeeecceEEEEE
Confidence            3578999999877761          24455566678899988887765555444445566777888887774

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=85.57  E-value=0.19  Score=40.80  Aligned_cols=21  Identities=33%  Similarity=0.553  Sum_probs=16.5

Q ss_pred             eeeccCCCCchhHHHHHHHHH
Q psy8456         154 VILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +++||+||||||.--.-+.+|
T Consensus         7 il~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           7 VLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             EEECCTTSSHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHh
Confidence            578999999999766555554

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=85.39  E-value=1.3  Score=40.63  Aligned_cols=34  Identities=15%  Similarity=0.303  Sum_probs=23.8

Q ss_pred             CCccEEEEccccChH-H-HHHHHHHHHhCCCEEEEEe
Q psy8456          71 KDIDVIGIDEGQFFP-D-VVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        71 ~~~dvV~IDEaQFF~-d-Iv~l~~~l~~~G~~VivaG  105 (353)
                      ...|+|+|||+...+ . +..+...+ ..|..+|..|
T Consensus       260 l~~d~lIIDEaSmv~~~l~~~ll~~~-~~~~~lILvG  295 (359)
T d1w36d1         260 LHLDVLVVDEASMIDLPMMSRLIDAL-PDHARVIFLG  295 (359)
T ss_dssp             CSCSEEEECSGGGCBHHHHHHHHHTC-CTTCEEEEEE
T ss_pred             cccceeeehhhhccCHHHHHHHHHHh-cCCCEEEEEC
Confidence            358999999999996 3 34444332 4578888766

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.17  E-value=0.21  Score=43.56  Aligned_cols=68  Identities=18%  Similarity=0.170  Sum_probs=40.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcc--cCCCccEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIP--HTKDIDVIGID  229 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~--~~~~~~~i~ID  229 (353)
                      -.+++||.|+|||+ |++.+.+  ..+..++.+.+..-.-       +..|..     ...+..+..  ....+.+|+||
T Consensus        40 giLL~GppGtGKT~-l~~ala~--~~~~~~~~i~~~~l~~-------~~~g~~-----~~~l~~~f~~A~~~~p~il~iD  104 (258)
T d1e32a2          40 GILLYGPPGTGKTL-IARAVAN--ETGAFFFLINGPEIMS-------KLAGES-----ESNLRKAFEEAEKNAPAIIFID  104 (258)
T ss_dssp             EEEEECCTTSSHHH-HHHHHHH--HTTCEEEEECHHHHTT-------SCTTHH-----HHHHHHHHHHHHHTCSEEEEES
T ss_pred             eeEEecCCCCCchH-HHHHHHH--HhCCeEEEEEchhhcc-------cccccH-----HHHHHHHHHHHHhcCCeEEEeh
Confidence            35899999999997 5555443  4688888776643111       111111     112333321  23567899999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |++-+
T Consensus       105 eid~l  109 (258)
T d1e32a2         105 ELDAI  109 (258)
T ss_dssp             SGGGT
T ss_pred             hhhhh
Confidence            99964

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=85.00  E-value=0.37  Score=43.93  Aligned_cols=38  Identities=16%  Similarity=0.034  Sum_probs=30.6

Q ss_pred             eeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCC
Q psy8456         155 ILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRY  192 (353)
Q Consensus       155 i~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~  192 (353)
                      |+||.||||||-+-+-+..+...|++|-++.--..+.+
T Consensus        56 itG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~~   93 (323)
T d2qm8a1          56 ITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTR   93 (323)
T ss_dssp             EECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGGS
T ss_pred             eeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccHH
Confidence            79999999999999988888889988876654444443

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=84.73  E-value=0.23  Score=39.90  Aligned_cols=20  Identities=25%  Similarity=0.127  Sum_probs=14.7

Q ss_pred             eeeccCCCCchhHHHHHHHH
Q psy8456         154 VILGPMFSGKTTELIRRIRR  173 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~  173 (353)
                      +++|+|||||||---.-+.+
T Consensus         6 il~G~~GsGKSTia~~LA~~   25 (170)
T d1e6ca_           6 FMVGARGCGMTTVGRELARA   25 (170)
T ss_dssp             EEESCTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            67899999999854444443

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=84.51  E-value=0.17  Score=41.96  Aligned_cols=21  Identities=33%  Similarity=0.381  Sum_probs=16.6

Q ss_pred             eeeccCCCCchhHHHHHHHHH
Q psy8456         154 VILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +++||+||||||.--+-+.+|
T Consensus        10 iliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1          10 AIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             EEECCTTSSHHHHHHHHHHHB
T ss_pred             EEECCCCCCHHHHHHHHHHHH
Confidence            678999999999866655554

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=84.34  E-value=0.4  Score=43.87  Aligned_cols=33  Identities=15%  Similarity=0.011  Sum_probs=28.0

Q ss_pred             eeeccCCCCchhHHHHHHHHHHHhCCEEEEEee
Q psy8456         154 VILGPMFSGKTTELIRRIRRYQYANYRCMIVRY  186 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~  186 (353)
                      =|+||.||||||-+-+-+..+...|++|-++.-
T Consensus        58 gitG~pGaGKSTLi~~l~~~~~~~g~~vavlav   90 (327)
T d2p67a1          58 GVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAV   90 (327)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EeeCCCCCCHHHHHHHHHHHHHhcCCceeeecC
Confidence            379999999999999999999999988765543

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=84.07  E-value=0.4  Score=42.54  Aligned_cols=100  Identities=11%  Similarity=0.080  Sum_probs=51.4

Q ss_pred             CCCCchHHHHHHHHHHHH-HcCceEEEEeeccCCC---------CCC--Cceee--ccCCce------ee-eecCChhhh
Q psy8456           8 DRINPYIVHFCRRIRRYQ-YANYRCMIVRYAKDDR---------YDT--EKVAT--HDQQKL------TA-VSAVELNKL   66 (353)
Q Consensus         8 ~~~~GKSteLLrr~~ry~-~agkkvlv~Kp~iDtR---------y~~--~~I~S--r~G~~~------~A-i~i~~l~ei   66 (353)
                      ..-+|||.-....++.+. ..+.++|++-|...=-         ++.  ...+.  ..|...      .+ +.+.....+
T Consensus       136 pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~~~~g~~~~~~~~~~~~i~i~t~qs~  215 (282)
T d1rifa_         136 PTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQTV  215 (282)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECSTTCSSTTCCCTTCSEEEECHHHH
T ss_pred             EcccCccHHHHHHHHHhhhcccceEEEEEcCchhHHHHHHHHHHhhccccccceeecceecccccccccceEEEEeeehh
Confidence            346899976666665554 4567899999952110         111  11111  112111      11 222333222


Q ss_pred             c----ccCCCccEEEEccccChH--HHHHHHHHHHhCCCEEEEEeccccc
Q psy8456          67 I----PHTKDIDVIGIDEGQFFP--DVVSFAESMANAGKIVVVAALDGTF  110 (353)
Q Consensus        67 ~----~~~~~~dvV~IDEaQFF~--dIv~l~~~l~~~G~~VivaGLd~DF  110 (353)
                      .    ...+++++|++||||-+.  .+..+   +......-+..||..+-
T Consensus       216 ~~~~~~~~~~f~~VIvDEaH~~~a~~~~~i---l~~~~~~~~rlGlTaT~  262 (282)
T d1rifa_         216 VKQPKEWFSQFGMMMNDECHLATGKSISSI---ISGLNNCMFKFGLSGSL  262 (282)
T ss_dssp             TTSCGGGGGGEEEEEEETGGGCCHHHHHHH---TTTCTTCCEEEEECSSC
T ss_pred             hhhcccccCCCCEEEEECCCCCCchhHHHH---HHhccCCCeEEEEEeec
Confidence            2    123579999999999996  34333   32221122346887764

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=83.98  E-value=0.28  Score=42.40  Aligned_cols=23  Identities=35%  Similarity=0.569  Sum_probs=18.5

Q ss_pred             ccceeeeeccCCCCchhHHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      ..++.+++||.|||||+ +|+++.
T Consensus        23 ~~~lnvlvG~NgsGKS~-iL~Ai~   45 (308)
T d1e69a_          23 SDRVTAIVGPNGSGKSN-IIDAIK   45 (308)
T ss_dssp             CSSEEEEECCTTTCSTH-HHHHHH
T ss_pred             CCCeEEEECCCCCcHHH-HHHHHH
Confidence            35688999999999998 566664

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.76  E-value=0.33  Score=39.99  Aligned_cols=19  Identities=21%  Similarity=0.162  Sum_probs=15.0

Q ss_pred             ceeeeeccCCCCchhHHHH
Q psy8456         151 EKEVILGPMFSGKTTELIR  169 (353)
Q Consensus       151 eI~vi~G~M~sGKt~~Li~  169 (353)
                      .+-+++||.+|||||-+-+
T Consensus         4 k~ivl~Gpsg~GK~tl~~~   22 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNT   22 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHH
Confidence            3568999999999976533

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=83.28  E-value=0.28  Score=39.27  Aligned_cols=21  Identities=33%  Similarity=0.279  Sum_probs=15.2

Q ss_pred             eeeccCCCCchhHHHHHHHHH
Q psy8456         154 VILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       154 vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +++|+|||||||-.-.-+..+
T Consensus         4 ~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           4 VFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             EEECCTTSCHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHh
Confidence            678999999997654444443

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=83.22  E-value=1.2  Score=37.51  Aligned_cols=20  Identities=20%  Similarity=0.032  Sum_probs=14.9

Q ss_pred             eeeeccCCCCchhHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~  172 (353)
                      -+++||.|+||||-....++
T Consensus        37 ~Ll~Gp~G~GKtt~a~~~~~   56 (239)
T d1njfa_          37 YLFSGTRGVGKTSIARLLAK   56 (239)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            47899999999985443333

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=83.20  E-value=0.44  Score=40.69  Aligned_cols=35  Identities=14%  Similarity=0.086  Sum_probs=27.4

Q ss_pred             CCccEEEEccccChH-HHHHHHHHHHhCCCEEEEEe
Q psy8456          71 KDIDVIGIDEGQFFP-DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        71 ~~~dvV~IDEaQFF~-dIv~l~~~l~~~G~~VivaG  105 (353)
                      +++++|+|||+|-++ -..+++..+...+..+++.|
T Consensus       205 ~~~~~i~vDE~QD~~~~~~~~l~~~~~~~~~~~~~G  240 (306)
T d1uaaa1         205 NKIRYLLVDEYQDTNTSQYELVKLLVGSRARFTVVG  240 (306)
T ss_dssp             TTCSEEEESCGGGCBHHHHHHHHHHHTTTCCEEEEC
T ss_pred             HHhhHHHHHHHHHhhHHHHhhhhhcccCCCcceEee
Confidence            478999999999996 45567777777777776654

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=83.19  E-value=1.4  Score=37.08  Aligned_cols=23  Identities=13%  Similarity=0.304  Sum_probs=18.6

Q ss_pred             ccHHHHHHHHHhCCCEEEEEecc
Q psy8456         281 PDVVSFAESMANAGKIVVVAALD  303 (353)
Q Consensus       281 ~~~~~~~~~~~~~g~~Vi~~gLd  303 (353)
                      ..+..+|..+.+.|..|+|+...
T Consensus        84 ~r~~~~a~~~~~~g~~viv~~i~  106 (208)
T d1m7ga_          84 RRIAEVAKLFADSNSIAITSFIS  106 (208)
T ss_dssp             HHHHHHHHHHHHTTCEEEEECCC
T ss_pred             HHHHHHHHHHhccCCceeeeccc
Confidence            34667778888999999999883

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=82.83  E-value=0.28  Score=45.09  Aligned_cols=75  Identities=20%  Similarity=0.164  Sum_probs=39.3

Q ss_pred             ccccceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhcccCCCccEE
Q psy8456         147 RIGQEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPHTKDIDVI  226 (353)
Q Consensus       147 Ri~geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~~i  226 (353)
                      |...+.-+++||.|+||| .|.+.+..-.-++...+.++.+        .+.++    .-......+.+++.......+|
T Consensus       120 ~~~~g~~l~~G~pG~GKT-~la~ala~~~~~~~~~~~~~~~--------~~~~~----~~G~~e~~~~~~f~~a~~~~il  186 (321)
T d1w44a_         120 RYASGMVIVTGKGNSGKT-PLVHALGEALGGKDKYATVRFG--------EPLSG----YNTDFNVFVDDIARAMLQHRVI  186 (321)
T ss_dssp             EEESEEEEEECSSSSCHH-HHHHHHHHHHHTTSCCEEEEBS--------CSSTT----CBCCHHHHHHHHHHHHHHCSEE
T ss_pred             ccCCceEEEECCCCccHH-HHHHHHHHHhcCCCCeEEEEhh--------Hhhhc----ccchHHHHHHHHHHHHhhccEE
Confidence            444455566899999998 4555554433333333333321        12221    1112233444554332335699


Q ss_pred             EEeccccc
Q psy8456         227 GIDEGQFV  234 (353)
Q Consensus       227 ~IDE~QF~  234 (353)
                      +|||++-+
T Consensus       187 f~DEid~~  194 (321)
T d1w44a_         187 VIDSLKNV  194 (321)
T ss_dssp             EEECCTTT
T ss_pred             Eeehhhhh
Confidence            99999974

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=82.71  E-value=0.14  Score=41.82  Aligned_cols=33  Identities=21%  Similarity=0.159  Sum_probs=27.8

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEE
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCM  182 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~  182 (353)
                      +.+.++.|+.++|||+-.++.+.+....++.++
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~   66 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFY   66 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEEC
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCce
Confidence            568899999999999999999998876655443

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=82.33  E-value=0.48  Score=41.48  Aligned_cols=37  Identities=14%  Similarity=0.064  Sum_probs=33.9

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeec
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAK  188 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~  188 (353)
                      ..++.|..|||||.=.++.+...-.+|+.|+++-|.+
T Consensus        78 ~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~  114 (233)
T d2eyqa3          78 DRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTT  114 (233)
T ss_dssp             EEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSH
T ss_pred             CeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHH
Confidence            4588999999999999999999999999999999963

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=82.19  E-value=0.36  Score=39.98  Aligned_cols=37  Identities=22%  Similarity=0.099  Sum_probs=28.4

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHh------CCEEEEEee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYA------NYRCMIVRY  186 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~------~~~~~~~k~  186 (353)
                      +.+.+++||.+||||+-.++-+.+....      +.+++.+..
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~   78 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDT   78 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEES
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEec
Confidence            4578999999999999999999887532      445555544

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.18  E-value=0.23  Score=40.60  Aligned_cols=38  Identities=13%  Similarity=0.190  Sum_probs=29.3

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHH------hCCEEEEEeee
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQY------ANYRCMIVRYA  187 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~------~~~~~~~~k~~  187 (353)
                      +.+.+++||.+||||+-.++-+.+.+.      .|.+++.+...
T Consensus        34 G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2          34 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            468899999999999999998877643      25567666543

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.91  E-value=0.45  Score=39.46  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=16.6

Q ss_pred             eeeeccCCCCchhHHHHHHHHH
Q psy8456         153 EVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       153 ~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      -+++||-|+||||-+-.-++..
T Consensus        38 lLl~Gp~G~GKttl~~~la~~l   59 (227)
T d1sxjc2          38 LLFYGPPGTGKTSTIVALAREI   59 (227)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCChhHHHHHHHHHh
Confidence            4789999999998665555543

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=81.74  E-value=0.33  Score=39.62  Aligned_cols=25  Identities=24%  Similarity=0.339  Sum_probs=18.6

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      ..+-+++||.||||||.--+-+.+|
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3456789999999999665555544

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=81.72  E-value=0.52  Score=40.84  Aligned_cols=34  Identities=18%  Similarity=0.121  Sum_probs=27.6

Q ss_pred             CccEEEEccccChH-HHHHHHHHHHhCCCEEEEEe
Q psy8456          72 DIDVIGIDEGQFFP-DVVSFAESMANAGKIVVVAA  105 (353)
Q Consensus        72 ~~dvV~IDEaQFF~-dIv~l~~~l~~~G~~VivaG  105 (353)
                      .+++|+|||+|-++ -..++...+...+..++++|
T Consensus       216 ~~~~i~iDE~QD~s~~q~~~~~~l~~~~~~~~~~g  250 (318)
T d1pjra1         216 KFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVG  250 (318)
T ss_dssp             HCSEEEESSGGGCCHHHHHHHHHHHTTTCCEEEEE
T ss_pred             ccchhhhHHHHHHHHHHHHHHHHHHHhhcceeeec
Confidence            48899999999997 44677777777778888777

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=81.58  E-value=0.6  Score=36.97  Aligned_cols=30  Identities=7%  Similarity=-0.041  Sum_probs=26.5

Q ss_pred             CCchHHHHHHHHHHHHHcCceEEEEeeccC
Q psy8456          10 INPYIVHFCRRIRRYQYANYRCMIVRYAKD   39 (353)
Q Consensus        10 ~~GKSteLLrr~~ry~~agkkvlv~Kp~iD   39 (353)
                      =|||||-+-+-+.++..+|.+|.++|...-
T Consensus        11 gSGKTTli~~l~~~L~~~g~~v~vik~d~~   40 (165)
T d1xjca_          11 HSGKTTLMEKWVAAAVREGWRVGTVKHHGH   40 (165)
T ss_dssp             TSSHHHHHHHHHHHHHHTTCCEEEEECCC-
T ss_pred             CCCHHHHHHHHHHHHHhCCCeEEEEEeccC
Confidence            489999999999999999999999997643

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=81.11  E-value=0.65  Score=40.72  Aligned_cols=68  Identities=22%  Similarity=0.178  Sum_probs=39.5

Q ss_pred             eeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCcccceeecccHhhhccc--CCCccEEEEe
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAVSAVELNKLIPH--TKDIDVIGID  229 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~~~~~~~~~~~~--~~~~~~i~ID  229 (353)
                      --+++||.|+|||+- ++.+-  ...|..++.++++.       -+....|     .....+.+++..  ...+-+++||
T Consensus        47 ~iLL~GppGtGKT~l-a~~iA--~~~~~~~~~i~~~~-------l~~~~~g-----~~~~~l~~~f~~A~~~~P~il~iD  111 (256)
T d1lv7a_          47 GVLMVGPPGTGKTLL-AKAIA--GEAKVPFFTISGSD-------FVEMFVG-----VGASRVRDMFEQAKKAAPCIIFID  111 (256)
T ss_dssp             EEEEECCTTSCHHHH-HHHHH--HHHTCCEEEECSCS-------STTSCCC-----CCHHHHHHHHHHHHTTCSEEEEET
T ss_pred             eEEeeCCCCCCccHH-HHHHH--HHcCCCEEEEEhHH-------hhhcchh-----HHHHHHHHHHHHHHHcCCEEEEEE
Confidence            358999999999864 55544  34477777665531       0111112     112234444432  4566799999


Q ss_pred             ccccc
Q psy8456         230 EGQFV  234 (353)
Q Consensus       230 E~QF~  234 (353)
                      |++-+
T Consensus       112 eiD~l  116 (256)
T d1lv7a_         112 EIDAV  116 (256)
T ss_dssp             THHHH
T ss_pred             Chhhh
Confidence            99853

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=80.38  E-value=0.062  Score=42.14  Aligned_cols=25  Identities=16%  Similarity=0.177  Sum_probs=18.9

Q ss_pred             ccccceeeeeccCCCCchhHHHHHHH
Q psy8456         147 RIGQEKEVILGPMFSGKTTELIRRIR  172 (353)
Q Consensus       147 Ri~geI~vi~G~M~sGKt~~Li~~~~  172 (353)
                      .+..++.+|+||.+|||||- +..+.
T Consensus        21 ~f~~~~tvi~G~NGsGKSti-l~Ai~   45 (222)
T d1qhla_          21 DLDELVTTLSGGNGAGKSTT-MAAFV   45 (222)
T ss_dssp             CHHHHHHHHHSCCSHHHHHH-HHHHH
T ss_pred             EcCCCeEEEECCCCCCHHHH-HHHHH
Confidence            33467899999999999964 45554

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=80.36  E-value=0.75  Score=40.84  Aligned_cols=82  Identities=18%  Similarity=0.180  Sum_probs=52.1

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHHHHhCCEEEEEeeecCCCCCCCceeeccCccccee---e---cccHhhhc---ccC
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRYQYANYRCMIVRYAKDDRYDTEKVSTHDQQKLTAV---S---AVELNKLI---PHT  220 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~~~~~~~~~~~k~~~D~R~~~~~i~s~~g~~~~a~---~---~~~~~~~~---~~~  220 (353)
                      +.+..++||-.||||+-.++.+.+++..|.+|+.+....--  +.+ ...+-|.-..-+   .   .++..+++   ...
T Consensus        57 g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~--~~~-~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~  133 (268)
T d1xp8a1          57 GRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHAL--DPV-YARALGVNTDELLVSQPDNGEQALEIMELLVRS  133 (268)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCC--CHH-HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTT
T ss_pred             ceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccC--CHH-HHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhc
Confidence            34788999999999999999999999999999988765321  111 122223221111   1   11222222   224


Q ss_pred             CCccEEEEeccccc
Q psy8456         221 KDIDVIGIDEGQFV  234 (353)
Q Consensus       221 ~~~~~i~IDE~QF~  234 (353)
                      .++++|+||=+.-+
T Consensus       134 ~~~~liIiDSi~al  147 (268)
T d1xp8a1         134 GAIDVVVVDSVAAL  147 (268)
T ss_dssp             TCCSEEEEECTTTC
T ss_pred             CCCcEEEEeccccc
Confidence            67999999988653

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=80.26  E-value=0.3  Score=41.39  Aligned_cols=22  Identities=36%  Similarity=0.299  Sum_probs=17.4

Q ss_pred             ccceeeeeccCCCCchhHHHHHH
Q psy8456         149 GQEKEVILGPMFSGKTTELIRRI  171 (353)
Q Consensus       149 ~geI~vi~G~M~sGKt~~Li~~~  171 (353)
                      .|++..++||.||||||-| +.+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl-~~i   47 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLL-KTI   47 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHH-HHH
T ss_pred             CCCEEEEECCCCChHHHHH-HHH
Confidence            4678889999999999854 444

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.09  E-value=1.2  Score=37.28  Aligned_cols=25  Identities=24%  Similarity=0.139  Sum_probs=18.2

Q ss_pred             cceeeeeccCCCCchhHHHHHHHHH
Q psy8456         150 QEKEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       150 geI~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      |..-++-|+.||||||..-.-..++
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHH
Confidence            4566789999999999864444333

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=80.04  E-value=0.48  Score=38.43  Aligned_cols=23  Identities=26%  Similarity=0.086  Sum_probs=19.0

Q ss_pred             eeeeeccCCCCchhHHHHHHHHH
Q psy8456         152 KEVILGPMFSGKTTELIRRIRRY  174 (353)
Q Consensus       152 I~vi~G~M~sGKt~~Li~~~~~~  174 (353)
                      +-.|.||.||||||.--.-+.+|
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            45788999999999877777766